EP4680677A1 - Benzothienopyrrole cyanine dyes - Google Patents

Abstract

The present disclosure provides novel benzothienopyrrole (Bt)-cyanine(Cy) fluorescent compounds, water-soluble BtCy fluorescent dyes, water-soluble BtCy binding partner conjugates, and tandem dyes thereof. The BtCy fluorescent compounds, conjugates, and tandem dyes can be excited using yellow, orange, red, NIR, or IR wavelengths. The fluorescent dyes may be conjugated to a binding partner for detection of target analytes in biological samples and are suitable for use in flow cytometry analyses. Those dyes have the following generic formula wherein Ar¹ is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, polycyclic aryl group, monocyclic heteroaryl group, and polycyclic heteroaryl group.

Description

BENZOTHIENOPYRROLE CYANINE DYES

[0001] This application is being filed March 15, 2024, as a PCT International Patent application and claims the benefit of and priority to U.S. Provisional application Serial No. 63/490,932, filed March 17, 2023, and U.S. Provisional application Serial No. 63/510,018, filed June 23, 2023, each of which is incorporated by reference herein in its entirety.

BACKGROUND

[0002] There is an increasing demand for a variety of fluorescent dyes and dye conjugates for use in flow cytometers as well as in spectral flow instruments. Water soluble fluorescent compounds and their conjugates can be used in a variety of biological applications by generating signals which can be monitored in real time and provide simple and rapid methods for the detection of biological targets and events, e.g., in diagnostic kits, in microscopy or in drug screening.

[0003] Molecular recognition involves the specific binding of two molecules. Molecules which have binding specificity for a target biomolecule find use in a variety of research and diagnostic applications, such as the labelling and separation of analytes, flow cytometry, in situ hybridization, enzyme-linked immunosorbent assay s (ELISAs), western blot analysis, magnetic cell separations and chromatography. Target biomolecules may be detected by labelling with a fluorescent dye.

[0004] Several fluorescent dyes and their antibody conjugates have previously been developed which are excitable with 355 nm and 405 nm lasers. For example, US Pat. No. 11,208,527 describes water soluble dihydrophenanthrene (DHP) based fluorescent polymer dyes, for example, exhibiting excitation maxima between 395-415 nm with emitted light between about 415-475 nm. US Patent Application Publication US 2020/0190253 describes water soluble DHP based violet excitable polymers and tandem dyes.

[0005] Demands have increased for multicolor panels for both conventional and spectral flow cytometry that require additional fluorescent dyes excitable with other lasers (e.g., 488, 563, 638, and 808 nm). Parameters considered by a user in choosing a fluorescent dye may include excitation wavelength maximum, the emission wavelength maximum, brightness of the dye, and the fluorescence lifetime. Brightness of a dye is an overall contribution from the extinction coefficient (e, measure of the amount of light absorbed at a particular wavelength) and fluorescence quantum yield (0, measure of the light emitted in the form of radiation from its singlet excited state).

[0006] Water-soluble fluorescent dyes that can be excited using blue, green, yellow, orange, red, near infrared (NIR), and infrared (IR) wavelengths are desirable. [0007] SUMMARY

[0008] The present disclosure provides benzothienopyrrole-cyanine (BtCy) compounds, that can be water-soluble fluorescent BtCy dyes. BtCy tandem dyes are also provided comprising a BtCy fluorescent compound as an acceptor or donor chromophore. Labeled specific binding partners are also provided comprising a BtCy compound or BtCy tandem dye according to the invention conjugated to a specific binding partner, and their complexes. The BtCy compounds, labeled specific binding partners, and tandem dyes according to the present disclosure are useful in biological applications, including for the detection of target analytes and use in diagnostic kits, etc. For example, labeled specific binding partners comprising a specific binding partner and BtCy compound(s) or BtCy tandem dye(s) according to the invention are useful in methods for detecting analytes in a sample.

[0009] Novel fluorescent dyes based on benzo[4,5]thieno[2,3b]pyrrole- cyanine structures are provided. Water solubility has been improved by addition of water-solubilizing moieties. Synthetic routes have been designed for conjugation to antibodies and for preparation of tandem dyes.

[0010] The disclosure provides a fluorescent compound comprising a structure according to Formula (I): is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, polycyclic aryl group, monocyclic heteroaryl group, and polycyclic heteroaryl group; is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, and polycyclic aryl group; each T is independently NR^4’, CR¹, CR¹R², O, S, Se, or Te; V is NR¹¹, CR⁸, CR⁸R⁹, O, S, Se, or Te, or each T-V together can stand for a structural element selected from the group consisting of SO2, -CR¹-O-, -O-CR¹-, -CO- O-, -O-CO-, -CO-NR¹¹-, or -NR^4’-CO-; G is C or N; each R¹, R², R⁸, and R⁹ is independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, binding partner, linked binding partner, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, alkoxy sulfonate, carboxylic acid, carboxylate, alkyl carboxylate, alkoxy carboxylate, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkyl sulfonamide PEG, alkylamide,

; each R⁴, R^4’, R¹⁰, and R¹¹ is independently selected from the group consisting of a linker moiety, a chromophore, linked chromophore, reactive group, linked reactive group, conjugation tag, linked conjugation tag, water-solubilizing moiety, linked water- solubilizing moiety, binding partner, linked binding partner, E, linked E, H, halogen alkyl, alkenyl, alkynyl, a PEG group, a linked PEG group, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, carboxylic acid, carboxylate, alkyl carboxylate, alkyl sulfonamide, alkyl sulfonamide PEG, alkyl amide, alkyl amide-PEG,

