CN113480620B

CN113480620B - Mutant of porin monomer, protein hole and application thereof

Info

Publication number: CN113480620B
Application number: CN202110950708.3A
Authority: CN
Inventors: 刘少伟; 谢馥励; 何京雄; 岳飞飞; 李倩雯
Original assignee: Chengdu Qitan Technology Ltd
Current assignee: Chengdu Qitan Technology Ltd
Priority date: 2021-08-18
Filing date: 2021-08-18
Publication date: 2024-02-06
Anticipated expiration: 2041-08-18
Also published as: CN113480620A

Abstract

The invention belongs to the technical field of characterization of target analyte characteristics, and particularly provides a mutant of a porin monomer, a protein hole containing the mutant, and application of the mutant in detecting target analyte, wherein the amino acid of the mutant of the porin monomer comprises a sequence shown in SEQ ID NO. 1 or a sequence with at least 99%, 98%, 97%, 96%, 95%, 90%, 80%, 70%, 60% or 50% identity with the sequence, and the amino acid of the mutant of the porin monomer comprises mutation at one or more positions corresponding to T71, S75 and F76 of SEQ ID NO. 1.

Description

Mutant of porin monomer, protein hole and application thereof

Technical Field

The invention belongs to the technical field of characterization of target analyte characteristics, and particularly relates to a mutant of a porin monomer, a protein hole containing the mutant and application of the mutant in detection of target analytes.

Background

Along with the research on the structure and sequence of nucleic acid, the nucleic acid sequencing technology is continuously developed, becomes the core field of life science research, and plays a great promotion role in the technical development of the fields of biology, chemistry, electricity, life science, medicine and the like. The use of nanopores to develop novel rapid, accurate, low cost, high precision and high throughput nucleic acid sequencing techniques is one of the hot spots of the latter human genome project.

Nanopore (Nanopore) sequencing, also known as fourth generation sequencing, is a genetic sequencing technique that uses single-stranded nucleic acid molecules as sequencing elements, and utilizes a Nanopore that provides ion current channels so that single-stranded nucleic acid molecules pass through the Nanopore under electrophoretic driving, and when nucleic acid passes through the Nanopore, the current of the Nanopore is reduced, and sequence information is read in real time for the different signals generated.

Nanopore sequencing is mainly characterized in that: the read length is long, the accuracy is high, and the error region mostly occurs in the region of the homopolymeric oligonucleotide. Nanopore sequencing not only can realize natural DNA and RNA sequencing, but also can directly acquire base modification information of DNA and RNA, for example, methylated cytosine can be directly read out, and the genome does not need to be subjected to bisulfite (bisufite) treatment in advance like a second-generation sequencing method, so that the method has a great promotion on directly researching epigenetic related phenomena at the genome level. The nanopore detection technology is used as a novel platform, and has the advantages of low cost, high flux, no marking and the like.

Nanopore analysis techniques originate from the invention of Coulter counters and single channel current recording techniques. The physiological and medical Nobel prize acquirers Neher and Sakamann measure membrane potential in 1976 by using a patch clamp technology, research membrane proteins and ion channels, and promote the practical application process of the nanopore sequencing technology. In 1996, kasianowicz et al proposed a new concept for DNA sequencing using alpha-hemolysin, a milestone marker for biological nanopore single molecule sequencing. Subsequently, research reports of biological nanopores such as MspA porin, phage Phi29 connector and the like enrich the research of nanopore analysis technology. Li et al opened a new era of solid state nanopore research in 2001. Solid state nanopore sequencing has evolved slowly, limited by the development of the semiconductor and materials industry.

One of the key points of nanopore sequencing technology is that a special biological nanopore is designed, a read head structure formed by a constriction zone in the pore can cause blockage of pore current when a single-stranded nucleic acid (e.g. ssDNA) molecule passes through the nanopore, so that the intensity of the current flowing through the nanopore is briefly influenced (the variation amplitude of the current influenced by each base is different), and finally, high-sensitivity electronic equipment detects the changes to identify the passed base. At present, protein pores are used as nanopores for sequencing, and the porin mainly uses escherichia coli as a source.

At present, the nanopore protein is single, and alternative nanopore protein needs to be developed to realize a nanopore sequencing technology. Porin is also closely related to sequencing precision, and the porin also relates to mode change of interaction with the speed control protein, so that stability of an interaction interface of the porin and the speed control protein is further optimized, and consistency and stability of sequencing data are improved. The accuracy of nanopore sequencing technology is also to be improved, and therefore, there is a need to develop improved nanopore proteins to further increase the resolution of nanopore sequencing.

Disclosure of Invention

To solve the above problems, an object of embodiments of the present invention is to provide a mutant of an alternative porin monomer, a protein pore including the same, and applications thereof.

In a first aspect, embodiments of the present invention provide a mutant of a porin monomer, wherein the amino acid of the mutant of a porin monomer comprises or consists of the sequence shown in SEQ ID No. 1 or a sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 80%, 70%, 60% or 50% identity thereto, and the amino acid of the mutant of a porin monomer comprises a mutation at one or more positions of T71, S75, F76 corresponding to SEQ ID No. 1;

one or more of T71, S75, F76 are specifically T71, S75, F76, T71 and S75, S75 and F76, T71 and S76, or T71 and S75 and F76.

Preferably, the amino acids of the mutant of the porin monomer comprise mutations at one or more positions corresponding to positions 62-175, 62-104, 68-175, 64-79, 71-76, or 69-76 of SEQ ID NO. 1.

Preferably, the amino acids of the mutant of the porin monomer include:

(1) Insertions, deletions and/or substitutions of amino acids at one or more positions of K69, P70, T71, P72, a73, S74, S75 and F76 corresponding to SEQ ID No. 1; (2) An insertion, deletion and/or substitution of an amino acid at one or more positions corresponding to Q64, T65, G66, Q67, Y68, K69, P70, T71, P72, a73, S74, S75, F76, S77, T78, and S79 of SEQ ID No. 1; (3) Insertions, deletions and/or substitutions of amino acids at one or more positions of R62, D63, Y68, K69, T71, S75, F76, and E104 corresponding to SEQ ID NO. 1; or (4) has amino acid insertions, deletions and/or substitutions at one or more positions corresponding to Y68, K69, P70, T71, P72, A73, S74, S75, F76, E171 and D175 of SEQ ID NO. 1.

In one embodiment, the amino acid mutation of the mutant of the porin monomer is selected from the group consisting of:

(a) The amino acids KPTPASSF corresponding to positions 69-76 of SEQ ID NO. 1 are mutated into M ₁ M ₂ M ₃ M ₄ M ₅ M ₆ M ₇ M ₈ Wherein M is ₁ 0 to 3 selected from R, K, H; m is M ₂ 0 to 1 selected from P; m is M ₃ From 0 to 10 selected from S, G, C, U, T, M, A, V, L, I; m is M ₄ 0 to 1 selected from P; m is M ₅ 0 to 5 selected from A, G, V, L, I; m is M ₆ 0 to 5 selected from S, C, U, T, M; m is M ₇ From 0 to 10 selected from A, T, G, V, L, I, S, C, U, M; m is M ₈ 0 to 7 selected from Q, D, E, N, K, H, R;

(b) Amino acids QTGQYKPTPASSFSTS corresponding to positions 64-79 of SEQ ID NO. 1 are mutated to M ₉ M ₁₀ M ₁₁ M ₁₂ M ₁ ₃ M ₁₄ M ₁₅ M ₁₆ M ₁₇ M ₁₈ M ₁₉ M ₂₀ M ₂₁ M ₂₂ M ₂₃ M ₂₄ Wherein M is ₉ 0 to 5 selected from L, G, A, V, I; m is M ₁₀ 0 to 5 selected from T, S, C, U, M; m is M ₁₁ 0 to 5 selected from G, A, V, L, I; m is M ₁₂ 0 to 4 selected from Q, D, E, N; m is M ₁₃ 0 to 3 selected from Y, F, W; m is M ₁₄ 0 to 3 selected from R, H, K; m is M ₁₅ 0 to 1 selected from P; m is M ₁₆ 0 to 5 selected from S, C, U, T, M; m is M ₁₇ 0 to 1 selected from P; m is M ₁₈ 0 to 5 selected from A, G, V, L, I; m is M ₁₉ 0 to 5 selected from S, C, U, T, M; m is M ₂₀ 0 to 5 selected from A, G, V, L, I; m is M ₂₁ 0 to 9 selected from N, D, E, Q, L, G, A, V, I; m is M ₂₂ 0 to 5 selected from S, C, U, T, M; m is M ₂₃ 0 to 5 selected from T, S, C, U, M; m is M ₂₄ 0 to 5 selected from A, G, V, L, I;

(c) The 62-bit mutation corresponding to SEQ ID NO. 1 is 0 to 5 in S, C, U, T, M; mutation at position 63 into 0 to 5 of V, G, A, L, I; mutation at position 68 to 0 to 2 in F, W; mutation at position 69 to 0 to 2 of R, H; mutation at position 71 to 0 to 4 in S, C, U, M; mutation at position 75 to 0 to 5 in A, G, V, L, I; mutation at position 76 to 0 to 4 in Q, D, E, N; mutations at position 104 to 0 to 5 of V, G, A, L, I; and

(d) Amino acids YKPTPASSF corresponding to positions 68-76 of SEQ ID NO. 1 are mutated to M ₂₅ M ₂₆ M ₂₇ M ₂₈ M ₂₉ M ₃₀ M ₃₁ M ₃₂ M ₃₃ And mutation at position 171 to 0 to 3 of N, D, Q; mutation at position 175 to 0 to 3 in N, E, Q wherein M ₂₅ 0 to 3 selected from F, Y, W; m is M ₂₆ 0 to 3 selected from R, H, K; m is M ₂₇ 0 to 1 selected from P; m is M ₂₈ 0 to 5 selected from S, C, U, T, M; m is M ₂₉ 0 to 1 selected from P; m is M ₃₀ 0 to 5 selected from A, G, V, L, I; m is M ₃₁ 0 to 5 selected from S, C, U, T, M; m is M ₃₂ 0 to 5 selected from A, G, V, L, I; m is M ₃₃ From 0 to 4 of Q, D, E, N.

(a) The amino acids KPTPASSF corresponding to positions 69-76 of SEQ ID NO. 1 are mutated into M ₁ M ₂ M ₃ M ₄ M ₅ M ₆ M ₇ M ₈ Wherein M is ₁ Selected from R, K or H; m is M ₂ Selected from P; m is M ₃ Selected from S, G, C, U, T, M, A, V, L or I; m is M ₄ Selected from P; m is M ₅ Selected from A, G, V, L or I; m is M ₆ Selected from S, C, U, T or M; m is M ₇ Selected from A, T, G, V, L, I, S, C, U or M; m is M ₈ Selected from Q, D, E, N, K, H or R;

(b) Amino acids QTGQYKPTPASSFSTS corresponding to positions 64-79 of SEQ ID NO. 1 are mutated to M ₉ M ₁₀ M ₁₁ M ₁₂ M ₁ ₃ M ₁₄ M ₁₅ M ₁₆ M ₁₇ M ₁₈ M ₁₉ M ₂₀ M ₂₁ M ₂₂ M ₂₃ M ₂₄ Wherein M is ₉ Selected from L, G, A, V or I; m is M ₁₀ Selected from T, S, C, U or M; m is M ₁₁ Selected from G, A, V, L or I; m is M ₁₂ Selected from Q, D, E or N; m is M ₁₃ Selected from Y, F or W; m is M ₁₄ Selected from R, H or K; m is M ₁₅ Selected from P; m is M ₁₆ Selected from S, C, U, T or M; m is M ₁₇ Selected from P; m is M ₁₈ Selected from A, G, V, L or I; m is M ₁₉ Selected from S, C, U, T or M; m is M ₂₀ Selected from A, G, V, L or I; m is M ₂₁ Selected from N, D, E, Q, L, G, A, V or I; m is M ₂₂ Selected from S, C, U, T or M; m is M ₂₃ Selected from T, S, C, U or M; m is M ₂₄ Selected from A, G, V, L or I;

(c) The R62 corresponding to SEQ ID NO. 1 is mutated to R62S, R62C, R62U, R T or R62M; d63 is mutated to D63V, D63G, D63A, D L or D63I; y68 is mutated to Y68F or Y68W; k69 is mutated to K69R or K69H; t71 is mutated into T71S, T, 71C, T, 71U or T71M; the S75 mutation is S75A, S75G, S75V, S L or S75I; the F76 is mutated into F76Q, F, 76D, F E or F76N; the E104 is mutated into E104V, E, 104G, E, A, E L or E104I; and

(d) Amino acids YKPTPASSF corresponding to positions 68-76 of SEQ ID NO. 1 are mutated to M ₂₅ M ₂₆ M ₂₇ M ₂₈ M ₂₉ M ₃₀ M ₃₁ M ₃₂ M ₃₃ And E171 is mutated to E171N, E171D or E171Q; mutation of D175 to D175N, D175E or D175Q, wherein M ₂₅ Selected from F, Y or W; m is M ₂₆ Selected from R, H or K; m is M ₂₇ Selected from P; m is M ₂₈ Selected from S, C, U,T or M; m is M ₂₉ Selected from P; m is M ₃₀ Selected from A, G, V, L or I; m is M ₃₁ Selected from S, C, U, T or M; m is M ₃₂ Selected from A, G, V, L or I; m is M ₃₃ Selected from Q, D, E, or N.