, or protected groups thereof, or one, two, three, or four of R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ together form an unsubstituted or substituted unsaturated or partially unsaturated C3- C₁₀ cycloalkyl group; unsubstituted or substituted unsaturated or partially unsaturated C3-C10 heterocycloalkyl optionally substituted with O; unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃-C₈ polycycloalkyl group; or unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3 - C₈ polyheterocycloalkyl group optionally substituted with O; each R³ is independently selected from the group consisting of H, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl, (hetero)arylamino, alkyl sulfonate, alkyl carboxylate, a water-solubilizing moiety, a linked water-solubilizing moiety, a chromophore, a linked chromophore, functional moiety, linked functional moiety, conjugation tag, linked conjugation tag, binding partner, linked binding partner, a PEG group, and a linked PEG group; each Q is independently a bond, O, NH, NR⁴, C₁-C₁₂ alkylene, CHR⁴, or CH₂; each Z is independently CH2, CHR⁴, O, NR⁴, or NH; each W¹ is independently a water-solubilizing moiety; L¹, L², and L³ are each independently selected linker moieties; each E is independently selected from the group consisting of a chromophore, a functional moiety, a substrate, a reactive group, conjugation tag, linked conjugation tag, and a binding partner; each R⁷ is independently selected from the group consisting of H, hydroxyl, C₁- C12 alkyl, C1-C12 heteroalkyl, C2-C12 alkene, C2-C12 alkyne, C3-C12 cycloalkyl, C1- C₁₂ haloalkyl, C₁-C₁₂ alkoxy, C₂-C₁₈ (hetero)aryloxy, C₂-C₁₈ (hetero)arylamino, carboxylate, carboxylic acid, C2-C12 alkyl carboxylic acid, C2-C12 alkyl carboxylate, C2- C₁₂ alkyl carboxylate ester, aryl carboxylic acid, aryl carboxylate ester, C₁-C₁₂ alkoxy, a water-solubilizing moiety, a PEG moiety, a protected or unprotected functional group, a chemoselective functional group, conjugation tag, linked conjugation tag, a linker, sulfonic acid, sulfonate, C1-C12 alkyl sulfonate, sulfonamide, and combinations thereof; each R¹² , R¹³ and R¹⁴ is independently selected from the group consisting of hydrogen, halogen, one or more heteroatoms, substituted or unsubstituted C1-C6 alkyl, substituted or unsubstituted C1-C6 heteroalkyl, substituted or unsubstituted C1-C6 alkene, substituted or unsubstituted C3-C10 cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted C3-C10 heterocycloalkyl, CO₂R¹, CONR¹R², -O-CH₂CH₂-PEG-R⁷, -S-CH₂CH₂-PEG-R⁷, -N- CH2CH2-PEG-R⁷, O-aryl, S-aryl, N-aryl, -O-alkyl, S-alkyl, N-alkyl, wherein each alkyl or aryl can optionally be substituted with one or more R⁷, PEG, or PEG-R⁷, optionally wherein each R¹² , R¹³ and R¹⁴ is independently substituted with one or more R⁷ groups; or at least two of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, optionally including, but not limited to, one, two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ form an unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ cycloalkyl group, unsubstituted or substituted unsaturated or partially unsaturated C3- C₁₀ heterocycloalkyl optionally substituted with O, an unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3-C8 polycycloalkyl group, or unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃- C8 polyheterocycloalkyl group optionally substituted with O; each K is independently a covalent bond, O, S, Se, P, NR¹, or CR¹R²; each f is independently an integer from 0 to 50, 1 to 30, or 2 to 20; each m and m’ is independently 0, 1, 2, or 3; each n is independently an integer from 1 to 20; 1 to 10; or 0, 1, 2, or 3; each p is independently 1, 2, 3, or 4; each s is independently 1 or 2; each t is independently 0, 1, 2, 3, or 4; and X is a counterion. [0011] In some cases, m is 0 or 1. [0012] In some cases, p is 1, 2, or 3. In some cases p is 1. In some cases, p is 2. In some cases, p is 3. In some cases, p is 4. [0013] In some cases, when m is 0, each T is independently CR¹ or CR¹R². In some cases, when m is 0, T is not NR^4’, S or O. In some cases, when m is 1, each T is independently NR^4’, O, S, Se, or Te. In some cases, when m is 1, T is not CR¹ or CR¹R². [0014] A BtCy tandem dye is provided, comprising: a fluorescent BtCy compound of the present disclosure; and a chromophore, donor dye, or acceptor dye covalently linked to the fluorescent BtCy compound or labeled specific binding partner. The BtCy compounds of the present invention can be a donor dye. The BtCy compounds of the present invention can be an acceptor dye. [0015] A labeled specific binding partner is provided, comprising: a fluorescent BtCy compound or BtCy tandem dye according to the present disclosure; and a specific binding partner covalently linked to the fluorescent BtCy compound. [0016] A method for detecting a target analyte in a sample is provided, the method comprising: providing a sample that is suspected of containing the analyte; and contacting the sample with a specific binding partner conjugated to a fluorescent BtCy compound or BtCy tandem dye of the present disclosure, wherein the specific binding partner is capable of interacting with the target analyte. [0017] A kit is provided comprising at least one fluorescent BtCy compound, labeled specific binding partner, or tandem dye according to the present disclosure. The compound or tandem dye may include a conjugation tag. BRIEF DESCRIPTION OF THE DRAWINGS [0018] FIG.1 shows chemical structures of prior art indole-cyanine dyes Cy3, C5 and Cy7 and inventive benzothienopyrrole-cyanine dyes BtCy3, BtCy5, and BtCy7. The spectra of the BtCy3, BtCy5, and BtCy7 compounds are red shifted by about 200 nm compared to common indole-cyanine compounds Cy3, Cy5, and Cy7. [0019] FIG.2 shows Schemes 1 and 2 showing representative synthetic routes to benzothienopyrrole intermediates 3 and 6, respectively. Scheme 1 shows synthesis of intermediate compound 3: 3-(2,3,3-trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium- 1-yl)propane-1-sulfonate from starting 2-iodobenzo[b]thiophene. Scheme 2 shows synthesis of intermediate compound 6: 3-(2,3-dimethyl-3-(3-sulfopropyl)-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate from starting ethyl 2- methyl-3-oxobutanoate. [0020] FIG.3 shows Schemes 3A, 3B and 4 showing representative synthetic routes to benzothienopyrrole intermediates 7 and 8, and indole intermediate 10, respectively. As shown in Scheme 3A, benzothienopyrrole intermediate compound 7: 1-(2-carboxyethyl)-2,3,3-trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium iodide was made from intermediate compound 2 and 3-iodopropanoic acid. As shown in Scheme 3B, benzothienopyrrole intermediate compound 8: 1-(2-carboxyethyl)-2,3-dimethyl-3- (3-sulfopropyl)-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium iodide was made from intermediate compound 5 and 3-iodopropanoic acid. As shown in Scheme 4, indole intermediate compound 10: 5-((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-1-(2- carboxyethyl)-2,3,3-trimethyl-3H-indol-1-ium iodide was made in two steps from 2,3,3-trimethyl-3H-indol-5-ol. [0021] FIG.4 shows Schemes 5, 6, and 7 illustrating representative synthetic routes to symmetric benzothienopyrrole-cyanine dye compounds 11 (BtCy3), 12 (BtCy5), and 13 (BtCy7), respectively, from benzothienopyrrole intermediate compound 3. [0022] FIG.5 shows Scheme 8 with representative synthetic route to symmetric benzothienopyrrole-cyanine dye compound 14 from benzothienopyrrole intermediate compound 6. [0023] FIG.6 shows Schemes 9 and 10 illustrating representative synthetic routes to asymmetric benzothienopyrrole-cyanine dye compounds 15 and 17. Scheme 9 shows preparation of compound 15: 4-((Z)-3,3-dimethyl-2-((2E,4E)-5-(1,3,3-trimethyl- 3H-indol-1-ium-2-yl)penta-2,4-dien-1-ylidene)-2,3-dihydro-1H-benzo[4,5]thieno[2,3- b]pyrrol-1-yl)butane-1-sulfonate from 1,2,3,3-tetramethyl-3H-indol-1-ium iodide and intermediate compound 3. Scheme 10 shows preparation of compound 17: sodium 1- (2-carboxyethyl)-2-((1E,3E,5Z)-5-(3,3-dimethyl-1-(4-sulfonatobutyl)-1,3-dihydro-2H- benzo[4,5]thieno[2,3-b]pyrrol-2-ylidene)penta-1,3-dien-1-yl)-3,3-dimethyl-3H-indol-1- ium-5-sulfonate from 1-(2-carboxyethyl)-2,3,3-trimethyl-5-sulfo-3H-indol-1-ium iodide intermediate compound 16 and benzothienopyrrole intermediate compound 3. [0024] FIG.7 shows Schemes 11 and 12 illustrating representative synthetic routes to asymmetric benzothienopyrrole-cyanine dye compounds 19 and 20, respectively. Scheme 11 shows preparation of compound 19: 1-(2-carboxyethyl)-3,3-dimethyl-2- ((1E,3E,5E,7Z)-7-(3-methyl-1,3-bis(3-sulfopropyl)-1,3-dihydro-2H- benzo[4,5]thieno[2,3-b]pyrrol-2-ylidene)hepta-1,3,5-trien-1-yl)-3H-indol-1-ium iodide from indole intermediate compound 18 and benzothienopyrrole intermediate compound 6. Scheme 12 shows preparation of compound 20: 3-(2-((1E,3E,5E)-7-((Z)-5- ((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-1-(2-carboxyethyl)-3,3- dimethylindolin-2-ylidene)hepta-1,3,5-trien-1-yl)-3-methyl-3-(3-sulfopropyl)-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate was produced from indole intermediate compound 10 and benzothienopyrrole intermediate compound 6. [0025] FIG.8 shows Scheme 13 illustrating a representative synthetic route to asymmetric benzothienopyrrole-cyanine dye compound 21: 1-(2-carboxyethyl)-3,3- dimethyl-2-((1E,3Z)-3-(3-methyl-1,3-bis(3-sulfopropyl)-1,3-dihydro-2H- benzo[4,5]thieno[2,3-b]pyrrol-2-ylidene)prop-1-en-1-yl)-3H-indol-1-ium iodide from indole intermediate compound 18 and benzothienopyrrole intermediate compound 6 using N,N'-diphenylformamidine. [0026] FIG.9 shows Schemes 14 and 15 illustrating representative synthetic routes to asymmetric benzothienopyrrole-cyanine dye compound 24. Scheme 14 illustrates a synthetic route to intermediate compound 23: 1-(2-carboxyethyl)-2,3,3-trimethyl-5-(3- sulfopropoxy)-3H-indol-1-ium iodide from 2,3,3-trimethyl-3H-indol-5-ol. Scheme 15 illustrates representative synthetic route to compound 24 from indole intermediate compound 23 and benzothienopyrrole intermediate compound 6. [0027] FIG.10 shows the chemical structure of symmetric benzothienopyrrole- cyanine dye compound 12 (BtCy5). Absorption spectra of BtCy5 is shown at lower left exhibiting an extinction coefficient ε at 859 nm of 88k in MeOH. BtCy5 emission spectra is shown at the lower right exhibiting a max λ em 878 nm in methanol (MeOH). [0028] FIG.11 shows the chemical structure of asymmetric benzothienopyrrole- cyanine compound 15. Absorption spectrum of compound 15 in methanol (MeOH) is shown at lower left exhibiting max λ abs of 740 nm and an extinction coefficient at 740 nm of ≈ 90k. Emission spectra of compound 15 in MeOH is shown at lower right having max λem of 765 nm. [0029] FIG.12 shows the chemical structure of symmetric benzothienopyrrole- cyanine dye compound 13 (BtCy7). Absorption spectrum of BtCy7 is shown at lower left having max λ abs of 973 nm. Emission spectra in methanol of BtCy7 after excitation at either 972 nm (a) or 808 nm (b) is shown at lower right. Symmetric benzothienopyrrole-cyanine dye compound 13 exhibits max λem of 997 nm. [0030] FIG.13 shows the chemical structure and absorption spectra of symmetric benzothienopyrrole-cyanine dye compound 12 in MeOH (max λabs 860 nm) overlaid with the absorption spectra of symmetric benzothienopyrrole-cyanine dye compound 14 in MeOH (max λabs 863 nm) or PBS. [0031] FIG 14 shows an exemplary synthetic scheme for preparing and purifying a BtCy-antibody conjugate. [0032] FIG.15 shows Scheme 17 illustrating representative synthetic route to asymmetric benzothienopyrrole-cyanine dye compound 25 from indole intermediate compound and benzothienopyrrole intermediate compound 3. [0033] FIG.16 shows Schemes 18 and 19 illustrating representative synthetic route to benzothienopyrrole intermediate compound 26, and asymmetric benzothienopyrrole- cyanine dye compound 27. [0034] FIG.17 shows Schemes 20 and 21 illustrating representative synthetic route to indole intermediate compound 28 and asymmetric benzothienopyrrole-cyanine dye compound 29. [0035] FIG.18 shows Scheme 22 illustrating representative synthetic route to asymmetric benzothienopyrrole-cyanine dye compound 30. [0036] FIG 19 shows Schemes 23 and 24 illustrating representative synthetic routes to benzo indole intermediate compound 32 and asymmetric benzothienopyrrole- cyanine dye compound 33. DETAILED DESCRIPTION OF THE INVENTION I. General [0037] The present disclosure provides novel BtCy fluorescent compounds, labeled specific binding partners comprising the BtCy compounds with covalently linked specific binding partners. In some embodiments, BtCy compounds and labeled specific binding partners have been designed to be water soluble. The disclosure also provides tandem dyes comprising the BtCy compounds and/or labeled specific binding partners. [0038] The BtCy compounds of the present disclosure exhibit excitation maxima in a range of from about 500 -1200 nm, 575-1200 nm, or 750-1200 nm, or 600-1000 nm. [0039] In some embodiments, BtCy compounds of the present disclosure can be excited using blue, green, yellow, orange, red, near infrared (NIR), or infrared (IR) wavelengths. [0040] In some embodiments, BtCy compounds of the present disclosure can be excited using yellow, orange, red, or near infrared (NIR) wavelengths. [0041] Methods are provided for detecting target analytes in a sample using fluorescent BtCy compounds or BtCy tandem dyes conjugated to binding partners. [0042] Kits comprising at least one fluorescent BtCy compound, labeled specific binding partner, or tandem dye according to the present disclosure are also provided. The fluorescent BtCy compound or tandem dye may include a conjugation tag. II. Definitions [0043] The abbreviations used herein have their conventional meaning within the chemical and biological arts. [0044] Reference will now be made in detail to certain embodiments of the disclosed subject matter, examples of which are illustrated in part in the accompanying drawings. While the disclosed subject matter will be described in conjunction with the enumerated claims, it will be understood that the exemplified subject matter is not intended to limit the claims to the disclosed subject matter. [0045] Throughout this document, values expressed in a range format should be interpreted in a flexible manner to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited. For example, a range of “about 0.1% to about 5%” or “about 0.1% to 5%” should be interpreted to include not just about 0.1% to about 5%, but also the individual values (e.g., 1%, 2%, 3%, and 4%) and the sub-ranges (e.g., 0.1% to 0.5%, 1.1% to 2.2%, 3.3% to 4.4%) within the indicated range. The statement “about X to Y” has the same meaning as “about X to about Y,” unless indicated otherwise. Likewise, the statement “about X, Y, or about Z” has the same meaning as “about X, about Y, or about Z,” unless indicated otherwise. [0046] In this document, the terms “a,” “an,” or “the” are used to include one or more than one unless the context clearly dictates otherwise. The term “or” is used to refer to a nonexclusive “or” unless otherwise indicated. The statement “at least one of A and B” or “at least one of A or B” has the same meaning as “A, B, or A and B.” In addition, it is to be understood that the phraseology or terminology employed herein, and not otherwise defined, is for the purpose of description only and not of limitation. Any use of section headings is intended to aid reading of the document and is not to be interpreted as limiting; information that is relevant to a section heading may occur within or outside of that particular section. All publications, patents, and patent documents referred to in this document are incorporated by reference herein in their entirety, as though individually incorporated by reference. In the event of inconsistent usages between this document and those documents so incorporated by reference, the usage in the incorporated reference should be considered supplementary to that of this document; for irreconcilable inconsistencies, the usage in this document controls. [0047] In the methods described herein, the acts can be carried out in any order without departing from the principles of the present disclosure, except when a temporal or operational sequence is explicitly recited. Furthermore, specified acts can be carried out concurrently unless explicit claim language recites that they be carried out separately. For example, a claimed act of doing X and a claimed act of doing Y can be conducted simultaneously within a single operation, and the resulting process will fall within the literal scope of the claimed process. [0048] The term “about” as used herein can allow for a degree of variability in a value or range, for example, within 10%, within 5%, or within 1% of a stated value or of a stated limit of a range, and includes the exact stated value or range. The term “substantially” as used herein refers to a majority of, or mostly, as in at least about 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.9%, 99.99%, or at least about 99.999% or more, or 100%. The term “substantially free of” as used herein can mean having none or having a trivial amount of, such that the amount of material present does not affect the material properties of the composition including the material, such that about 0 wt% to about 5 wt% of the composition is the material, or about 0 wt% to about 1 wt%, or about 5 wt% or less, or less than or equal to about 4.5 wt%, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.01, or about 0.001 wt% or less, or about 0 wt%. [0049] The term “ambient room temperature” refers to about 23 deg C. [0050] Unless otherwise specified, the term “percent” or “%” refers to weight percent. [0051] The term “reactive group” refer to a functional group that can selectively react with another compatible functional group to form a covalent bond, in some cases, after optional activation of one of the functional groups. Chemoselective functional groups of interest include, but are not limited to, thiols, maleimides, halogenated maleimides, iodoacetamides, amines, alkyl carboxylates, alkyl sulfonates, carboxylic amines, carbamate, carboxylate esters, N-hydroxysuccinimidyl (NHS), imido ester, halogen, boronic esters, boronic acids, hydrazonyl, carboxylic acids or active esters thereof, as well as groups that can react with one another via Click chemistry, e.g., azide and alkyne groups (e.g., cyclooctyne groups), tetrazine and alkene groups (e.g., cyclooctene groups), dienes and dienophiles, sulfur (VI) fluoride exchange chemistry (SuFEX), sulfonyl fluoride, as well as hydroxyl, hydrazido, hydrazino, aldehyde, ketone, azido, alkyne, phosphine, epoxide, and the like, or protected groups thereof. The reactive group may be a conjugation tag. The chemoselective functional group may be protected or unprotected. [0052] The term “amine-reactive group” refers to any group that forms a chemical bond with a primary amine. Amine-reactive groups of interest include, but are not limited to, isothiocyanates, isocyanates, acyl azides, NHS esters, imidoesters, sulfonyl chlorides, aldehydes, glyoxals, epoxides, oxiranes, carbonates, aryl halides, imidoesters, carbodiimides, anhydrides, and fluorophenyl esters. The amine-reactive group can be a NHS ester or imidoesters. [0053] In some cases, non-covalent linking may involve specific binding between two moieties of interest (e.g., two affinity moieties such as a hapten and an antibody or a biotin moiety and a streptavidin, etc.). In certain cases, non-covalent linking may involve absorption to a substrate. [0054] The term “symmetric” in reference to a compound of the present disclosure refers to wherein each terminal heterocyclic ring system is the same, and substituents may be the same or different. In some symmetric compounds, n=2. [0055] The term “asymmetric” in reference to a compound of the present disclosure refers to wherein each terminal heterocyclic ring system is different. In some asymmetric compounds, n=3. [0056] The term “counterion” refers to an ion that is charge balancing to the fluorescent compound according to the disclosure. The counter ion may be a cation. The counterion may be an anion. In some cases the counterion may be a halogen ion, perchlorate ion, PF^6-, phosphate ion, sulfate ion, and the like. The counterion may be, F- , Cl-, Br-, I-, ClO4-, CF3CO2-, CH3CO2-, PO4^3-, SO4^2-, BF4-, and the like. In some cases the counterion may be Na⁺, K⁺, Mg⁺⁺, Ca⁺⁺, and the like. [0057] For example, benzothienopyrrole-cyanine dye-labeled antibodies according to the present disclosure find use in flow cytometry as reagents exhibiting a fluorescent signal. Additionally, orthogonal “functional group(s)” can be included that can be used for either bioconjugation or the attachment of acceptor signaling chromophores in donor acceptor benzothienopyrrole tandem dyes. [0058] The term “organic group” as used herein refers to any carbon-containing functional moiety. Examples can include an oxygen-containing group such as an alkoxy group; aryloxy group; aralkyloxy group; oxo(carbonyl) group; an amine group, including alkyl amine esters, and sulfonamide groups; a carboxyl group including a carboxylic acid, carboxylate, and a carboxylate ester; a sulfur-containing group such as an alkyl and aryl sulfide group, thiol, thiol reactive group, and sulfone group; maleimide; iodoacetamide; azide group; alkyne group; and other heteroatom-containing groups. Non-limiting examples of organic groups include OR, OOR, OC(O)N(R)₂, CN, CF3, OCF3, R, C(O)R, methylenedioxy, ethylenedioxy, N(R)2, N3, S(H)R, SOR, SO₂R, SO₂N(R)₂, SO₃R, C(O)R, C(O)C(O)R, C(O)CH₂C(O)R, C(S)R, C(O)OR, OC(O)R, C(O)N(R)2, OC(O)N(R)2, C(S)N(R)2, (CH2)0-2N(R)C(O)R, (CH2)0- ₂N(R)N(R)₂, N(R)N(R)C(O)R, N(R)N(R)C(O)OR, N(R)N(R)CON(R)₂, N(R)SO₂R, N(R)SO2N(R)2, N(R)C(O)OR, N(R)C(O)R, N(R)C(S)R, N(R)C(O)N(R)2, N(R)C(S)N(R)₂, N(COR)COR, N(OR)R, C(=NH)N(R)₂, C(O)N(OR)R, C(=NOR)R, and substituted or unsubstituted (C1-C100)hydrocarbyl, wherein R can be hydrogen (in examples that include other carbon atoms) or a carbon-based moiety, and wherein the carbon-based moiety can be substituted or unsubstituted. [0059] The term “heteroatom” as used herein refers to any appropriate atom that is not carbon, such as, for example, N, O, S, Se, P, B, Al, Si, and Ge, inserted between adjacent carbon atoms in an organic group. The organic group may be a cyclic, aryl, or straight or branched chain group (e.g., alkyl or alkene). More than one heteroatom (e.g., 1, 2, 3, 4 or 5heteroatoms) may be inserted between adjacent carbon atoms. The heteroatoms can be oxidized to form moieties such as, but not limited to, -S(O)- and S(O)₂-, sulfinate, sulfonamide. [0060] The term “substituted” as used herein in conjunction with a molecule or an organic group as defined herein refers to the state in which one or more hydrogen atoms contained therein are replaced by one or more non-hydrogen atoms, such as, for example an alkyl, aryl, or a functional group. The “substituted” group may include one or more groups selected from halogen, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. [0061] The terms “functional group,” “functional moiety,” or “substituent” as used herein refers to a group that can be or is substituted onto a molecule or onto an organic group. Examples of substituents or functional groups can include, but are not limited to, a halogen (e.g., F, Cl, Br, and I); alkene; an oxygen atom in groups such as hydroxy groups, alkoxy groups, aryloxy groups, aralkyloxy groups, oxo(carbonyl) groups, carboxyl groups including carboxylic acids, carboxylates, and carboxylate esters; a sulfur atom in groups such as thiol groups, alkyl and aryl sulfide groups, sulfoxide groups, sulfone groups, sulfonyl groups, and sulfonamide groups; a nitrogen atom in groups such as amines, hydroxyamines, nitriles, nitro groups, N-oxides, hydrazides, azides, tetrazines, imides (e.g., maleimide), and enamines; and other heteroatoms in various other groups. Non-limiting examples of substituents that can be bonded to a substituted carbon (or other) atom include F, Cl, Br, I, OR, OC(O)N(R)2, CN, NO, NO₂, ONO₂, azido, CF₃, OCF₃, R, O (oxo), S (thiono), C(O), S(O), methylenedioxy, ethylenedioxy, N(R)2, SR, SOR, SO2R, SO2N(R)2, SO3R, C(O)R, C(O)C(O)R, C(O)CH₂C(O)R, C(S)R, C(O)OR, OC(O)R, C(O)N(R)₂, OC(O)N(R)₂, C(S)N(R)₂, (CH2)0-2N(R)C(O)R, (CH2)0-2N(R)N(R)2, N(R)N(R)C(O)R, N(R)N(R)C(O)OR, N(R)N(R)CON(R)₂, N(R)SO₂R, N(R)SO₂N(R)₂, N(R)C(O)OR, N(R)C(O)R, N(R)C(S)R, N(R)C(O)N(R)2, N(R)C(S)N(R)2, N(COR)COR, N(OR)R, C(=NH)N(R)2, C(O)N(OR)R, and C(=NOR)R, wherein R can be hydrogen or a carbon-based moiety; for example, R can be hydrogen, (C1-C100)hydrocarbyl, alkyl, acyl, cycloalkyl, aryl, aralkyl, heterocyclyl, heteroaryl, or heteroarylalkyl; or wherein two R groups bonded to a nitrogen atom or to adjacent nitrogen atoms can together with the nitrogen atom or atoms form a heterocyclyl. The subject fluorescent compounds can include one or more “functional group(s)” that provide for bioconjugation. In some cases, such functionality may be used to covalently attach a biomolecule or binding partner such as a protein, peptide, affinity ligand, antibody, antibody fragment, polynucleotide, or aptamer. In some cases the functional group may be selected from the group consisting of amine, carbamate, carboxylic acid, carboxylate, maleimide, activated ester, N- hydroxysuccinimidyl, hydrazine, hydrazide, hydrazone, isothiocyanato, azide, alkyne, alkene, tetrazine, aldehyde, thiol, and protected groups thereof for conjugation to a substrate, acceptor dye, functional moiety, or binding partner. The functional group may be protected or unprotected. The functional group may be a reactive or chemoselective functional group that can react with another group via Click chemistry, such as, for example, cycloalkene (e.g., cyclooctene); alkyne; cycloalkyne (e.g., cyclooctyne group, such as, for example, bicyclo[6.1.0] nonyne (BCN)), Dibenzocyclooctyne (DBCO)); cycloalkene (e.g., cyclooctene group, such as, for example, CO trans-cyclooctene(TCO)); azide group; and tetrazine group. [0062] As used herein, the term “activated ester” or “active esters” by itself or as part of another substituent refers to carboxyl-activating groups employed in peptide chemistry to promote facile condensation of a carboxyl group with a free amino group of an amino acid derivative. Descriptions of these carboxyl-activating groups are found in general textbooks of peptide chemistry, for example K. D. Kopple, “Peptides and Amino Acids”, W. A. Benjamin, Inc., New York, 1966, pp.50-51 and E. Schroder and K. Lubke, “The Peptides”; Vol.1, Academic Press, New York, 1965, pp.77-128 which are each incorporated herein by reference in their entireties. [0063] As used herein, the term “ammonium” by itself or as part of another substituent refers to a cation having the formula NHR3⁺ where each R group, independently, is hydrogen or a substituted or unsubstituted alkyl, aryl, aralkyl, or alkoxy group. Preferably, each of the R groups is hydrogen. [0064] The term “hydrocarbon” or “hydrocarbyl” as used herein refers to a molecule or functional group that includes carbon and hydrogen atoms. The term can also refer to a molecule or functional group that normally includes both carbon and hydrogen atoms but wherein some or all the hydrogen atoms are substituted with other functional groups. The term “hydrocarbyl” refers to a functional group derived from a straight chain, branched, or cyclic hydrocarbon, and can be alkyl, alkenyl, alkynyl, aryl, cycloalkyl, acyl, or any combination thereof. Hydrocarbyl groups can be shown as (Ca- C_b)hydrocarbyl, wherein a and b are integers and mean having any of a to b number of carbon atoms. For example, (C1-C4)hydrocarbyl means the hydrocarbyl group can be methyl (C₁), ethyl (C₂), propyl (C₃), or butyl (C₄), and (C₀-C_b)hydrocarbyl means in certain embodiments there is no hydrocarbyl group. A hydrocarbylene group is a diradical hydrocarbon, e.g., a hydrocarbon that is bonded at two locations. [0065] As used herein, the term “alkyl” by itself or as part of another substituent refers to a straight or branched, saturated, aliphatic radical having the number of carbon atoms indicated. Alkyl groups can be optionally substituted alkyl groups. For example, C1-C6 alkyl includes, but is not limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, etc. Other alkyl groups include, but are not limited to heptyl, octyl, nonyl, decyl, etc. Alkyl can include any number of carbons, such as 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 2-3, 2-4, 2-5, 2-6, 3-4, 3-5, 3-6, 4-5, 4-6 and 5-6. Alkyl can also refer to alkyl groups having up to 20 carbons atoms, such as, but not limited to heptyl, octyl, nonyl, decyl, etc. Alkyl groups can be substituted or unsubstituted. Unless otherwise specified, “substituted alkyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. The alkyl group is typically monovalent, but can be divalent, such as when the alkyl group links two moieties together. [0066] As used herein, the term “alkylene” refers to an alkyl group, as defined above, linking at least two other groups (i.e., a divalent alkyl radical). The two moieties linked to the alkylene group can be linked to the same carbon atom or different carbon atoms of the alkylene group. [0067] As used herein, the term “alkoxy” by itself or as part of another substituent refers to an alkyl group, as defined above, having an oxygen atom that connects the alkyl group to the point of attachment. Alkoxy groups include, for example, methoxy, ethoxy, propoxy, iso-propoxy, butoxy, 2-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, pentoxy, hexoxy, etc. The alkoxy groups can be further substituted with a variety of substituents described within. For example, the alkoxy groups can be substituted with halogens to form a “halo-alkoxy” group. [0068] As used herein, the term “alkene” or “alkenyl” by itself or as part of another substituent refers to either a straight chain, branched chain, or cyclic hydrocarbon, having at least one double bond between two carbon atoms. Examples of alkene groups include, but are not limited to, vinyl, propenyl, isopropenyl, 1-butenyl, 2-butenyl, isobutenyl, butadienyl, 1-pentenyl, 2-pentenyl, isopentenyl, 1,3-pentadienyl, 1,4- pentadienyl, 1-hexenyl, 2-hexenyl, 3-hexenyl, 1,3-hexadienyl, 1,4-hexadienyl, 1,5- hexadienyl, 2,4-hexadienyl, or 1,3,5-hexatrienyl. The alkene group is typically monovalent, but can be divalent, such as when the alkenyl group links two moieties together. [0069] As used herein, the term “alkyne” or “alkynyl” by itself or as part of another substituent refers to either a straight chain or branched hydrocarbon, having at least one triple bond between two carbon atoms. Examples of alkynyl groups include, but are not limited to, acetylenyl, propynyl, 1-butynyl, 2-butynyl, isobutynyl, sec-butynyl, butadiynyl, 1-pentynyl, 2-pentynyl, isopentynyl, 1,3-pentadiynyl, 1,4-pentadiynyl, 1- hexynyl, 2-hexynyl, 3-hexynyl, 1,3-hexadiynyl, 1,4-hexadiynyl, 1,5-hexadiynyl, 2,4- hexadiynyl, or 1,3,5-hexatriynyl. The alkynyl group is typically monovalent, but can be divalent, such as when the alkynyl group links two moieties together. [0070] The term “acyl” as used herein refers to a group containing a carbonyl moiety wherein the group is bonded via the carbonyl carbon atom. The carbonyl carbon atom is bonded to a hydrogen forming a “formyl” group or is bonded to another carbon atom, which can be part of an alkyl, aryl, aralkyl cycloalkyl, cycloalkylalkyl, heterocyclyl, heterocyclylalkyl, heteroaryl, heteroarylalkyl group or the like. An acyl group can include 0 to about 12, 0 to about 20, or 0 to about 40 additional carbon atoms bonded to the carbonyl group. An acyl group can include double or triple bonds within the meaning herein. An acyl group can optionally also include heteroatoms within the meaning herein. Examples of acyl groups include, but are not limited to, a nicotinoyl group (pyridyl-3-carbonyl) acetyl, benzoyl, phenylacetyl, pyridylacetyl, cinnamoyl, and acryloyl groups and the like. When the group containing the carbon atom that is bonded to the carbonyl carbon atom contains a halogen, the group is termed a “haloacyl” group. An example is a trifluoroacetyl group. [0071] As used herein, the term “aldehyde” by itself or as part of another substituent refers to a chemical compound that has a —CHO group. [0072] As used herein, the term “aryl” by itself or as part of another substituent refers to cyclic aromatic hydrocarbon groups that do not contain heteroatoms in the aromatic ring assembly. “Aryl” groups can be a monocyclic or fused bicyclic, tricyclic, tetracyclic, pentacyclic, or greater, aromatic ring assembly containing 6 to 22, 14 to 22, 17 to 22, or 6 to 16 ring carbon atoms. For example, aryl may be, but is not limited to, phenyl, azulenyl, heptalenyl, biphenyl, indacenyl, fluorenyl, phenanthrenyl, triphenylenyl, pyrenyl, naphthacenyl, chrysenyl, biphenylenyl, anthracenyl, benzyl, or naphthyl, and the like. In some cases, the aryl may be phenyl. [0073] The term “monocyclic aryl” refers to an unsubstituted or substituted aryl ring system comprising 1 aryl ring with or without fused cycloalkyl or cycloalkenyl rings. [0074] The term “monocyclic heteroaryl” refers to an unsubstituted or substituted heteroaryl ring system comprising 1 aryl ring with or without fused cycloalkyl or cycloalkenyl rings, and wherein the monocyclic ring system comprises one or more, two or more, three or more, or four or more heteroatoms. Nonlimiting examples of a monocyclic heteroaryl group are substituted or unsubstituted pyridinyl, pyranyl, thiophenyl, furanyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl. [0075] The term “polycyclic aryl” refers to an unsubstituted or substituted polycyclic ring system comprising 2 to 9, 2 to 8, or 2 to 6 aryl rings with or without fused cycloalkyl or cycloalkenyl rings. Examples of polycyclic aryl groups may include fluorene, 9H-fluorene, phenanthrene, dihydrophenanthrene, 9,10-dihydrophenanthrene, naphthalene, anthracene, tetracene, pentacene, and the like. [0076] The term “polycyclic heteroaryl” refers to an unsubstituted or substituted polycyclic ring system comprising 2 to 9, 2 to 8, or 2 to 6 aryl rings with or without fused cycloalkyl or cycloalkenyl rings, and wherein the polycyclic ring system comprises one or more, two or more, three or more, or four or more heteroatoms. Non- limiting examples of polycyclic heteroaryl systems may include quinoline, benzoxazole, benzothiazole, benzimidazole, indole, benzindole, pyridinium, benzopyrylium, thiopyrylium, 6,8-dihydro-5H-naphtho[2,1-f]indole, 4,5-dihydro-3H- naphtho[2,1-e]indole, 6,7-dihydro-3H-naphtho[2,1-g]indole, 5,6- dihydrophenanthro[3,2-d]thiazole, 4,5-dihydrophenanthro[2,1-d]thiazole, 6,7- dihydrophenanthro[4,3-d]thiazole, 5,6-dihydrophenanthro[3,2-d]oxazole, 4,5- dihydrophenanthro[2,1-d]oxazole, 6,7-dihydrophenanthro[4,3-d]oxazole, 5,6- dihydronaphtho[2,1-g]quinoline, 7,8-dihydronaphtho[2,1-h]quinoline, 5,6- dihydronaphtho[2,1-f]quinoline, 5,6-dihydro-8 ^2-phenanthro[3,2-d]imidazole, 4,5- dihydro-3 ^2-phenanthro[2,1-d]imidazole, 6,7-dihydro-3 ^2-phenanthro[4,3- d]imidazole, 5,6-dihydronaphtho[1,2-g]quinoxaline, 5,6-dihydronaphtho[2,1- f]quinoxaline, 7,8-dihydronaphtho[1,2-f]quinoxaline, 5,6-dihydropentapheno[3,2,1- cd:10,11,12-c'd']diindole, 3,8-dihydrophenanthro[2,3-e:7,6-e']diindole, 3,5,6,8- tetrahydrophenanthro[2,3-e:7,6-e']diindole, 1,2,3,5,6,8-hexahydrophenanthro[2,3-e:7,6- e']diindole-1,10-diium salt, 3,5,6,8-tetrahydrophenanthro[2,3-e:7,6-e']diindole--ethane (1/1), 5,6-dihydropentapheno[3,4-d:10,9-d']bis(oxazole), 1,2,5,6,9,10- hexahydropentapheno[3,4-d:10,9-d']bis(thiazole)-1,10-diium, pentapheno[3,4-d:10,9- d']bis(thiazole), 1,2,9,10-tetrahydropentapheno[3,4-d:10,9-d']bis(thiazole)-1,10-diium, 6,7-dihydrophenanthro[2,3-f:7,6-f']diquinoline-1,12-diium, 6,7-dihydrophenanthro[2,3- f:7,6-f']diquinoline, 2,6,7,11-tetrahydrobenzo[1,2-g:4,3-g']dichromene, 2,11- dihydrobenzo[1,2-g:4,3-g']dichromene, 5,10-dihydro-6H-naphtho[2,1-g]chromene, 10H-naphtho[2,1-g]chromene, 2,6,7,11-tetrahydrobenzo[1,2-g:4,3- g']bis(thiochromene), 2,11-dihydrobenzo[1,2-g:4,3-g']bis(thiochromene), and the like. [0077] The term “Arylene” refers to a divalent radical derived from an aryl group. Aryl groups can be mono-, di- or tri-substituted by one, two or three radicals selected from alkyl, alkoxy, aryl, hydroxy, halogen, cyano, amino, amino-alkyl, trifluoromethyl, alkylenedioxy and oxy-C₂-C₃-alkylene; all of which are optionally further substituted, for instance as hereinbefore defined; or 1- or 2-naphthyl; or 1- or 2-phenanthrenyl. Alkylenedioxy is a divalent substitute attached to two adjacent carbon atoms of phenyl, e.g., methylenedioxy or ethylenedioxy. Oxy-C2-C3-alkylene is also a divalent substituent attached to two adjacent carbon atoms of phenyl, e.g., oxyethylene or oxypropylene. An example for oxy-C2-C3-alkylene-phenyl is 2,3-dihydrobenzofuran-5- yl. [0078] Aryl groups can include substituted aryl groups. Substituted aryl groups include, e.g., but are not limited to, naphthyl or phenyl, optionally mono- or disubstituted by alkoxy, phenyl, halogen, alkyl or trifluoromethyl, hydroxyl, C1- C₁₂ alkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁-C₁₂ haloalkyl, C₁- C12 alkoxy, C2-C18 (hetero)aryloxy, C2-C18 (hetero)arylamino, carboxylate, carboxylic acid, C₂-C₁₂ alkyl carboxylic acid, C₂-C₁₂ alkyl carboxylate, C₂-C₁₂ alkyl carboxylate ester, C1-C12 alkoxy, a water-solubilizing group (WSG), a functional group, sulfonic acid, sulfonate, C₁-C₁₂ alkyl sulfonate. In some cases, the substituted aryl group, such as for example naphthyl or phenyl, may be mono- or disubstituted by a functional group, a WSG, optionally a WSG comprising a functional group, alkoxy, halogen or trifluoromethyl.The WSG can be a branched WSG, optionally comprising a functional group, such as, for example, a WSG comprising PEG and a functional group. [0079] As used herein, the term “aryloxy” by itself or as part of another substituent refers to a O-aryl group, wherein aryl is as defined above. An aryloxy group can be unsubstituted or substituted with one or two suitable substituents. The term “phenoxy” refers to an aryloxy group wherein the aryl moiety is a phenyl ring. The term “(hetero)aryloxy” as used herein means an —O-heteroaryl group, wherein heteroaryl is as defined below. The term “(hetero)aryloxy” is used to indicate the moiety is either an aryloxy or (hetero)aryloxy group. [0080] The term “aralkyl” as used herein refers to alkyl groups as defined herein in which a hydrogen or carbon bond of an alkyl group is replaced with a bond to an aryl group as defined herein. Representative aralkyl groups include benzyl and phenylethyl groups and fused (cycloalkylaryl)alkyl groups such as 4-ethyl-indanyl. Aralkenyl groups are alkenyl groups as defined herein in which a hydrogen or carbon bond of an alkyl group is replaced with a bond to an aryl group as defined herein. [0081] As used herein, the term “amine” by itself or as part of another substituent as used herein refers to an alkyl groups as defined within, having one or more amino groups. The amino groups can be primary, secondary or tertiary. The alkyl amine can optionally be further substituted, for example, with a hydroxy group. Amines useful in the present disclosure include, but are not limited to, ethyl amine, propyl amine, isopropyl amine, ethylene diamine and ethanolamine. The amino group can link the alkyl amine to the point of attachment with the rest of the compound, be at the omega position of the alkyl group, or link together at least two carbon atoms of the alkyl group. One of skill in the art will appreciate that other alkyl amines are useful in the present disclosure. [0082] The term “amino group” as used herein refers to a substituent of the form - NH₂, -NHR, -NR₂, -NR₃ ⁺, wherein each R is independently selected, and protonated forms of each, except for -NR3⁺, which cannot be protonated. Accordingly, any compound substituted with an amino group can be viewed as an amine. An “amino group” within the meaning herein can be a primary, secondary, tertiary, or quaternary amino group. An “alkylamino” group may include a monoalkylamino, dialkylamino, or trialkylamino group. [0083] The term “amide” refers to a functional group having a carbonyl group attached to an amine group, having the general formula RC(=O)NR’R’’, where R, R’, and R’’ represent organic groups or hydrogen atoms. The term “amido” refers to a substituent containing an amide group. [0084] As used herein, the term “carbamate” by itself or as part of another substituent refers to the functional group having the structure —NR″CO2R′, where R′ and R″ are independently selected from hydrogen, (C1-C8)alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C1-C4)alkyl, and (unsubstituted aryl)oxy-(C1-C4)alkyl. Examples of carbamates include t-Boc, Fmoc, benzyloxy- carbonyl, alloc, methyl carbamate, ethyl carbamate, 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluorenylmethyl carbamate, Tbfmoc, Climoc, Bimoc, DBD- Tmoc, Bsmoc, Troc, Teoc, 2-phenylethyl carbamate, Adpoc, 2-chloroethyl carbamate, 1,1-dimethyl-2-haloethyl carbamate, DB-t-BOC, TCBOC, Bpoc, t-Bumeoc, Pyoc, Bnpeoc, V-(2-pivaloylamino)-1,1-dimethylethyl carbamate, NpSSPeoc. [0085] As used herein, the term “carboxylic acid” by itself or as part of another substituent refers to a structure R-COOH where R is a carbon-containing group of atoms. [0086] As used herein, the term “carboxylate” by itself or as part of another substituent refers to the conjugate base of a carboxylic acid, which generally can be represented by the formula RCOO-. For example, the term “magnesium carboxylate” refers to the magnesium salt of the carboxylic acid The term “carboxylate ester” as used herein by itself or as part of another substituent refers to a compound derived from a carboxylic acid, which generally can be represented by the formula RCOOR′ where R′ can be an alkyl, alkene, alkyne, haloalkyl, heteroalkyl, cycloalkyl, aryl, heteroaryl, (unsubstituted aryl)alkyl, and (unsubstituted aryl)oxy-alkyl or other carbon-containing group of atoms. R′ can optionally contain functional groups. [0087] As used herein, the term “cycloalkyl” by itself or as part of another substituent refers to a saturated or partially unsaturated, monocyclic, fused bicyclic or bridged polycyclic ring assembly containing from 3 to 12 ring atoms or the number of atoms indicated. Cycloalkyl can include any number of carbons, such as C_3-6, C_4-6, C5-6, C3-8, C4-8, C5-8, C6-8, C3-9, C3-10, C3-11, and C3-12. Saturated monocyclic cycloalkyl rings include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cyclooctyl. Saturated bicyclic and polycyclic cycloalkyl rings include, for example, norbornane, [2.2.2] bicyclooctane, decahydronaphthalene and adamantane. Cycloalkyl groups can also be partially unsaturated, having one or more double or triple bonds in the ring. Representative cycloalkyl groups that are partially unsaturated include, but are not limited to, cyclobutene, cyclopentene, cyclohexene, cyclohexadiene (1,3- and 1,4-isomers), cycloheptene, cycloheptadiene, cyclooctene, cyclooctadiene (1,3-, 1,4- and 1,5-isomers), norbornene, and norbornadiene. When cycloalkyl is a saturated monocyclic C3-8 cycloalkyl, exemplary groups include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and cyclooctyl. When cycloalkyl is a saturated monocyclic C3-6 cycloalkyl, exemplary groups include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Cycloalkyl groups can be substituted or unsubstituted. Unless otherwise specified, “substituted cycloalkyl” groups can be substituted with one or more groups selected from halo, hydroxy, amino, alkylamino, amido, acyl, nitro, cyano, and alkoxy. Cycloalkyl groups can be substituted with K-R¹³, H, halogen, O-C_1-6 alkyl, S-C_1-6 alkyl, O-aryl, S-aryl, NHC1-6alkyl, Ph-NCS, Ph-CO2H, and Ph-(CH2)1-4CO2H. The term “lower cycloalkyl” refers to a cycloalkyl radical having from three to seven carbons including, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl. Monocyclic rings include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cyclooctyl. Bicyclic and polycyclic rings include, for example, norbornane, decahydronaphthalene and adamantane. For example, C_3-8cycloalkyl includes cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclooctyl, and norbornane. Polycyclic ring systems may be substituted or unsubstituted. [0088] As used herein, the term “cycloalkylene” refers to a cycloalkyl group, as defined above, linking at least two other groups (i.e., a divalent cycloalkyl radical). The two moieties linked to the cycloalkylene group can be linked to the same atom or different atoms of the cycloalkylene group. [0089] As used herein, the term “haloalkyl” by itself or as part of another substituent refers to alkyl as defined above where some or all of the hydrogen atoms are substituted with halogen atoms. Halogen (halo) preferably represents chloro or fluoro, but may also be bromo or iodo. For example, haloalkyl includes trifluoromethyl, flouromethyl, 1,2,3,4,5-pentafluoro-phenyl, etc. The term “perfluoro” defines a compound or radical which has at least two available hydrogens substituted with fluorine. For example, perfluorophenyl refers to 1,2,3,4,5-pentafluorophenyl, perfluoromethane refers to 1,1,1-trifluoromethyl, and perfluoromethoxy refers to 1,1,1- trifluoromethoxy. [0090] As used herein, the term “halogen” by itself or as part of another substituent refers to fluorine, chlorine, bromine, and iodine. [0091] As used herein, the term “heteroaryl” by itself or as part of another substituent refers to a monocyclic or fused polycyclic, such as bicyclic, tricyclic, tetracyclic, or pentacylic aromatic ring assembly, for example, containing 5 to 22, 14 to 22, 17 to 22, 6 to 16, or 5 to 16 ring atoms, where from 1 to 4 of the ring atoms may be a heteroatom, such as N, O, or S. Additional heteroatoms can also be useful, including, but not limited to, B, Al, Si, or P. The heteroaryl may be substituted or unsubstituted. Substituted heteroaryl may include one or more K-R¹³, halogen, O-C1-6 alkyl, S-C1-6 alkyl, O-aryl, S-aryl, NHC_1-6alkyl, Ph-NCS, Ph-CO₂H, Ph-(CH₂)_1-4CO₂H substituents. [0092] As used herein, the terms “heteroalkyl” or “heteroalkoxy” by itself or as part of another substituent refers to an alkyl or alkoxy group, preferably a C₁-C₁₂ alkyl group or C1-C12 alkoxy group where a C is substituted by a heteroatom such as N, O or S. For example, heteroalkyl or heteroalkoxy can include ethers, thioethers and alkyl-amines. Additional heteroatoms can also be useful, including, but not limited to, B, Al, Si, or P. The heteroatoms can be oxidized to form moieties such as, but not limited to, -S(O)- , -S(O)2-, sulfinate, sulfonamide. The heteroatom portion of the heteroalkyl can replace a hydrogen atom of the alkyl group to form a hydroxy, thio or amino group. Alternatively, the heteroatom portion can be the connecting atom, or be inserted between two carbon atoms. For example, heteroaryl may include pyridyl, indolyl, indazolyl, quinoxalinyl, quinolinyl, isoquinolinyl, benzothienyl, benzofuranyl, furanyl, pyrrolyl, thiazolyl, benzothiazolyl, oxazolyl, isoxazolyl, triazolyl, tetrazolyl, pyrazolyl, imidazolyl, thienyl, or any other radicals substituted, especially mono- or di- substituted, by, e.g., alkyl, nitro or halogen. Pyridyl may represent 2-, 3- or 4-pyridyl, advantageously 2- or 3-pyridyl. Thienyl may represent 2- or 3-thienyl. Quinolinyl may represent preferably 2-, 3- or 4-quinolinyl. Isoquinolinyl may represent preferably 1-, 3- or 4-isoquinolinyl. Benzopyranyl, benzothiopyranyl represents preferably 3- benzopyranyl or 3-benzothiopyranyl, respectively. Thiazolyl may represent preferably 2- or 4-thiazolyl, and most preferred, 4-thiazolyl. Triazolyl may represent preferably 1-, 2- or 5-(1,2,4-triazolyl). Tetrazolyl is preferably 5-tetrazolyl. The heteroaryl may include aryloxy or arylamino groups. In some embodiments, heteroaryl is pyridyl, indolyl, quinolinyl, pyrrolyl, thiazolyl, isoxazolyl, triazolyl, tetrazolyl, pyrazolyl, imidazolyl, thienyl, furanyl, benzothiazolyl, benzofuranyl, isoquinolinyl, benzothienyl, oxazolyl, indazolyl, or any of the radicals substituted, especially mono- or di- substituted. [0093] The term “heterocycloalkyl” by itself or as part of another substituent refers to a monocyclic or fused polycyclic, such as bicyclic, tricyclic, tetracyclic, or pentacylic aromatic ring assembly, for example, containing 5 to 22, 14 to 22, 17 to 22, 6 to 16, or 5 to 16 ring atoms, where from 1 to 4 of the ring atoms may be a heteroatom each independently selected from N, O, or S. Additional heteroatoms can also be useful, including, but not limited to, B, Al, Si, or P. The heterocycloalkyl may be substituted or unsubstituted. Substituted heterocycloalkyl may include one or more K- R¹³, halogen, O-C_1-6 alkyl, S-C_1-6 alkyl, O-aryl, S-aryl, NHC_1-6alkyl, Ph-NCS, Ph- CO2H, Ph-(CH2)1-4CO2H substituents. [0094] As used herein, the term “heteroalkylene” refers to a heteroalkyl group, as defined above, linking at least two other groups (i.e., a divalent heteroalkyl radical). The two moieties linked to the heteroalkylene group can be linked to the same atom or different atoms of the heteroalkylene group. [0095] As used herein, the term “(hetero)arylamino” by itself or as part of another substituent refers an amine radical substituted with an aryl group (e.g., —NH-aryl). An arylamino may also be an aryl radical substituted with an amine group (e.g., -aryl- NH2). Arylaminos may be substituted or unsubstituted. [0096] In some embodiments, substituents for the aryl, heteroaryl, and heteroalkylene groups are varied and are selected from: -halogen, —OR′, —OC(O)R′, —C(O)R′,—NR′R″, —SR′, —R′, —CN, —NO₂, —CO₂R′, —CONR′R″, —C(O)R′, — OC(O)NR′R″, —NR″C(O)R′, —NR″C(O)2R′, —NR′—C(O)NR″R′″, —NH— C(NH₂)═NH, —NR′C(NH₂)═NH, —NH—C(NH₂)═NR′, —S(O)R′, —S(O)₂R′, — S(O)2NR′R″, —N3, —CH(Ph)2, perfluoro(C1-C4)alkoxy, and perfluoro(C1-C4)alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R′, R″ and R′″ are independently selected from hydrogen, (C1- C₅)alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C₁- C4)alkyl, and (unsubstituted aryl)oxy-(C1-C4)alkyl. [0097] Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -T-C(O)—(CH2)q—U—, wherein T and U are independently —NH—, —O—, —CH₂— or a single bond, and q is an integer of from 0 to 2. Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH2)r—B—, wherein A and B are independently —CH2—, —O—, —NH—, — S—, —S(O)—, —S(O)₂—, —S(O)₂NR′— or a single bond, and r is an integer of from 1 to 3. One of the single bonds of the new ring so formed may optionally be replaced with a double bond. Alternatively, two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula — (CH2)s—X’—(CH2)t—, where s and t are independently integers of from 0 to 3, and X’ is —O—, —NR′—, —S—, —S(O)—, —S(O)₂—, or —S(O)₂NR′—. The substituent R′ in —NR′— and —S(O)2NR′— is selected from hydrogen or unsubstituted (C1- C₆)alkyl. [0098] As used herein, the term “oligoether” is understood to mean an oligomer containing structural repeat units having an ether functionality. As used herein, an “oligomer” is understood to mean a molecule that contains one or more identifiable structural repeat units of the same or different formula. [0099] The terms “polyethylene oxide”, “PEO”, “polyethylene glycol” and “PEG” are used interchangeably and refer to a polymeric moiety including a chain described by the formula -(CH2-CH2-O)n- or a derivative thereof. The PEG can be linear or branched. In some embodiments, “n” is 5000 or less, such as 1000 or less, 500 or less, 200 or less, 100 or less, 50 or less, 40 or less, 30 or less, 20 or less, 15 or less, such as 3 to 15, or 10 to 15. As used herein, PEG groups include, but are not limited to, PEG, modified PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, alkyl sulfonamide-PEG and alkoxy sulfonamide-PEG. It is understood that the PEG polymeric moiety may be of any convenient length and may include a variety of terminal groups and/or further substituent groups, including but not limited to, alkyl, aryl, hydroxyl, amino, acyl, acyloxy, and amido terminal and/or substituent groups. PEG groups that may be adapted for use with the subject compounds include those PEGs described by S. Zalipsky in “Functionalized poly(ethylene glycol) for preparation of biologically relevant conjugates”, Bioconjugate Chemistry 1995, 6 (2), 150-165; by Zhu et al in “Water-Soluble Conjugated Polymers for Imaging, Diagnosis, and Therapy”, Chem. Rev., 2012, 112 (8), pp 4687-4735; by J.M. Harris in “Poly(ethylene glycol) Chemistry: Biotechnical and Biomedical Applications”, Plenum Press, New York, N.Y. (1992); and by J.M. Harris and S Zalipsky in “Poly(ethylene glycol) Chemistry and Biological Applications”, ACS (1997). In some instances, PEG and modified PEG moieties can be, for example, those taught in International Patent Applications: WO 90/13540, WO 92/00748, WO 92/16555, WO 94/04193, WO 94/14758, WO 94/17039, WO 94/18247, WO 94/28937, WO 95/11924, WO 96/00080, WO 96/23794, WO 98/07713, WO 98/41562, WO 98/48837, WO 99/30727, WO 99/32134, WO 99/33483, WO 99/53951, WO 01/26692, WO 95/13312, WO 96/21469, WO 97/03106, WO 99/45964 U.S. Pat. Nos.4,179,337; 5,075,046; 5,089,261; 5,100,992; 5,134,192; 5,166,309; 5,171,264; 5,213,891; 5,219,564; 5,275,838; 5,281,698; 5,298,643; 5,312,808; 5,321,095; 5,324,844; 5,349,001; 5,352,756; 5,405,877; 5,455,027; 5,446,090; 5,470,829; 5,478,805; 5,567,422; 5,605,976; 5,612,460; 5,614,549; 5,618,528; 5,672,662; 5,637,749; 5,643,575; 5,650,388; 5,681,567; 5,686,110; 5,730,990; 5,739,208; 5,756,593; 5,808,096; 5,824,778; 5,824,784; 5,840,900; 5,874,500; 5,880,131; 5,900,461; 5,902,588; 5,919,442; 5,919,455; 5,932,462; 5,965,119; 5,965,566; 5,985,263; 5,990,237; 6,011,042; 6,013,283; 6,077,939; 6,113,906; 6,127,355; 6,177,087; 6,180,095; 6,194,580; 6,214,966 each of which are incorporated herein by reference. [00100] As used herein, the term “sulfonate functional group” or “sulfonate” either by itself or as part of another substituent refers to both the free sulfonate anion (— S(=O)₂O—) and salts thereof. Therefore, the term sulfonate encompasses sulfonate salts such as sodium, lithium, potassium and ammonium sulfonate. [00101] As used herein, the term “sulfonamide” by itself or as part of another substituent refers to a group of formula —SO2NR2 where each R can independently be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or functional group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non-ionic water-soluble polymer, such as, for example, PEG, or modified PEG terminated with a carboxylic acid or a carboxylic ester. The “sulfonamide” attached to another molecule by a linker or bond. The “sulfonamide” can be, for example, sulfonamide-PEG, alkyl sulfonamide, alkoxy sulfonamide, alkyl sulfonamide PEG, alkoxy sulfonamide PEG, alkyl sulfonamide PEG carboxylate, alkoxy sulfonamide PEG carboxylate. [00102] As used herein, the term “sulfonamido” by itself or as part of another substituent refers to a group of formula —SO₂NR— where R can be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or functional group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non-ionic water-soluble polymer, such as, for example, PEG, or modified PEG terminated with a carboxylic acid or a carboxylic ester. The “sulfonamido” can be attached to another molecule by a linker or bond. The “sulfonamido” can be, for example, sulfonamido-PEG, alkyl sulfonamido, alkoxy sulfonamido, alkyl sulfonamido PEG, alkoxy sulfonamido PEG, alkyl sulfonamido PEG carboxylate, alkoxy sulfonamido PEG carboxylate. [00103] As used herein, the term “sulfinamide” by itself or as part of another substituent refers to a group of formula —SONR₂ where each R can independently be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or functional group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non-ionic water-soluble polymer, such as, for example, PEG, or modified PEG terminated with a carboxylic acid or a carboxylic ester. The “sulfinamide” can be attached to another molecule by a linker or bond. The “sulfinamide” can be, for example, sulfinamide-PEG, alkyl sulfinamide, alkoxy sulfinamide, alkyl sulfinamide PEG, alkoxy sulfinamide PEG, alkyl sulfinamide PEG carboxylate, alkoxy sulfinamide PEG carboxylate. [00104] As used herein, the terms “hydrazine” and “hydrazide” by themselves or as part of another substituent refer to compounds that contain singly bonded nitrogens, one of which is a primary amine functional group. For example, the term “hydrazine” refers to a moiety having the structure –NHNH₂. [00105] As used herein, the term “thiol” by itself or as part of another substituent refers to a compound that contains the functional group composed of a sulfur-hydrogen bond. The general chemical structure of the thiol functional group is R—SH, where R represents an alkyl, alkene, aryl, or other carbon-containing group of atoms. [00106] As used herein, the term “silyl” by itself or as part of another substituent refers to Si(R^z)₃ wherein each R^z independently is alkyl, aryl or other carbon-containing group of atoms. [00107] As used herein, the term “diazonium salt” by itself or as part of another substituent refers to a group of organic compounds with a structure of R—N2⁺X⁻, wherein R can be any organic group (e.g., alkyl or aryl) and X is an inorganic or organic anion (e.g., halogen). [00108] As used herein, the term “triflate” by itself or as part of another substituent also referred to as trifluoromethanesulfonate, is a group with the formula CF3SO3. [00109] As used herein, the term “boronic acid” by itself or as part of another substituent refers to a structure -B(OH)2. It is recognized by those skilled in the art that a boronic acid may be present as a boronate ester. Boronic acid is meant to include such esters. The term “boronic ester” or “boronate ester” as used herein refers to a chemical compound containing a —B(Z¹)(Z²) moiety, wherein Z¹ and Z² together form a moiety where the atom attached to boron in each case is an oxygen atom. In some embodiments, the boronic ester moiety is a 5-membered ring. In some other embodiments, the boronic ester moiety is a 6-membered ring. In some other embodiments, the boronic ester moiety is a mixture of a 5-membered ring and a 6- membered ring. [00110] As used herein, the term “maleimide” by itself or as part of another substituent refers a structure where R can be, for example, a water solubilizing moiety, hydrogen , alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, halogen, or other group and can contain carboxylic groups. R can be a water- solubilizing polymer including, but not limited to, a Ypolymer comprising 6 or more monomeric units, a non-ionic water-soluble polymer, PEG, modified PEG terminated with a carboxylic acid or a carboxylic ester. [00111] As used herein, the term “hydrazone” by itself or as part of another substituent refers to a structure where R can be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or other group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non- ionic water-soluble polymer, PEG, modified PEG terminated with a carboxylic acid or a carboxylic ester. [00112] As used herein, the term “azide” by itself or as part of another substituent refers to a structure-N3. [00113] As used herein, the term “N h i i i l” by itself or as part of another substituent refers to a structure can be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or other group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non-ionic water-soluble polymer, PEG, modified PEG terminated with a carboxylic acid or a carboxylic ester. [00114] As used herein, the term “phosphoramide” by itself or as part of another substituent refers to a structure where R can be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or other group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non- ionic water-soluble polymer, such as, for example, PEG, or modified PEG terminated with a carboxylic acid or a carboxylic ester. The “phosphoramide” can be attached to another molecule by a linker or bond. The “phosphoramide” can be, for example, phosphoramide-PEG, alkyl phosphoramide, alkoxy phosphoramide, alkyl phosphoramide PEG, alkoxy phosphoramide PEG, alkyl phosphoramide PEG carboxylate, alkoxy phosphoramide PEG carboxylate. [00115] As used herein, the term “phosphonamidate” by itself or as part of another substituent refers to a structure where R can be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or other group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non- ionic water-soluble polymer, such as, for example, PEG, or modified PEG terminated with a carboxylic acid or a carboxylic ester. The “phosphonamidite” can be attached to another molecule by a linker or bond. The “phosphonamidite”can be, for example, phosphonamidite-PEG, alkyl phosphonamidite, alkoxy phosphonamidite, alkyl phosphonamidite PEG, alkoxy phosphonamidite PEG, alkyl phosphonamidite PEG carboxylate, alkoxy phosphonamidite PEG carboxylate. [00116] As used herein, the term “phosphinamide” by itself or as part of another substituent refers to a structure where R can be, for example, a water solubilizing moiety, hydrogen, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, aryl, or other group and can contain carboxylic groups. R can be a water-solubilizing polymer including, but not limited to, a polymer comprising 6 or more monomeric units, a non- ionic water-soluble polymer, such as, for example, PEG, modified PEG terminated with a carboxylic acid or a carboxylic ester. The “phosphinamide” can be attached to another molecule by a linker or bond. The “phosphinamide” can be, for example, phosphinamide-PEG, alkyl phosphinamide, alkoxy phosphinamide, alkyl phosphinamide PEG, alkoxy phosphinamide PEG, alkyl phosphinamide PEG carboxylate, alkoxy phosphinamide PEG carboxylate. [00117] The term “fluorescent” as used herein refers to a compound which, when irradiated by light of a wavelength that the compound absorbs, emits light of a (typically) different wavelength. Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. In most cases, the emitted light has a longer wavelength than the absorbed light. [00118] The term “absorbance maxima” or “Abs ^ max” or “max ^ abs” refer to wavelength of maximum absorbance measured by UV Vis spectroscopy. [00119] The term “excitation wavelength” or “ ^ ^ex” refers to the wavelength where the compound can be excited to induce fluorescence emission, it does not necessarily have to be at the Abs ^ max. [00120] The term “chromophore” refers to a molecular entity or a portion thereof consisting of an atom or a group of atoms in which the electronic transition responsible for a given spectral band is approximately localized. In some instances, the “chromophore” may itself be fluorescent. As used herein, the terms “fluorescent chromophore” and “fluorescent dye” are used interchangeably and refer to a compound which has a structure capable of harvesting light with a particular absorption maximum wavelength and converting it to emitted light at a longer emission maximum wavelength. A chromophore may have a reactive group (e.g., a carboxylate moiety, an amino moiety, a haloalkyl moiety, or the like) that can be covalently bonded. Examples of suitable chromophores include, but are not limited to, those described in U.S. Pat. Nos.7,687,282; 7,671,214; 7,446,202; 6,972,326; 6,716,979; 6,579,718; 6,562,632; 6,399,392; 6,316,267; 6,162,931; 6,130,101; 6,005,113; 6,004,536; 5,863,753; 5,846,737; 5,798,276; 5,723,218; 5,696,157; 5,658,751; 5,656,449; 5,582,977; 5,576,424; 5,573,909; and 5,187,288, which patents are incorporated herein by reference in their entirety. [00121] The term “moiety” refers to a group as a portion of a molecule, which may be a functional group, or a portion of a molecule with multiple groups which share common structural and/or functional aspects. Examples of group or moiety include but are not limited to a linker moiety, a functional group, a water-solubilizing moiety, a PEG moiety, according to the present disclosure. [00122] The term “linker”, “linked,” or “linkage” refers to a linking moiety that connects two groups and has a backbone of 100 atoms or less in length. A linker or linkage may be a covalent bond that connects two groups or a chain of between 1 and 100 atoms in length, for example a chain of 1, 2, 3, 4, 5, 6, 8, 10, 12, 14, 16, 18, 20 or more carbon atoms in length, where the linker may be linear, branched, cyclic or a single atom. In some embodiments, the linker is a branching linker that refers to a linking moiety that connects three or more groups. In certain cases, one, two, three, four or five or more carbon atoms of a linker backbone may be optionally substituted with a sulfur, nitrogen or oxygen heteroatom. In some embodiments, the linker backbone includes a linking functional group, such as an ether, thioether, amino, amide, carbonyl, acyl, sulfonamide, a sulfinamide, a disulfonamide, a disulfinamide, a sultam, an amide, a secondary amine, a phosphonamide, a phosphinamide, a phosphonamidate, a selenonamide, a seleninamide, carbamate, thiocarbamate, urea, thiourea, ester, thioester or imine. In some embodiments, the linker backbone includes a linking functional group, such as an amino, amide, carbonyl, sulfonamide, sulfinamide, a disulfonamide, a disulfinamide, a sultam, an amide, a secondary amine, a phosphonamide, a phosphinamide, a phosphonamidate, a selenonamide, or a seleninamide. The bonds between backbone atoms may be saturated or unsaturated, and in some cases not more than one, two, or three unsaturated bonds are present in a linker backbone. The linker may include one or more substituent groups, for example with an alkyl, aryl or alkenyl group. A linker may include, without limitations, polyethylene glycol, ethers, thioethers, tertiary amines, alkyls, which may be straight or branched, e.g., methyl, ethyl, n-propyl, 1-methylethyl (iso-propyl), n-butyl, n-pentyl, 1,1- dimethylethyl (t-butyl), and the like. The linker backbone may include a cyclic group, for example, an aryl, a heterocycle or a cycloalkyl group, where 2 or more atoms, e.g., 2, 3 or 4 atoms, of the cyclic group are included in the backbone. [00123] The phrase “conjugated water-soluble fluorescent compound” refers to a water-soluble fluorescent compound having a binding partner conjugated thereto. [00124] In chemical structures, “ ” represents either a single or double bond. [00125] In chemical structures, represents an aryl group, for example, a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, polycyclic aryl group, monocyclic heteroaryl group, or polycyclic heteroaryl group. [00126] In chemical structures, is an optionally substituted cycloalkenyl or polycycloalkenyl moiety which ma y be partially unsaturated. The optionally substituted cycloalkenyl may be an optionally substituted cyclohex-1-en-1-yl. The optionally substituted cycloalkenyl may be substituted with a halogen, such as a chloro group, or a phenylthio group. The optionally substituted polycycloalkenyl moiety may be an optionally substituted naphthalenyl moiety. The optionally substituted cycloalkenyl or polycycloalkenyl moiety may be partially unsaturated. [00127] The phrase “binding partner” refers to any molecule or complex of molecules capable of specifically binding to a target analyte. A binding partner of the present disclosure includes for example, a protein (e.g., an antibody or an antibody fragment), a small organic molecule, a carbohydrate (e.g., a polysaccharide), an oligonucleotide, a polynucleotide, a lipid, an affinity ligand, an aptamer, or the like. In some embodiments, the binding partner is an antibody or fragment thereof. Specific binding in the context of the present disclosure refers to a binding reaction which is determinative of the presence of a target analyte in the presence of a heterogeneous population. Thus, under certain assay conditions, the specified binding partners bind preferentially to a particular protein or isoform of the particular protein and do not bind in a significant amount to other proteins or other isoforms present in the sample. [00128] In some cases, the antibody includes intravenous immunoglobulin (IVIG) and/or antibodies from (e.g., enriched from, purified from, e.g., affinity purified from) IVIG. IVIG is a blood product that contains IgG (immunoglobulin G) pooled from the plasma (e.g., in some cases without any other proteins) from many (e.g., sometimes over 1,000 to 60,000) normal and healthy blood donors. IVIG is commercially available. Aspects of IVIG are described, for example, in US. Pat. Appl. Pub. Nos. 2010/0150942; 2004/0101909; 2013/0177574; 2013/0108619; and 2013/0011388. [00129] In some cases, the antibody is a monoclonal antibody of a defined sub-class (e.g., IgG1, IgG2, IgG3, or IgG4). If combinations of antibodies are used, the antibodies can be from the same subclass or from different subclasses. For example, the antibodies can be IgG1 antibodies. In some embodiments, the monoclonal antibody is humanized. [00130] The phrase “water-soluble fluorescent complex” refers to a water-soluble fluorescent compound of the present disclosure conjugated with a binding partner. [00131] The phrase “protected group” (also referred to as "protecting group" or “protected”) refers to a reversibly formed derivative of an existing functional group in a molecule attached to decrease reactivity so that the protected functional group does not react under synthetic conditions to which the molecule is subjected. Examples of amine protecting groups include, but are not limited to, benzyloxycarbonyl; 9-fluorenylmethyloxycarbonyl (Fmoc); tert-butyloxycarbonyl (Boc); allyloxycarbonyl (Alloc); p-toluene sulfonyl (Tos); 2,2,5,7,8-pentamethylchroman-6-sulfonyl (Pmc); 2,2,4,6,7-pentamethyl-2,3-dihydrobenzofuran-5-sulfonyl (Pbf); mesityl-2-sulfonyl (Mts); 4-methoxy-2,3,6-trimethylphenylsulfonyl (Mtr); acetamido; phthalimido; and the like. These and other protecting groups for amines, carboxylic acids, alcohols, and further functional groups can be added to and removed from polymers of the present disclosure using known techniques as described, for example, by Green and Wuts (Protective Groups in Organic Synthesis, 4^th Ed.2007, Wiley-Interscience, New York). [00132] The term “sample” refers to a material or mixture of materials, in some cases in liquid form, containing one or more analytes of interest. In some embodiments, the term as used in its broadest sense, refers to any plant, animal or bacterial material containing cells or producing cellular metabolites, such as, for example, tissue or fluid isolated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment. The term “sample” may also refer to a “biological sample”. As used herein, the term “a biological sample” refers to a whole organism or a subset of its tissues, cells or component parts (e.g. body fluids, including, but not limited to, blood, mucus, lymphatic fluid, synovial fluid, cerebrospinal fluid, saliva, amniotic fluid, amniotic cord blood, urine, vaginal fluid and semen). A “biological sample” can also refer to a homogenate, lysate or extract prepared from a whole organism or a subset of its tissues, cells or component parts, or a fraction or portion thereof, including but not limited to, plasma, serum, spinal fluid, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, blood cells, tumors and organs. In certain embodiments, the sample has been removed from an animal or plant. Biological samples may include cells. The term “cells” is used in its conventional sense to refer to the basic structural unit of living organisms, both eukaryotic and prokaryotic, having at least a nucleus and a cell membrane. In certain embodiments, cells include prokaryotic cells, such as from bacteria. In other embodiments, cells include eukaryotic cells, such as cells obtained from biological samples from animals, plants or fungi. [00133] The term “substrate” refers to a solid material having a variety of configurations. The substrate can be, for example, a sheet, bead, or other structure, such as a plate with wells, a polymer, particle, a semiconductor surface, nanotubes, a fibrous mesh, hydrogels, porous matrix, a pin, a microarray surface, a chromatography support, and the like. In some instances, the substrate is selected from the group consisting of a particle, a planar solid substrate, a fibrous mesh, a hydrogel, a porous matrix, a pin, a microarray surface and a chromatography support. [00134] The term “water” as used herein refers to any aqueous solution that is primarily water and is compatible with physiological conditions. In some instances, the aqueous solution contains more than 50% water, such as more than 60% water, more than 70% water, more than 80% water, more than 90% water, or more than 95% water. The term “water” includes, for example, biological buffers and other aqueous solutions that may contain additives such as salts, detergents, stabilizers, and other water-soluble components, for example, sugars, proteins, amino acids, and nucleotides. In some instances, “water” may be an aqueous solution containing up to 10% miscible organic solvent (e.g., up to 10% DMSO in water). The term “water” does not include pure solvents or solvent combinations different from water, such as pure alcohols, for example pure methanol or ethanol, pure ethers, for example pure diethyl ether or tetrahydrofuran, or any other pure solvent either miscible or not miscible with water. [00135] The term “water-solubilizing moiety” or “water-solubilizing group” (WSG or W) as used herein by itself or part of another group refers to any hydrophilic group that is well solvated in aqueous environments, for example such as under physiological conditions, and is capable of increasing the water solubility of the molecule to which it is attached. Any convenient WSG may be included in the dyes described herein to provide for increased water-solubility. A water-solubilizing moiety can increase the solubility of a compound in a predominantly aqueous solution, as compared to a control compound which lacks the water-solubilizing moiety. The water-solubilizing moiety may be any convenient hydrophilic moiety that is well solvated in aqueous environments. In some instances, the water-solubilizing moiety can be capable of imparting solubility in water (e.g., aqueous buffer) > 1 mg/mL, > 2 mg/mL, > 3 mg/mL, > 4 mg/mL, > 5 mg/mL, > 6 mg/mL, > 7 mg/mL, > 8 mg/mL, > 9 mg/mL, or >10 mg/mL. In some instances, the water-solubilizing moiety can be capable of imparting solubility in water of > 10 mg/mL , > 20 mg/mL, > 30 mg/mL, > 40 mg/mL, > 50 mg/mL, > 60 mg/mL, > 70 mg/mL, > 80 mg/mL, > 90 mg/mL or > 100 mg/mL. [00136] The increase in water solubility of the molecule can vary depending upon the moiety attached. In some instances, the increase in water solubility (as compared to the solubility of the molecule without the moiety attached) is 2 fold or more, 5 fold or more, 10 fold or more, 25 fold or more, 50 fold or more, or 100 fold or more. In some cases, the water-solubilizing moiety is charged, e.g., a positively or negatively charged hydrophilic moiety. In some instances, the water-solubilizing moiety is a neutral hydrophilic moiety. In some instances, the water-solubilizing moiety is branched (e.g., as described herein). In some instances, the water-solubilizing moiety is linear. Water- solubilizing moieties include, but are not limited to, those taught in US Patent Publication No.2022/0348770 which is incorporated herein by referenced in its entirety. [00137] A “water-soluble compound” may exhibit solubility in water (e.g., aqueous buffer) of > 1 mg/mL, > 2 mg/mL, > 3 mg/mL, > 4 mg/mL, > 5 mg/mL, > 6 mg/mL, > 7 mg/mL, > 8 mg/mL, > 9 mg/mL, or >10 mg/mL at ambient room temperature. In some instances, the water-soluble compound can exhibit solubility in water of > 10 mg/mL , > 20 mg/mL, > 30 mg/mL, > 40 mg/mL, > 50 mg/mL, > 60 mg/mL, > 70 mg/mL, > 80 mg/mL, > 90 mg/mL and/or > 100 mg/mL at ambient room temperature [00138] Any convenient WSG may be included in the dyes described herein to provide for increased water-solubility. WSGs may be, but are not limited to, carboxylate, carboxylic acid, phosphonate, phosphate, sulfonate, sulfate, sulfinate, sulfonium, ester, polyethylene glycols (PEG) and modified PEGs, linear PEG groups, branched PEG groups, hydroxyl, amine, amino acid, ammonium, guanidinium, pyridinium, polyamine and sulfonium, polyalcohols, straight chain or cyclic saccharides, primary, secondary, tertiary, or quaternary amines and polyamines, phosphonate groups, phosphinate groups, ascorbate groups, glycols, including, polyethers, a zwitterionic derivative, a peptide sequence, nucleotides (DNA and RNA), a peptoid, a carbohydrate, an oxazoline, a polyol, a dendron, a dendritic polyglycerol, a cellulose, a chitosan, —COOM′, —SO3M′, —PO3M′, —NR³+, Y′, (CH2CH2O)pR and mixtures thereof, where Y′ can be any halogen, sulfate, sulfonate, or oxygen containing anion, p can be 1 to 500, each R can be independently H or an alkyl (such as methyl) and M′ can be a cationic counterion such as Na⁺, K⁺, and the like, or hydrogen, — (CH2CH2O)yyCH2CH2XR^yy, —(CH2CH2O)yyCH2CH2X—, — X(CH₂CH₂O)_yyCH₂CH₂—, glycol, and polyethylene glycol, wherein yy is selected from 1 to 1000, X is selected from O, S, and NR^ZZ, and R^ZZ and R^YY are independently selected from H and C_1-3 alkyl, and combinations or derivatives thereof. In some instances, WSGs include, but are not limited to, PEG, a modified PEG, a peptide sequence, a peptoid, a carbohydrate, an oxazoline, a polyol, a dendron, a dendritic polyglycerol, a cellulose, a chitosan, or a derivative thereof. WSGs may be unsubstituted or substituted. [00139] In some instances, the WSGs may be a hydrophilic polymer. For example, hydrophilic polymers that can be utilized in the WSG include, but are not limited to, polyalkylene oxide based polymers comprising an ethylene oxide repeat unit of the formula —(CH₂—CH₂—O)_n— or —(O—CH₂—CH₂)_n—, such as, for example, PEG, polyamide alkylene oxide, or derivatives thereof. Further examples of polymers of interest include a polyamide having a molecular weight greater than 1,000 Daltons of the formula —[C(O)—X—C(O)—NH—Y—NH]n- or —[NH—Y—NH—C(O)—X— C(O)]_n—, where X and Y are divalent radicals that may be the same or different and may be branched or linear, and n is a discrete integer from 2-100, such as from 2 to 50, and where either or both of X and Y comprises a biocompatible, substantially non- antigenic water-soluble repeat unit that may be linear or branched. The number of such water-soluble repeat units can vary significantly, with the number of such units being from 2 to 500, 2 to 400, 2 to 300, 2 to 200, 2 to 100, 6-100, for example from 2 to 50 or 6 to 50. An example of an embodiment is one in which one or both of X and Y is selected from: —((CH₂)_n1—(CH₂—CH₂—O)_n2—(CH₂)— or —((CH₂)_n1—(O—CH₂— CH2)n2—(CH2)n1—), where n1 is 1 to 6, 1 to 5, 1 to 4, or 1 to 3, and where n2 is 2 to 50, 2 to 25, 2 to 15, 2 to 10, 2 to 8, or 2 to 5. In some instances, the water-soluble polymer is a group of 1-50 monomeric units, such as 1-40, 1-30, 1-20, 2-24, 2-20, 2-10 or 2-6 monomeric units. A further example of an embodiment is one in which X is — (CH2—CH2)—, and where Y is —(CH2—(CH2—CH2—O)3—CH2—CH2—CH2)— or —(CH₂—CH₂—CH₂—(O—CH₂—CH₂)₃—CH₂)—. In certain instances, any one of the formulae described herein may be substituted with a water-soluble moiety that is a dendron, as known in art. [00140] In some instances, hydrophilic polymers can be, for example, PEG, a peptide sequence, a peptoid, a carbohydrate, an oxazoline, a polyol, a dendron, a dendritic polyglycerol, a cellulose, a chitosan, or a derivative thereof. [00141] In some cases, a WSG is (CH₂)_x(OCH₂CH₂)_yOCH₃ where each x is independently an integer from 0-20, each y is independently an integer from 0 to 50. In some instances, the water-soluble polymer is a PEG group or modified PEG polymer of 6-24 monomeric units, such as 10-30, 10-24, 10-20, 12-24, 12-20, 12-16 or 16-20 monomeric units. [00142] In some cases, the WSG includes a non-ionic polymer (e.g., a PEG polymer) substituted at the terminal with an ionic group (e.g., a sulfonate). In some embodiments of the formulae, the WSG includes a substituent selected from (CH₂)_x(OCH₂CH₂)_yOCH₃ where each x is independently an integer from 0-20, each y is independently an integer from 0 to 50; and a benzyl optionally substituted with one or more halogen, hydroxyl, C₁-C₁₂ alkoxy, or (OCH₂CH₂)_zOCH₃ where each z is independently an integer from 0 to 50. In some instances, the WSG is (CH₂)₃(OCH₂CH₂)₁₁OCH₃. In some embodiments, one or more of the substituents is a benzyl substituted with at least one WSG groups (e.g., one or two WSG groups) selected from (CH₂)_x(OCH₂CH₂)_yOCH₃ where each x is independently an integer from 0-20 and each y is independently an integer from 0 to 50. It is understood that hydroxy- terminated polymer chains (e.g., PEG chains) instead of methoxy-terminated polymer chains (e.g., PEG chains) may be utilized in any of the water-solubilizing moieties. [00143] The term modified polymer, such as a modified PEG, refers to water soluble polymers that have been modified or derivatized at either or both terminals, e.g., to include a terminal substituent (e.g., a terminal alkyl, substituted alkyl, alkoxy or substituted alkoxy, etc.) and/or a terminal linking functional group (e.g., an amino or carboxylic acid group suitable for attachment via amide bond formation) suitable for attached of the polymer to a molecule of interest (e.g., to a light harvesting chromophore via a branching group). The subject water-soluble polymers can be adapted to include any convenient linking groups. It is understood that in some cases, the water-soluble polymer can include some dispersity with respect to polymer length, depending on the method of preparation and/or purification of the polymeric starting materials. In some instances, the water-soluble polymers are monodisperse. [00144] The water-soluble polymer can include one or more spacers or linkers. Examples of spacers or linkers include linear or branched moieties comprising one or more repeat units employed in a water-soluble polymer, diamino and or diacid units, natural or unnatural amino acids or derivatives thereof, as well as aliphatic moieties, including alkyl, aryl, heteroalkyl, heteroaryl, alkoxy, and the like, which can contain, for example, up to 18 carbon atoms or even an additional polymer chain. [00145] The water-soluble polymer moiety, or one or more of the spacers or linkers of the polymer moiety when present, may include polymer chains or units that are biostable or biodegradable. For example, polymers with repeat linkages have varying degrees of stability under physiological conditions depending on bond lability. Polymers with such bonds can be categorized by their relative rates of hydrolysis under physiological conditions based on known hydrolysis rates of low molecular weight analogs, e.g., from less stable to more stable, e.g., polyurethanes (—NH—C(O)—O— )>polyorthoesters (—O—C((OR)(R′))—O—)>polyamides (—C(O)—NH—). Similarly, the linkage systems attaching a water-soluble polymer to a target molecule may be biostable or biodegradable, e.g., from less stable to more stable: carbonate (— O—C(O)—O—)>ester (—C(O)—O—)>urethane (—NH—C(O)—O—)>orthoester (—O—C((OR)(R′))—O—)>amide (—C(O)—NH—). In general, it may be desirable to avoid use of a sulfated polysaccharide, depending on the lability of the sulfate group. In addition, it may be less desirable to use polycarbonates and polyesters. These bonds are provided by way of example, and are not intended to limit the types of bonds employable in the polymer chains or linkage systems of the water-soluble polymers useful in the WSGs disclosed herein. [00146] In some instances, the water-solubilizing moieties include, but are not limited to, hydroxy, alkoxy, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl carboxylate, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylcarboxylate, alkylamide, alkoxy sulfonate, alkyl sulfonate, alkyl sulfonate salt, , ,