(a) The 69-76 amino acids KPTPASSF corresponding to SEQ ID NO. 1 are mutated into RPSPASAQ;

(b) The amino acids KPTPASSF corresponding to positions 69-76 of SEQ ID NO. 1 are mutated into KPGPASTK;

(c) Amino acids QTGQYKPTPASSFSTS corresponding to positions 64-79 of SEQ ID NO. 1 are mutated to LTGQYRPSPASANSTA;

(d) Amino acids QTGQYKPTPASSFSTS corresponding to positions 64-79 of SEQ ID NO. 1 are mutated to LTGQYRPSPASALSTA;

(e) R62S, D63V, Y F, K69R, T71S, S75A, F76Q, and E104V corresponding to SEQ ID NO 1; and

(f) Amino acids YKPTPASSF corresponding to positions 68-76 of SEQ ID NO. 1 are mutated to FRPSPASAQ, and E171N and D175N corresponding to SEQ ID NO. 1.

In a second aspect, embodiments of the present invention provide a protein pore comprising a mutant of at least one pore protein monomer.

In a third aspect, embodiments of the present invention provide a complex for characterizing a target analyte, characterized by: the protein hole and the speed control protein combined with the protein hole.

In a fourth aspect, embodiments of the invention provide nucleic acids encoding mutants, protein pores, or complexes of a porin monomer.

In a fifth aspect, embodiments of the invention provide a vector or genetically engineered host cell comprising the nucleic acid.

In a sixth aspect, embodiments of the invention provide the use of a mutant of a porin monomer, a protein pore, complex, nucleic acid, vector or host cell thereof to detect the presence, absence or one or more characteristics of a target analyte or to prepare a product to detect the presence, absence or one or more characteristics of a target analyte.

In a seventh aspect, embodiments of the present invention provide a method of producing a protein pore or polypeptide thereof, comprising transforming said host cell with said vector, and inducing said host cell to express said protein pore or polypeptide thereof.

In an eighth aspect, embodiments of the present invention provide a method for determining the presence, absence or one or more characteristics of a target analyte, comprising:

a. contacting a target analyte with a protein pore, a complex, or a protein pore in a complex such that the target analyte moves relative to the protein pore; and

b. One or more measurements are taken while the target analyte moves relative to the protein aperture to determine the presence, absence, or one or more characteristics of the target analyte.

In one embodiment, the method comprises: the target analyte interacts with the protein pores present in the membrane such that the target analyte moves relative to the protein pores.

In one embodiment, the target analyte is a nucleic acid molecule.

In one embodiment, a method for determining the presence, absence, or one or more characteristics of a target analyte includes coupling the target analyte to a membrane; and the target analyte interacts with the protein pores present in the membrane such that the target analyte moves relative to the protein pores.

In a ninth aspect, embodiments of the invention provide a kit for determining the presence, absence or one or more characteristics of a target analyte comprising mutants of said porin monomer, said protein pore, said complex, said nucleic acid, or said vector or host, and components of said membrane.

In a tenth aspect, embodiments of the present invention provide a device for determining the presence, absence or one or more characteristics of a target analyte, comprising the protein pore or the complex, and the membrane.

In one embodiment, the target analyte comprises a polysaccharide, a metal ion, an inorganic salt, a polymer, an amino acid, a peptide, a protein, a nucleotide, an oligonucleotide, a polynucleotide, a dye, a drug, a diagnostic agent, an explosive, or an environmental contaminant;

preferably, the target analyte comprises a polynucleotide,

more preferably, the polynucleotide comprises DNA or RNA; and/or, the one or more features are selected from (i) the length of the polynucleotide; (ii) identity of said polynucleotides; (iii) the sequence of the polynucleotide; (iv) A secondary structure of said polynucleotide and (v) whether said polynucleotide is modified; and/or, the rate controlling protein in the complex comprises a polynucleotide binding protein.

Drawings

The drawings described are only schematic and are non-limiting.

Fig. 1 illustrates the basic working principle of a nanopore according to one embodiment.

FIG. 2 shows a schematic diagram of DNA sequencing according to one embodiment.

FIG. 3 illustrates corresponding pore blocking signals as a nucleotide passes through a protein pore according to one embodiment.

FIGS. 4A, 4B and 4C illustrate wild-type protein pore channel surface structures and streamer patterns according to one embodiment. Fig. 4A is a side view of a surface structural model, fig. 4B is a top view of a streamer structural model, and fig. 4C is a streamer structural model.

Fig. 5A and 5B show amino acid model diagrams of the mutation hole 1 according to an embodiment, fig. 5A is a top view, and fig. 5B is a side view.

Fig. 6 shows the size information of the various parts of the abrupt hole 1 according to one embodiment.

Fig. 7 shows a monomeric amino acid model diagram of porin mutant 1 according to one embodiment, (b) is (a) the core amino acid composition of the constriction zone (eye loop) shown enlarged.

FIG. 8 shows negative staining electron microscopy results for porin mutant 1 according to one embodiment.

Fig. 9A shows a cryo-electron micrograph of porin mutant 1 and fig. 9B shows a 2D classification result according to one embodiment.

Fig. 10A and 10B show the results of local refinement fourier shell correlation coefficient (FSC) of porin mutant 1, a: an rIn FSC unshielded graph; b: an rIn FSC phase random mask; c: an rIn FSC correction chart; d: rIn FSC mask.

FIG. 11 illustrates a three-dimensional reconstruction of porin mutant 1 by cryoelectron microscopy, according to one embodimentElectron density map of resolution.

FIG. 12 shows that porin mutant 1 is in accordance with one embodimentElectron density map below.

FIG. 13 shows the structure of the DNA construct BS7-4C3-SE1 according to an embodiment.

FIG. 14 shows the structure of the DNA construct BS7-4C3-PLT according to one embodiment.

Fig. 15A shows the pore current and its gating characteristics for a mutant pore 1 at a voltage of ±180mV according to one embodiment.

FIG. 15B shows a nucleic acid via condition of mutant well 1 at a voltage of +180mV, according to one embodiment.

FIGS. 16A and 16B illustrate example current traces when helicase Mph-MP1-E105C/A362C controls the displacement of DNA construct BS7-4C3-PLT through mutant well 1, according to one embodiment.

Fig. 17 is an enlarged view showing a region of a single signal in the embodiment of fig. 16B.

Fig. 18A shows the pore current and its gating characteristics for a snap hole 2 at a voltage of ±180mV, according to one embodiment.

FIG. 18B shows a nucleic acid via condition of mutant well 2 at a voltage of +180mV, according to one embodiment.

FIGS. 19A and 19B show example current traces when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant well 2, according to one embodiment.

Fig. 20 is an enlarged view showing the area of a single signal in the embodiment of fig. 19A and B.

Fig. 21A shows the pore current and its gating characteristics for the abrupt pore 3 at a voltage of ±180mV according to one embodiment.

FIG. 21B shows a nucleic acid via condition of mutant well 3 at a voltage of +180mV, according to one embodiment.

FIGS. 22A and 22B illustrate example current traces when helicase Mph-MP1-E105C/A362C controls the displacement of DNA construct BS7-4C3-PLT through mutant pore 3, according to one embodiment.

Fig. 23 is an enlarged view showing the area of a single signal in the embodiment of fig. 22A.

Fig. 24A shows the pore current and its gating characteristics for a snap hole 4 at a voltage of ±180mV, according to one embodiment.

FIG. 24B shows a nucleic acid via condition of mutant well 4 at a voltage of +180mV, according to one embodiment.

FIGS. 25A and 25B illustrate example current traces when the helicase Mph-MP1-E105C/A362C control DNA construct BS7-4C3-PLT is shifted through the mutant pore 4 according to one embodiment.

Fig. 26 is an enlarged view showing the area of a single signal in the embodiment of fig. 25A and 25B.

FIG. 27 shows the pore current and its gating characteristics for a snap hole 5 at a voltage of 180mV, according to one embodiment.

FIG. 28 shows an example current trace when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant pore 5, according to one embodiment.

Fig. 29 is an enlarged view of the embodiment of fig. 28 showing a single signal in an area.

Fig. 30A shows the pore current and its gating characteristics for a mutant pore 6 at a voltage of ±180mV according to one embodiment.

FIG. 30B shows a nucleic acid via condition of mutant well 6 at a voltage of +180mV, according to one embodiment.

FIGS. 31A and 31B illustrate example current traces when the helicase Mph-MP1-E105C/A362C controls the displacement of the DNA construct BS7-4C3-PLT through the mutant hole 6 according to one embodiment.

Fig. 32 is an enlarged view of a single signal area of the embodiment of fig. 31A.

FIG. 33 shows the result of SDS-PAGE electrophoresis of mutant 1 according to an embodiment.

FIG. 34 shows a mutant 1 protein size exclusion chromatogram according to one embodiment.

Detailed Description

It will be appreciated that the unused application of the disclosed products and methods may be adapted to the specific needs of the art. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments of the invention only and is not intended to be limiting.

Further, as used in this specification and the claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. For example, reference to "a nucleotide" includes two or more nucleotides and reference to "a helicase" includes two or more helicases.

As used herein, the term "comprising" means that any recited element must be included, and other elements may also be optionally included. "consisting of" means that not all elements not listed are included. Embodiments defined by each of these terms are within the scope of the present invention.

As used herein, "nucleotide sequence," "DNA sequence," or "nucleic acid molecule" refers to a polymeric form of nucleotides of any length (ribonucleotides or deoxyribonucleotides). The term refers to only the primary structure of the molecule. Thus, the term includes double and single stranded DNA and RNA.

The term "nucleic acid" as used herein refers to a single-or double-stranded covalently linked nucleotide sequence in which the 3 'and 5' ends on each nucleotide are linked by a phosphodiester linkage. The nucleotides may consist of deoxyribonucleotide bases or ribonucleotide bases. Nucleic acids may include DNA and RNA, and may be synthetically prepared in vitro or isolated from natural sources. The nucleic acid may further comprise modified DNA or RNA, such as methylated DNA or RNA, or post-translationally modified RNA, such as 5 '-capping with 7-methylguanosine, 3' -end processing, such as cleavage and polyadenylation, and splicing. Nucleic acids may also include synthetic nucleic acids (XNA), such as Hexitol Nucleic Acids (HNA), cyclohexene nucleic acids (CeNA), threose Nucleic Acids (TNA), glycerol Nucleic Acids (GNA), locked Nucleic Acids (LNA) and Peptide Nucleic Acids (PNA). The size of a nucleic acid (or polynucleotide) is typically expressed in terms of the number of base pairs (bp) of a double-stranded polynucleotide, or in the case of a single-stranded polynucleotide, the number of nucleotides (nt). 1 kilobase pair (kb) is equal to 1 kilobp or nt. Polynucleotides less than about 40 nucleotides in length are commonly referred to as "oligonucleotides" and may comprise primers for use in DNA manipulation, such as by Polymerase Chain Reaction (PCR).

Polynucleotides, e.g., nucleic acids, are macromolecules comprising two or more nucleotides. The polynucleotide or nucleic acid may comprise any combination of any nucleotides. The nucleotides may be naturally occurring or synthetic. One or more nucleotides in the polynucleotide may be oxidized or methylated. One or more nucleotides in the polynucleotide may be damaged. For example, the polynucleotide may comprise a pyrimidine dimer. Such dimers are generally associated with damage caused by ultraviolet light and are a major contributor to cutaneous melanoma. One or more nucleotides in the polynucleotide may be modified, for example with a conventional label or tag. The polynucleotide may comprise one or more nucleotides that are abasic (i.e., lack nucleobases), or lack nucleobases and sugars (i.e., are C3).

The nucleotides in the polynucleotides may be linked to each other in any manner. The nucleotides are typically linked by their sugar and phosphate groups, as in nucleic acids. The nucleotides may be linked by their nucleobases, as in the crying dimers.

The polynucleotide may be single-stranded or double-stranded. At least a portion of the polynucleotide is preferably double-stranded. The polynucleotide may be a nucleic acid, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). A polynucleotide may comprise one RNA strand that is hybridized to one DNA strand. The polynucleotide may be any synthetic nucleic acid known in the art, such as Peptide Nucleic Acid (PNA), glycerol Nucleic Acid (GNA), threose Nucleic Acid (TNA), locked Nucleic Acid (LNA) or other synthetic polymer having a nucleotide side chain. The PNA backbone is composed of repeating N- (2-aminoethyl) -glycine units linked by peptide bonds. The GNA backbone is composed of repeating ethylene glycol units linked by phosphodiester linkages. The TNA backbone is composed of repeating threosyl groups linked together by phosphodiester linkages. LNA is formed from the ribonucleic acid described above, with an additional bridging structure linking the 2 'oxygen and 4' carbon in the ribose moiety. Bridged Nucleic Acids (BNA) are modified RNA nucleotides. They may also be referred to as limited or inaccessible RNA13BNA monomers may contain 5-, 6-or even 7-membered bridging structures and carry a "fixed" C3 '-endo-sugar folding structure (C3' -endo sugar puckering). The bridging structure is synthesized to introduce the 2',4' _ position of ribose to produce the 2',4' -BNA monomer.

Most preferably, the polynucleotide is ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). The polynucleotide may be of any length. For example, the polynucleotide may be at least 10, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, or at least 500 nucleotides or nucleotide pairs in length. The polynucleotide may be 1000 or more nucleotides or nucleotide pairs in length, 5000 or more nucleotides or nucleotide pairs, or 100000 or more nucleotides or nucleotide pairs.