[00147] In some instances, the subject compounds may comprise multiple water- solubilizing moieties attached at a single location in the subject compounds, for example, via a branching linker, such as, for example, an aralkyl substituent further di- substituted with water solubilizing groups. As such, in some cases, the branching linker group is a substituent of the dye that connects the dye to two or more water solubilizing groups. In some instances, multiple water-solubilizing moieties may be attached to the subject compounds via groups having, for example, the following formulas:

(VId), wherein X¹, X² are branching points, L¹, L², L³ are linkers, m’ is an integer from 1, 2, or 3; W¹ is a water-solubilizing moiety. [00148] In some instances, one or more water-solubilizing moieties may be attached to the subject compounds via a group comprising linkers according to the disclosure, for example, as taught in US Published Application No.2020/0190253A1, which is incorporated herein by reference in its entirety. A linker moiety can be attached to the cyanine bridge or the heterocycloaryl groups of the fluorescent compounds of the instant disclosure. A linker may be cleavable or non-cleavable. [00149] One or more water-solubilizing moieties can also be attached to the subject compounds via a group comprising linkers, such as, for example, but not limited to, the following linker formula (VIe): - (L³)_m –(X¹)_m’-(( L¹)_m”-(W¹)_s)_t-R³ (VIe) wherein: each optional L¹ and L³ is an independently selected linker moiety; X¹, optionally present, is a branching point; W¹ is a water-soluble moiety, including, but not limited to, a water-soluble polymer comprising 2-50, 4-30, or 6-24 monomeric units; each m is independently 0 or 1; each m’ is independently 0 or 1; each m” is independently 0 or 1; each s is independently 1 or 2; each t is independently 0, 1, 2, or 3; and R³ is as defined herein. [00150] In some instances, L¹, L³, and X are absent and W¹ is a water-solubilizing moiety, for example, a water-soluble polymer comprising 2-50, 4-30, or 6-24 monomeric units, such as 10-30, 10-24, 10-20, 12-24, 12-20, 12-16 or 16-20 monomeric units. In some cases, the water-solubilizing moiety may be a linear water- solubilizing moiety. For example, L¹ and X may be absent, L³ is a linker (e.g., as disclosed herein), and W¹ is a water-solubilizing moiety. [00151] In some cases, at least one of, at least two of, or all three of L¹, L² and/or L³ may be selected from an alkyl or substituted alkyl linker, an alkenyl or substituted alkenyl linker, an alkynyl or substituted alkynyl linker, an alkoxy or substituted alkoxy linker, a PEG linker, a sulfonamido-alkyl or substituted sulfonamido-alkyl linker, an amido-alkyl or substituted amido-alkyl linker and an alkyl-amido-alkyl or substituted alkyl-amido-alkyl linker. In certain cases, the linker comprises a carbonyl group. A linker moiety can be a covalent bond, an alkoxy, sulfonamide, disulfonamide, a selenomide, a sulfinamide, a sultam, a disulfinamide, an amide, carbonyl, a seleninamide, a phosphonamide, a phosphinamide, a phosphonamidate, or a secondary amine. [00152] In some instances, L² and L³ may be linker moieties each independently selected from the group consisting of a covalent bond, C_1-8 alkylene, 2- to 8-membered heteroalkylene, and a chain of between 2 and 200 backbone atoms in length, wherein the chain comprises a linear chain, a branched chain, and/or a cyclic moiety [00153] In some instances, L¹ can be a sulfonamide, a sulfinamide, a disulfonamide, a disulfinamide, a sultam, an amide, a secondary amine, a phosphonamide, a phosphinamide, a phosphonamidate, a selenonamide, or a seleninamide. [00154] In some instances, L³ can be a linker having a backbone of 20 atoms or less in length and W¹ is a water-solubilizing moiety (e.g., as described herein). In some instances, L³ can be selected from an alkyl or substituted alkyl linker, an alkenyl or substituted alkenyl linker, an alkynyl or substituted alkynyl linker, an acyl or substituted acyl, an alkoxy or substituted alkoxy linker, a PEG linker, a sulfonamido- alkyl or substituted sulfonamido-alkyl linker, an amido-alkyl or substituted amido-alkyl linker and an alkyl-amido-alkyl or substituted alkyl-amido-alkyl linker. In some instances, L³ can be a bond. In some instances, L³ can be an alkyl or substituted alkyl linker, an alkenyl or substituted alkenyl linker, an alkynyl or substituted alkynyl linker, an alkoxy or substituted alkoxy linker and X can be an aryl group. [00155] In some instances, L¹ and L³ are each independently selected from a C1- C₁₂ alkyl or substituted alkyl linker, a C₁-C₁₂ alkenyl or substituted alkenyl linker, a C₁- C12 alkynyl or substituted alkynyl linker, a C1-C12 acyl or substituted acyl linker, a C1- C₁₂ alkoxy or substituted alkoxy linker, a C₁-C₁₂ amido-alkyl or substituted amido-alkyl linker, a C1-C12 alkyl-amido-alkyl or substituted alkyl-amido-alkyl linker, a sulfonamide, a sulfinamide, a disulfonamide, a disulfinamide, a sultam, an amide, a secondary amine, a phosphonamide, a phosphinamide, a phosphonamidate, a selenonamide, and a seleninamide. In certain cases, L³ comprises a carbonyl group or alkoxy group, and L¹ is a C1-C12 alkyl or substituted alkyl, a sulfonamide, a sulfinamide, a disulfonamide, a disulfinamide, a sultam, an amide, a secondary amine, a phosphonamide, a phosphinamide, a phosphonamidate, a selenonamide, and a seleninamide. In some instances, L³ can be an alkoxy or substituted alkoxy linker, X can be absent, and L¹ can be a sulfonamide, a sulfinamide, a disulfonamide, a disulfinamide, a sultam, an amide, a secondary amine, a phosphonamide, a phosphinamide, a phosphonamidate, a selenonamide, or a seleninamide. [00156] In some instances, the branching point X¹ is selected from N, CR′, C(═O)N, SO₂N, a tri-substituted aryl moiety (e.g., a 1,3,5-phenyl), a tetra-substituted aryl moiety (e.g., a 1, 3, 4, 5-phenyl), and a tri-substituted heteroaryl group. In certain instances, the branching point X¹ is a nitrogen atom. In other instances, the branching point X¹ is CR′, where R′ is selected from hydrogen, alkyl, substituted alkyl, or -L³-W¹ (e.g., as described herein). [00157] The term “sulfonamide,” refers to a moiety –S(O)2NR-; the term “disulfonamide,” refers to a moiety –S(O)₂NRS(O)₂-; the term “selenonamide,” refers to a moiety –Se(O)2NR-; the term “sulfinamide,” refers to a moiety –S(O)NR2; the term “disulfinamide,” refers to a moiety –S(O)NRS(O)-; the term “seleninamide,” refers to a moiety –Se(O)NR-; the term “phosphonamide,” refers to a moiety –NR-PR(O)NR-; the term “phosphinamide,” refers to a moiety –PR(O)NR-; and the term “phosphonamidate,” refers to a moiety –O-PR(O)NR-; and the term “sultam” refers to a cyclic sulfonamide (e.g., wherein the R group is bonded to the sulfur atom via an alkylene moiety); wherein for each term the R group is independently H, alkyl, haloalkyl, or aryl. [00158] The term “cyanine” (Cy) as used herein refers to a substituted or unsubstituted bridge unit permitting delocalization across the BtCy molecules of the invention. In some embodiments, the “cyanine” is a substituted or unsubstituted methine or polymethine unit, such as a tri-, penta- or heptamethine unit. For example, in some embodiments, “cyanine” refers to substituted and unsubstituted groups, such as the following: In some embodiments, the cyanine is In other embodiments, the cyanine is In some embodiments, the cyanine is still other embodiments, the cyanine is In some embodiments, the cyanine is embodiments the “cyanine” is a substituted or unsubstituted “cyclic group” such as, for example, a “squaraine” cycloalkenyl or polycycloalkenyl moiety, which may be substituted or unsubstituted. [00159] The term “squaraine” as used herein refers to a substituted or unsubstituted cyclic group, such as a 4-membered, 5-membered, or 6-membered ring. In addition, the molecules of the invention include other cyanine cyclic groups and heterocyclic groups, including, but not limited to, substituted or unsubstituted five- or six-membered cyclic and heterocyclic groups. For example, cyanine cyclic groups include, but are not limited to, substituted or unsubstituted cyanine cyclic and heterocyclic groups such as the following:

, , or , wherein C is a four-, five- or six-membered cyclic, heterocyclic, or fused polycyclic group. In some embodiments, the cyanine cyclic group is a squaraine group such as . In some embodiments, the cyanine cyclic group is . In some embodiments, the cyanine cyclic group is . In other embodiments, the cyanine cyclic group is

. In still other embodiments, the cyanine cyclic group is . In some embodiments, the cyanine cyclic group is . In some embodiments, the cyanine cyclic group is . In some embodiments, the cyanine cyclic R¹⁶ m_{' R} ¹⁶ m_' 5 group is . In some embodiments, the cyanine cyclic group is

III. Benzothienopyrrole-cyanine Compounds [00160] The disclosure provides benzothienopyrrole-cyanine (BtCy) compounds, and methods for making BtCy compounds. The BtCy compounds can be a fluorescent water-soluble dye. The disclosure provides BtCy tandem dyes comprising BtCy compounds and a donor or acceptor dye. The disclosure also provides labeled specific binding partners comprising the BtCy compounds or BtCy tandem dyes and specific binding partners covalently linked to the BtCy compounds or BtCy tandem dyes. The BtCy tandem dyes include the BtCy compounds or labeled specific binding partners having an acceptor or donor chromophore attached thereto. Methods for detecting a target analyte in a sample using labeled specific binding partners of the invention, or tandem dye labeled specific binding partners, are also provided in the disclosure. The disclosure additionally provides kits containing a BtCy compound(s), labeled specific binding partner(s), and/or tandem dye(s) according to the invention. In addition to the specific structures disclosed herein, structural isomers of the disclosed structures are also included. [00161] Known cyanine compounds comprise two indole moieties and a cyanine bridge. Structures of known Cy3, Cy5, and Cy7 compounds are shown in FIG.1. Prior art Cy3 exhibit typical excitation wavelength (λex) and emission wavelengths (λem) of about 555 nm/569 nm (λex/λem, PBS), respectively. Prior art Cy5 exhibits λex and λem of about 651 nm/670 nm (( λex/ λem, PBS), respectively. Prior art Cy7 exhibits λex and λem of about 750 nm/780 nm (( λex/ λem, PBS), respectively. [00162] The BtCy compounds of the present disclosure each comprise at least one benzothienopyrrole moiety or derivative thereof and exhibit λex in a range of from about 500 nm to about 1100 nm and λem of about 550 nm to about 1200 nm. [00163] In some cases, the BtCy compounds of the present disclosure each comprise at least one benzothienopyrrole moiety or derivative thereof and exhibit λex in a range of from about 600 nm to about 1100 nm and λem of about 650 nm to about 1300 nm. [00164] In some cases, the BtCy compounds of the present disclosure exhibit λex in a range of from about 625 nm to about 1000 nm and λem of about 660 nm to about 1050 nm. [00165] In some cases, the BtCy3 compounds of the present disclosure exhibit λex in a range of from about 600 nm to about 775 nm and λem of about 650 nm to about 800 nm. [00166] In some cases, the BtCy5 compounds of the present disclosure exhibit λex in a range of from about 725 nm to about 875 nm and λem of about 750 nm to about 900 nm. [00167] In some cases, the BtCy7 compounds of the present disclosure exhibit λex in a range of from about 825 nm to about 975 nm and λem of about 850 nm to about 1000 nm. [00168] The BtCy compounds according to the disclosure may comprise a structure according to Formula (I): (I), wherein is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, polycyclic aryl group, monocyclic heteroaryl group, and polycyclic heteroaryl group; is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, and polycyclic aryl group; each T is independently NR^4’, CR¹, CR¹R², O, S, Se, or Te; V is NR¹¹, CR⁸, CR⁸R⁹, O, S, Se, or Te, or each T-V together can stand for a structural element selected from the group consisting of SO2, -CR¹-O-, -O-CR¹-, -CO- O-, -O-CO-, -CO-NR¹¹-, or -NR^4’-CO-; G is C or N; each R¹, R², R⁸, and R⁹ is independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, binding partner, linked binding partner, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, alkoxy sulfonate, carboxylic acid, carboxylate, alkyl carboxylate, alkoxy carboxylate, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkyl sulfonamide PEG, alkylamide, ,

; each R⁴, R^4’, R¹⁰, and R¹¹ is independently selected from the group consisting of a linker moiety, a chromophore, linked chromophore, reactive group, linked reactive group, conjugation tag, linked conjugation tag, water-solubilizing moiety, linked water- solubilizing moiety, binding partner, linked binding partner, E, linked E, H, halogen alkyl, alkenyl, alkynyl, a PEG group, a linked PEG group, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, carboxylic acid, carboxylate, alkyl carboxylate, alkyl sulfonamide, alkyl sulfonamide PEG, alkyl amide, alkyl amide-PEG, , r protected groups thereof, or one, two, three, or four of R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ together form an unsubstituted or substituted unsaturated or partially unsaturated C₃- C10 cycloalkyl group; unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ heterocycloalkyl optionally substituted with O; unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3-C8 polycycloalkyl group; or unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃ - C8 polyheterocycloalkyl group optionally substituted with O; each R³ is independently selected from the group consisting of H, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl, (hetero)arylamino, alkyl sulfonate, alkyl carboxylate, a water-solubilizing moiety, a linked water-solubilizing moiety, a chromophore, a linked chromophore, functional moiety, linked functional moiety, conjugation tag, linked conjugation tag, binding partner, linked binding partner, a PEG group, and a linked PEG group; each Q is independently a bond, O, NH, NR⁴, C1-C12 alkylene, CHR⁴, or CH2; each Z is independently CH₂, CHR⁴, O, NR⁴, or NH; each W¹ is independently a water-solubilizing moiety; L¹, L², and L³ are each independently selected linker moieties; each E is independently selected from the group consisting of a chromophore, a functional moiety, a substrate, a reactive group, conjugation tag, linked conjugation tag, and a binding partner; each R⁷ is independently selected from the group consisting of H, hydroxyl, C1- C₁₂ alkyl, C₁-C₁₂ heteroalkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁- C12 haloalkyl, C1-C12 alkoxy, C2-C18 (hetero)aryloxy, C2-C18 (hetero)arylamino, carboxylate, carboxylic acid, C₂-C₁₂ alkyl carboxylic acid, C₂-C₁₂ alkyl carboxylate, C₂- C12 alkyl carboxylate ester, aryl carboxylic acid, aryl carboxylate ester, C1-C12 alkoxy, a water-solubilizing moiety, a PEG moiety, a protected or unprotected functional group, conjugation tag, linked conjugation tag, a chemoselective functional group, a linker, sulfonic acid, sulfonate, C₁-C₁₂ alkyl sulfonate, sulfonamide; each R¹² , R¹³ and R¹⁴ is independently selected from the group consisting of hydrogen, halogen, one or more heteroatoms, substituted or unsubstituted C₁-C₆ alkyl, substituted or unsubstituted C1-C6 heteroalkyl, substituted or unsubstituted C1-C6 alkene, substituted or unsubstituted C3-C10 cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted C3-C10 heterocycloalkyl, CO2R¹, CONR¹R², O-aryl, S-aryl, N-aryl, -O-alkyl, S-alkyl, N-alkyl, wherein each alkyl or aryl can optionally be substituted with one or more R⁷, PEG, or PEG-R⁷, optionally wherein each R¹² , R¹³ and R¹⁴ is independently substituted with one or more R⁷ groups; or at least two of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, optionally including, but not limited to, one, two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ form an unsubstituted or substituted unsaturated or partially unsaturated C3-C10 cycloalkyl group, unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ heterocycloalkyl optionally substituted with O or N, an unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃-C₈ polycycloalkyl group, or unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3- C₈ polyheterocycloalkyl group optionally substituted with O or N; each K is independently a covalent bond, O, S, Se, P, NR¹, or CR¹R²; each f is independently an integer from 0 to 50, 1 to 30, or 2 to 20; each m and m’ is independently 0, 1, 2, or 3; each n is independently an integer from 1 to 20; 1 to 10; or 0, 1, 2, or 3; each p is independently 1, 2, 3, or 4; each s is independently 1 or 2; each t is independently 0, 1, 2, 3, or 4; and X is a counterion. [00169] In some cases, p is 1, 2, or 3. In some cases p is 1. In some cases, p is 2. In some cases, p is 3. In some cases, p is 4. [00170] In some cases, m is 0. In some cases, m is 1. In some cases, when m is 0, each T is independently CR¹ or CR¹R². In some cases, when m is 0, T is not NR^4’, S or O. In some cases, when m is 1, each T is independently NR^4’, O, S, Se, or Te. In some cases, when m is 1, T is not CR¹ or CR¹R². [00171] The BtCy compounds according to the present disclosure may comprise a structure according to any one of formulae (IIa), (IIb), (IIc), (IId), (IIe), (IIf), (IIg), (IIh), (IIi), (IIj), (IIk), (IIl), (IIm), (IIn), and (IIo): (IIa), (IIb),