Any number of polynucleotides may be studied. For example, the methods of the embodiments may involve characterizing 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 100, or more polynucleotides. If two or more polynucleotides are characterized, they may be different polynucleotides or the case of the same polynucleotide.

Polynucleotides may be naturally occurring or synthetic. For example, the method can be used to verify the sequence of the prepared oligonucleotides. The method is typically performed in vitro.

In the context of the present disclosure, the term "amino acid" is used in its broadest sense and is meant to include a compound comprising an amine (NH ₂ ) And organization of the Carboxyl (COOH) functional groups and of the side chains specific for each amino acid (for example R groups) And (3) a compound. In some embodiments, an amino acid refers to a naturally occurring lα -amino acid or residue. Common single-letter and three-letter abbreviations for naturally occurring amino acids are used herein: a=ala; c=cys; d=asp; e=glu; f=phe; g=gly; h=his; i=ile; k=lys; l=leu; m=met; n=asn; p=pro; q=gln; r=arg; s=ser; t=thr; v=val; w=trp; and y=tyr (Lehning e r, a.l. (1 975) biochem try, 2 nd edition, pages 71-92, worth Publishers, new York). The generic term "amino acid" also includes D-amino acids, retro-retro amino acids, and chemically modified amino acids (such as amino acid analogs), naturally occurring amino acids that are not normally incorporated into proteins (such as norleucine) and chemically synthesized compounds having properties known in the art to be characteristic of amino acids (such as β -amino acids). For example, analogs or mimetics of phenylalanine or proline are included in the definition of amino acids that allow the same conformational restriction of peptide compounds as do natural Phe or Pro. Such analogs and mimetics are referred to herein as "functional equivalents" of the corresponding amino acid. Roberts and Vellaccio, the Peptides: analysis, synthesis, biology, gross and Meiehofer, vol.5, page 341, academic Press, inc., N.Y.1983 list other examples of amino acids, which are incorporated herein by reference.

The terms "protein," "polypeptide," and "peptide" are further used interchangeably herein to refer to polymers of amino acid residues as well as variants and synthetic analogs of amino acid residues. Thus, these terms apply to amino acid polymers in which one or more amino acid residues is a synthetic non-naturally occurring amino acid, such as a chemical analog of the corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. Polypeptides may also undergo maturation or post-translational modification processes, which may include, but are not limited to: glycosylation, proteolytic cleavage, lipidation, signal peptide cleavage, propeptide cleavage, phosphorylation, and the like.

"homologues" of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified or wild-type protein in question and having similar biological and functional activity to the unmodified protein from which they are derived. As used herein, the term "amino acid identity" refers to the degree of sequence identity on an amino acid-to-amino acid basis in a comparison window. Thus, the "percent sequence identity" is calculated by: comparing the two optimally aligned sequences in a comparison window, determining the number of positions in the two sequences at which the same amino acid residue (e.g., ala, pro, ser, thr, gly, val, leu, ile, phe, tyr, trp, lys, arg, his, asp, glu, asn, gln, cys and Met) occurs to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the comparison window (i.e., window size), and multiplying the result by 100 to yield the percent sequence identity.

Sequence identity may also be a fragment or portion of a full-length polynucleotide or polypeptide. Thus, a sequence may have only 50% overall sequence identity to a full-length reference sequence, but a sequence of a particular region, domain or subunit may have 80%, 90% or up to 99% sequence identity to a reference sequence.

The term "wild-type" refers to a gene or gene product isolated from a naturally occurring source. Wild-type genes are the most commonly observed genes in a population, and are therefore arbitrarily designed as "normal" or "wild-type" forms of the genes. Conversely, the term "modified," "mutation," or "variant" refers to a gene or gene product that exhibits sequence modification (e.g., substitution, truncation, or insertion), post-translational modification, and/or functional properties (e.g., altered characteristics) as compared to the wild-type gene or gene product. Note that naturally occurring mutants can be isolated; these mutants are identified by the fact that they have altered characteristics compared to the wild-type gene or gene product. Methods for introducing or substituting naturally occurring amino acids are well known in the art. For example, methionine (M) may be replaced with arginine (R) by replacing the codon for methionine (ATG) with the codon for arginine (CGT) at the relevant position in the polynucleotide encoding the mutated monomer. Methods of introducing or substituting non-naturally occurring amino acids are also well known in the art. For example, non-naturally occurring amino acids can be introduced by including a synthetic aminoacyl-tRNA in the IVTT system for expressing the mutated monomer. Alternatively, non-naturally occurring amino acids can be introduced by expressing mutated monomers in a taeniasis (Pseudomonas taeanensis MS-3), which is auxotrophic for those particular amino acids in the presence of synthetic (i.e., non-naturally occurring) analogs of those particular amino acids. If the mutated monomers are produced using partial peptide synthesis, they may also be produced by naked ligation. Conservative substitutions replace an amino acid with other amino acids having similar chemical structures, similar chemical properties, or similar side-chain volumes. The amino acids introduced may have similar polarity, hydrophilicity, hydrophobicity, basicity, acidity, neutrality, or charge as the amino acids they replace. Alternatively, conservative substitutions may introduce another aromatic or aliphatic amino acid instead of the pre-existing aromatic or aliphatic amino acid. Conservative amino acid changes are well known in the art and may be selected based on the nature of the 20 major amino acids defined in table 1 below. In the case of amino acids of similar polarity, this can also be determined with reference to the hydrophilicity scale of the amino acid side chains in Table 2.

TABLE 1 chemical Properties of amino acids

TABLE 2 hydrophilicity scale

Side chain	Hydrophilic properties
		Ile,I	4.5
Val,V	4.2
		Leu,L	3.8
Phe,F	2.8
		Cys,C	2.5
Met,M	1.9
		Ala,A	1.8
Gly,G	-0.4
		Thr,T	-0.7
Ser,S	-0.8
		Trp,W	-0.9
Tyr,Y	-1.3
		Pro,P	-1.6
His,H	-3.2
		Glu,E	-3.5
Gln,Q	-3.5
		Asp,D	-3.5
Asn,N	-3.5
		Lys,K	-3.9
Arg,R	-4.5

It is well known that conservative substitutions of amino acids of similar nature with respect to each other typically do not affect the activity of the peptide sequence, and are shown in Table 3.

TABLE 3 conservative amino acid substitutions

The mutated or modified protein, monomer or peptide may also be chemically modified at any site in any manner. The mutated or modified monomer or peptide is preferably chemically modified by attachment of the molecule to one or more cysteines (cysteine linkages), attachment of the molecule to one or more lysines, attachment of the molecule to one or more unnatural amino acids, enzymatic modification of an epitope or modification of a terminus. Suitable methods for making such modifications are well known in the art. Mutants of modified proteins, monomers or peptides may be chemically modified by attachment of any molecule. For example, modified mutants of proteins, monomers or peptides may be chemically modified by attachment of dyes or fluorophores. In some embodiments, the mutant or modified monomer or peptide is chemically modified with a molecular adaptor that facilitates interaction between a pore comprising the monomer or peptide and the target nucleotide or target polynucleotide sequence. The molecular adaptors are preferably cyclic molecules, cyclodextrins, substances capable of hybridizing, DNA binders or intercalators, peptides or peptide analogues, synthetic polymers, aromatic planar molecules, positively charged small molecules or small molecules capable of hydrogen bonding.

The presence of the adaptors improves the host-guest chemistry of the pore and nucleotide or polynucleotide sequences, thereby improving the sequencing ability of the pore formed from the mutated monomer. The principles of host-guest chemistry are well known in the art. The adaptors have an effect on the physical or chemical properties of the pore, which improves the interaction of the pore with the nucleotide or polynucleotide sequence. The adaptors may alter the charge of the barrel or channel of the well, or specifically interact or bind with the nucleotide or polynucleotide sequence, thereby facilitating its interaction with the well.

A "protein pore" is a transmembrane protein structure that defines a channel or pore that allows translocation of molecules and ions from one side of the membrane to the other. Translocation of ionic species through the pore may be driven by a potential difference applied to either side of the pore. "nanopore" is a protein pore in which the smallest diameter of a channel through which a molecule or ion passes is on the order of nanometers (10 ^-9 Rice). In some embodiments, the protein pore may be a transmembrane protein pore. The transmembrane protein structure of the protein pore may be monomeric or oligomeric in nature. Typically, the pore comprises a plurality of polypeptide subunits arranged about a central axis, thereby forming a protein-lined channel extending substantially perpendicular to the membrane in which the nanopore resides. The number of polypeptide subunits is not limited. Typically, the number of subunits is from 5 to 30, suitably the number of subunits is from 6 to 10. Alternatively, the number of subunits is not as defined as in the case of perfringens lysin (perfringens) or associated large membrane pores. The protein subunit portion within the nanopore forming the protein-lined channel typically comprises a secondary structural motif that may include one or more transmembrane β -barrel and/or α -helical portions.

In one embodiment, the protein pores comprise one or more pore protein monomers. Each porin monomer may be from a cestode pseudomonas. In one embodiment, the protein pores comprise mutants of one or more pore protein monomers (i.e., monomers of one or more pore protein mutations).

In one embodiment, the porin is from a wild-type protein of the kingdom, a wild-type homolog, or a mutant thereof. The mutant may be a modified porin or a porin mutant. Modifications in mutants include, but are not limited to, any one or more of the modifications disclosed herein or combinations of such modifications. In one embodiment, the wild-type protein of the kingdom is a protein from cestode pseudomonas.

In one embodiment, a porin homolog refers to a polypeptide having at least 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50% complete sequence identity to the protein shown in SEQ ID NO. 1.

In one embodiment, a porin homolog refers to a polynucleotide that has at least 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50% complete sequence identity to a polynucleotide encoding a protein set forth in SEQ ID NO. 2. The polynucleotide sequence may comprise a sequence that differs from SEQ ID NO. 2 based on the degeneracy of the genetic code.

The polynucleotide sequence may be derivatized and replicated using methods standard in the art. Chromosomal DNA encoding wild-type porins may be extracted from pore-producing organisms such as P.taenii. The gene encoding the pore subunit may be amplified using PCR including specific primers. The amplified sequence may then be subject to site-directed mutagenesis. Suitable methods for site-directed mutagenesis are known in the art and include, for example, combinatorial chain reactions. The constructed polynucleotides encoding the examples may be prepared using techniques well known in the art, such as those described in Sambrook, j.and Russell, d. (2001) Molecular Cloning A Laboratory Manual,3rd Edition.Cold Spring Harbor Laboratory Press,Cold Spring Harbor,NY.

The resulting polynucleotide sequence may then be integrated into a recombinant replicable vector, such as a cloning vector. The vector may be used to replicate the polynucleotide in a compatible host cell. The polynucleotide sequence may thus be prepared by introducing the polynucleotide into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which cause replication of the vector. The vector may be recovered from the host cell.

Basic principle of operation of nanopores or protein pores

In one embodiment, in the electrolyte filled chamber 100, the insulating film 102 with the nanoscale pores divides the chamber into 2 cells, as shown in FIG. 1, when a voltage is applied to the electrolyte chamber, ions or other small molecular species pass through the pores under the force of an electric field, forming a stable detectable ionic current. By grasping the size and surface characteristics of the nano-pores, the applied voltage and the solution conditions, different types of biomolecules can be detected.

Because the molecular structures and the volumes of four bases adenine (A), guanine (G), cytosine (C) and thymine (T) which form DNA are different, when single-stranded DNA (ssDNA) passes through a nano-scale small hole under the drive of a speed-controlling enzyme and an electric field, the chemical property difference of different bases causes the variation amplitude of current caused when the DNA passes through the nano-pore or a protein pore to be different, so that the sequence information of the detected nucleic acid such as DNA is obtained.

FIG. 2 shows a schematic diagram 200 of DNA sequencing. As shown in fig. 2, in a typical nanopore/protein pore sequencing experiment, the nanopore is the only channel through which ions on both sides of the phospholipid membrane pass. A rate controlling protein, such as a polynucleotide binding protein, acts as a motor protein for a nucleic acid molecule, such as DNA, pulling the DNA strand through the nanopore/protein pore in sequence in steps of individual nucleotides. Every time a nucleotide passes through a nanopore/protein pore, the corresponding pore blocking signal is recorded (fig. 3). By analyzing the current signals associated with these sequences by a corresponding algorithm, sequence information of nucleic acid molecules such as DNA can be deduced.

In an embodiment, porins are screened from different species in nature (mainly bacteria and archaea) by bioinformatics means and evolutionary perspective. In one embodiment, the porin is from any organism, preferably from a cestode pseudomonas. Through sequence analysis, porins possess a complete functional domain. The structural biological means is utilized to predict and analyze a porin 3D structural model, and a channel protein with a proper read head architecture is selected. Then, by means of genetic engineering, protein engineering, directed evolution of proteins, computer aided protein design and the like, candidate channel proteins (or porins) are modified, tested and optimized, and a plurality of homologous protein mutants, preferably six (different homologous protein frameworks) with different signal characteristics and signal distribution modes are obtained through a plurality of iterations.

The porins in the examples are applicable to fourth generation sequencing techniques. In one embodiment, the porin is a nanopore protein. In one embodiment, porins may be used for solid state pore sequencing.

In one embodiment, a new protein backbone is employed to form a new constriction zone (read head region) structure, thereby providing a completely new mode of action during sequencing. The porins of the examples have good edge-jump distribution and efficiency of recombination with phospholipid membranes.

In one embodiment, the wild-type pore protein monomer is subjected to genetic mutation to alter the mutant of the pore protein monomer. In one embodiment, the amino acids of the mutant of the porin monomer comprise the sequence shown in SEQ ID NO. 1 or comprise a sequence having at least 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, or 50% identity thereto, and the amino acids of the mutant of the porin monomer have mutations at one or more of positions 62-79, 104, 170, and 175 of SEQ ID NO. 1.

In one embodiment, the mutation comprises an insertion, deletion and/or substitution of an amino acid. In one embodiment, the mutation at one or more of positions 62-79, 104, 170 and 175 of SEQ ID NO. 1 is an amino acid insertion, deletion and/or substitution at one or more of positions 62-79, 104, 170 and 175 of SEQ ID NO. 1.

In one embodiment, the amino acids of the mutant of the porin monomer correspond to one or more of positions (1) 69-76, (2) 64-79, (3) 62, 63, 68, 69, 71, 75, 76, and 104, or (4) positions 68-76 and 171, and 175 of SEQ ID NO. 1.

In one embodiment, the amino acids of the mutant of the porin monomer correspond to positions (1) 69-76, (2) 64-79, (3) 62, 63, 68, 69, 71, 75, 76, and 104 of SEQ ID NO. 1, or (4) one or more of positions 68-76 and 171 and 175 have amino acid insertions, deletions, and/or substitutions.

In one embodiment, the amino acids of the mutant of the porin monomer have mutations only at positions 69-76 (i.e., K69, P70, T71, P72, A73, S74, S75, F76) corresponding to SEQ ID NO. 1, or have insertions, deletions and/or substitutions of amino acids at one or more positions.

In one embodiment, the amino acids of the mutant of the porin monomer have mutations only at positions 64-79 (i.e., Q64, T65, G66, Q67, Y68, K69, P70, T71, P72, A73, S74, S75, F76, S77, T78 and S79) corresponding to SEQ ID NO. 1, or have insertions, deletions and/or substitutions of amino acids at one or more positions.

In one embodiment, the amino acids of the mutant of the porin monomer have mutations only at positions R62, D63, Y68, K69, T71, S75, F76Q, and E104 corresponding to SEQ ID NO. 1, or have amino acid insertions, deletions, and/or substitutions at one or more positions.

In one embodiment, the amino acids of the mutant of the porin monomer have mutations only at positions 68-76 (i.e., Y68, K69, P70, T71, P72, A73, S74, S75 and F76), E171 and D175, or have amino acid insertions, deletions and/or substitutions at one or more positions corresponding to SEQ ID NO. 1.

In one embodiment, the position corresponding to SEQ ID NO. 1 refers to the relative position where the sequence numbering is unchanged, whether by amino acid insertion or deletion or by the use of an identical sequence, the numbering of the SEQ ID NO. 1 sequence may still be used. For example, Q64 corresponding to SEQ ID NO. 1 may be mutated to Q64L, and even if the SEQ ID NO. 1 sequence number varies or a sequence having identity as defined herein with SEQ ID NO. 1 is employed, amino acid Q corresponding to position 64 of SEQ ID NO. 1 (even if it is not at position 64 in another sequence) may be mutated to L, which is within the scope of the present invention.

In one embodiment, the amino acids of the mutant of the porin monomer consist of the sequence shown in SEQ ID NO. 1, or consist of a sequence having at least 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 85%, 80%, 75% or 70%, 65%, 60%, 55%, or 50% identity thereto, and the amino acids of the mutant of the porin monomer have mutations at one or more of positions 62-79, 104, 170, and 175 of SEQ ID NO. 1.

In one embodiment, the sequence of SEQ ID NO. 1 of the porin monomer is from Pseudomonas cestodiae. The nucleotide sequence of the amino acid sequence encoding SEQ ID NO. 1 is SEQ ID NO. 2.

In one embodiment, the amino acids KPTPASSF at positions 69-76 are mutated to M ₁ M ₂ M ₃ M ₄ M ₅ M ₆ M ₇ M ₈ Wherein M is ₁ Selected from R, K or H; m is M ₂ Selected from P; m is M ₃ Selected from S, G, C, U, T, M, A, V, L or I; m is M ₄ Selected from P; m is M ₅ Selected from A, G, V, L or I; m is M ₆ Selected from S, C, U, T or M; m is M ₇ Selected from A, T, G, V, L, I, S, C, U or M; m is M ₈ Selected from Q, D, E, N, K, H or R.

In one embodiment, amino acids QTGQYKPTPASSFSTS corresponding to positions 64-79 of SEQ ID NO. 1 are mutated to M ₉ M ₁₀ M ₁₁ M ₁₂ M ₁₃ M ₁₄ M ₁₅ M ₁₆ M ₁₇ M ₁₈ M ₁₉ M ₂₀ M ₂₁ M ₂₂ M ₂₃ M ₂₄ Wherein M is ₉ Selected from L, G, A, V or I; m is M ₁₀ Selected from T, S, C, U or M; m is M ₁₁ Selected from G, A, V, L or I; m is M ₁₂ Selected from Q, D, E or N; m is M ₁₃ Selected from Y, F or W; m is M ₁₄ Selected from R, H or K; m is M ₁₅ Selected from P; m is M ₁₆ Selected from S, C, U, T or M; m is M ₁₇ Selected from P; m is M ₁₈ Selected from A, G, V, L or I; m is M ₁₉ Selected from S, C, U, T or M; m is M ₂₀ Selected from A, G, V, L or I; m is M ₂₁ Selected from N, D, E, Q, L, G, A, V or I; m is M ₂₂ Selected from S, C, U, T or M; m is M ₂₃ Selected from T, S, C, U or M; m is M ₂₄ Selected from A, G, V, L or I.

In one embodiment, R62 corresponding to SEQ ID NO. 1 is mutated to R62S, R62C, R62U, R T or R62M; d63 is mutated to D63V, D63G, D63A, D L or D63I; y68 is mutated to Y68F or Y68W; k69 is mutated to K69R or K69H; t71 is mutated into T71S, T, 71C, T, 71U or T71M; the S75 mutation is S75A, S75G, S75V, S L or S75I; the F76 is mutated into F76Q, F, 76D, F E or F76N; the E104 mutation is E104V, E, 104G, E, A, E L or E104I.

In one embodiment, amino acids YKPTPASSF corresponding to positions 68-76 of SEQ ID NO. 1 are mutated to M ₂₅ M ₂₆ M ₂₇ M ₂₈ M ₂₉ M ₃₀ M ₃₁ M ₃₂ M ₃₃ And E171 is mutated to E171N, E171D or E171Q; mutation of D175 to D175N, D175E or D175Q, wherein M ₂₅ Selected from F, Y or W; m is M ₂₆ Selected from R, H or K; m is M ₂₇ Selected from P; m is M ₂₈ Selected from S, C, U, T or M; m is M ₂₉ Selected from P; m is M ₃₀ Selected from A, G, V, L or I; m is M ₃₁ Selected from S, C, U, T or M; m is M ₃₂ Selected from A, G, V, L or I; m is M ₃₃ Selected from Q, D, E, or N.

In one embodiment, mutants of the porin monomer, wherein the amino acid mutation is selected from the group consisting of:

In one embodiment, the amino acid sequence of the mutant of the porin monomer comprises or consists of SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 27, SEQ ID NO. 28, SEQ ID NO. 29 or SEQ ID NO. 30.

In one embodiment, the protein pore comprises a mutant of at least one pore protein monomer (or a mutant pore protein monomer). In one embodiment, the protein wells comprise mutants of at least two, three, four, five, six, seven, eight, nine, or ten or more protein monomers. In one embodiment, the protein pore comprises mutants of at least two pore protein monomers, which may be the same or different. In one embodiment, the protein well comprises a mutant of two or more pore protein monomers, preferably the same mutant of two or more monomers. In one embodiment, the diameter of the constriction zone pore canal of the protein pore is 0.7nm-2.2nm, 0.9nm-1.6nm, 1.4-1.6nm or

Use of a mutant of a porin monomer or a protein pore comprising the same for detecting the presence, absence or one or more characteristics of a target analyte. In one embodiment, mutants of porin monomers or protein wells are used to detect the sequence of a nucleic acid molecule, or to characterize polynucleotide sequences, such as sequencing polynucleotide sequences, because they can distinguish between different nucleotides with high sensitivity. Mutants of or protein wells comprising the porin monomers can distinguish between four nucleotides in DNA and RNA, even methylated and unmethylated nucleotides, and the resolution is unexpectedly high. Mutants of porin monomers or protein wells showed almost complete separation of all four DNA/RNA nucleotides. Deoxycytosine monophosphate (dCMP) and methyl-dCMP are further distinguished based on the residence time in the protein pores and the current flowing through the protein pores.

Mutants of porin monomers or protein pores can also distinguish between different nucleotides under a range of conditions. In particular, mutants of the porin monomers or protein pores distinguish nucleotides under conditions that favor nucleic acid characterization, such as sequencing. By varying the applied potential, salt concentration, buffer, temperature and the presence of additives such as urea, betaine and DTT, the degree to which mutants of the porin monomers or protein pores distinguish between different nucleotides can be controlled. This allows the function of mutants of porin monomers or protein pores to be finely tuned, especially in sequencing. Mutants of porin monomers or protein pores may also be used to identify polynucleotide polymers by interactions with one or more monomers rather than on nucleotide-based nucleotides.

Mutants of porin monomers or protein pores may be isolated, substantially isolated, purified or substantially purified. Mutants of the porin monomers or protein wells of the examples are isolated or purified if they are completely free of any other component, such as liposomes or other protein wells/porins. A mutant of a porin monomer or a protein pore is substantially isolated if it is mixed with a carrier or diluent that does not interfere with its intended use. For example, a mutant of a porin monomer or a protein pore is substantially isolated or substantially purified if the mutant of a porin monomer or protein pore is present in a form comprising less than 10%, less than 5%, less than 2%, or less than 1% of other components such as triblock copolymers, liposomes, or other protein pores/porins. Alternatively, mutants of the porin monomer or protein pores may be present in the membrane.

For example, the membrane is preferably an amphiphilic layer. The amphiphilic layer is a layer formed of amphiphilic molecules, for example, phospholipids, which have hydrophilicity and lipophilicity. The amphiphilic molecules may be synthetic or naturally occurring. The amphiphilic layer may be a single layer or a double layer. The amphiphilic layer is generally planar. The amphiphilic layer may be curved. The amphiphilic layer may be supported. The membrane may be a lipid bilayer. Lipid bilayers are formed from two opposing layers of lipids. The two layers of lipids are arranged such that their hydrophobic tail groups face each other to form a hydrophobic interior. The hydrophilic head groups of the lipids face outwards towards the aqueous environment on each side of the bilayer. The film includes a solid layer. The solid layer may be formed of organic and inorganic materials. If the membrane comprises a solid layer, the pores are typically present in the amphiphilic membrane or in a layer comprised within the solid layer, e.g. in holes, wells, gaps, channels, grooves or slits within the solid layer.

Characterization of analytes

Embodiments provide a method of determining the presence, absence, or one or more characteristics of a target analyte. The method involves contacting the target analyte with a mutant of a porin monomer or a protein pore such that the target analyte moves relative to, e.g., through, the mutant of a porin monomer or the protein pore, and obtaining one or more measurements when the target analyte moves relative to the mutant of a porin monomer or the protein pore, thereby determining the presence, absence, or one or more characteristics of the target analyte. The target analyte may also be referred to as a template analyte or analyte of interest.

The target analyte is preferably a polysaccharide, a metal ion, an inorganic salt, a polymer, an amino acid, a peptide, a polypeptide, a protein, a nucleotide, an oligonucleotide, a polynucleotide, a dye, a drug, a diagnostic agent, an explosive or an environmental contaminant. The method may involve determining the presence, absence, or one or more characteristics of two or more target analytes of the same class, e.g., two or more proteins, two or more nucleotides, or two or more drugs. Alternatively, the method may involve determining the presence, absence, or one or more characteristics of two or more different classes of target analytes, e.g., one or more proteins, one or more nucleotides, and one or more drugs.

The method includes contacting the target analyte with a mutant or protein pore of a porin monomer such that the target analyte moves through the mutant or protein pore of the porin monomer. The protein pore generally comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 monomers with a pore protein mutation, e.g., 7,8,9, or 10 monomers. The protein pores comprise the same monomer or different porin monomers, preferably comprising 8 or 9 identical monomers. One or more of the monomers, for example 2, 3, 4, 5, 6, 7,8,9 or 10, are preferably chemically modified as discussed above. In one embodiment, the amino acid of each monomer comprises SEQ ID NO. 1 and mutants thereof as described above. In one embodiment, the amino acid of each monomer consists of SEQ ID NO. 1 and mutants thereof as described above.

The methods of the embodiments may measure two, three, four, or five or more characteristics of a polynucleotide. The one or more characteristics are preferably selected from (i) the length of the polynucleotide, (ii) the identity of the polynucleotide, (iii) the sequence of the polynucleotide, (iv) the secondary structure of the polynucleotide, and (v) whether the polynucleotide is modified. In one embodiment, any combination of (i) to (v) may be measured.