),

T is NR , CR , CR R , O, or S; V is NR¹¹, CR⁸, CR⁸R⁹, O, or S; each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; R¹⁶ is K-R¹³, optionally H, halogen, O-C1-6 alkyl, S-C1-6 alkyl, O-aryl, S-aryl, NHC_1-6alkyl, Ph-NCS, Ph-CO₂H, Ph-(CH₂)_1-4CO₂H; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. [00172] The BtCy compounds according to the present disclosure may comprise a structure according to any one of formulae (IIIa), (IIIb), (IIIc), (IIId), (IIIe), (IIIf), (IIIg), (IIIh), (IIIi), (IIIj), (IIIk), (IIIl), (IIIm), and (IIIn): (IIIa),

wherein each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. [00173] The BtCy compounds according to the present disclosure may comprise a structure according to any one of formulae (IVa), (IVb), (IVc), (IVd), (IVe), (IVf), (IVg), (IVh), (IVi), (IVj), (IVk), (IVl), (IVm), (IVn), (IVo), (IVp), (IVq), (IVr), (IVs), (IVt), (IVu), (IVv), (IVw), and (IVx): 



wherein each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. [00174] The BtCy compounds according to the present disclosure may comprise a structure according to any one of Formulae (Va), (Vb), (Vc), (Vd), (Ve), (Vf), (Vg), (Vh), (Vi), (Vj), (Vk), and (Vl):

wherein Ar¹, Ar², R¹, R², R³, R⁴, R⁵, R⁶, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, R¹⁴, K, T, V, X, and m, are as defined herein, and Y is selected from the group consisting of NR⁴, CR¹, CR¹R², O, and S. In some cases, the polycyclic cyanine bridge may be substituted or unsubstituted. In some cases, the polycyclic cyanine bridge may be substituted with one or more R¹⁶ groups. Polycycloalkenyl cyanine bridges may be prepared according to the methods of Michie et al.2017 JACS, 139, 12406-12409, or Bandi et al., 2022, Nature Methods, 19, 353-358, each of which is incorporated by reference herein in its entirety. [00175] The BtCy compounds of the present disclosure may comprise a structure according to Formula (I), for example, Formulas (IIa)-(IIo), Formulas (IIIa)-(IIIn), Formulas (Iva)-(IVx), Formulas (Va)-(Vk) and (Vl), or a modified structures thereof, wherein one or both of the Ar¹ and Ar² aryl rings may be fused at any two adjacent carbons on the terminal heteroaryl ring systems. [00176] In some examples, at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises an E or linked E. [00177] In some examples, at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a binding partner or linked binding partner. [00178] In some examples, at least one, at least two, at least three, or at least four of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a water-solubilizing moiety or a linked water-solubilizing moiety. The water-solubilizing moiety or linked-water solubilizing moiety can be selected from, for example, carboxylates, carboxylic acids, phosphonates, phosphates, sulfonates, sulfonamides, sulfates, sulfinates, sulfoniums, esters, polyaklylene oxides, polyethylene oxides comprising an ethylene oxide repeat unit of the formula —(CH2—CH2—O)n—, polyamidealkylene oxides comprising an ethylene oxide repeat unit of the formula —(CH₂—CH₂—O)n—, polyethylene glycols (PEGs), modified PEGs, linked PEGs, amide-PEGs, sulfonamide-PEGs, phosphoramide-PEGs, hydroxyls, amines, amino acids, ammoniums, guanidiniums, pyridiniums, polyamines and sulfoniums, polyalcohols, straight chain or cyclic saccharides, primary, secondary, tertiary, or quaternary amines and polyamines, glycols, polyethers, —COOX, —SO3X, —PO3X, —NR3+X, (CH2CH2O)fR¹⁵ and mixtures thereof, wherein R¹⁵ is hydrogen, a substituted or unsubstituted C₁-C₆ alkyl, or a substituted or unsubstituted C1-C6 alkoxy, and X is a counterion. [00179] In some examples, at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a reactive group, linked reactive group, conjugation tag, or linked conjugation tag. [00180] In some examples, at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a chromophore or linked chromophore. [00181] In some examples, p is 1, 2, or 3. In some cases p is 1. In some cases, p is 2. In some cases, p is 3. In some cases, p is 4. [00182] In some examples, m is 0. In some examples, m is 1. In some examples, when m is 0, each T is independently CR¹ or CR¹R². In some examples, when m is 0, T is not NR^4’, S or O. In some examples, when m is 1, each T is independently NR^4’, O, S, Se, or Te. In some examples, when m is 1, T is not CR¹ or CR¹R². [00183] In some examples, the fluorescent compound according to the present disclosure is symmetric. [00184] In some examples, the fluorescent compound according to the present disclosure is asymmetric. [00185] In some examples, X is a counterion selected from the group consisting of F-, Cl-, Br-, I-, ClO₄-, CF₃CO₂-, CH₃CO₂-, PO₄ ^3-, SO₄ ^2-, BF₄-, Na⁺, K⁺, Mg⁺⁺, and Ca⁺⁺. [00186] In some examples, the reactive group or conjugation tag is selected from the group consisting of thiols, maleimides, halogenated maleimide, iodoacetamides, amines, alkyl carboxylates, alkyl sulfonates, carboxylic amines, carbamate, carboxylate esters, N-hydroxysuccinimidyl, halogen, boronic esters, boronic acids, hydrazonyl, carboxylic acids or active esters thereof, azide, alkyne, cyclooctyne, cyclooctene, tetrazine, cyclooctene, dienes, dienophiles, sulfur (VI) fluoride (SuFEX), sulfonyl fluoride, hydroxyl, hydrazido, hydrazino, aldehyde, ketone, azido, alkyne, phosphine, epoxide, and protected groups thereof. [00187] In some cases, when m is 0, each T is independently CR¹ or CR¹R². In some cases, when m is 0, T is not NR^4’, S or O. In some cases, when m is 1, each T is independently NR^4’, O, S, Se, or Te. In some cases, when m is 1, T is not CR¹ or CR¹R². [00188] The fluorescent compound according to the disclosure may comprise a structure selected from the group consisting of:

,

[00189] In the present disclosure, benzothienopyrrole intermediate compounds can be prepared via a number of synthetic routes, for example, as illustrated in FIG.2, Schemes 1 and 2, FIG.3, Schemes 3A, 3B and 4, FIG.9, Scheme 14, FIG, 16, Scheme18, FIG.17, Scheme 20, FIG.19, Scheme 23, and detailed in Examples 1A,1B, IC, ID, 3F, 3I, 3J, and 3L. [00190] As shown in Scheme 1, 2-iodobenzo[b]thiophene and tert-butyl hydrazinecarboxylate in DMF can be treated with Cs₂CO₃ and 1,10 phenanthroline and CuI to provide benzothiophene hydrazine compound 1: tert-butyl 1-(benzo[b]thiophen- 2-yl)hydrazine-1-carboxylate. Compound 1 can be treated with 3-methylbutan-2-one and para-tolunensulfonic acid (pTSA) to obtain compound 2: 2,3,3-trimethyl-3H- benzo[4,5]thieno[2,3-b]pyrrole. Compound 2 can be treated with 1,3-propane sultone to obtain benzothienopyrrole intermediate compound 3: 3-(2,3,3-trimethyl-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate. [00191] As shown in Scheme 2, ethyl 2-methyl-3-oxobutanoate in t-butanol can be treated with potassium tert-butoxide and 1,3-propanesultone to provide compound 4: 4- methyl-5-oxohexane-1-sulfonic acid. Compound 4 can be treated with benzothiophene hydrazine compound 1 to obtain compound 5: 3-(2,3-dimethyl-3H- benzo[4,5]thieno[2,3-b]pyrrol-3-yl)propane-1-sulfonic acid. Compound 5 can be treated with 1,3-propanesultone to obtain benzothienopyrrole intermediate compound 6:3-(2,3-dimethyl-3-(3-sulfopropyl)-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1- yl)propane-1-sulfonate. [00192] The benzothienopyrrole intermediates can be further derivatized, for example, as shown in Figure 3, Schemes 3A, 3B, and detailed in Examples 1C and 1D. Scheme 3A shows derivatization of compound 2 by treating with 3-iodopropanoic acid to provide benzothienopyrrole (Bt) intermediate compound 7: 1-(2-carboxyethyl)-2,3,3- trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium iodide. Scheme 3B shows derivatization of compound 5 by treating with 3-iodopropanoic acid to provide Bt intermediate compound 8: 1-(2-carboxyethyl)-2,3-dimethyl-3-(3-sulfopropyl)-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium iodide. [00193] Various indole intermediate compounds may also be prepared for use in the synthesis of asymmetric BtCy dyes, for example as shown in Figure 3, Scheme 4, and detailed in Example 1E. shows an exemplary synthetic route to indole intermediate compound 10: 5-((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-1-(2-carboxyethyl)- 2,3,3-trimethyl-3H-indol-1-ium iodide was made in two steps by treating 2,3,3- trimethyl-3H-indol-5-ol with a PEG-tosyl group to provide pegylated intermediate compound 9. Compound 9 can be treated with 3-iodopropanoic acid to provide indole intermediate compound 10. [00194] Symmetric BtCy compounds can be prepared, for example, as shown in Figures 4 and 5, Schemes 5, 6, 7, and 8 and as detailed in Example 2A-2D. [00195] As illustrated in Figure 4, Scheme 5, benzothienopyrrole intermediate compounds can be treated with N,N'- diphenylformamidine, acetic anhydride and NaOAc to obtain symmetric BtCy3 fluorescent dyes, for example, compound 11. [00196] As illustrated in Figures 4 and 5, Schemes 6 and 8, benzothienopyrrole (Bt) intermediate compounds can be treated with N-((1E,3E)-3-(phenylimino)prop-1-en-1- yl)aniline, acetic acid and NaOAc to obtain symmetric BtCy5 fluorescent dyes, for example, compounds 12 and 14, respectively. [00197] As illustrated in Figure 4, Scheme 7, benzothienopyrrole (Bt) intermediate compounds can be treated with N-((1E,3E,5Z)-5-(phenylimino)penta-1,3-dien-1- yl)aniline, acetic acid and NaOAc to obtain symmetric ByCy3, BtCy5, and BtCy7 fluorescent dyes, compounds 13-15, respectively. [00198] Asymmetric BtCy compounds can be prepared, for example, as shown in FIGS.6, 7, 8, and 9, Schemes 9-15 and 17-22 and as detailed in Examples 3A-3K. [00199] As illustrated in Figure 6, Scheme 9, indole intermediate 1,2,3,3- tetramethyl-3H-indol-1-ium iodide can be treated with acetic anhydride, then N- ((1E,3E)-3-(phenylimino)prop-1-en-1-yl)aniline, then benzothienopyrrole intermediate compound 3 to provide asymmetric benzothienopyrrol-Cy5 compound 15. About 1:1 molar ratio of indole and benzothienopyrrole monomers can be employed. [00200] As illustrated in Figure 6, Scheme 10, indole intermediate 16 can be treated with acetic anhydride, then N-((1E,3E)-3-(phenylimino)prop-1-en-1-yl)aniline, then benzothienopyrrole intermediate compound 3 to provide asymmetric benzothienopyrrol-Cy5 compound 17. [00201] As illustrated in Figure 7, Scheme 11, indole intermediate 18 can be treated with acetic anhydride, then N-((1E,3E,5Z)-5-(phenylimino)penta-1,3-dien-1-yl)aniline, then benzothienopyrrole intermediate compound 6 to provide asymmetric benzothienopyrrol-Cy5 compound 19. [00202] As illustrated in Figure 7, Scheme 12, indole intermediate 10 can be treated with acetic anhydride, then N-((1E,3E,5Z)-5-(phenylimino)penta-1,3-dien-1-yl)aniline, then benzothienopyrrole intermediate compound 6 to provide asymmetric benzothienopyrrol-Cy5 compound 20. [00203] As illustrated in Figure 8, Scheme 13, compound 21: 1-(2-carboxyethyl)- 3,3-dimethyl-2-((1E,3Z)-3-(3-methyl-1,3-bis(3-sulfopropyl)-1,3-dihydro-2H- benzo[4,5]thieno[2,3-b]pyrrol-2-ylidene)prop-1-en-1-yl)-3H-indol-1-ium iodide can be made from intermediate compound 18, by addition of acetic anhydride, and N,N'- diphenylformamidine, then adding compound 6 to provide compound 21. [00204] As illustrated in Figure 9, Scheme 15, asymmetric BtCy compound 24 can be made from intermediate compound 23 by adding acetic anhydride, N-((1E,3E,5Z)-5- (phenylimino)penta-1,3-dien-1-yl)aniline, and compound 6 to provide compound 24. [00205] As illustrated in Figure 15, Scheme 17, asymmetric BtCy compound 25 can be made from 1,2,3,3-tetramethyl-3H-indol-1-ium iodide by adding acetic anhydride, N-((E)-(2-chloro-3-((E)-(phenylimino)methyl)cyclohex-2-en-1-ylidene)methyl)aniline, and intermediate compound 3, to provide asymmetric BtCy compound 25. [00206] As illustrated in FIG.16, Scheme 18, intermediate compound 26 can be made by exposing compound 3 to fuming sulfuric acid. [00207] As illustrated in FIG.16, Scheme 19, asymmetric BtCy compound 27 can be made from 1,2,3,3-tetramethyl-3H-indol-1-ium iodide by adding acetic anhydride, N-((E)-(2-chloro-3-((E)-(phenylimino)methyl)cyclohex-2-en-1-ylidene)methyl)aniline, and intermediate compound 26 to provide asymmetric BtCy compound 27. [00208] As illustrated in Figure 17, Scheme 20, intermediate compound 28 can be prepared by treating 2,3,3-trimethyl indole with 6-bromohexanoic acid. [00209] As illustrated in Figure 17, Scheme 21, asymmetric BtCy compound 29 can be prepared by treating intermediate compound 28 with acetic anhydride, N-((E)-(2- chloro-3-((E)-(phenylimino)methyl)cyclohex-2-en-1-ylidene)methyl)aniline, and intermediate compound 26 to provide asymmetric BtCy compound 29. [00210] As illustrated in Figure 18, Scheme 22, asymmetric BtCy compound 30 can be prepared by treating BtCy compound 29 with thiophenol and Cs2CO3. [00211] As illustrated in Figure 19, Scheme 23, intermediate compound 32 can be prepared by treating naphthalen-2-ylhydrazine HCl with 7-oxooctanoic acid in acetic acid in a sealed flask to provide intermediate compound 31, then treating compound 31 with 1,3-propanesultone to provide intermediate compound 32. [00212] As illustrated in Figure 19, Scheme 24, asymmetric BtCy compound 33 can be prepared by treating intermediate compound 32 with acetic anhydride, N-((E)-(2- chloro-3-((E)-(phenylimino)methyl)cyclohex-2-en-1-ylidene)methyl)aniline, and intermediate compound 26 to provide asymmetric BtCy compound 33. [00213] The present disclosure provides a labeled specific binding partner, comprising a BtCy compound or BtCy tandem dye according to the present disclosure; and a specific binding partner covalently linked to the BtCy compound. [00214] In some examples, the specific binding partner is selected from the group consisting of a protein, peptide, affinity ligand, antibody, antibody fragment, carbohydrate, lipid, nucleic acid, and an aptamer. In some examples, the specific binding partner is an antibody. The specific binding partner may specifically bind a target analyte. The specific binding partner may specifically bind a target antigen. [00215] The present disclosure provides a BtCy tandem dye, comprising a BtCy compound or a labeled specific binding partner of the present disclosure; and a chromophore, fluorophore, or acceptor chromophore covalently linked to the BtCy compound or labeled specific binding partner. The BtCy compound can also be an acceptor dye attached to a fluorescent compound. In this instance, the BtCy tandem dye can also comprise a fluorescent dye and BtCy compound of the present disclosure covalently linked to the fluorescent dye. [00216] The BtCy compound, labeled specific binding partner, or tandem dye according to the present disclosure may be a water-soluble fluorescent dye. The fluorescent compound, labeled specific binding partner, or tandem dye according to the present disclosure may exhibit solubility in water at ambient room temperature of > 1 mg/mL, > 2 mg/mL, > 3 mg/mL, > 4 mg/mL, > 5 mg/mL, > 6 mg/mL, > 7 mg/mL, > 8 mg/mL, > 9 mg/mL, >10 mg/mL, > 20 mg/mL, > 30 mg/mL, >40 mg/mL, >50 mg/mL, > 80 mg/mL, or >100 mg/mL. [00217] The BtCy compound, labeled specific binding partner, or tandem dye according to the present disclosure may exhibit a excitation maxima ( λex) at a wavelength of >500 nm, >600 nm, >700 nm, >800 nm, >850 nm, >900 nm, >950 nm, >1,000 nm, or >1,050 nm, >1,100 nm, or within a range of between about 500 nm and 1200 nm, about 500 nm to about 1,100, about 550 nm to about 1150 nm, about 550 nm to about 1,075 nm, about 550 nm to about 1,050 nm, about 575 nm to about 1,000 nm, or about 600 nm to about 950 nm. [00218] The BtCy compound, BtCy labeled specific binding partner comprising a BtCy compound or BtCy tandem dye, or BtCy tandem dye comprising a BtCy compound according to the present disclosure may exhibit an emission maxima ( λem) of >550 nm, > 650 nm, >750 nm, >850 nm, > 900 nm, >1000, >1050 nm, >1100, >1150 nm, >1200 nm, or > 1250 nm, or within a range of between about 550 nm to about 1300 nm, about 600 nm to about 1300 nm, about 600 nm to about 1200 nm, about 650 nm to about 1150 nm, or about 550 nm to about 1050 nm, or about 650 nm to about 1050 nm. [00219] The BtCy dyes, tandem dyes, labeled specific binding partners, compositions, methods and systems as described herein may find use in a variety of applications, including diagnostic and research applications, in which the labelling, detection and/or analysis of a target of interest is desirable. Such applications include methodologies such as, for example, cytometry, microscopy, immunoassays (e.g. competitive or non-competitive), fluorescence in situ hybridization (FISH), cell tracing, receptor labeling, fluorescence spectroscopy, assessment of a free analyte, assessment of receptor bound ligand, and so forth. The compositions, system and methods described herein may be useful in analysis of any of a number of samples, including but not limited to, biological fluids, cell culture samples, and tissue samples. In certain aspects, the compositions, system and methods described herein may find use in methods where analytes are detected in a sample, if present, using fluorescent labels, such as in fluorescent activated cell sorting or analysis, immunoassays, immunostaining, and the like. In certain instances, the compositions and methods find use in applications where the evaluation of a sample for the presence of a target analyte is of interest. In some cases, the methods and compositions find use in any assay format where the detection and/or analysis of a target from a sample is of interest, including but not limited to, flow cytometry, fluorescence microscopy, in-situ hybridization, enzyme-linked immunosorbent assays (ELISAs), western blot analysis, magnetic cell separation assays and fluorochrome purification chromatography. In certain instances, the methods and compositions find use in any application where the fluorescent labelling of a target molecule is of interest. The subject compositions may be adapted for use in any convenient applications where pairs of specific binding members find use, such as biotin-streptavidin and hapten-anti-hapten antibody. [00220] The disclosure provides a method for detecting a target analyte in a sample comprising: providing a sample that is suspected of containing the analyte; and contacting the sample with a specific binding partner conjugated to a BtCy compound or tandem dye of the present disclosure, wherein the specific binding partner is capable of interacting with the target analyte. The specific binding partner may be a target analyte-specific antibody or antigen-binding fragment thereof. [00221] In some examples, the method is configured for flow cytometry. [00222] In some examples, the water-soluble fluorescent compound is bound to a substrate. [00223] In some examples, the analyte is a protein expressed on a cell surface. [00224] In some examples, the method is configured as an immunoassay. In some examples, the method further comprises providing additional binding partners for detecting additional analytes simultaneously. [00225] The disclosure provides a kit comprising at least one BtCy compound, labeled specific binding partner, or tandem dye according to the present disclosure. Aspects of the invention further include kits for use in practicing the subject methods and compositions. The compositions of the invention can be included as reagents in kits either as starting materials or provided for use in, for example, the methodologies described above. [00226] A kit can include a BtCy dye, BtCy tandem dye or BtCy labeled specific binding member as described herein and a container. Any convenient containers can be utilized, such as tubes, bottles, or wells in a multi-well strip or plate, a box, a bag, an insulated container, and the like. In some instances, the subject kits can include one or more components selected from a BtCy dye, BtCy tandem dye, a fluorophore, a chromophore, a specific binding member, a specific binding member conjugate, a support bound specific binding member, a cell, a support, a biocompatible aqueous elution buffer, and instructions for use. In some embodiments of the kit, the BtCy dye or BtCy tandem dye is covalently linked to a specific binding member. [00227] In some instances, the subject kits can be a “labeling kit” that include a BtCy dye or BtCy tandem dye comprising a sidechain chemoselective functional group such as, for example, a BtCy-NHS ester and the like, (also referred to as a “conjugation tag”) to which any convenient target moiety of interest (e.g., a donor or acceptor dye, fluorophore, chromophore, a specific binding partner, a support) can be conjugated. The chemoselective functional group may include a reactive group (e.g., biotin) that targets specific functional groups on biomolecules (e.g., proteins or antibodies), such as, for example, primary amines, sulfhydryls, carboxyls, or carbohydrates. The chemoselective functional group can be one used in “click chemistry” reactions. [00228] In certain instances, the conjugation tag includes a maleimide functional group and the target moiety includes a thiol functional group, or vice versa. In some instances, the conjugation tag includes an alkyne (e.g., a cyclooctyne group) functional group and the target moiety includes an azide functional group, or vice versa, which can be conjugated via Click chemistry. In certain instances, the conjugation tag includes an alkene (e.g., a cyclooctene group) functional group and the target moiety includes a tetrazine functional group, or vice versa, which can be conjugated via inverse–demand Diels–Alder cycloaddition reaction. In some instances, the conjugation tag includes an amine-reactive chemical group, such as, for example, a NHS ester (N-hydroxysuccinimde esters) or imidoester functional group and the target moiety includes a NH2 functional group, or vice versa. In some instances, the conjugation tag includes a biotin-binding protein (e.g., Avidin, Streptavidin, or NeutrAvidin) and the target moiety includes a biotin molecule, or vice versa, which can non-covalently interact. [00229] In some instances, the target moiety is a specific binding partner. In some instances, the specific binding partner is an antibody. In certain instances, the specific binding partner is an antibody fragment or binding derivative thereof. In certain cases, the antibody fragment or binding derivative thereof is selected from the group consisting of a Fab fragment, a F(ab′)₂ fragment, a scFv, a diabody and a triabody. [00230] In some instances, the target moiety is a fluorophore or chromophore. In some instances, the fluorophore or chromophore is an acceptor dye. In some instances, the fluorophore or chromophore is a donor dye. [00231] Table 1 shows exemplary inventive symmetric and asymmetric BtCy compounds of the present disclosure along with their fluorescence properties including maximum excitation wavelength ( λex) and emission wavelengths ( λem). The BtCy3, BtCy5, and BtCy7 compounds are red shifted by about 200 nm compared to common indole-cyanine compounds Cy3, Cy5, and Cy7. [00232] Table 1. BtCy Compounds with excitation and emission data