For (i), the length of the polynucleotide may be measured, for example, by determining the number of interactions between the polynucleotide and the mutant/protein pore of the protein monomer or the duration of interactions between the polynucleotide and the mutant/protein pore of the protein monomer.

For (ii), the identity of the polynucleotide may be measured in a variety of ways, and the identity of the polynucleotide may be measured in conjunction with or without measurement of the polynucleotide sequence. The former is simpler; the polynucleotides are sequenced and identified. The latter can be accomplished in several different ways. For example, the presence of a particular motif in a polynucleotide may be measured (without measuring the remaining sequence of the polynucleotide). Alternatively, measurement of specific electrical and/or optical signals in the method may identify that the polynucleotide is from a specific source.

For (iii), the sequence of the polynucleotide may be determined as previously described. Suitable sequencing methods, in particular sequencing methods using electrical measurement methods, are described in Stoddart D et al ProC Natl Acad Sci,12;106 (19) 7702-7,Lieberman KR et al,J Am Chem SoC.2010;132 (50) 17961-72 and International application W02000/28312.

For (iv), the secondary structure can be measured using a variety of methods. For example, if the method involves an electrical measurement method, the secondary structure may be measured using a change in residence time or a change in current flowing through the pores. This allows the regions of single-stranded and double-stranded polynucleotides to be distinguished.

For (v), it can be measured whether any modifications are present. The method preferably comprises determining whether the polynucleotide is modified by methylation, oxidation, damage, with one or more proteins or with one or more labels, tags or with no bases or lack of nucleobases and sugars. Specific modifications will result in specific interactions with the well, which can be measured using the method described below. For example, methylcytosine can be distinguished from cytosine based on the current that flows through the pore during its interaction with each nucleotide.

The target polynucleotide is contacted with a mutant of a protein monomer/protein well, e.g., a mutant of a protein monomer/protein well as in the examples. Mutants of the protein monomers/protein pores are typically present in the membrane. Suitable membranes are as described hereinbefore. The method can be performed using any device suitable for studying membrane/protein pores or mutant systems of porin monomers, wherein mutants of protein monomers/protein pores are present in the membrane. The method can be performed using any device suitable for use on the sensory side of a transmembrane pore. For example, the device includes a chamber containing an aqueous solution and a barrier dividing the chamber into two parts. The barrier typically has holes in which a film comprising holes is formed. Or the barrier forms a membrane in which mutants of protein monomers/protein pores are present. The process may be carried out using the apparatus described in International application No. PCT/GB08/000562 (WO 2008/102120).

Various different types of measurements may be made. This includes, but is not limited to, electrical and optical measurements. Electrical measurements include voltage measurements, capacitance measurements, current measurements, impedance measurements, tunneling measurements (tunnelling measurement) (Ivanov AP et al, nano lett.201110nn 12;11 (I): 279-85) and FET measurements (international application TO 2005/124888). The optical measurement may be combined with an electrical measurement (Soni GV et al, rev Sci Instrom.2010Jan; 81 (1) 014301). The measurement may be a transmembrane current measurement, for example a measurement of the ion current flowing through the aperture. In one embodiment, the electrical or optical measurement may take the form of conventional electrical or optical measurements.

Electrical measurements can be made using the methods described in Stoddart D et al ProC Natl Acad Sci,12;106 (19) 7702-7,Lieberman KR et al,J Am Chem SoC.2010;132 (50) 17961-72 and International application WO 2000/28312. Alternatively, the electrical measurements may be performed using a multichannel system, for example as described in international application W02009/077734 and international application WO 2011/067559.

The method is preferably carried out using a potential applied across the membrane. The applied potential may be a voltage potential. Alternatively, the applied potential may be a chemical potential. An example of this is by salt gradients across a membrane, such as an amphiphilic layer. Salt gradients are disclosed in Holden et al, J Am Chem soc.2007jul 11;129 (27) 8650-5. In some cases, the current flowing through the mutant/protein pore of the protein monomer as the polynucleotide moves relative to the mutant/protein pore of the protein monomer is used to estimate or determine the sequence of the polynucleotide. This is strand sequencing.

The method may comprise measuring the current flowing through the pore as the polynucleotide moves relative to the pore. The apparatus used in the method may therefore also include circuitry capable of applying an electrical potential and measuring an electrical signal across the membrane and the well. The method may be performed using patch clamp or voltage clamp.

May include measuring the current flowing through the pore as the polynucleotide moves relative to the pore. Suitable conditions for measuring ion flow through transmembrane protein pores are known in the art and disclosed in the examples. The method is typically performed by applying a voltage across the membrane and the pores. The voltages used are generally from +5V to-5V, for example from +4V to-4V, from +3V to-3V or from +2V to-2V. The voltages used are typically from-600 mV to +600V or-400 mV to +400mV. The voltages used are preferably in the range having a lower limit selected from-400 mV, -300mV, -200mV, -150mV, -100mV, -50mV, -20mV and 0mV and an upper limit independently selected from +10mV, +20mV, +50mV, +100mV, +150mV, +200mV, +300nA P+400 mV. The voltage used is more preferably in the range of 100mV to 240mV and most preferably in the range of 120mV to 220 mV. By using an increased applied potential, the recognition of different nucleotides by the pore can be increased.

The process is generally carried out in the presence of any charge carrier, for example a metal salt such as an alkali metal salt, a halide salt such as a chloride salt, for example an alkali metal chloride salt. The charge carrier may comprise an ionic liquid or an organic salt, such as tetramethylammonium chloride, trimethylphenylammonium chloride, phenyltrimethylammonium chloride or 1-ethyl-3-methylimidazole chloride. In the above exemplary device, the salt is present in an aqueous solution in the chamber. Usually potassium chloride (KCl), sodium chloride (NaCl), cesium chloride (CsCl) or a mixture of potassium ferrocyanide and potassium ferricyanide is used. Mixtures of KCl, naCl and potassium ferrocyanide and potassium ferricyanide are preferred. The charge carriers may be asymmetric on the membrane. For example, the type and/or concentration of charge carriers may be different on each side of the membrane.

The concentration of the salt may be saturated. The concentration of the salt may be 3M or less, and is typically 0.1 to 2.5M,0.3 to 1.9M,0.5 to 1.8M,0.7 to 1.7M,0.9 to 1.6M, or 1M to 1.4M. The concentration of the salt is preferably 150mM to 1M. The method is preferably carried out using a salt concentration of at least 0.3M, for example at least 0.4M, at least 0.5M, at least 0.6M, at least 0.8M, at least 1.0M, at least 1.5M, at least 2.0M, at least 2.5M or at least 3.0M. The high salt concentration provides a high signal to noise ratio and allows the presence of the nucleotide to be identified in the context of normal current fluctuations to be indicated by the current.

The process is generally carried out in the presence of a buffer. In the above exemplary device, the buffer is present in an aqueous solution in the chamber. Any buffer may be used in the methods of the invention. Typically, the buffer is a phosphate buffer. Other suitable buffers are HEPES or Tris-HCl buffers. The process is typically carried out at a pH of 4.0 to 12.0, 4.5 to 10.0, 5.0 to 9.0, 5.5 to 8.8, 6.0 to 8.7, 7.0 to 8.8, or 7.5 to 8.5. The pH used is preferably about 7.5.

The process may be carried out at a temperature of from 0 ℃ to 100 ℃,15 ℃ to 95 ℃,16 ℃ to 90 ℃,17 ℃ to 85 ℃,18 ℃ to 80 ℃,19 ℃ to 70 ℃, or 20 ℃ to 60 ℃. The process is usually carried out at room temperature. The process is optionally carried out at a temperature that supports the function of the enzyme, for example at about 37 ℃.

In one embodiment, a method for determining the presence, absence, or one or more characteristics of a target analyte (e.g., a polynucleotide) includes coupling the target analyte to a membrane; and the target analyte interacts with (e.g., contacts) the protein pore present in the membrane such that the target analyte moves relative to (e.g., through) the protein pore. In one embodiment, the current through the protein pore as the target analyte moves relative to the protein pore is measured to determine the presence, absence, or one or more characteristics (e.g., the sequence of a polynucleotide) of the target analyte.

Polynucleotide binding proteins

The characterization method of an embodiment preferably comprises contacting the polynucleotide with a polynucleotide binding protein such that the protein controls movement of the polynucleotide relative to, e.g., through, a mutant of a protein monomer/protein pore.

More preferably, the method comprises (a) contacting the polynucleotide with a mutant/protein pore of a protein monomer and a polynucleotide binding protein such that the protein controls movement of the polynucleotide relative to the mutant/protein pore of the protein monomer, e.g., through the mutant/protein pore of the protein monomer, and (b) obtaining one or more measurements as the polynucleotide moves relative to the mutant/protein pore of the protein monomer, wherein the measurements are indicative of one or more characteristics of the polynucleotide, thereby characterizing the polynucleotide.

More preferably, the method comprises (a) contacting the polynucleotide with a mutant/protein pore of a protein monomer and a polynucleotide binding protein such that the protein controls movement of the polynucleotide relative to the mutant/protein pore of the protein monomer, e.g., through the mutant/protein pore of the protein monomer, and (b) measuring the current through the mutant/protein pore of the protein monomer as the polynucleotide moves relative to the mutant/protein pore of the protein monomer, wherein the current is indicative of one or more characteristics of the polynucleotide, thereby characterizing the polynucleotide.

The polynucleotide binding protein may be any protein capable of binding a polynucleotide and controlling its movement through a pore. The polynucleotide binding protein typically interacts with and modifies at least one property of the polynucleotide. The protein may be modified by cleaving the polynucleotide to form individual nucleotides or short strands of nucleotides (e.g., dinucleotides or trinucleotides). The protein may be modified by orienting the polynucleotide or moving it to a specific location, i.e., controlling its movement.

The polynucleotide binding protein is preferably derived from a polynucleotide handling enzyme. A polynucleotide handling enzyme is a polypeptide that is capable of interacting with a polynucleotide and modifying at least one property of the polynucleotide. The enzyme may modify a polynucleotide by cleaving it to form individual nucleotides or short strands of nucleotides (e.g., dinucleotides or trinucleotides). The enzyme may modify a polynucleotide by orienting it or moving it to a specific location. The polynucleotide processive enzyme need not exhibit enzymatic activity so long as it is capable of binding the polynucleotide and controlling its movement through the pore. For example, the enzyme may be modified to remove its enzymatic activity, or may be used under conditions that prevent its use as an enzyme.

The polynucleotide handling enzymes are preferably polymerases, exonucleases, helicases and topoisomerases, e.g., gyrases. In one embodiment, the enzyme is preferably a helicase, such as Hel308Mbu, hel308Csy, hel308Tga, hel308Mhu, tral Eco, XPD Mbu, dda, or variants thereof. Any helicase may be used in the examples.

In one embodiment, any number of helicases may be used. For example, I,2,3,4,5,6,7,8,9, 10 or more helicases may be used. In some embodiments, different numbers of helicases may be used.

The method of embodiments preferably comprises contacting the polynucleotide with two or more helicases. The two or more helicases are typically the same helicase. The two or more helicases may be different helicases.

The two or more helicases may be any combination of the above helicases. The two or more helicases may be two or more Dda helicases. The two or more helicases may be one or more Dda helicases and one or more TrwC helicases. The two or more helicases may be different variants of the same helicase.

The two or more helicases are preferably linked to each other. The two or more helicases are more preferably covalently linked to each other. The helicases may be attached in any order and using any method.

Kit for detecting a substance in a sample

The invention also provides a kit for characterizing a target analyte (e.g., a target polynucleotide). The kit comprises the components of the wells and membranes of the examples. The film is preferably formed from components. The pores are preferably present in the membrane. The kit may comprise components of any of the films disclosed above (e.g., amphiphilic layer or triblock copolymer film). The kit may further comprise a polynucleotide binding protein. Any of the polynucleotide binding proteins discussed above may be used.

In one embodiment, the membrane is an amphiphilic layer, a solid state layer, or a lipid bilayer.

The kit may further comprise one or more anchors for coupling the polynucleotide to the membrane.

The kit is preferably for characterizing double stranded polynucleotides and preferably comprises a Y-adaptor and a hairpin loop adaptor.

The Y adaptor preferably has one or more helicases attached, and the hairpin loop adaptor preferably has one or more molecular stoppers attached. The Y-adaptor preferably comprises one or more first anchors for coupling the polynucleotide to the membrane, the hairpin loop adaptor preferably comprises one or more second anchors for coupling the polynucleotide to the membrane, and the strength of the hairpin loop adaptor coupling to the membrane is preferably greater than the strength of the Y-adaptor coupling to the membrane.

The kit may additionally comprise one or more other reagents or instruments that enable any of the embodiments mentioned above. Such reagents or instruments include one or more of the following: suitable buffers (aqueous solutions), means for obtaining a sample from an individual (e.g., a container or instrument containing a needle), means for amplifying and/or expressing a polynucleotide, or a voltage or patch clamp device. The reagents may be present in the kit in dry form such that the fluid sample re-suspends the reagents. The kit may also optionally contain instructions that enable the kit to be used with the method of the invention or details about what organisms can use the method.

Equipment (or apparatus)

The invention also provides an apparatus for characterizing a target analyte (e.g., a target polynucleotide). The device comprises a mutant/protein well of single or multiple protein monomers, and a single or multiple membranes. The mutant/protein pore of the protein monomer is preferably present in the membrane. The number of holes and membranes is preferably equal. Preferably, there is a single hole in each membrane.

The apparatus preferably further comprises instructions for implementing the method in the embodiment. The device may be any conventional device for analyte analysis, such as an array or chip. Any of the embodiments discussed in connection with the method of the embodiments are equally applicable to the apparatus. The device may also include any of the features present in the kit. The apparatus used in the examples may specifically be an zipcotechnique gene sequencer QNome-9604.

The prior art mentioned above is incorporated herein by reference in its entirety.

The following examples illustrate the invention without limiting it.

Example 1

In an embodiment, the wild-type porin is from Pseudomonas cestodiae and the amino acid sequence of the wild-type porin is SEQ ID NO. 1 and the nucleotide sequence encoding this amino acid sequence is shown as SEQ ID NO. 2. Mutant 1 of the porin monomer is that the wild type porin has mutation at 69-76 positions corresponding to SEQ ID NO. 1, particularly KPTPASSF at 69-76 positions is replaced by RPSPASASAQ. The protein well of mutant 1, which includes a porin monomer, is mutant well 1. The amino acid sequence of the mutant 1 of the protein monomer is shown as SEQ ID NO. 24, and the nucleic acid sequence is shown as SEQ ID NO. 25.

Example 2

In an embodiment, the wild-type porin is from P.taenii and the amino acid sequence of the wild-type porin is SEQ ID NO. 1 and the nucleotide sequence encoding the sequence of this amino acid is shown as SEQ ID NO. 2. Mutant 2 of the porin monomer is a wild-type porin having a mutation at positions 69-76 corresponding to SEQ ID NO. 1, in particular KPTPASSF at positions 69-76 is replaced with KPGPASTK. The protein wells of mutant 2, which include porin monomers, are mutant wells 2. The amino acid sequence of mutant 2 of protein monomer is shown as SEQ ID NO. 26.

Example 3

In an embodiment, the wild-type porin is from P.taenii and the amino acid sequence of the wild-type porin is SEQ ID NO. 1 and the nucleotide sequence encoding the sequence of this amino acid is shown as SEQ ID NO. 2. Mutant 3 of the porin monomer is a wild type porin having a mutation at positions 64-79 corresponding to SEQ ID NO. 1, specifically a substitution of LTGQYRPSPASANSTA at QTGQYKPTPASSFSTS at positions 64-79. The protein well of mutant 3, which includes a porin monomer, is mutant well 3. The amino acid sequence of mutant 3 of protein monomer is shown as SEQ ID NO. 27.

Example 4

In an embodiment, the wild-type porin is from P.taenii and the amino acid sequence of the wild-type porin is SEQ ID NO. 1 and the nucleotide sequence encoding the sequence of this amino acid is shown as SEQ ID NO. 2. Mutant 4 of the porin monomer is a wild type porin having a mutation at positions 64-79 corresponding to SEQ ID NO. 1, specifically a substitution of LTGQYRPSPASALSTA at QTGQYKPTPASSFSTS at positions 64-79. The protein wells of mutant 4, which include porin monomers, are mutant wells 4. The amino acid sequence of mutant 4 of protein monomer is shown in SEQ ID NO. 28.

Example 5

In an embodiment, the wild-type porin is from P.taenii and the amino acid sequence of the wild-type porin is SEQ ID NO. 1 and the nucleotide sequence encoding the sequence of this amino acid is shown as SEQ ID NO. 2. Mutant 5 of the porin monomer is a mutation of the wild-type porin at the following positions corresponding to SEQ ID NO: 1: R62S, D63V, Y F, K69R, T3871S, S75A, F Q, and E104V. The protein wells of mutant 5, which include porin monomers, are mutant wells 5. The amino acid sequence of mutant 5 of protein monomer is shown in SEQ ID NO. 29.

Example 6

In an embodiment, the wild-type porin is from P.taenii and the amino acid sequence of the wild-type porin is SEQ ID NO. 1 and the nucleotide sequence encoding the sequence of this amino acid is shown as SEQ ID NO. 2. Mutant 6 of the porin monomer is a wild-type porin having mutations at positions 68-76, 171 and 175 corresponding to SEQ ID NO. 1, specifically a substitution of YKPTPASSF at positions 68-76 with FRPSPASAQ, a substitution of E at position 171 with N and a substitution of D at position 175 with N. The protein wells of mutant 6, which include porin monomers, are mutant wells 6. The amino acid sequence of mutant 6 of protein monomer is shown as SEQ ID NO. 30.

Example 7

The SWISS MODEL is adopted to carry out homology modeling on the wild type porin, and the amino acid of the wild type porin monomer is shown as SEQ ID NO. 1. Fig. 4A is a side view 400 of a model of predicted protein structure, wherein the darker portion shows a protein monomer 402. Fig. 4B is a top view 404 of a ribbon structural model, where the darker portion shows a protein monomer 406. Fig. 4C is a ribbon structure model 408 with darker portions of protein monomers 410.

Mutant well 1 was homologously modeled using SWISS MODEL. FIGS. 5A and 5B show amino acid model diagrams of mutant well 1, wherein the plus sign "+" indicates a water molecule.

FIG. 6 shows the size of each portion of mutant 1 of a porin monomer, mutants of two porin monomers (i.e., two mutated porin monomers) 602 and604, the diameter of the pore canal of the constriction zone in the middle is at mostSecondly, is->Minimum diameter of +.>The two mutated porin monomers are head-to-tail separated by +.>And->Mutant porin monomer full length +.> The head distance of the mutant porin monomer from the pore canal of the constriction zone is +.>The height of the tunnel part of the constriction zone is shown as +.>And->

FIG. 7 shows a monomeric amino acid model of mutant 1 of porin, with an enlarged representation of the amino acid composition of the constriction zone structure, namely Gln76, ser74 and Ser71.

Example 8

The negative staining electron microscopy results for mutant 1 of porin are shown in fig. 8, as can be seen by the negative staining EM results: mutant 1 particles were homogeneous, less aggregated, and many significantly correct protein particles were seen.

The cryo-electron micrograph and 2D classification results for mutant 1 of porin are shown in fig. 9A and 9B, where the 2D results only show the better classification part.

FIGS. 10A and 10B show results of local refinement of Fourier shell correlation coefficient (FSC), showing that mutant 1 of porin has different regional resolution results and final single particle reconstruction resolution of cryoelectron microscopy of The reconstruction resolution is determined based on the gold standard FSC 0.143 standard and the high resolution noise substitution. FIG. 11 shows three-dimensional reconstruction of porin mutant 1 by cryoelectron microscopy>Electron density map of resolution. FIG. 12 shows that mutant 1 of porin is +.>Electron density map below. The map shows the channel eye-loop area and is overlaid on the final refined model.

The data of the porin mutant 1 in the cryo-electron microscopy are shown in Table 4.

Table 4 cryo-electron microscopy data for mutant 1 of porin

EXAMPLE 9 preparation of DNA constructs

Two DNA constructs, BS7-4C3-SE1 and BS7-4C3-PLT, respectively, were prepared. The structure of BS7-4C3-SE1 is shown in FIG. 13, and the sequence information is as follows:

a:30*C3

5'-TTTTT TTTTT-3' (i.e. SEQ ID NO: 3)

Speed-controlling protein

d:4*C18

e:5’-AATGT ACTTC GTTCA GTTAC GTATTGCT-3' (i.e. SEQ ID NO: 4)

f:5’P-GC AATAC GTAAC TGAAC GAAGT 3' (i.e. SEQ ID NO: 5)

g cholesterol label

h:5’-3' (i.e. SEQ ID NO: 6)

i. 5'-AAAAA AAAAA AAAAA AAAAA AAAAA AAAAA AAAAA AAAAA AAGCA ATACG TAACT GAACG AAGTA CATTA AAAAA AAAAA AAAAA AAAA-3' (i.e. SEQ ID NO: 7)

5'-ATCCT TTTTT TTTTT TTTTT TTTT-3' (i.e. SEQ ID NO: 8)

k 5'-AATGT ACTTC GTTCA GTTAC GTATT GCTTT TTTTT TTTTT TTTTT TTT-3' (i.e. SEQ ID NO: 9)

l:dSpacer

m 5'-TTTTT TTTTT TTTTT TTTTT-3' (i.e. SEQ ID NO: 10)

The structure of BS7-4C3-PLT is shown in FIG. 14, and the sequence information is as follows:

a:30*C3

5'-TTTTT TTTTT-3' (i.e. SEQ ID NO: 11)

Speed-controlling protein

d:4*C18

e 5'-AATGT ACTTC GTTCA GTTAC GTATT GCT-3' (SEQ ID NO: 12)

f 5'P-GC AATAC GTAAC TGAAC GAAGT TCACTATCGCATTCTCATGA-3' (i.e. SEQ ID NO: 13)

g cholesterol label

h 5'-TCATG AGAAT GCGAT AGTGA-3' (i.e. SEQ ID NO: 14)

i 5'-AAAAAAAAAAAAAAAAAAAAAAAAAAAA (i.e. SEQ ID NO: 15)/dSpacer/AAAAAAAAAA (i.e. SEQ ID NO: 16)/dSpacer/AAAAAAAAAAAAAATCTCTGAATCTCTGAATCTCTGAATCTCTAAAAAAAAAAAAGAAAAAAAAAAAACAAAAAAAAAAAATAAAAAAAAAAAAAGCAATACGTAACTGAACGAAGTACATTAAAAAAAAAA (i.e. SEQ ID NO: 17) -3'

j:5'-ATCCTTTTTTTTTTAATGTACTTCGTTCAGTTACGTATTGCT-3' (i.e. SEQ ID NO: 18)

k 5'P-TTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTTTTTTTCTTTTTTTTTTTTAGAGATTCAGAGATTCAGAGATTCAGAGATTTTTTTTTTTTTT (i.e. SEQ ID NO: 19)/dSpacer/TTTTTTTTTTTT (i.e. SEQ ID NO: 20)/iSpC 3/TTTTTTTTTTTTTTTTTTTTTTTTTTTT (i.e. SEQ ID NO: 21) -3'

C3, C18, dSpacer and iSpC3 are marker sequences introduced to indicate the pore sequencing resolution features.

In this example, the C-speed controlling protein in FIGS. 13 and 14 is helicase Mph-MP1-E105C/A362C (with mutation E105C/A362C), the amino acid sequence is SEQ ID NO:22, and the nucleic acid sequence is SEQ ID NO:23.

Example 10

Mutant hole 1 was used as a protein hole and was detected by single well sequencing. After insertion of a single porin with the amino acid sequence mutant 1 into the phospholipid bilayer, the buffer (625mM KCl,10mM HEPES pH 8.0, 50mM MgCl ₂ ) Flows through the system to remove any excess mutant 1 nanopores. DNA construct BS7-4C3-SE1 (data not shown) or BS7-4C3-PLT (1-2 nM final concentration) was added to the mutant 1 nanopore assay system and after mixing, buffer (625mM KCl,10mM HEPES pH 8.0, 50mM MgCl) ₂ ) Flows through the system to remove any excess DNA construct BS7-4C3-SE1 or BS7-4C3-PLT. A helicase (Mph-MP 1-E105C/A362C,15nM final concentration), fuel (ATP 3mM final concentration) premix was then added to the single mutant 1 nanopore experimental system and the sequencing of mutant 1 porin was monitored at +180 mV.

Abrupt pore 1 opens at a voltage of 180 mV. FIG. 15A shows the pore current and gating characteristics of mutant pore 1 at +180mV voltage. FIG. 15B shows the single stranded nucleic acid via condition of mutant well 1 at +180mV voltage. The nucleic acid may be via. After addition of single stranded nucleic acid, the downward line shows the nucleic acid via signal.

Sequencing the DNA construct BS7-4C3-PLT through the mutation hole 1 by adopting a single-hole sequencing technology method, and adding a nucleic acid sequencing signal generated by a sequencing system after hole embedding is completed. FIGS. 16A and 16B show example current traces when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant well 1. Based on this signal feature, the mutant pore 1 can be used for nucleic acid sequencing.

Fig. 17 is an enlarged result of displaying the current trace on the portion of fig. 16B. The graph (middle graph) with a dashed box and an arrow is the result after the original signal filtering process (y-axis coordinates of two traces=current (pA), x-axis coordinates=time (s)). The dotted arrow indicates the enlarged result of the current trace. The region of this single signal is shown in enlarged form, further demonstrating that mutant well 1 can be used for nucleic acid sequencing.

Example 11

Similar to example 10, example 11 uses abrupt holes 2 for void and via detection.

Fig. 18A shows the open cell current and its gating characteristics for abrupt cell 2 at a voltage of 180 mV. FIG. 18B shows the single stranded nucleic acid via condition of mutant well 2 at +180mV voltage. The nucleic acid may be via. After addition of single stranded nucleic acid, the downward line shows the nucleic acid via signal.

Sequencing the DNA construct BS7-4C3-PLT through the mutation hole 2 by adopting a single-hole sequencing technology method, and adding a nucleic acid sequencing signal generated by a sequencing system after hole embedding is completed. FIGS. 19A and 19B show example current traces when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant well 2. According to the signal characteristics, relevant characteristics such as sequencing resolution, stability, signal consistency and the like of the mutant hole 2 can be obtained. The hole has clear steps and obvious jump distribution, and has high-precision sequencing capability. From the signal characteristics, the consistency of the sequencing signals is higher.