[00233] With respect to values shown in Table 1, unless otherwise indicated, absorption/emission spectra were taken in methanol. * measured in DMF. [00234] As shown in Table 1, inventive benzothienopyrrole cyanine dyes BtCy3 compound 11, BtCy5 compound 12, and BtCy7 compound 13 exhibited about 200 nm Abs/Em red shift versus comparative prior art indole cyanine dyes Cy3, Cy5, and Cy7, respectively. The benzothienopyrrole cyanine dyes of Table 1 exhibit absorbance maxima in a range of 642-972 nm. The benzothienopyrrole cyanine dyes of Table 1 exhibit emission maxima in a range of 662-997 nm. IV. Binding Partners [00235] A “binding partner” or “specific binding partner” of the present disclosure can be any molecule or complex of molecules capable of specifically binding to a target analyte. A binding partner of this disclosure includes, for example, proteins, small organic molecules, carbohydrates (including polysaccharides), oligonucleotides, polynucleotides, lipids, affinity ligand, antibody, antibody fragment, an aptamer and the like. In some embodiments, the binding partner is an antibody or fragment thereof. Specific binding in the context of the present disclosure refers to a binding reaction which is determinative of the presence of a target analyte in the presence of a heterogeneous population. Thus, under designated assay conditions, the specified binding partners bind preferentially to a particular protein or isoform of the particular protein and do not bind in a significant amount to other proteins or other isoforms present in the sample. [00236] When the binding partners are antibodies, they may be monoclonal or polyclonal antibodies. The term antibody as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules. Such antibodies include, but are not limited to, polyclonal, monoclonal, mono-specific polyclonal antibodies, antibody mimics, chimeric, single chain, Fab, Fab′ and F(ab′)2 fragments, Fv, and a Fab expression library. [00237] In general, water-soluble fluorescent compounds of the present disclosure can be conjugated to binding partners to form a conjugated water-soluble fluorescent compound complex using techniques known to those of skill in the art or using methods known in the art in combination with methods described herein. [00238] A labeled specific binding partner is provided comprising a fluorescent BtCy compound according to the present disclosure; and a specific binding partner covalently linked to the fluorescent compound. The specific binding partner may be an antibody. The specific binding partner may be specific for a target analyte. [00239] In some embodiments, fluorescent compounds of the present disclosure can be conjugated to binding partners using a method of direct modification similar to that described in US2020/0190253, which is incorporated herein by reference in its entirety. For example, a BtCy dye-antibody complex can be prepared according to the general scheme as shown in Figure 14, Scheme 16. [00240] For example, preparation of BtCy-NHS ester can proceed as follows. Using a clean vial, dissolve 5 mg of BtCy in 1 mL dry CH₃CN. To this, add 2 mg N,N,N’,N’- tetramethyl-O-(N-succinimidyl)uranium tetrafluoroborate (TSTU) and stir for 2 more minutes. To this, add 20 uL N,N-diisopropylethylamine (DIPEA) and continue stirring for ~1hour with the cap sealed with parafilm. Later evaporate off the organic solvents in the reaction mixture. Crude BtCy-NHS may be isolated by extraction/purified and used immediately for labeling antibody. [00241] Conjugation of BtCy NHS with anti-CD4 antibody can proceed as follows. Take the BtCy-NHS into DMSO (˜10 uL), add to 0.6 mg of CD4 and mix with 100 uL of 0.5M Borate buffer (pH 9.0). Vortex quickly for 30 seconds and allow to mix for 3-4 hours in the coulter mixture. [00242] Purification of BtCy-antibody conjugate can proceed as follows. [00243] Approach 1: Purification of BtCy-antibody conjugate through SEC column can proceed as follows. Load the crude conjugate containing free dye and the conjugate to the Size Exclusion Column, using 1×PBS. Pool the tubes after checking the absorption spectra and concentrate in an Amicon Ultra-15 having a 30 KDa MWCO centrifugal concentrator. [00244] Approach 2: the conjugation reaction mixture can be loaded to a pre- equilibrated (PBS 1x) size exclusion spin column with appropriate cut off (10k, 20K or 40K Zeba) to obtain the purified BtCy-antibody conjugate. [00245] Approach 3: Purification of BtCy-antibody conjugate through an Anti- mouse anti-H+L antibody-agarose bead can proceed as follows. Mix crude BtCy- antibody conjugate mixture with anti-mouse anti-H+L antibody-agarose bead in a biological buffer having a pH between about 6 to about 8 for about 30 minutes at room temperature. The anti-mouse anti H+L antibody-agarose bead will bind to the BtCy- antibody conjugate. Remove unreacted BtCy by washing with the above-mentioned biological buffer using a benchtop centrifuge with a speed of 300 g for 3 minutes. Repeat the washing process at least three times. To elute the BtCy-antibody conjugate, apply an IgG elution buffer with a pH ranging from about 2 to about 4 to the washed antibody-agarose bead and incubate for about 10 to 15 min. Centrifuge to collect the flow through that contains the antibody conjugate. V. Tandem Dyes [00246] The compounds of the present disclosure can be either a donor dye or an acceptor dye. The compounds and labeled specific binding partners of the present disclosure are capable of transferring energy to a linked acceptor chromophore or accepting energy from a linked donor chromophore. When the compounds and labeled specific binding partners of the disclosure are donor dyes, an acceptor chromophore can be covalently linked to a DHP bridged compound or labeled specific binding partner according to the disclosure in energy-receiving proximity such that excitation of the donor DHP bridged compound or labeled specific binding partner leads to energy transfer to, and emission from, the covalently attached acceptor signaling chromophore. When the compounds and labeled specific binding partners of the disclosure are acceptor dyes, they can be covalently linked to a donor chromophore in energy- receiving proximity such that excitation of the donor leads to energy transfer to, and emission from, the covalently attached acceptor signaling chromophore. Mechanisms for energy transfer between the compounds and labeled specific binding partners of the present disclosure and a linked donor or acceptor chromophore include, for example, resonant energy transfer (e.g., Fӧrster (or fluorescence) resonant energy transfer, FRET), quantum charge exchange (Dexter energy transfer) and the like. In some cases, the “chromophore” may be a “fluorophore”. In some cases, the “chromophore” may be an acceptor dye. In some cases the ”chromophore” may be a donor dye. [00247] As such, in some embodiments, the fluorescent BtCy compounds, water- soluble fluorescent BtCy compounds of the disclosure, and labeled specific binding partners, include additional fluorophores, donor dyes, acceptor dyes, or chromophores attached to the fluorescent compounds. In some cases, the BtCy compounds are donor dyes. In some cases, the BtCy compounds are acceptor dyes. When a light source excites the donor compound, the fluorophores, acceptor dyes or chromophores can absorb energy of an appropriate wavelength and emit or transfer energy. [00248] The fluorophore (FP), chromophore, donor, or acceptor dye linked to the fluorescent dyes of the invention may have an absorption or emission profile with a degree of overlap with the absorption or emission profile of the BtCy compounds of the disclosure. The FP, chromophore, donor, or acceptor dye linked to the fluorescent dyes of the invention can be a fluorescent dye that has absorption maximum longer than 405 nm or 575 nm, and emission maximum longer than 428 nm, 450 nm, or 600 nm, and optionally may exhibit with fluorescence quantum yield larger than 2%, 3%, 4%, 5%, 6%, 7%, 8%, or 10%. The fluorophore may be selected from coumarins, fluoresceins, rhodamines, cyanines, bodipys, or other polycyclic aromatics. Many fluorophores are commercially available and may be selected from but are not limited to, for example, any dye available from Beckman Coulter, Inc., including, but not limited to, SuperNova polymer dyes; any dye available from Becton Dickinson Biosciences, including, but not limited to, BD Horizon Brilliant™ polymer dyes; any dye available from ThermoFisher Scientific, including, but not limited to, Super Bright polymer dyes, and Alexa Fluor dyes, including, but not limited to, Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 647, Alexa Fluor 660, Alexa Fluor 680; ATTO 390, ATTO 465, ATTO 488, ATTO 495, ATTO 514, ATTO 532, ATTO 550, ATTO 565, ATTO 590, ATTO 594, ATTO 610, ATTO 620, ATTO 633, ATTO 647, ATTO 647N, ATTO 655, ATTO 665, ATTO 680, ATTO 700, ATTO 725, ATTO 740, 5-carboxy-2,7-dichlorofluorescein, 5-Carboxyfluorescein (5-FAM), 5-Carboxynapthofluorescein, 5-Carboxytetramethylrhodamine (5- TAMRA), 5-FAM (5-Carboxyfluorescein), 5-ROX, 6-TAMRA, 6-Carboxyrhodamine 6G, 6-CR6G, 6-JOE, 6-FAM, 6-ROX, Bodipy 492/515, Bodipy 493/503, Bodipy 500/510, Bodipy 505/515, Bodipy 530/550, Bodipy 542/563, Bodipy 558/568, Bodipy 564/570, Bodipy 576/589, Bodipy 581/591, Bodipy 630/650-X, Bodipy 650/665- X, Bodipy 665/676, Bodipy Fl, Bodipy R6G, Bodipy TMR, Bodipy TR, CF 488A, CF 555,CF 568, CF 594ST, CF 633, CF 640R, CF 647, CF 660C, CF 680, CF680R, CF 750, CF 770, CF 790, CL- NERF, CMFDA, Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, DDAO, DiA, DiD, DiI, DyLight 488, DyLight 550, DyLight 594, DyLight 633, DyLight 650, DyLight 680, DyLight 755, DyLight 800, DiO, DiR, DM- NERF, DsRed, DTAF, DY-490, DY-495, DY-505, DY-530, DY-547, DY-548, DY- 549, DY-549P1, DY-550, DY-554, DY-555, DY-556, DY-560, DY-590, DY-591, DY- 594, DY-605, DY-610, DY-615, DY-630, DY-631, DY-632, DY-633, DY-634, DY- 635, DY-636, DY-647, DY-648, DY-649, DY-649P1, DY-650, DY-651, DY-652, DY- 654, DY-675, DY-676, DY-677, DY-678, DY-679, DY-679P1, DY-680, DY-681, DY- 682, DY-700, DY-701, DY-703, DY-704, DY-730, DY-731, DY-732, DY-734, DY- 749, DY-750, DY-751, DY-752, DY-754, DY-776, DY-777, DY-778, DY-780, DY- 781, DY-782, DY-800, DY-831, Eosin, Erythrosin, FITC, Fluo-3, Fluo-4, Fluor- Ruby, FluorX, FM 1-43, FM 1-46, iFluor 488, iFluor 555, iFluor 594, iFluor 647, iFluor 680, iFluor 700, iFluor 750, iFluor 780, Lyso Tracker Green, Lyso Tracker Yellow, Mitotracker Green, Mitotracker Orange, Mitotracker Red, NBD, Oregon Green 488, Oregon Green 514, PKH26, PKH67, Resorufin, RH 414, Rhod- 2, Rhodamine, Rhodamine 110, Rhodamine 123, Rhodamine 6G, Rhodamine B, Rhodamine Green, Rhodamine Red, Rose Bengal, Spectrum Green, Spectrum Orange, Spectrum Red, SYTO 11, SYTO 12, SYTO 13, SYTO 14, SYTO 15, SYTO 16, SYTO 17, SYTO 18, SYTO 20, SYTO 21, SYTO 22, SYTO 23, SYTO 24, SYTO 25, SYTO 40, SYTO 41, SYTO 42, SYTO 43, SYTO 44, SYTO 45, SYTO 59, SYTO 60, SYTO 61, SYTO 62, SYTO 63, SYTO 64, SYTO 80, SYTO 81, SYTO 82, SYTO 83, SYTO 84, SYTO 85, SYTOX Blue, SYTOX Green, SYTOX Orange, Texas Red, Tide Fluor 2 (TF2), Tide Fluor 2WS (TF2WS), Tide Fluor 3 (TF3), Tide Fluor 3WS(TF3WS), Tide Fluor 4 (TF4), Tide Fluor 5WS (TF5WS), Tide Fluor 6WS (TF6WS), Tide Fluor 7WS (TF7WS), Tide Fluor 8WS (TF8WS), TRITC, and XTRITC. [00249] In some cases, the fluorophore, chromophore, donor dye, or acceptor dyes useful in the disclosure may include, for example, a cyanine dye, a xanthene dye, a coumarin dye, a thiazine dye, an acridine dye, FITC, CY3B, Cy55, Alexa 488, Texas red, Cy5, Cy7, Alexa 750, Cy55, Cy3B, Cy3.5, Alexa 750, 800 CW, Biotium CF 555, diethyl coumarin, DY705 (Dyomics), DY431, DY485XL, DY500XL, DY610, DY640, DY654, DY 682, DY 700, DY 701, DY 704, DY 730, DY 731, DY732, DY 734, DY 752, DY 778, DY 782, DY 800, DY 831and 800CW. [00250] In some cases, the BtCy compounds may act as acceptor dyes with fluorescent polymer dyes/protein dyes as a donor. The fluorescent polymer dye may be any appropriate fluorescent polymer dye. For example, fluorescent polymer dyes are disclosed in US Pat Nos.11,208,527; 11,584,825; 11,119,107; 11485825; 11492493; 9159465; 11,215,612; 11,209,43; 10,288,620; 8,969,509; 8431416; 11,099,190; 10,604,657; 10,533,092; 10,920,082; and U.S. Published Patent Applications US2020/0048469; US 2022/0082568; US2022/0276255; US2021/0373029; US 2022/0340813; US 2021/0108083; and US 2022/0348770; each of which is incorporated by reference herein in its entirety. The polymer dye can also be a BD Horizon Brilliant™ polymer dye (Becton Dickinson Biosciences) or Super Bright polymer dye (ThermoFisher Scientific). [00251] The acceptor dye may be a pendant acceptor dye. The tandem dye may comprise a benzothienopyrrole-cyanine compound according to the present disclosure, optionally comprising one or more, or two or more, additional fluorophore, chromophore, or acceptor dye moieties. The tandem dye may comprise a fluorophore or chromophore donor dye and a BtCy acceptor dye according to the present invention. [00252] Fluorescent tandem dyes can be prepared using techniques known to those of skill in the art or using methods known in the art in combination with methods described herein. The tandem dyes can be water-soluble. [00253] In some embodiments, instead of being attached directly to the compound, the fluorophore, acceptor dye, chromophore, and/or functional moiety(ies) and binding partner(s) can be attached to BtCy compounds of the present disclosure through a linker moiety using the method of direct modification as described in US2020/0190253, which is incorporated herein by reference in its entirety. In some embodiments, the present disclosure provides a tandem dye comprising: a fluorescent compound, or labeled specific binding partner according to the disclosure; and a fluorophore, chromophore, or acceptor dye covalently linked to the fluorescent compound, or labeled specific binding partner. VI. Methods of Detecting an Analyte [00254] The present disclosure provides methods for detecting a target analyte in a sample, the method comprising: providing a sample that is suspected of containing a target analyte; and contacting the sample with a specific binding partner conjugated to a fluorescent BtCy or BtCy tandem dye compound of the present disclosure, wherein the binding partner is capable of interacting with the target analyte. [00255] A light source is applied to the sample that can excite the fluorescent compound or a donor dye; and light emitted from the conjugated fluorescent compound complex or an acceptor dye is detected. In the typical assay, water-soluble fluorescent compounds of the present disclosure are excitable with a light having wavelength between about 500 nm and about 1200 nm, about 550 nm and about 1150 nm, about 575 nm and about 1100 nm, about 600 nm and about 1000 nm and the emitted light is typically between about 600 nm and about 1200 nm, about 650 and about 1150 nm, or about 700 nm and about 1100 nm. [00256] Alternatively, excitation light can have a wavelength between about 600 nm and about 1100 nm and the emitted light can have a wavelength between about 650 nm and about 1200 nm. The fluorescent compounds of the present disclosure may have an excitation spectrum tuned to the yellow, orange, red and NIR or another laser depending on design of the compound. [00257] In the method of the present disclosure, the fluorescent BtCy compound can be any water-soluble fluorescent BtCy compound or BtCy tandem dye of the present disclosure as disclosed herein. The binding partner may be a protein, peptide, affinity ligand, antibody, antibody fragment, carbohydrate, lipid, nucleic acid or an aptamer. When the binding partner is an antibody, the method may be configured for flow cytometry; the water-soluble fluorescent BtCy dye or tandem dye may be bound to a substrate; the analyte may be a protein expressed on a cell surface; the method may be configured as an immunoassay; or the method may further comprise providing additional specific binding partners for detecting additional analytes simultaneously. Samples [00258] The sample in the methods of the present disclosure can be, for example, blood, bone marrow, spleen cells, lymph cells, bone marrow aspirates (or any cells obtained from bone marrow), urine (lavage), serum, saliva, cerebral spinal fluid, urine, amniotic fluid, interstitial fluid, feces, mucus, or tissue (e.g., tumor samples, disaggregated tissue, disaggregated solid tumor). In certain embodiments, the sample is a blood sample. In some embodiments, the blood sample is whole blood. The whole blood can be obtained from the subject using standard clinical procedures. In some embodiments, the sample is a subset of one or more cells of whole blood (e.g., erythrocyte, leukocyte, lymphocyte (e.g., T cells, B cells or NK cells), phagocyte, monocyte, macrophage, granulocyte, basophil, neutrophil, eosinophil, platelet, or any cell with one or more detectable markers). In some embodiments, the sample can be from a cell culture. [00259] The subject can be a human (e.g., a patient suffering from a disease), a commercially significant mammal, including, for example, a monkey, cow, or horse. Samples can also be obtained from household pets, including, for example, a dog or cat. In some embodiments, the subject is a laboratory animal used as an animal model of disease or for drug screening, for example, a mouse, a rat, a rabbit, or guinea pig. [00260] Analytes [00261] An “analyte” or “target analyte” as used herein, refers to a substance, e.g., molecule, whose abundance/concentration is determined by some analytical procedure. For example, in the present disclosure, an analyte can be a protein, peptide, nucleic acid, lipid, carbohydrate small molecule, or a target-associated biomolecule. [00262] The target analyte may be, for example, nucleic acids (DNA, RNA, mRNA, tRNA, or rRNA), peptides, polypeptides, proteins, lipids, ions, monosaccharides, oligosaccharides, polysaccharides, lipoproteins, glycoproteins, glycolipids, or fragments thereof. In some embodiments, the target analyte is a protein and can be, for example, a structural microfilament, microtubule, and intermediate filament proteins, organelle-specific markers, proteasomes, transmembrane proteins, surface receptors, nuclear pore proteins, protein/peptide translocases, protein folding chaperones, signaling scaffolds, ion channels and the like. The protein can be an activatable protein or a protein differentially expressed or activated in diseased or aberrant cells, including but not limited to transcription factors, DNA and/or RNA- binding and modifying proteins, nuclear import and export receptors, regulators of apoptosis or survival and the like. [00263] Assays [00264] Assay systems utilizing a binding partner and a fluorescent label to quantify bound molecules are well known. Examples of such systems include flow cytometers, scanning cytometers, imaging cytometers, fluorescence microscopes, and confocal fluorescent microscopes. [00265] In some embodiments, flow cytometry is used to detect fluorescence. A number of devices suitable for this use are available and known to those skilled in the art. Examples include BCI Navios, Gallios, Aquios, and CytoFLEX flow cytometers. [00266] In other embodiments, an assay is used. The assay can be an immunoassay. Examples of immunoassays useful in the disclosure include, but are not limited to, fluoroluminescence assay (FLA), and the like. The assays can also be carried out on protein arrays. [00267] When the binding partners are antibodies, antibody or multiple antibody sandwich assays can also be used. A sandwich assay refers to the use of successive recognition events to build up layers of various binding partners and reporting elements to signal the presence of a particular analyte. Examples of sandwich assays are disclosed in U.S. Pat. No.4,486,530 and in the references noted therein. VII. EXAMPLES Example 1. Synthesis of Benzothienopyrrole and Indole Intermediate Compounds [00268] Intermediate and product compounds were characterized by mass spectrometry and/or ¹H-NMR. [00269] Example 1A. Synthesis of Benzothienopyrrole Intermediate 3: 3-(2,3,3- trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate [00270] Synthesis of benzothienopyrrole intermediate 3 was performed as illustrated in FIG.2, Scheme 1. [00271] Compound 1. tert-butyl 1-(benzo[b]thiophen-2-yl)hydrazine-1- carboxylate [00272] In a round bottom flask 5.7g of 2-iodobenzo[b]thiophene (21.9 mmoles) and 7.24g of tert-butyl hydrazinecarboxylate (54.8 mmoles) were dissolved in 10 mL of DMF. Then 10g of Cs2CO3 (30.7 mmoles) and 0.39g of 1,10 phenanthroline (2.19 mmoles) and 42 mg of CuI (0.22 mmoles) were added. The mixture was purged with Nitrogen for 10 minutes and then reacted at 48 ℃ for 4 days. [00273] After that 15 ml of H₂O was added to the reaction mixture and stirred for 10 minutes. The mixture was diluted with 1/1 brine /water mix and extracted with ethyl acetate 3 times. The organic portions were combined, washed with brine and then concentrated. The residue was purified with an automated chromatography system using neutral Alumina as stationary phase and Hexanes/ethyl acetate as mobile phase. Product 1.36 g (23%) was collected as orange solid to provide compound 1.¹H NMR and MS confirmed desired structure.¹H NMR D6DMSO (500MHz): 7.75 (1H, d, J = 13.1 Hz), 7.61 (1H, d, J = 13.1 Hz), 7.75 (1H, t, J = 12.8 Hz), 7.15 (1H, t, J = 12.8 Hz), 5.59(2H, bs), 1.55 (9H, s). HRMS (ESI +): m/z found 248.0465 [M + H -NH2]. [00274] Compound 2.2,3,3-trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrole To a flask containing 300 mg of compound 1 (1.14 mmoles) dissolved in 5 mL of ethanol, 243 uL of 3-methylbutan-2-one (2.27 mmoles) and 648 mg of para- tolunensulfonic acid (pTSA) (3.4 mmoles) were added. The mixture was heated to 85 ℃ for 6 hours then left at room temperature overnight. After that, 8 mL of water were added, and the resulting solution brought to pH=9 by addition of 3 mL of 2M Na2CO3. The mixture was extracted with CHCl₃, the organic portions were combined and concentrated. The residue was purified with an automated chromatography system using neutral silica as stationary phase and Hexanes/ethyl acetate as mobile phase. Product 175 mg g (71%) was collected as orange oil to provide compound 2. HRMS (ESI +): m/z found 216.0839 [M + H]. [00275] Compound 3.3-(2,3,3-trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1- ium-1-yl)propane-1-sulfonate [00276] 175 mg of compound 2 (0.81 mmoles) was dissolved in 1 mL of hot 1,2- dichlorobenzene and 109 mg of 1,3-propane sultone (0.9 mmoles) added with the help of 0.25 mL of THF. The mixture was heated at 120 ℃ for 3 hours and then cooled down to room temperature.1 mL of hexanes was added, the liquid decanted. Then 0.6 toluene was added, the mix sonicated and then decanted. The resulting solid was dissolved in 0.5 mL of MeOH and precipitated again by adding diethyl ether. The solid compound 3245 mg was collected (89%).¹H-NMR and Mass spectra confirmed the desired structure of compound 3.¹H NMR D₆DMSO (500MHz): 8.12 (1H, d, J = 7.4 Hz), 8.06 (1H, d, J = 7.4 Hz), 7.63-7.55 (2H, m), 4.19 (2H, m), 2.60-2.55 (2H, m), 2.58 (3H, s), 2.16-2.10 (2H, m), 1.59 (6H, s). HRMS (ESI +): m/z found 360.0699 [M + Na]. [00277] Example 1B. Synthesis of Benzothienopyrrole Intermediate 6: 3-(2,3- dimethyl-3-(3-sulfopropyl)-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1- sulfonate [00278] Synthesis of benzothienopyrrole intermediate 6 was performed as shown in FIG.2, Scheme 2. [00279] Compound 4.4-methyl-5-oxohexane-1-sulfonic acid [00280] To a solution of 3.56 g of potassium tert-butoxide (31.9 mmoles) in 52 mL of tert-butanol, 3.84 g of ethyl 2-methyl-3-oxobutanoate (26.16 mmoles) were added. While stirring, 3.25g of 1,3-propanesultone (26.6 mmoles) was added portion wise. The mixture was heated to 110 ℃ for 2 hours and then left to cool to room temperature. The solvents were evaporated, and the residue dissolved in 30 mL of water. The resulting solution was washed with hexanes, the organic portions were discarded and the aqueous layer acidified to pH=1 using concentrated HCl. The solvent was evaporated, 80 mL of MeOH were added to the residue and the mixture sonicated 5 minutes. The insoluble residue was filtered off and the methanolic solution collected. [00281] 3.6g of NaOH (86.3 mmoles) were dissolved in 18 mL of water and the solution added to the methanolic solution from above, the resulting mixture was heated to 50 ℃ for 12 hours. After that MeOH was evaporated off and the residue acidified to pH=1 using concentrated HCl. The solvent was removed using a rotavapor. To the residue, 60 mL of acetone was added, and the mixture sonicated for 10 minutes. The insoluble material was filtered off and acetone evaporated to afford 2.6 g of product compound 4 as a pale yellow oil (50%). ¹H-NMR confirmed the desired structure of compound 4. ¹H NMR D6DMSO (500MHz): 2.53-2.46 (3H, m), 2.08 (3H, s), 1.65- 1.58 (1H, m), 1.55-1.45-(2H, m), 1.36-1.29 (1H, m), 0.97(3H, d, J=7.1Hz). [00282] Compound 5.3-(2,3-dimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-3- yl)propane-1-sulfonic acid [00283] 340 mg of compound 4 (1.75 mmoles) and 420 mg of benzothiophene hydrazine compound 1 (1.5 mmoles) were dissolved in 8 mL acetic acid and the mixture heated to 92 ℃ for 12 hours. After that the solvent was evaporated, the residue dissolved in about 8 mL MeOH and then 8 mL of water were added to induce precipitation. The mixture was centrifuged, and the supernatant collected and concentrated. The resulting material was the purified by c18 reverse phase chromatography eluting with 1/1 MeOH /H2O as mobile phase to afford 440 mg of compound 5 (91%) as a dark orange solid which can be used as is in the next steps. ¹H- NMR and Mass spectra confirmed the desired structure of compound 5. ¹H NMR D6DMSO (500MHz): 7.84 (1H, d, J= 7.6Hz), 7.64 (1H, d, J= 7.6Hz), 7.37-7.29 (2H, m), 2.29-2.25 (5H, m), 1.96-1.90 (1H, m), 1.77-1.71 (1H, m), 1.24 (3H, s), 1.18-1.06 (2H, m). HRMS (ESI+): m/z found 324.1005 [M + H]. [00284] Compound 6.3-(2,3-dimethyl-3-(3-sulfopropyl)-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate [00285] 90mg of compound 5 (0.28 mmoles) was dissolved in 1 mL of hot 1,2- dichlorobenzene and 41mg of 1,3-propanesultone (0.33 mmoles) added. The mixture was heated at 120 ℃ for 1 hour and then cooled down to room temperature.1 mL of hexanes was added, the liquid decanted. Then 0.6mL of toluene was added, the mix sonicated and then decanted. The resulting solid was washed with hexanes and the residue purified by preparative HPLC using a C8 column as stationary phase and MeOH/H₂O as mobile phase.80 mg (64%) of product compound 6 was collected as dark purple solid.¹H-NMR and Mass spectra confirmed the desired structure of compound 6. ¹H NMR D₆DMSO (500MHz): 8.15 (1H, d, J= 8.6Hz), 8.08 (1H, d, J= 8.6Hz), 7.63-7.56 (2H, m),4.25-4.10 (2H, m), 2.59-2.86 (5H, m), 2.40-2.28 (4H, m), 2.20-2.06 (2H, m), 1.61 (3H, s), 0.99-0.91 (2H, m). HRMS (ESI-): m/z found 444.1738 [M-H ]. [00286] Example 1C. Synthesis of Benzothienopyrrole Intermediate Compound 7: 1-(2-carboxyethyl)-2,3,3-trimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium iodide. [00287] As shown in FIG.3, Scheme 3A, compound 7 was made from compound 2 in a similar manner as employed for compound 3 except 3-iodopropanoic acid was used instead of 1,3-propane sultone.