Fig. 20 shows an enlarged result of a partial current trace. The graph with the dashed box and arrow is the result after the original signal filtering process (y-axis coordinates of two traces=current (pA), x-axis coordinates=time (s)). The dotted arrow indicates the enlarged result of the current trace. The region of the single signal is shown in an enlarged view, indicating that the mutant wells have high resolution for nucleic acid sequencing.

Example 12

Similar to example 10, example 12 uses abrupt holes 3 for void and via detection.

FIG. 21A shows the pore current and its gating characteristics for abrupt pore 3 at a voltage of 180 mV. FIG. 21B shows the single stranded nucleic acid via condition of mutant well 3 at +180mV voltage. The nucleic acid may be via. After addition of single stranded nucleic acid, the downward line shows the nucleic acid via signal.

Sequencing the DNA construct BS7-4C3-PLT through the mutation hole 3 by adopting a single-hole sequencing technology method, and adding a nucleic acid sequencing signal generated by a sequencing system after hole embedding is completed. FIGS. 22A and 22B show example current traces when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant well 3. Based on this signal feature, the mutant pore 3 can be used for nucleic acid sequencing.

Fig. 23 is an enlarged view of the current trace shown in fig. 22A. The graph with the dashed box and arrow is the result after the original signal filtering process (y-axis coordinates of two traces=current (pA), x-axis coordinates=time (s)). The dotted arrow indicates the enlarged result of the current trace. The region of this single signal is shown in enlarged form, further demonstrating that mutant well 3 can be used for nucleic acid sequencing.

Example 13

Similar to example 10, example 13 uses abrupt holes 4 for void and via detection.

Fig. 24A shows the open cell current and its gating characteristics for abrupt cell 4 at a voltage of 180 mV. FIG. 24B shows the single stranded nucleic acid via condition of mutant well 4 at +180mV voltage. The nucleic acid may be via.

Sequencing the DNA construct BS7-4C3-PLT through the mutation hole 4 by adopting a single-hole sequencing technology method, and adding a nucleic acid sequencing signal generated by a sequencing system after hole embedding is completed. FIGS. 25A and 25B show example current traces when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant well 4. Based on this signal feature, the mutant pore 4 can be used for nucleic acid sequencing.

Fig. 26 is an enlarged view showing the current trace of the embodiment of fig. 25A and 25B. The graph with the dashed box and arrow is the result after the original signal filtering process (y-axis coordinates of two traces=current (pA), x-axis coordinates=time (s)). The dotted arrow indicates the enlarged result of the current trace. The region of this single signal is shown in enlarged form, further demonstrating that the mutant wells 4 can be used for nucleic acid sequencing.

Example 14

Similar to example 10, example 14 uses abrupt holes 5 for void and via detection.

FIG. 27 shows the current drawn by the mutant wells 5 at +180 mV and their gating characteristics.

Sequencing the DNA construct BS7-4C3-PLT through the mutation hole 5 by adopting a single-hole sequencing technology method, and adding a nucleic acid sequencing signal generated by a sequencing system after hole embedding is completed. FIG. 28 shows an example current trace when the helicase Mph-MP1-E105C/A362C control DNA construct BS7-4C3-PLT is translocated through the mutant pore 5. Based on this signal feature, the mutant pore 5 can be used for nucleic acid sequencing.

Fig. 29 is an enlarged view of the embodiment of fig. 28 partially showing the current trace. The graph with the dashed box and arrow is the result after the original signal filtering process (y-axis coordinates of two traces=current (pA), x-axis coordinates=time (s)). The dotted arrow indicates the enlarged result of the current trace. The region of this single signal is shown in enlarged form, further demonstrating that the mutant wells 5 can be used for nucleic acid sequencing.

Example 15

Similar to example 10, example 15 uses abrupt holes 6 for void and via detection.

FIG. 30A shows the pore current and its gating characteristics for mutant pore 6 at a voltage of 180 mV. FIG. 30B shows the single stranded nucleic acid via condition of mutant pore 6 at +180mV voltage. The nucleic acid may be via. After addition of single stranded nucleic acid, the downward line shows the nucleic acid via signal.

Sequencing the DNA construct BS7-4C3-PLT through the mutation hole 6 by adopting a single-hole sequencing technology method, and adding a nucleic acid sequencing signal generated by a sequencing system after hole embedding is completed. FIGS. 31A and 31B show example current traces when helicase Mph-MP1-E105C/A362C controls the translocation of DNA construct BS7-4C3-PLT through mutant well 6. According to the signal characteristics, relevant characteristics such as sequencing resolution, stability, signal consistency and the like of the mutation hole 6 can be obtained. The hole has clear steps and obvious jump distribution, and has high-precision sequencing capability. From the signal characteristics, the consistency of the sequencing signals is higher.

Fig. 32 is an enlarged view of the current trace shown in fig. 31A. The graph with the dashed box and arrow is the result after the original signal filtering process (y-axis coordinates of two traces=current (pA), x-axis coordinates=time (s)). The dotted arrow indicates the enlarged result of the current trace. The region of the single signal is shown in an enlarged view, indicating that the mutant wells have high resolution for nucleic acid sequencing.

Example 16

Recombinant plasmids containing mutant 1 nucleic acid sequences (SEQ ID NO: 25) of porin monomers were transformed into BL21 (DE 3) competent cells by a thermal shock method, 0.5ml of LB medium was added, and after 1 hour of culture at 30 ℃, an appropriate amount of bacterial liquid was taken and spread on an ampicillin-resistant solid LB plate, and culture was carried out overnight at 37 ℃, and monoclonal colonies were picked the next day and inoculated into 50ml of ampicillin-resistant liquid LB medium for culture overnight at 37 ℃. The culture was transferred to an ampicillin-resistant TB liquid medium at 1% inoculum size for expansion at 37℃and 220rpm, and the OD600 was measured continuously. When OD600 = 2.0-2.2, the broth in TB medium was cooled to 16 ℃ and Isopropyl Thiogalactoside (IPTG) was added to induce expression to a final concentration of 0.015mM. After 20-24h of induced expression, the thalli are collected by centrifugation. The thalli are crushed under high pressure after being resuspended by a crushing buffer solution, purified by a Ni-NTA affinity chromatography method, and the target eluting sample is collected. Mutants 2 to 6 of the porin monomer were purified as described above.

For example, FIG. 33 shows the results of protein purification for mutant 1, with lanes 1-4 showing SDS-PAGE detection of the different fractions isolated. Fig. 34 shows an example of mutant 1 protein Size Exclusion Chromatography (SEC) (25 mL of Superose-6ge healthcare, x-axis label = elution volume (mL), Y-axis label = absorbance (mAu)).

SEQUENCE LISTING

<110> Chengdu carbon technology Co., ltd

<120> mutant of porin monomer, protein pore and use thereof

<130> SPI213793-23

<160> 30

<170> PatentIn version 3.5

<210> 1

<211> 283

<212> PRT

<213> Pseudomonas taeanensis

<400> 1

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Arg Asp Gln

50 55 60

Thr Gly Gln Tyr Lys Pro Thr Pro Ala Ser Ser Phe Ser Thr Ser Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Glu Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Glu Tyr Arg Val Asp Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