¹H-NMR and Mass spectra confirmed the desired structure of compound 7. ¹H NMR D₆DMSO (500MHz):8.14-8.05 (2H, m), 7.65-7.58 (2H, m), 4.24 (2H, t, J= 13.6 Hz),2.93-2.85 (2H, m), 2.59 (3H, s), 1.61 (6H, s). HRMS (ESI+): m/z found 288.1044 [M+]. [00288] Example 1D. Synthesis of Benzothienopyrrole Intermediate Compound 8.1-(2-carboxyethyl)-2,3-dimethyl-3-(3-sulfopropyl)-3H-benzo[4,5]thieno[2,3- b]pyrrol-1-ium iodide. [00289] As shown in FIG.3, Scheme 3B, compound 8 was made in a similar manner as compound 7, except compound 5 was used instead of compound 2. ¹H- NMR and Mass spectra confirmed the desired structure of compound 8. ¹H NMR D6DMSO (500MHz):8.16-8.06 (2H, m), 7.69-7.51 (2H, m), 4.26-4.21(2H, m), 2.96- 2.86 (2H, m), 2.67-2.57 (5H, m),2.38-2.33 (2H, m), 1.61 (3H, s), 0.99-0.92 (2H, m). HRMS (ESI-): m/z found 394.1062 [M-2H]. [00290] Example 1E. Synthesis of Indole Intermediate Compound 10: 5- ((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-1-(2-carboxyethyl)-2,3,3-trimethyl- 3H-indol-1-ium [00291] Synthesis of Indole Intermediate Compound 10 was performed as shown in FIG.3, Scheme 4. [00292] Compound 9: 5-((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-2,3,3- trimethyl-3H-indole [00293] Starting material 2,3,3-trimethyl-3H-indol-5-ol was produced per literature protocols. Tomasulo et al., 2007, J Org Chem 72, 2, 595-605.130 mg of 2,3,3-trimethyl-3H-indol-5-ol (0.74 mmoles) and 406 mg of compound m-PEG8-Tos PEG linker containing a Tosyl group BP22358 from BroadPharm (0.82 mmoles) were dissolved in 10 mL of acetone and 0.4g of K₂CO₃ (2.9 mmoles) added. The mixture was heated to 60 ℃ for 14 hours and then the solvents evaporated. The residue was purified by automated chromatography system using silica as stationary phase and CHCl3/MeOH as mobile phase. Product 240 mg compound 9 (50%) was collected.¹H- NMR confirmed the desired structure of compound 9. ¹H NMR CDCl3 (500MHz): 7.51 (1H, d, J= 8.6 Hz), 6.92 (1H, d, J= 3.5Hz), 6.87 (1H, dd, J= 8.6Hz, J= 3.5 Hz), 4.17 (2H, t, J= 4.5 Hz), 3.89 (2H, t, J= 5.1 Hz), 3.76-3.74 (2H, m), 3.71-3.65 (20H, m), 3.57-3.55 (2H, m), 3.39 (3H, s), 2.38 (3H, s), 1.34 (6H, s). [00294] Compound 10: 5-((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-1-(2- carboxyethyl)-2,3,3-trimethyl-3H-indol-1-ium iodide. [00295] 105 mg of compound 9 (0.21 mmoles) and 47 mg of 3-iodopropanoic acid (0.23 mmoles) were dissolved in 1 mL of toluene. The mixture was heated to 100 ℃ for 12 hours and then the solvents evaporated. The residue was washed with hexanes then dissolved in 0.5 mL of EtOAc and precipitated by addition of 20 mL hexanes to afford 143 mg (98%) of compound 10.¹H-NMR and Mass spectra confirmed the desired structure of compound 10. HRMS (ESI+): m/z found 570.3019 (M⁺- I). ¹H NMR CDCl3 (500MHz): 7.69 (1H, d, J= 8.8 Hz), 7.13 (1H, dd, J= 9.0Hz, J= 2.3Hz ), 7.10 (1H, d, J= 2.2 Hz), 4.84 (2H, t, J= 6.4 Hz), 4.24 (2H, t, J= 4.7 Hz), 3.89 (2H, t, J= 4.5 Hz), 3.73-3.71 (2H, m), 3.67-3.62 (20H, m), 3.55-3.53 (2H, m), 3.37 (3H, s), 3.23 (2H, t, J= 5.5 Hz), 2.97 (3H, s), 1.58 (6H, s). [00296] Example 2. Synthesis of Symmetric BtCy Dyes [00297] Symmetric BtCy dyes were prepared as outlined in FIG.4 and FIG.5. [00298] Example 2A. Compound 11 (BtCy3): sodium 3-(2-((1E,3Z)-3-(3,3- dimethyl-1-(3-sulfonatopropyl)-1,3-dihydro-2H-benzo[4,5]thieno[2,3-b]pyrrol-2- ylidene)prop-1-en-1-yl)-3,3-dimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1- yl)propane-1-sulfonate was prepared as shown in FIG.4, Scheme 5. [00299] In a glass vial 9 mg of compound 3 (26.7 umoles) was dissolved in 0.2 mL of EtOH then 2.3 mg of N,N'-diphenylformamidine (11.6 umoles), 0.6 mL of acetic anhydride and 30 mg NaOAc (36 umoles) was added. The mixture was heated to 80 ℃ for 1 hour. After that the solvents were evaporated and the residue purified by automated column chromatography using Silica as stationary phase and chloroform/ methanol as mobile phase to provide compound 11. For compound 11, UV Vis showed an absorbance max at 758 nm (MeOH) and emission at 769 nm (MeOH). [00300] Example 2B. Compound 12 (BtCy5): sodium 3-(2-((1E,3E,5Z)-5-(3,3- dimethyl-1-(3-sulfonatopropyl)-1,3-dihydro-2H-benzo[4,5]thieno[2,3-b]pyrrol-2- ylidene)penta-1,3-dien-1-yl)-3,3-dimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1- yl)propane-1-sulfonate was produced as shown in FIG.4, Scheme 6. [00301] In a glass vial 20 mg of compound 3 (59 umoles) was dissolved in 0.3 mL of EtOH then 4.4 mg of N-((1E,3E)-3-(phenylimino)prop-1-en-1-yl)aniline (17 umoles), 0.8 mL pf acetic anhydride and 50 mg NaOAc (61 umoles) was added. The mixture was heated to 90 ℃ for 2 hours. After that the solvents were evaporated and the residue purified by automated column chromatography using Silica as stationary phase and chloroform/ methanol as mobile phase to afford 11 mg of product compound 12. ESI-TOF mass spectrum: calc. exact mass:709.15 g/mol; M.W.709.93; m/z: 709.15 (100%). For compound 12, UV Vis showed an absorbance max at 860 nm (MeOH) and emission at 875 nm (MeOH).¹H-NMR and Mass spectra confirmed the desired structure of compound 12. HRMS (ESI-): m/z found 709.1495 (M-). ¹H NMR D6DMSO (500MHz):7.96 (2H, d, J= 7.2Hz), 7.91 (2H, d, J= 8.1Hz), 7.84 (2H, t, J= 13.3Hz), 7.47 (2H, t, J= 7.9Hz), 7.31 (2H, t, J= 7.7Hz),3.81-6.74 (3H, m), 3.90 (4H, t, J= 8.0 Hz), 2.57 (4H, t, J= 7.1 Hz), 2.09-2.06 (4H, m), 1.71 (s, 12H). [00302] Example 2C. Compound 13 (BtCy7): sodium 3-(2-((1E,3E,5E,7Z)-7- (3,3-dimethyl-1-(3-sulfonatopropyl)-1,3-dihydro-2H-benzo[4,5]thieno[2,3-b]pyrrol-2- ylidene)hepta-1,3,5-trien-1-yl)-3,3-dimethyl-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium- 1-yl)propane-1-sulfonate was produced as shown in FIG.4, Scheme 7. [00303] In a glass vial 9 mg of compound 3 (27 umoles) was dissolved in 0.6 mL of EtOH then 3.5 mg of N-((1E,3E,5Z)-5-(phenylimino)penta-1,3-dien-1-yl)aniline (12 umoles), 0.6 mL pf acetic anhydride and 0.2 mL pyridine was added. The mixture was heated to 110 ℃ for 1 hour. After that the solvents were evaporated and the residue purified by automated column chromatography using Silica as stationary phase and chloroform/ methanol as mobile phase to afford 5 mg of product compound 13. For compound 13, UV Vis showed an absorbance max at 972 nm (MeOH) and emission at 997 nm (MeOH). ESI (negative mode) showed peak with m/z = 735.22. HRMS (ESI-): m/z found 735.2250 (M-). [00304] Example 2D. Compound 14: sodium 3-(3-methyl-2-((1E,3E,5Z)-5-(3- methyl-1-(3-sulfonatopropyl)-3-(3-sulfopropyl)-1,3-dihydro-2H-benzo[4,5]thieno[2,3- b]pyrrol-2-ylidene)penta-1,3-dien-1-yl)-3-(3-sulfopropyl)-3H-benzo[4,5]thieno[2,3- b]pyrrol-1-ium-1-yl)propane-1-sulfonate, was produced as shown in FIG.5, Scheme 8. Compound 14 was made using a similar experimental protocol as Compound 12 but Compound 6 was used as starting material instead of Compound 3. For compound 14, UV Vis showed an absorbance max at 863 nm (MeOH) and emission at 887nm (MeOH). Example 3. Synthesis of Asymmetric BtCy Dyes [00305] Asymmetric BtCy dyes were prepared as outlined in FIG.6, FIG.7, FIG.8, and FIG.9. [00306] Example 3A. Compound 15: 4-((Z)-3,3-dimethyl-2-((2E,4E)-5-(1,3,3- trimethyl-3H-indol-1-ium-2-yl)penta-2,4-dien-1-ylidene)-2,3-dihydro-1H- benzo[4,5]thieno[2,3-b]pyrrol-1-yl)butane-1-sulfonate was produced as shown in FIG.6, Scheme 9. [00307] Starting 1,2,3,3-tetramethyl-3H-indol-1-ium iodide was made per literature reference EP2289563, and is also commercially available (Aldrich, CAS 5418-63-3). [00308] In a glass vial 30 mg of 1,2,3,3-tetramethyl-3H-indol-1-ium iodide (0.1 mmoles) was dissolved in 0.6 mL of acetic anhydride then 25.6 mg of N-((1E,3E)-3- (phenylimino)prop-1-en-1-yl)aniline (0.1 mmoles) was added and the mixture heated to 90 ℃ for 40 minutes. After that 35 mg of compound 3 (0.11 mmoles) dissolved in 0.4 mL EtOH was added together with 66 mg of NaOAc (0.8 mmoles). The mixture was heated to 90 ℃ for 1 hour. After that the solvents were evaporated and the residue purified by automated column chromatography using Silica as stationary phase and chloroform/ methanol as mobile phase to afford 6 mg of product compound 15. For compound 15, UV Vis showed an absorbance max at 740 nm (MeOH) and emission at 766 nm (MeOH). ESI MS (positive mode) showed peak with m/z 547.2 and M+Na 569.2. HRMS (ESI+): m/z found 547.2089 (M+H) and 569.1891 (M+Na). [00309] Example 3B. Compound 17: sodium 1-(2-carboxyethyl)-2- ((1E,3E,5Z)-5-(3,3-dimethyl-1-(4-sulfonatobutyl)-1,3-dihydro-2H- benzo[4,5]thieno[2,3-b]pyrrol-2-ylidene)penta-1,3-dien-1-yl)-3,3-dimethyl-3H-indol-1- ium-5-sulfonate was produced as shown in FIG.6, Scheme 10. [00310] Compound 17 was made using a similar experimental protocol as Compound 15 but Compound 16 was used as starting material instead of 1,2,3,3- tetramethyl-3H-indol-1-ium iodide. Compound 161-(2-carboxyethyl)-2,3,3-trimethyl- 5-sulfo-3H-indol-1-ium iodide was made per literature protocols. Tomasulo et al., 2007, J Org Chem 72, 2, 595-605. For compound 17, UV Vis showed an absorbance max at 747 nm (DMF) and emission at 777 nm (DMF. [00311] Example 3C. Compound 19: 1-(2-carboxyethyl)-3,3-dimethyl-2- ((1E,3E,5E,7Z)-7-(3-methyl-1,3-bis(3-sulfopropyl)-1,3-dihydro-2H- benzo[4,5]thieno[2,3-b]pyrrol-2-ylidene)hepta-1,3,5-trien-1-yl)-3H-indol-1-ium iodide was produced as shown in FIG.7, Scheme 11. [00312] Compound 19 was made using a similar experimental protocol as compound 15 but compound 18 was used as starting material instead of 1,2,3,3- tetramethyl-3H-indol-1-ium iodide and compound 6 was used instead of compound 3. Compound 18: 1-(2-carboxyethyl)-2,3,3-trimethyl-3H-indol-1-ium iodide was produced according to literature protocols. Fissi et al., Macromolecules 1995, 28, 302- 309. For compound 19, UV Vis showed an absorbance max at 842 nm (MeOH) and emission at 885 nm (MeOH). [00313] Example 3D. Compound 20: 3-(2-((1E,3E,5E)-7-((Z)-5- ((2,5,8,11,14,17,20-heptaoxadocosan-22-yl)oxy)-1-(2-carboxyethyl)-3,3- dimethylindolin-2-ylidene)hepta-1,3,5-trien-1-yl)-3-methyl-3-(3-sulfopropyl)-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate was produced as shown in FIG.7, Scheme 12. Compound 20 was made using a similar experimental protocol as compound 15 but compound 10 was used as starting material instead of 1,2,3,3-tetramethyl-3H-indol-1- ium iodide and compound 6 instead of compound 3. For compound 20, UV Vis showed an absorbance max at 859 nm (MeOH). [00314] Example 3E. Compound 21: 1-(2-carboxyethyl)-3,3-dimethyl-2- ((1E,3Z)-3-(3-methyl-1,3-bis(3-sulfopropyl)-1,3-dihydro-2H-benzo[4,5]thieno[2,3- b]pyrrol-2-ylidene)prop-1-en-1-yl)-3H-indol-1-ium iodide was produced as shown in FIG.8, Scheme 13. [00315] Compound 21 was made from compound 18 and compound 6 using a similar experimental protocol as compound 19 except N,N'-diphenylformamidine was used instead of N-((1E,3E)-3-(phenylimino)prop-1-en-1-yl)aniline. For compound 21, UV Vis showed an absorbance max at 642 nm (MeOH) and emission at 662 nm (MeOH). ESI MS (negative mode) showed peak m/z=685.25. HRMS (ESI-): m/z found 685.2531. [00316] Example 3F. Compound 24: 3-(2-((1E,3E,5E)-7-((Z)-1-(2- carboxyethyl)-3,3-dimethyl-5-(3-sulfopropoxy)indolin-2-ylidene)hepta-1,3,5-trien-1- yl)-3-methyl-3-(3-sulfopropyl)-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane- 1-sulfonate was produced as shown in FIG.9, Schemes 14 and 15. [00317] Intermediate Compound 22: 3-((2,3,3-trimethyl-3H-indol-5- yl)oxy)propane-1-sulfonic acid was made as shown in FIG.9, Scheme 14. [00318] 70 mg of 2,3,3-trimethyl-3H-indol-5-ol (0.4 mmoles) was dissolved in acetone (10 mL) to form a solution. 166 mg of K₂CO₃ (1.2 mmoles) and 51mg of 1,3- propanesultone (0.42 mmoles) were added to the solution. The mixture was heated to 70 ℃ for 12h hours and then the solvent evaporated. The residue was dissolved in 2 mL of H2O and then acidified with HCl 1M to pH<2. The resulting precipitate was collected to afford 120 mg (99%) of product compound 22.¹H-NMR and Mass spectra confirmed the desired structure of compound 22. HRMS (ESI-): m/z found 296.2177. ¹NMR: D₆DMSO (500MHz): 7.27 (1H, d, J= 8.3 Hz), 7.02 (1H, d, J= 2.5 Hz), 6.78 (1H, dd, J¹ = 8.3Hz, J²= 2.5 Hz), 4.04 (2H, t, J= 6.5 Hz), 2.55 (2H, t, J= 6.3 Hz), 2.15 (3H, s), 2.02-1.96 (2H, m), 1.21 (6H, s). [00319] Intermediate Compound 23: 1-(2-carboxyethyl)-2,3,3-trimethyl-5-(3- sulfopropoxy)-3H-indol-1-ium iodide was made as shown in FIG.9, Scheme 14. [00320] 120 mg of compound 22 (0.4 mmoles) were dissolved in 1 mL of dichlorobenzene and 104 mf of 3-iodopropanoic acid (0.48 mmoles) were added. The mixture was reacted at 120 ℃ for 14 hours. After that, the solvent was decanted, the residue washed with Hexanes and finally with CHCl₃. The residue was purified by preparative HPLC using a C8 column as stationary phase and MeOH/H2O as mobile phase.200 mg (99%) of product compound 23 was collected as dark brown solid. ¹H- NMR and Mass spectra confirmed the desired structure of compound 23. HRMS (ESI- ): m/z 368.2203 (M-I).¹NMR: D6DMSO (500MHz): 7.86 (1H, d, J= 8.8 Hz), 7.49 (1H, d, J= 2.5 Hz), 7.12 (1H, dd, J¹= 8.9Hz, J²= 2.5 Hz), 4.59 (2H, t, J = 7.0 Hz), 4.18 (2H, t, J = 6.6 Hz), 2.94 (2H, t, J = 7.0 Hz), 2.77 (3H, s), 2.56 (2H, t, J = 7.2 Hz), 2.02 (2H, m), 1.50 (6H, s). [00321] Example 3G. Compound 24: 1-((l1-oxidaneyl)dioxo-l6-sulfaneyl)-3- (2-((1E,3E,5E)-7-((Z)-1-(2-carboxyethyl)-3,3-dimethyl-5-(3-sulfopropoxy)indolin-2- ylidene)hepta-1,3,5-trien-1-yl)-3-methyl-3-(3-sulfopropyl)-3H-benzo[4,5]thieno[2,3- b]pyrrol-1-ium-1-yl)propan-1-ide was made as shown in FIG.9, Scheme 15. [00322] Compound 24 was made using a similar experimental protocol as Compound 20 but Compound 23 was used as starting material instead of Compound 10. For compound 24, UV Vis showed an absorbance max at 869 nm (MeOH) and emission at 899 nm (MeOH). [00323] Example 3H. Compound 25: 3-(2-((E)-2-((E)-2-chloro-3-(2-((E)-1,3,3- trimethylindolin-2-ylidene)ethylidene)cyclohex-1-en-1-yl)vinyl)-3,3-dimethyl-3H- benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate [00324] Compound 25 was made as illustrated in FIG.15, Scheme 17. [00325] In a glass vial 40 mg of 1,2,3,3-tetramethyl-3H-indol-1-ium iodide (0.13 mmoles) was dissolved in 1.4 mL of acetic anhydride then 55 mg of N-((E)-(2-chloro- 3-((E)-(phenylimino)methyl)cyclohex-2-en-1-ylidene)methyl)aniline (0.15 mmoles) was added and the mixture heated to 100℃ for 30 minutes. After that the solvents were evaporated, to the residue Et2O was added and after vortex decanted. The purified residue was dissolved in fresh acetic anhydride (1 mL) and 55 mg of compound 3 (0.16 mmoles) dissolved in 0.8 mL EtOH was added together with 65 mg of NaOAc (0.8 mmoles). The mixture was heated to 90 ℃ for 2.5 hour. After that the solvents were evaporated, and the residue purified by automated column chromatography using Silica as stationary phase and chloroform/methanol as mobile phase to afford 28 mg of product. Compound 25 structure was confirmed by ¹H NMR. ¹H NMR: D6DMSO (500MHz): 8.3 (1H, s), 8.08 (1H, d), 8.05 (1H, d), 7.58-7.51 (2H, m), 7.44-7.37 (2H, m), 7.26 (1H, t), 7.17 (1H, d), 7.07 (1H, d), 7.00 (1H, t), 6.82 (1H, d), 5.75 (1H, d), 4.12 (2H, t), 3.37 (3H, s), 2.71 (2H, m), 2.64-2.56 (4H, m), 2.13 (2H, m) 1.85 (2H, m), 1.67 (6H, s), 1.54 (6H, s). For compound 25, UV Vis showed an absorbance max at 875 nm ( ) and emission at 895 nm (MeOH). [00326] Example 3I. Compound 27: 3-(2-((E)-2-((E)-2-chloro-3-(2-((E)-1,3,3- trimethylindolin-2-ylidene)ethylidene)cyclohex-1-en-1-yl)vinyl)-3,3-dimethyl-5-sulfo- 3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane-1-sulfonate [00327] Asymmetric benzothienopyrrole-cyanine dye compound 27 was made as illustrated in FIG.16. [00328] Intermediate compound 26: 2,3,3-trimethyl-5-sulfo-1-(3-sulfopropyl)- 3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium was prepared as shown in FIG.16, Scheme 18. [00329] 90 mg of compound 3 was added to a vial containing 1 mL of fuming sulfuric acid previously chilled at -20 ºC for 1 h. The mixture was stirred in an ice bath and allowed to warm up to room temperature overnight. After that, the mixture was transferred to a centrifuge vial containing 10 mL of ethyl acetate and the resulting mixture centrifuged. Compound 26 was collected as the precipitate, washed with diethyl ether and used as is for the next steps. ESI (positive mode) showed peak with m/z = 418.02 (M+). HRMS (ESI+): m/z found 418.0243.¹NMR: D₆DMSO (500MHz): 8.11 (1H, d, J= 1.5 Hz), 8.01 (1H, d, J= 8.5 Hz), 7.81 (1H, dd, J= 2 Hz, J= 8.5 Hz), 4.18 (2H, m), 2.62-2.55 (5H, m), 2.13 (2H, m), 1.59 (6H, s). [00330] Compound 27 was made as illustrated in FIG.16, Scheme 19. In a glass vial 20 mg of 1,2,3,3-tetramethyl-3H-indol-1-ium iodide (0.066 mmoles) was dissolved in 0.6 mL of acetic anhydride then 27 mg of N-((E)-(2-chloro-3-((E)- (phenylimino)methyl)cyclohex-2-en-1-ylidene)methyl)aniline (0.076 mmoles) was added and the mixture heated to 100℃ for 30 minutes. After that, the solvents were evaporated, to the residue Et₂O was added and after vortex decanted. The purified residue was dissolved in fresh acetic anhydride (1 mL) and 33 mg of compound 26 (0.08 mmoles) dissolved in 0.3 mL EtOH was added together with 33 mg of NaOAc (0.398 mmoles). The mixture was heated to 90 ℃ for 3 hours. After that, the solvents were evaporated, and the residue purified by automated column chromatography using Silica as stationary phase and chloroform/methanol as mobile phase to afford 7 mg of product compound 27. Mass spectra confirmed the desired structure of compound 27. ESI (negative mode) showed peak with m/z = 749.28 (M+Na). HRMS (ESI-): m/z = 749.2884 (M-+Na). Compound 27 exhibited an absorbance max at 883 nm (MeOH) and emission at 900 nm (MeOH). [00331] Example 3J. Compound 29: 3-(2-((E)-2-((E)-3-(2-((E)-1-(5- carboxypentyl)-3,3-dimethylindolin-2-ylidene)ethylidene)-2-chlorocyclohex-1-en-1- yl)vinyl)-3,3-dimethyl-5-sulfo-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1-yl)propane- 1-sulfonate [00332] Asymmetric benzothienopyrrole-cyanine dye compound 29 was made as illustrated in FIG.17, Schemes 20 and 21. [00333] Intermediate compound 281-(5-carboxypentyl)-2,3,3-trimethyl-3H- indol-1-ium, was prepared as shown in FIG.17, Scheme 20.1.1g of compound 2,3,3- trimethyl indole (6.9 mmoles) were dissolved in 5 mL of dichlorobenzene and 2.7g of 6-bromohexanoic acid (13.8 mmoles) were added. The mixture was reacted at 120 ℃ for 14 hours. After that, 10 mL hexanes were added, and the solvent was decanted. The residue was washed with Ethyl Acetate (3 times, 6 mL each time) and finally dissolved in 4 mL of MeOH. The solution was added slowly to a flask containing 140 mL of isopropyl ether and the precipitate collected to afford 2.1 g of compound 28.¹H-NMR and Mass spectra confirmed the desired structure of compound 28. ¹H-NMR: D₆DMSO (500MHz): 7.97 (1H, m), 7.84 (1H, m), 7.62 (2H, m), 4.46 (2H, t, J = 7.6 Hz), 2.84 (3H, s), 2.22 (2H, t, J = 7.0 Hz), 1.84 (2H, m), 1.60-1.52 (2H, m),1.53 (6H, s), 1.43 (2H, m). HRMS (ESI+): found 274.1685. [00334] Compound 29 was prepared using the same experimental procedure as Compound 27 but intermediate Compound 28 was used instead of 1,2,3,3-tetramethyl- 3H-indol-1-ium iodide. Compound 29 exhibited an absorbance max at 891 nm (MeOH) and emission at 908 nm (MeOH). HRMS (ESI-): found 825.2941. [00335] Example 3K. Compound 30: 3-(2-((E)-2-((E)-3-(2-((E)-1-(5- carboxypentyl)-3,3-dimethylindolin-2-ylidene)ethylidene)-2-(phenylthio)cyclohex-1- en-1-yl)vinyl)-3,3-dimethyl-5-sulfo-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-1- yl)propane-1-sulfonate [00336] Asymmetric benzothienopyrrole-cyanine dye compound 30 was made as illustrated in FIG.18, Scheme 22. In a glass vial 3 µL of thiophenol (0.029 mmoles) and 11 mg of Cs2CO3 (0.033 mmoles) were dispersed in 100ul of MeCN and the solution stirred under Nitrogen atmosphere at 0℃ for 45minutes. After that a solution of 17mg of compound 29 (0.021 mmoles) in 200uL DMF was added dropwise, and the reaction mixture was left to react overnight in the ice bath. After that, the mixture was filtered over a thin reverse phase C18 plug washing with MeOH. The solvent was evaporated off and the residue washed with cold diethyl ether and dried to afford 18mg of Compound 30. Compound 30 exhibited an absorbance max at 903 nm (MeOH) and emission at 925 nm (MeOH). [00337] Example 3L. Compound 33: 2-((E)-2-((E)-3-((E)-2-(1-(5- carboxypentyl)-1-methyl-3-(3-sulfonatopropyl)-1,3-dihydro-2H-benzo[e]indol-2- ylidene)ethylidene)-2-chlorocyclohex-1-en-1-yl)vinyl)-3,3-dimethyl-1-(3- sulfonatopropyl)-3H-benzo[4,5]thieno[2,3-b]pyrrol-1-ium-5-sulfonate [00338] Asymmetric benzothienopyrrole-cyanine dye compound 33 was made as illustrated in FIG.19, Schemes 23 and 24. [00339] Intermediate compound 316-(1,2-dimethyl-1H-benzo[e]indol-1- yl)hexanoic acid was prepared as shown in FIG.19, Scheme 23. In a sealed flask 964 mg of naphthalen-2-ylhydrazine HCl (4.95 mmoles) and 967mg of 7-oxooctanoic acid (5.2 mmoles) were dissolved in 10 mL of Acetic acid. The mixture was heated to 120 ℃ for 14 hours and then cooled down to room temperature. The solvents were evaporated off and the residue purified by automated column chromatography using Silica as stationary phase and Hexanes/ethyl acetate as mobile phase to afford 1.23 g (87%) of product. ¹NMR D6DMSO (500MHz): 8.07 (1H, d, J = 8.2 Hz), 8.00 (1H, d, J = 8.2 Hz), 7.90 (1H, d, J = 8.2 Hz), 7.67 (1H, d, J = 8.2 Hz), 7.57 (1H, t, J = 6.9 Hz), 7.46 (1H, t, J = 6.9 Hz), 2.38-2.32 (1H, m), 2.27 (3H, s), 2.03-1.94 (3H, m), 1.44 (3H, s), 1.22 (2H, t, J = 7.4 Hz), 1.09-0.98 (2H, m), 0.51-0.44 (1H, m), 0.21-0.14 (1H, m). HRMS (ESI-): m/z found 308.1948. [00340] Intermediate compound 321-(5-carboxypentyl)-1,2-dimethyl-3-(3- sulfopropyl)-1H-benzo[e]indol-3-ium, was prepared as shown in FIG.19, Scheme 23. 423mg of compound 31 (1.37 mmoles) was dissolved in 2 mL 1,2-dichlorobenzene and 217mg of 1,3-propanesultone (1.78 mmoles) added. The mixture was heated at 120 ℃ for 48 hours and then cooled down to room temperature.6 mL of hexanes was added, the liquid decanted. The residue was washed with Hexanes (3 times, 6 mL each time) then with Toluene (one time, 6 mL) and again with Hexanes (2 times, 6 mL each time). After drying 472 mg (80%) of compound 32 were collected. ¹NMR D6DMSO (500MHz): 8.34 (1H, d, J = 8.5 Hz), 8.30 (1H, d, J = 8.8 Hz), 8.25-8.21 (2H, m), 7.78 (1H, t, J = 6.1 Hz), 7.73(1H, t, J = 6.1 Hz), 4.82 (2H, m), 3.42 (2H, t, , J = 6.5 Hz), 2.97 (3H, s), 2.69-2.63 (2H, m), 2.21-2.17 (2H, m), 1.74 (3H, s), 1.69-1.78 (2H, m) 1.27- 1.20 (2H, m), 1.09-0.99 (2H, m), 0.61-0.55 (1H, m), 0.20-0.14 (1H, m). HRMS (ESI- ): m/z found 430.2076. [00341] Compound 33 was prepared using the same experimental procedure as Compound 27 but Compound 32 was used instead of 1,2,3,3-tetramethyl-3H-indol-1- ium iodide. Compound 33 exhibited an absorbance max at 907 nm (MeOH) and emission at 928 nm (MeOH). HRMS (ESI-): (M + CH3COO-) found 1043.2855. [00342] The above specification, examples and data provide a complete description of the manufacture and use of the compounds of the invention. Since many embodiments of the invention can be made without departing from the spirit and scope of the invention, the invention resides in the clauses and claims hereinafter appended. Clauses [00343] Clause 1. A fluorescent compound comprising a structure according to Formula (I): s se ecte rom t e group cons st ng o a su st tute or unsu stituted benzene, benzene derivative, monocyclic aryl group, polycyclic aryl group, monocyclic heteroaryl group, and polycyclic heteroaryl group; is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, and polycyclic aryl group; each T is independently NR^4’, CR¹, CR¹R², O, S, Se, or Te; V is NR¹¹, CR⁸, CR⁸R⁹, O, S, Se, or Te, or each T-V together can stand for a structural element selected from the group consisting of SO₂, -CR¹-O-, -O-CR¹-, -CO- O-, -O-CO-, -CO-NR¹¹-, or -NR^4’-CO-; G is C or N; each R¹, R², R⁸, and R⁹ is independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, binding partner, linked binding partner, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, alkoxy sulfonate, carboxylic acid, carboxylate, alkyl carboxylate, alkoxy carboxylate, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate phosphinamide alkoxy sulfonamide PEG alkyl sulfonamide PEG, each R , R , R , and R is independently selected from the group consisting of a linker moiety, a chromophore, linked chromophore, reactive group, linked reactive group, water-solubilizing moiety, linked water-solubilizing moiety, binding partner, linked binding partner, E, linked E, H, halogen alkyl, alkenyl, alkynyl, a PEG group, a linked PEG group, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, carboxylic acid, carboxylate, alkyl carboxylate, alkyl sulfonamide, alkyl sulfonamide PEG, alkyl amide, alkyl amide-PEG, , r protected groups thereof, or one, two, three, or four of R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ together form an unsubstituted or substituted unsaturated or partially unsaturated C₃- C10 cycloalkyl group; unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ heterocycloalkyl optionally substituted with O; unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3-C8 polycycloalkyl group; or unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃ - C8 polyheterocycloalkyl group optionally substituted with O; each R³ is independently selected from the group consisting of H, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl, (hetero)arylamino, alkyl sulfonate, alkyl carboxylate, a water-solubilizing moiety, a linked water-solubilizing moiety, a chromophore, a linked chromophore, functional moiety, linked functional moiety, binding partner, linked binding partner, a PEG group, and a linked PEG group; each Q is independently a bond, O, NH, NR⁴, C₁-C₁₂ alkylene, CHR⁴, or CH₂; each Z is independently CH2, CHR⁴, O, NR⁴, or NH; each W¹ is independently a water-solubilizing moiety; L¹, L², and L³ are each independently selected linker moieties; each E is independently selected from the group consisting of a chromophore, a functional moiety, a substrate, a reactive group, and a binding partner; each R⁷ is independently selected from the group consisting of H, hydroxyl, C1- C₁₂ alkyl, C₁-C₁₂ heteroalkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁- C12 haloalkyl, C1-C12 alkoxy, C2-C18 (hetero)aryloxy, C2-C18 (hetero)arylamino, carboxylate, carboxylic acid, C₂-C₁₂ alkyl carboxylic acid, C₂-C₁₂ alkyl carboxylate, C₂- C12 alkyl carboxylate ester, aryl carboxylic acid, aryl carboxylate ester, C1-C12 alkoxy, a water-solubilizing moiety, a PEG moiety, a protected or unprotected functional group, a chemoselective functional group, a linker, sulfonic acid, sulfonate, C1-C12 alkyl sulfonate, sulfonamide; each R¹² , R¹³ and R¹⁴ is independently selected from the group consisting of hydrogen, halogen, one or more heteroatoms, substituted or unsubstituted C₁-C₆ alkyl, substituted or unsubstituted C1-C6 heteroalkyl, substituted or unsubstituted C1-C6 alkene, substituted or unsubstituted C₃-C₁₀ cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted C3-C10 heterocycloalkyl, CO2R¹, CONR¹R², -O-CH2CH2-PEG-R⁷, -S-CH2CH2-PEG-R⁷, -N- CH2CH2-PEG-R⁷, O-aryl, S-aryl, N-aryl, -O-alkyl, S-alkyl, N-alkyl, wherein each alkyl or aryl can optionally be substituted with one or more R⁷, PEG, PEG-R⁷, or linking groups, optionally wherein each R¹² , R¹³ and R¹⁴ is independently substituted with a R⁷ group; or at least two of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, optionally including, but not limited to, one, two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ form an unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ cycloalkyl group, unsubstituted or substituted unsaturated or partially unsaturated C3-C10 heterocycloalkyl optionally substituted with O, an unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3-C8 polycycloalkyl group, or unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃- C8 polyheterocycloalkyl group optionally substituted with O; each K is independently a covalent bond, O, S, Se, P, NR¹, or CR¹R²; each f is independently an integer from 0 to 50, 1 to 30, or 2 to 20; each m and m’ is independently 0, 1, 2, or 3; each n is independently an integer from 1 to 20; 1 to 10; or 0, 1, 2, or 3; each p is independently 1, 2, 3, or 4; each s is independently 1 or 2; each t is independently 0, 1, 2, 3, or 4; and X is a counterion. [00344] Clause 2. The compound of clause 1, comprising a structure according to any one of formulae (IIa), (IIb), (IIc), (IId), (IIe), (IIf), (IIg), (IIh), (IIi), (IIj), (IIk), (IIl), (IIm), (IIn), and (IIo): (IIl), and (IIo), wherein T is NR^4’, CR¹, CR¹R², O, or S; V is NR¹¹, CR⁸, CR⁸R⁹, O, or S; each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; and R¹⁶ is K-R¹³, optionally H, halogen, O-C_1-6 alkyl, S-C_1-6 alkyl, O-aryl, S-aryl, NHC_{1- 6}alkyl, Ph-NCS, Ph-CO₂H, Ph-(CH₂)_1-4CO₂H; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety which may be partially unsaturated. [00345] Clause 3. The compound of clause 1 or 2, comprising a structure according to any one of formulae (IIIa), (IIIb), (IIIc), (IIId), (IIIe), (IIIf), (IIIg), (IIIh), (IIIi), (IIIj), (IIIk), (IIIl), (IIIm), or (IIIn):