<210> 2

<211> 852

<212> DNA

<213> Pseudomonas taeanensis

<400> 2

atgaacagac tactagcgat ggcgatgttg ctggccgccc tgcaaggctg cgccttgcgc 60

gaacccatgc cggcggagct ggaaaacgcg actccgaccc tgacgccgcg ggcctcgacc 120

tattacgact tgctggccct gccgcggccc aaaggccgcc tggttgccgc tgtgtacggc 180

ttccgcgacc agactgggca gtacaagccg acgcctgcca gttcgttctc caccagcgtg 240

actcagggcg ccgccagcat gctggtcgac gcgttgcagg ccagcggctg gttccgggtg 300

ctggagcgcg agggcctgca gaatatcctg accgaacgca agatcattcg cgcctcgcag 360

aacaagccca ataccccggt gaatatccag gccgatctgc cctcgttgca ggccgccaac 420

atccttctgg aaggcggggt gatcgcctac gacactaatg tacgtagcgg tggtgagggg 480

gctgcctacc tgggtatcag cctgtctcag gagtatcggg tggatcaggt ttcggtgaac 540

ctgcgtgcgg tggatgtgcg cagcggtcag gtactggcca acgtcatgac ctccaagacc 600

atctattcgg tcgggcgcaa tgccggcata ttcaaattca tcgagttcaa ggagctgttg 660

gaggccgagg cgggctacac gaccaatgaa ccggcgcagc tgtgtgtgct ctcggctatc 720

gaagccgccg tggctcatct ggtggcccag ggcatcgagc ggcgcctgtg gcaggctgct 780

gacgaaagct ccttcgataa gtcgtcactg cccaagtaca tgagccaggc gcgggccgat 840

ccactgcctt ag 852

<210> 3

<211> 10

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 3

tttttttttt 10

<210> 4

<211> 28

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 4

aatgtacttc gttcagttac gtattgct 28

<210> 5

<211> 42

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 5

gcaatacgta actgaacgaa gttcactatc gcattctcat ga 42

<210> 6

<211> 20

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 6

tcatgagaat gcgatagtga 20

<210> 7

<211> 89

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 7

aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aagcaatacg taactgaacg 60

aagtacatta aaaaaaaaaa aaaaaaaaa 89

<210> 8

<211> 24

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 8

atcctttttt tttttttttt tttt 24

<210> 9

<211> 48

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 9

aatgtacttc gttcagttac gtattgcttt tttttttttt tttttttt 48

<210> 10

<211> 20

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-SE1

<400> 10

tttttttttt tttttttttt 20

<210> 11

<211> 10

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 11

tttttttttt 10

<210> 12

<211> 28

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 12

aatgtacttc gttcagttac gtattgct 28

<210> 13

<211> 42

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 13

gcaatacgta actgaacgaa gttcactatc gcattctcat ga 42

<210> 14

<211> 20

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 14

tcatgagaat gcgatagtga 20

<210> 15

<211> 28

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 15

aaaaaaaaaa aaaaaaaaaa aaaaaaaa 28

<210> 16

<211> 12

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 16

aaaaaaaaaa aa 12

<210> 17

<211> 132

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 17

aaaaaaaaaa aaaatctctg aatctctgaa tctctgaatc tctaaaaaaa aaaaagaaaa 60

aaaaaaaaca aaaaaaaaaa ataaaaaaaa aaaaagcaat acgtaactga acgaagtaca 120

ttaaaaaaaa aa 132

<210> 18

<211> 42

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 18

atcctttttt ttttaatgta cttcgttcag ttacgtattg ct 42

<210> 19

<211> 94

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 19

tttttttttt ttattttttt tttttgtttt ttttttttct tttttttttt tagagattca 60

gagattcaga gattcagaga tttttttttt tttt 94

<210> 20

<211> 12

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 20

tttttttttt tt 12

<210> 21

<211> 28

<212> DNA

<213> Artificial Sequence

<220>

<223> part of BS7-4C3-PLT

<400> 21

tttttttttt tttttttttt tttttttt 28

<210> 22

<211> 441

<212> PRT

<213> Artificial Sequence

<220>

<223> helicase

<400> 22

Met Ile Thr Ile Asp Gln Leu Thr Glu Gly Gln Phe Asp Ser Leu Gln

1 5 10 15

Arg Ala Lys Val Leu Ile Gln Glu Ala Thr Lys Asn Asp Gly Asn Trp

20 25 30

Asn His Arg Thr Lys His Leu Thr Ile Asn Gly Pro Ala Gly Thr Gly

35 40 45

Lys Thr Thr Met Met Lys Phe Leu Val Ser Trp Leu Arg Asp Glu Gly

50 55 60

Ile Thr Gly Val Ala Leu Ala Ala Pro Thr His Ala Ala Lys Lys Val

65 70 75 80

Leu Ala Asn Ala Val Gly Glu Glu Val Ser Thr Ile His Ser Ile Leu

85 90 95

Lys Ile Asn Pro Thr Thr Tyr Glu Cys Lys Gln Phe Phe Glu Gln Ser

100 105 110

Ala Pro Pro Asp Leu Ser Lys Ile Arg Ile Leu Ile Cys Glu Glu Cys

115 120 125

Ser Phe Tyr Asp Ile Lys Leu Phe Glu Ile Leu Met Asn Ser Ile Gln

130 135 140

Pro Trp Thr Ile Ile Ile Gly Ile Gly Asp Arg Ala Gln Leu Arg Pro

145 150 155 160

Ala Asp Asp Lys Gly Ile Ser Arg Phe Phe Thr Asp Gln Arg Phe Glu

165 170 175

Gln Thr Tyr Leu Thr Glu Ile Lys Arg Ser Asn Met Pro Ile Ile Glu

180 185 190

Val Ala Thr Glu Ile Arg Asn Gly Gly Trp Ile Arg Glu Asn Ile Ile

195 200 205

Asp Asp Leu Gly Val Lys Gln Asp Lys Ser Val Ser Glu Phe Met Thr

210 215 220

Asn Tyr Phe Lys Val Val Lys Ser Ile Asp Asp Leu Tyr Glu Thr Arg

225 230 235 240

Met Tyr Ala Tyr Thr Asn Asn Ser Val Asp Thr Leu Asn Lys Ile Ile

245 250 255

Arg Lys Lys Leu Tyr Glu Thr Glu Gln Asp Phe Ile Val Gly Glu Pro

260 265 270

Ile Val Met Gln Glu Pro Leu Ile Arg Asp Ile Asn Tyr Glu Gly Lys

275 280 285

Arg Phe Gln Glu Ile Val Phe Asn Asn Gly Glu Tyr Leu Glu Val Ser

290 295 300

Glu Ile Lys Pro Met Glu Ser Val Leu Lys Cys Arg Asn Ile Asp Tyr

305 310 315 320

Gln Leu Val Leu His Tyr Tyr Gln Leu Lys Val Lys Ser Ile Asp Thr

325 330 335

Gly Glu Ser Gly Leu Ile Asn Thr Ile Ser Asp Lys Asn Glu Leu Asn

340 345 350

Lys Phe Tyr Met Phe Leu Gly Lys Val Cys Gln Asp Tyr Lys Ser Gly

355 360 365

Thr Ile Lys Ala Phe Trp Asp Asp Phe Trp Lys Ile Lys Asn Asn Tyr

370 375 380

His Arg Val Lys Pro Leu Pro Val Ser Thr Ile His Lys Gly Gln Gly

385 390 395 400

Ser Thr Val Asp Asn Ser Phe Leu Tyr Thr Pro Cys Ile Thr Lys Tyr

405 410 415

Ala Glu Pro Asp Leu Ala Ser Gln Leu Leu Tyr Val Gly Val Thr Arg

420 425 430

Ala Arg His Asn Val Asn Phe Val Gly

435 440

<210> 23

<211> 1326

<212> DNA

<213> Artificial Sequence

<220>

<223> helicase

<400> 23

atgatcacca tcgaccagct gaccgaaggt cagttcgact ctctgcagcg tgctaaagtt 60

ctgatccagg aagctaccaa aaacgacggt aactggaacc accgtaccaa acacctgacc 120

atcaacggtc cggctggtac cggtaaaacc accatgatga aattcctggt ttcttggctg 180

cgtgacgaag gtatcaccgg tgttgctctg gctgctccga cccacgctgc taaaaaagtt 240

ctggctaacg ctgttggtga agaagtttct accatccact ctatcctgaa aatcaacccg 300

accacctacg aatgcaaaca gttcttcgaa cagtctgctc cgccggacct gtctaaaatc 360

cgtatcctga tctgcgaaga atgctctttc tacgacatca aactgttcga aatcctgatg 420

aactctatcc agccgtggac catcatcatc ggtatcggtg accgtgctca gctgcgtccg 480

gctgacgaca aaggtatctc tcgtttcttc accgaccagc gtttcgaaca gacctacctg 540

accgaaatca aacgttctaa catgccgatc atcgaagttg ctaccgaaat ccgtaacggt 600

ggttggattc gtgaaaacat catcgacgac ctgggtgtta aacaggacaa atctgtttct 660

gaatttatga ccaactactt caaagttgtt aaatctatcg acgacctgta cgaaacccgt 720

atgtacgctt acaccaacaa ctctgttgac accctgaaca aaatcatccg taaaaaactg 780

tacgaaaccg aacaggactt catcgttggt gaaccgatcg ttatgcagga accgctgatc 840

cgtgacatca actacgaagg taaacgtttc caggaaatcg ttttcaacaa cggtgaatac 900

ctggaagttt ctgaaatcaa accgatggaa tctgttctga aatgccgtaa catcgactac 960

cagctggttc tgcactacta ccagctgaaa gttaaatcta tcgacaccgg tgaatctggt 1020

ctgatcaaca ccatctctga caaaaacgaa ctgaacaaat tctacatgtt cctgggtaaa 1080

gtttgccagg actacaaatc tggtaccatc aaagcgttct gggacgactt ctggaaaatc 1140

aaaaacaact accaccgtgt taaaccgctg ccggtttcta ccatccacaa aggtcagggt 1200

tctaccgttg acaactcttt cctgtacacc ccgtgcatca ccaaatacgc tgaaccggac 1260

ctggcttctc agctgctgta cgttggtgtt acccgtgctc gtcacaacgt taacttcgtt 1320

ggttaa 1326

<210> 24

<211> 283

<212> PRT

<213> Artificial Sequence

<220>

<223> mutant 1

<400> 24

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Arg Asp Gln

50 55 60

Thr Gly Gln Tyr Arg Pro Ser Pro Ala Ser Ala Gln Ser Thr Ser Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Glu Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Glu Tyr Arg Val Asp Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

<210> 25

<211> 849

<212> DNA

<213> Artificial Sequence

<220>

<223> mutant 1

<400> 25

atgaataggt tgttagcaat ggctatgcta ttggcggctt tgcaaggttg tgcactgcgt 60

gaaccgatgc cggcagaatt ggagaacgcg accccgaccc tgacgccacg tgcgtctacg 120

tactacgacc tgctggctct cccgcgtccg aagggtcgcc tggtggcggc ggtgtatggt 180

tttcgcgatc agactggtca gtaccgtccg tccccggcgt cagcacaaag caccagcgtc 240

acccagggtg cagcgtctat gctggttgac gcattacaag cgtccggctg gttccgcgtg 300

ctggagcgcg aaggcctgca aaacatcctt acggaacgta aaatcattcg tgcatctcag 360

aacaaaccga ataccccagt taatatccaa gcggatctgc cttcgttgca ggcggcgaac 420

attctgctcg agggtggcgt gattgcatac gacaccaatg ttcgttctgg cggtgaaggc 480

gctgcgtacc tgggtatcag cctgtcccaa gaatatcgcg ttgaccaggt tagcgttaac 540

ctgcgtgcgg ttgatgtccg tagcggccaa gtactggcga acgtgatgac ctcgaaaacc 600

atttatagcg tgggtcgtaa tgccggcatt tttaagttca tcgaattcaa agagttgttg 660

gaggcagaag cgggttatac cacaaacgag ccggcccaac tttgcgttct gagcgcaatc 720

gaggcggctg tggcccacct ggtcgcgcag ggcatcgagc gccgtctgtg gcaggctgcc 780

gatgagagct cctttgataa gagcagcttg ccgaagtaca tgagccaggc gagagccgac 840

ccgctgccg 849

<210> 26

<211> 283

<212> PRT

<213> Artificial Sequence

<220>

<223> mutant 2

<400> 26

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Arg Asp Gln

50 55 60

Thr Gly Gln Tyr Lys Pro Gly Pro Ala Ser Thr Lys Ser Thr Ser Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Glu Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Glu Tyr Arg Val Asp Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

<210> 27

<211> 283

<212> PRT

<213> Artificial Sequence

<220>

<223> mutant 3

<400> 27

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Arg Asp Leu

50 55 60

Thr Gly Gln Tyr Arg Pro Ser Pro Ala Ser Ala Asn Ser Thr Ala Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Glu Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Glu Tyr Arg Val Asp Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

<210> 28

<211> 283

<212> PRT

<213> Artificial Sequence

<220>

<223> mutant 4

<400> 28

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Arg Asp Leu

50 55 60

Thr Gly Gln Tyr Arg Pro Ser Pro Ala Ser Ala Leu Ser Thr Ala Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Glu Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Glu Tyr Arg Val Asp Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

<210> 29

<211> 283

<212> PRT

<213> Artificial Sequence

<220>

<223> mutant 5

<400> 29

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Ser Val Gln

50 55 60

Thr Gly Gln Phe Arg Pro Ser Pro Ala Ser Ala Gln Ser Thr Ser Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Val Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Glu Tyr Arg Val Asp Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

<210> 30

<211> 283

<212> PRT

<213> Artificial Sequence

<220>

<223> mutant 6

<400> 30

Met Asn Arg Leu Leu Ala Met Ala Met Leu Leu Ala Ala Leu Gln Gly

1 5 10 15

Cys Ala Leu Arg Glu Pro Met Pro Ala Glu Leu Glu Asn Ala Thr Pro

20 25 30

Thr Leu Thr Pro Arg Ala Ser Thr Tyr Tyr Asp Leu Leu Ala Leu Pro

35 40 45

Arg Pro Lys Gly Arg Leu Val Ala Ala Val Tyr Gly Phe Arg Asp Gln

50 55 60

Thr Gly Gln Phe Arg Pro Ser Pro Ala Ser Ala Gln Ser Thr Ser Val

65 70 75 80

Thr Gln Gly Ala Ala Ser Met Leu Val Asp Ala Leu Gln Ala Ser Gly

85 90 95

Trp Phe Arg Val Leu Glu Arg Glu Gly Leu Gln Asn Ile Leu Thr Glu

100 105 110

Arg Lys Ile Ile Arg Ala Ser Gln Asn Lys Pro Asn Thr Pro Val Asn

115 120 125

Ile Gln Ala Asp Leu Pro Ser Leu Gln Ala Ala Asn Ile Leu Leu Glu

130 135 140

Gly Gly Val Ile Ala Tyr Asp Thr Asn Val Arg Ser Gly Gly Glu Gly

145 150 155 160

Ala Ala Tyr Leu Gly Ile Ser Leu Ser Gln Asn Tyr Arg Val Asn Gln

165 170 175

Val Ser Val Asn Leu Arg Ala Val Asp Val Arg Ser Gly Gln Val Leu

180 185 190

Ala Asn Val Met Thr Ser Lys Thr Ile Tyr Ser Val Gly Arg Asn Ala

195 200 205

Gly Ile Phe Lys Phe Ile Glu Phe Lys Glu Leu Leu Glu Ala Glu Ala

210 215 220

Gly Tyr Thr Thr Asn Glu Pro Ala Gln Leu Cys Val Leu Ser Ala Ile

225 230 235 240

Glu Ala Ala Val Ala His Leu Val Ala Gln Gly Ile Glu Arg Arg Leu

245 250 255

Trp Gln Ala Ala Asp Glu Ser Ser Phe Asp Lys Ser Ser Leu Pro Lys

260 265 270

Tyr Met Ser Gln Ala Arg Ala Asp Pro Leu Pro

275 280

Claims

1. A mutant of a porin monomer, wherein the amino acid sequence of the mutant of the porin monomer consists of SEQ ID NO. 24, SEQ ID NO. 26, SEQ ID NO. 27, SEQ ID NO. 28, SEQ ID NO. 29 or SEQ ID NO. 30.

2. A protein pore comprising at least one mutant of the pore protein monomer of claim 1.

3. The protein well of claim 2, wherein said protein well comprises mutants of at least two of said porin monomers.

4. The protein pore of claim 2 or 3, wherein the protein pore has a constriction zone pore diameter of

5. A complex for characterizing a target analyte, characterized by: comprising the protein pore of any one of claims 2-4 and a rate controlling protein bound thereto.

6. A nucleic acid encoding a mutant of the porin monomer of claim 1, the protein pore of any one of claims 2-4, or the complex of claim 5.

7. A vector or genetically engineered host cell comprising the nucleic acid of claim 6.

8. A mutant of a porin monomer according to claim 1, a protein pore according to any one of claims 2 to 4, a complex according to claim 5, a nucleic acid according to claim 6, or a vector or host cell according to claim 7, use in or for the preparation of a product for detecting the presence, absence or one or more characteristics of a target analyte, which is not a diagnostic or therapeutic use for a disease.

9. A method of producing a protein pore or polypeptide thereof, comprising transforming the host cell of claim 7 with a vector comprising the vector of claim 7, and inducing the host cell to express the protein pore or polypeptide thereof of any one of claims 2-4.

10. A method for determining the presence, absence or one or more characteristics of a target analyte, comprising:

a. contacting a target analyte with the protein pore of any one of claims 2-4, the complex of claim 5, or the protein pore in the complex of claim 5 such that the target analyte moves relative to the protein pore; and

b. obtaining one or more measurements as the target analyte moves relative to the protein aperture, thereby determining the presence, absence, or one or more characteristics of the target analyte,

the method is not a diagnostic or therapeutic method for a disease.

11. The method of claim 10, wherein the method comprises:

the target analyte interacts with the protein pores present in the membrane such that the target analyte moves relative to the protein pores.

12. A kit for determining the presence, absence or one or more characteristics of a target analyte comprising a mutant of a porin monomer according to claim 1, a protein pore according to any one of claims 2 to 4, a complex according to claim 5, a nucleic acid according to claim 6, or a vector or host according to claim 7, and a component of a membrane as defined in claim 11.

13. A device for determining the presence, absence or one or more characteristics of a target analyte, comprising a protein pore according to any one of claims 2-4 or a complex according to claim 5, and a membrane as defined in claim 11.

14. The use, method, kit or device according to any one of claims 8-13, wherein the target analyte comprises an inorganic salt, a polymer, an amino acid or a nucleotide.

15. The use, method, kit or device according to any one of claims 8-13, wherein the target analyte comprises a dye, a drug, a diagnostic agent, an explosive or an environmental contaminant.

16. The use, method, kit or device according to any one of claims 8-13, wherein the target analyte comprises a metal ion, polysaccharide, peptide or polynucleotide.

17. The use, method, kit or device according to claim 16, wherein the polynucleotide comprises DNA or RNA.

18. The use, method, kit or device according to any one of claims 8-13, wherein the one or more features are selected from (i) the length of the polynucleotide; (ii) identity of said polynucleotides; (iii) the sequence of the polynucleotide; (iv) A secondary structure of said polynucleotide and (v) whether said polynucleotide is modified; and/or, the rate controlling protein in the complex comprises a polynucleotide binding protein.