wherein each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. [00346] Clause 4. The compound of clause 1 or 2, comprising a structure according to any one of formulae (Iva), (IVb), (IVc), (IVd), (IVe), (IVf), (IVg), (IVh), (IVi), (IVj), (IVk), (IVl), (IVm), (IVn), (IVo), (IVp), (IVq), (IVr), (IVs), (IVt), (IVu), (IVv), (IVw), and (IVx):

, wherein each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidite, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. [00347] Clause 5. The compound of any one of clauses 1 to 4, comprising a structure according to any one of formulae (Va), (Vb), (Vc), (Vd), (Ve), (Vf), (Vg), (Vh), (Vi), (Vj), (Vk), and (Vl): (Va), (Vb), (Vc),

wherein Y is selected from the group consisting of NR⁴, CR¹, CR¹R², O, and S. [00348] Clause 6. The compound of any one of clauses 1 to 5, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises an E or linked E. [00349] Clause 7. The compound of any one of clauses 1 to 6, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a binding partner or linked binding partner. [00350] Clause 8. The compound of any one of clauses 1 to 7, wherein at least one, at least two, at least three, or at least four of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a water-solubilizing moiety or a linked water-solubilizing moiety. [00351] Clause 9. The compound of any one of clauses 1 to 8, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a reactive group or linked reactive group. [00352] Clause 10. The compound of any one of clauses 1 to 9, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a chromophore or linked chromophore. [00353] Clause 11. The compound of any one of clauses 1 to 3 or 5 to 10, wherein the compound is symmetric. [00354] Clause 12. The compound of any one of clauses 1, 2, 4 or 5 to 10, wherein the compound is asymmetric. [00355] Clause 13. The compound of any one of clauses 1 to 12, wherein the water-solubilizing moiety is selected from the group consisting of carboxylates, carboxylic acids, phosphonates, phosphates, sulfonates, sulfonamides, sulfates, sulfinates, sulfoniums, esters, polyaklylene oxides, polyethylene oxides comprising an ethylene oxide repeat unit of the formula —(CH2—CH2—O)n—, polyamidealkylene oxides comprising an ethylene oxide repeat unit of the formula —(CH₂—CH₂—O)n—, polyethylene glycols (PEGs), modified PEGs, linked PEGs, amide-PEGs, sulfonamide- PEGs, phosphoramide-PEGs, hydroxyls, amines, amino acids, ammoniums, guanidiniums, pyridiniums, polyamines and sulfoniums, polyalcohols, straight chain or cyclic saccharides, primary, secondary, tertiary, or quaternary amines and polyamines, glycols, polyethers, —COOX, —SO3X, —PO3X, —NR3+X, (CH2CH2O)fR¹⁵ and mixtures thereof, wherein R¹⁵ is hydrogen, substituted or unsubstituted C₁-C₆ alkyl, or substituted or unsubstituted C1-C6 alkoxy, and X is a counterion. [00356] Clause 14. The compound according to any one of clauses 1 to 13, wherein X is a counterion selected from the group consisting of F-, Cl-, Br-, I-, ClO4-, CF₃CO₂-, CH₃CO₂-, PO₄ ^3-, SO₄ ^2-, BF₄-, Na⁺, K⁺, Mg⁺⁺, and Ca⁺⁺. [00357] Clause 15. The compound of any one of clauses 1 to 14, wherein the reactive group is selected from the group consisting of thiols, maleimides, halogenated maleimide, iodoacetamides, amines, alkyl carboxylates, alkyl sulfonates, carboxylic amines, carbamate, carboxylate esters, N-hydroxysuccinimidyl, halogen, boronic esters, boronic acids, hydrazonyl, carboxylic acids or active esters thereof, azide, alkyne, cyclooctyne, tetrazine, transcyclooctene, dienes, dienophiles, sulfur (VI) fluoride (SuFEX), sulfonyl fluoride, hydroxyl, hydrazido, hydrazino, aldehyde, ketone, azido, alkyne, phosphine, epoxide, and protected groups thereof. [00358] Clause 16. The compound according to any one of the preceding clauses, wherein when m is 0, each T is independently CR¹ or CR¹R². [00359] Clause 17. The compound according to any one of the preceding clauses, wherein when m is 0, T is not NR^4’, S or O. [00360] Clause 18. The compound according to any one of the preceding clauses, wherein when m is 1, each T is independently NR^4’, O, S, Se, or Te. [00361] Clause 19. The compound according to any one of the preceding clauses, wherein when m is 1, T is not CR¹ or CR¹R². [00362] Clause 20. The compound according to any one of the preceding clauses, comprising a structure selected from the group consisting of

[00363] Clause 21. A tandem dye, comprising the fluorescent compound of any one of clauses 1 to 20; and an acceptor or a donor chromophore covalently linked to the fluorescent compound. [00364] Clause 22. A labeled specific binding partner, comprising the fluorescent compound according to any one of clauses 1 to 20 or tandem dye according to clause 21; and a specific binding partner covalently linked to the fluorescent compound or tandem dye. [00365] Clause 23. The labeled specific binding partner according to clause 22, wherein the specific binding partner is selected from the group consisting of a protein, peptide, affinity ligand, antibody, antibody fragment, carbohydrate, lipid, nucleic acid, and an aptamer. [00366] Clause 24. The labeled specific binding partner according to clause 22 or 23, wherein the specific binding partner is an antibody. [00367] Clause 25. The compound of any one of clauses 1 to 20, tandem dye of clause 21, or labeled specific binding partner of any one of clauses 22 to 24, , wherein the compound exhibits solubility in water at ambient room temperature selected from the group consisting of > 1 mg/mL, > 2 mg/mL, > 3 mg/mL, > 4 mg/mL, > 5 mg/mL, > 6 mg/mL, > 7 mg/mL, > 8 mg/mL, > 9 mg/mL, >10 mg/mL, > 20 mg/mL, >30 mg/mL, >30 mg/mL, and > 50 mg/mL. [00368] Clause 26. The compound of any one of clauses 1 to 20, tandem dye of clause 21, or labeled specific binding partner of any one of clauses 22 to 24, wherein the compound exhibits an absorbance maxima of >500 nm, >600 nm, >700 nm, >800 nm, >850 nm, or in a range of from 500 nm to 1200 nm, 500 nm to 1,000 nm, or 600 nm to 950 nm. [00369] Clause 27. The compound of any one of clauses 1 to 20, tandem dye of clause 21, or labeled specific binding partner of any one of clauses 22 to 24, wherein the compound exhibits an emission maxima of >550 nm, > 650 nm, >750 nm, >850 nm, or > 900 nm, or in a range of from 550 nm to 1300 nm, 550 nm to 1,050 nm, or 650 to 1,000 nm. [00370] Clause 28. A method for detecting a target analyte in a sample comprising: providing a sample that is suspected of containing the analyte; and contacting the sample with a specific binding partner conjugated to a fluorescent compound of any one of clauses 1 to 20 or tandem dye of clause 21, wherein the specific binding partner is capable of interacting with the target analyte. [00371] Clause 29. The method of clause 28, wherein the binding partner is an antibody, optionally wherein: (a) the method is configured for flow cytometry; (b) the water-soluble fluorescent compound is bound to a substrate; (c) the analyte is a protein expressed on a cell surface; (d) the method is configured as an immunoassay; or (e) the method further comprises providing additional binding partners for detecting additional analytes simultaneously. [00372] Clause 30. A kit comprising at least one fluorescent compound of any one of clauses 1 to 20, tandem dye of clause 21, or labeled specific binding partner of any one of clauses 22 to 24, the compound or tandem dye optionally including a conjugation tag.

Claims

WE CLAIM: 1. A fluorescent compound comprising a structure according to Formula (I): (I), wherein is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, polycyclic aryl group, monocyclic heteroaryl group, and polycyclic heteroaryl group; is selected from the group consisting of a substituted or unsubstituted benzene, benzene derivative, monocyclic aryl group, and polycyclic aryl group; each T is independently NR^4’, CR¹, CR¹R², O, S, Se, or Te; V is NR¹¹, CR⁸, CR⁸R⁹, O, S, Se, or Te, or each T-V together can stand for a structural element selected from the group consisting of SO₂, -CR¹-O-, -O-CR¹-, -CO-O-, -O-CO-, -CO-NR¹¹-, or -NR^4’-CO-; G is C or N; each R¹, R², R⁸, and R⁹ is independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, binding partner, linked binding partner, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide- PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, alkoxy sulfonate, carboxylic acid, carboxylate, alkyl carboxylate, alkoxy carboxylate, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphoramidite, phosphinamide, alkoxy sulfonamide PEG, alkyl sulfonamide PEG, alkylamide,

, ; each R⁴, R^4’, R¹⁰, and R¹¹ is independently selected from the group consisting of a linker moiety, a chromophore, linked chromophore, reactive group, linked reactive group, conjugation tag, linked conjugation tag, water-solubilizing moiety, linked water- solubilizing moiety, binding partner, linked binding partner, E, linked E, H, halogen, alkyl, alkenyl, alkynyl, a PEG group, a linked PEG group, cycloalkyl, heterocycloalkyl, haloalkyl, aryl, heteroaryl, sulfonic acid, sulfonate, alkyl sulfonate, alkyl sulfonate salt, carboxylic acid, carboxylate, alkyl carboxylate, alkyl sulfonamide, alkyl sulfonamide PEG, alkyl amide, alkyl amide-PEG, , or protected groups thereof, or one, two, three, or four of R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ together form an unsubstituted or substituted unsaturated or partially unsaturated C3-C10 cycloalkyl group; unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ heterocycloalkyl optionally substituted with O; unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3-C8 polycycloalkyl group; or unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₄, C₃-C₁₀, or C₃ -C₈ polyheterocycloalkyl group optionally substituted with O; each R³ is independently selected from the group consisting of H, alkyl, alkene, alkyne, cycloalkyl, haloalkyl, alkoxy, (hetero)aryloxy, aryl, (hetero)arylamino, alkyl sulfonate, alkyl carboxylate, a water-solubilizing moiety, a linked water-solubilizing moiety, a chromophore, a linked chromophore, functional moiety, linked functional moiety, binding partner, linked binding partner, a PEG group, and a linked PEG group; each Q is independently a bond, O, NH, NR⁴, C₁-C₁₂ alkylene, CHR⁴, or CH₂; each Z is independently CH2, CHR⁴, O, NR⁴, or NH; each W¹ is independently a water-solubilizing moiety; L¹, L², and L³ are each independently selected linker moieties; each E is independently selected from the group consisting of a chromophore, a functional moiety, a substrate, a reactive group, a conjugation tag, and a binding partner; each R⁷ is independently selected from the group consisting of H, hydroxyl, C₁- C₁₂ alkyl, C₁-C₁₂ heteroalkyl, C₂-C₁₂ alkene, C₂-C₁₂ alkyne, C₃-C₁₂ cycloalkyl, C₁- C12 haloalkyl, C1-C12 alkoxy, C2-C18 (hetero)aryloxy, C2-C18 (hetero)arylamino, carboxylate, carboxylic acid, C₂-C₁₂ alkyl carboxylic acid, C₂-C₁₂ alkyl carboxylate, C₂- C12 alkyl carboxylate ester, aryl carboxylic acid, aryl carboxylate ester, C1-C12 alkoxy, a water-solubilizing moiety, a PEG moiety, a functional group, a chemoselective functional group, conjugation tag, linked conjugation tag, a linker, sulfonic acid, sulfonate, C₁-C₁₂ alkyl sulfonate, sulfonamide; each R¹² , R¹³ and R¹⁴ is independently selected from the group consisting of hydrogen, halogen, one or more heteroatoms, substituted or unsubstituted C₁-C₆ alkyl, substituted or unsubstituted C₁-C₆ heteroalkyl, substituted or unsubstituted C₁-C₆ alkene, substituted or unsubstituted C3-C10 cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted C₃-C₁₀ heterocycloalkyl, CO₂R¹, CONR¹R², O-aryl, S-aryl, N-aryl, -O-alkyl, S-alkyl, N-alkyl, wherein each alkyl or aryl can optionally be substituted with one or more R⁷, PEG, or PEG-R⁷, optionally wherein each R¹² , R¹³ and R¹⁴ is independently substituted with a R⁷ group; or at least two of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, optionally including, but not limited to, one, two, three, or four of R¹, R², R⁴, R^4’, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, and R¹⁴ together, including, but not limited to R⁴ and R¹² together; R¹⁴ and R¹⁰ together; R⁴ and R¹³ together; R¹³ and R¹⁰ together; R¹³ and R¹¹ together; R¹² and R¹⁴ together; R^4’ and R¹³ together; R^4’ and R¹² together; R¹³ and R¹⁰ together; R⁴, R¹², R¹⁴ and R¹⁰ together; R⁴, R¹³ and R¹⁰ together; R⁴, R¹³ and R¹¹ together; R⁴, R¹² and R¹⁴ together; R^4’, R¹³ and R¹¹ together; and R¹², R¹⁴ and R¹⁰ form an unsubstituted or substituted unsaturated or partially unsaturated C3-C10 cycloalkyl group, unsubstituted or substituted unsaturated or partially unsaturated C₃-C₁₀ heterocycloalkyl optionally substituted with O, an unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3-C8 polycycloalkyl group, or unsubstituted or substituted unsaturated or partially unsaturated C3-C14, C3-C10, or C3- C8 polyheterocycloalkyl group optionally substituted with O; each K is independently a covalent bond, O, S, Se, P, NR¹, or CR¹R²; each f is independently an integer from 0 to 50, 1 to 30, or 2 to 20; each m and m’ is independently 0, 1, 2, or 3; each n is independently an integer from 1 to 20; 1 to 10; or 0, 1, 2, or 3; each p is independently 1, 2, 3, or 4; each s is independently 1 or 2; each t is independently 0, 1, 2, 3, or 4; and X is a counterion. 2. The compound of claim 1, comprising a structure according to any one of formulae (IIa), (IIb), (IIc), (IId), (IIe), (IIf), (IIg), (IIh), (IIi), (IIj), (IIk), (IIl), (IIm), (IIn), and (IIo):

wherein T is NR^4’, CR¹, CR¹R², O, or S; V is NR¹¹, CR⁸, CR⁸R⁹, O, or S; each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide- PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphoramidite, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; each R¹⁶ is independently selected from K-R¹³, H, halogen, O-C1-6 alkyl, S-C1-6 alkyl, O- aryl, S-aryl, NHC_1-6alkyl, Ph-NCS, Ph-CO₂H, or Ph-(CH₂)_1-4CO₂H; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. 3. The compound of claim 1, comprising a structure according to any one of formulae (IIIa), (IIIb), (IIIc), (IIId), (IIIe), (IIIf), (IIIg), (IIIh), (IIIi), (IIIj), (IIIk), (IIIl), (IIIm), and (IIIn): (IIIa),

(IIIk), or (IIIn), wherein each R⁵ and R⁶ is independently selected from independently selected from the groupting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, hydrogen,xy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl,o)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG,horamide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoetherarbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylicarboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt,ate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate,hinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt,ally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen,ate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, ylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; each R¹⁶ is independently selected from K-R¹³, H, halogen, O-C_1-6 alkyl, S-C_1-6 alkyl, O--aryl, NHC1-6alkyl, Ph-NCS, Ph-CO2H, or Ph-(CH2)1-4CO2H ; and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety.

4. The compound of claim 1, comprising a structure according to any one of formulae (IVa), (IVb), (IVc), (IVd), (IVe), (IVf), (IVg), (IVh), (IVi), (IVj), (IVk), (IVl), (IVm), (IVn), (IVo), (IVp), (IVq), (IVr), (IVs), (IVt), (IVu), (IVv), (IVw), and (IVx):

wherein each R⁵ and R⁶ is independently selected from independently selected from the group consisting ter-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive linked reactive group, conjugation tag, linked conjugation tag, hydrogen, hydroxy, halogen,, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, nked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt,nium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl mide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonatealt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide,mide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate,ulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting ofen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group,ylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group; each R¹⁶ is independently selected from K-R¹³, H, halogen, O-C_1-6 alkyl, S-C_1-6 alkyl, O--aryl, NHC1-6alkyl, Ph-NCS, Ph-CO2H, or Ph-(CH2)1-4CO2H , and is an optionally substituted cycloalkenyl or polycycloalkenyl moiety. The compound of claim 1, comprising a structure according to any one of formulae (Va), (Vb), (Vc), (Vd), (Ve), (Vf), (Vg), (Vh), (Vi), (Vj), (Vk), and (Vl): (Va),

w e e Y is selected from the group consisting of NR⁴, CR¹, CR¹R², O, and S; and each R⁵ and R⁶ is independently selected from independently selected from the group consisting of a water-solubilizing moiety, linked water-solubilizing moiety, a linker moiety, E, a linked E, reactive group, linked reactive group, conjugation tag, linked conjugation tag, hydrogen, hydroxy, halogen, alkoxy, alkyl, alkenyl, alkynyl, cycloalkyl, haloalkyl, aryl, heteroaryl, (hetero)aryloxy, (hetero)arylamino, PEG, linked PEG, amide-PEG, sulfonamide-PEG, phosphoramide-PEG, ammonium alkyl salt, ammonium alkyloxy salt, ammonium oligoether salt, carbonyl, acyl, sulfonate, alkyl sulfonate, alkyl sulfonamide, phosphate group, carboxylic acid, carboxylate, alkyl carboxylate, sulfonic acid, sulfonate alkyl salt, sulfonate alkoxy salt, sulfonate oligoether salt, sulfonamido oligoether, sulfonamide, sulfinamide, phosphonamidate, phosphinamide, alkoxy sulfonamide PEG, alkylamide, alkoxy sulfonate, alkyl sulfonate salt, optionally wherein R⁵ and R⁶ are independently selected from the group consisting of hydrogen, sulfonate, alkyl sulfonate, alkyl sulfonamide, alkyl sulfonamide-PEG, phosphate group, carboxylic acid, carboxylate, amide, alkyl amide, amide-PEG, and a water-solubilizing group. 6. The compound of any one of claims 1-5, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises an E or linked E. 7. The compound of any one of claims 1-6, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a binding partner or linked binding partner. 8. The compound of any one of claims 1-7, wherein at least one, at least two, at least three, or at least four of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a water- solubilizing moiety or a linked water-solubilizing moiety. 9. The compound of any one of claims 1-8, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a reactive group or linked reactive group. 10. The compound of any one of claims 1-9, wherein at least one of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, and R¹¹ comprises a chromophore or linked chromophore. 11. The compound of claim 1, wherein the compound is symmetric. 12. The compound of claim 1, wherein the compound is asymmetric.

13. The compound of any one of claims 1-12, wherein the water-solubilizing moiety is selected from the group consisting of carboxylates, carboxylic acids, phosphonates, phosphates, sulfonates, sulfonamides, sulfates, sulfinates, sulfoniums, esters, polyaklylene oxides, polyethylene oxides comprising an ethylene oxide repeat unit of the formula — (CH2—CH2—O)n—, polyamidealkylene oxides comprising an ethylene oxide repeat unit of the formula —(CH₂—CH₂—O)n—, polyethylene glycols (PEGs), modified PEGs, linked PEGs, amide-PEGs, sulfonamide-PEGs, phosphoramide-PEGs, hydroxyls, amines, amino acids, ammoniums, guanidiniums, pyridiniums, polyamines and sulfoniums, polyalcohols, straight chain or cyclic saccharides, primary, secondary, tertiary, or quaternary amines and polyamines, glycols, polyethers, —COOX, —SO₃X, —PO₃X, — NR3+X, (CH2CH2O)fR¹⁵ and mixtures thereof, wherein R¹⁵ is hydrogen, substituted or unsubstituted C₁-C₆ alkyl, or substituted or unsubstituted C₁-C₆ alkoxy, and X is a counterion. 14. The compound of claim 1, wherein X is a counterion selected from the group consisting of F-, Cl-, Br-, I-, ClO₄-, CF₃CO₂-, CH₃CO₂-, PO₄ ^3-, SO₄ ^2-, BF₄-, Na⁺, K⁺, Mg⁺⁺, and Ca⁺⁺. 15. The compound of any one of claims 1-14, wherein the reactive group is selected from the group consisting of thiols, maleimides, halogenated maleimide, iodoacetamides, amines, alkyl carboxylates, alkyl sulfonates, carboxylic amines, carbamate, carboxylate esters, N- hydroxysuccinimidyl, halogen, boronic esters, boronic acids, hydrazonyl, carboxylic acids or active esters thereof, azide, alkyne, cyclooctyne, tetrazine, transcyclooctene, dienes, dienophiles, sulfur (VI) fluoride (SuFEX), sulfonyl fluoride, hydroxyl, hydrazido, hydrazino, aldehyde, ketone, azido, alkyne, phosphine, epoxide, and protected groups thereof. 16. The compound according to any one of claims 1 to 15, wherein when m is 0, each T is independently CR¹ or CR¹R². 17. The compound according to any one of claims 1 to 15, wherein when m is 0, T is not NR^4’, S or O.

18. The compound according to any one of claims 1 to 15, wherein when m is 1, each T is independently NR^4’, O, S, Se, or Te. 19. The compound according to any one of claims 1 to 15, wherein when m is 1, T is not CR¹ or CR¹R². 20. The compound of claim 1, comprising a structure selected from the group consisting of ,

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. 21. A tandem dye, comprising: the fluorescent compound of any one of claims 1-20; and an acceptor chromophore or a donor chromophore covalently linked to the fluorescent compound or labeled specific binding partner. 22. A labeled specific binding partner, comprising: the fluorescent compound according to any one of claims 1-20 or tandem dye according to claim 21; and a specific binding partner covalently linked to the fluorescent compound or tandem dye. 23. The labeled specific binding partner according to claim 22, wherein the specific binding partner is selected from the group consisting of a protein, peptide, affinity ligand, antibody, antibody fragment carbohydrate lipid nucleic acid and an aptamer

24. The labeled specific binding partner according to claim 23, wherein the specific binding partner is an antibody. 25. The compound of any one of claims 1-20, tandem dye of claim 21, or labeled specific binding partner of any one of claims 22-24, wherein the compound exhibits solubility in water at ambient room temperature of > 1 mg/mL, > 2 mg/mL, > 3 mg/mL, > 4 mg/mL, > 5 mg/mL, > 6 mg/mL, > 7 mg/mL, > 8 mg/mL, > 9 mg/mL, >10 mg/mL, > 20 mg/mL, >30 mg/mL, >30 mg/mL, or > 50 mg/mL. 26. The compound of any one of claims 1-20, tandem dye of claim 21, or labeled specific binding partner of any one of claims 22-24, wherein the compound exhibits an absorbance maxima of >500 nm, >600 nm, >700 nm, >800 nm, >850 nm, > 900 nm, >1000 nm, >1100 nm, or > 1200 nm. 27. The compound of any one of claims 1-20, tandem dye of claim 21 or labeled specific binding partner of any one of claims 22-24, wherein the compound exhibits an emission maxima of >550 nm, > 650 nm, >750 nm, >850 nm, >900 nm, > 1000 nm, > 1100 nm, > 1200 nm, or > 1300 nm. 28. A method for detecting a target analyte in a sample comprising: providing a sample that is suspected of containing the analyte; and contacting the sample with a specific binding partner conjugated to a fluorescent compound of any one of claims 1-20 or tandem dye of claim 21, wherein the specific binding partner is capable of interacting with the target analyte. 29. The method of claim 28, wherein the binding partner is an antibody, optionally wherein: a. the method is configured for flow cytometry; b. the water-soluble fluorescent compound is bound to a substrate; c. the analyte is a protein expressed on a cell surface; d. the method is configured as an immunoassay; or e. the method further comprises providing additional binding partners for detecting additional analytes simultaneously. 30. A kit comprising at least one fluorescent compound of any one of claims 1 to 20, tandem dye of claim 21, or labeled specific binding partner of any one of claims 22-24, the compound or tandem dye optionally including a conjugation tag.