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US20040110235A1 - Regulated aptamer therapeutics - Google Patents

Regulated aptamer therapeutics Download PDF

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US20040110235A1
US20040110235A1 US10/627,543 US62754303A US2004110235A1 US 20040110235 A1 US20040110235 A1 US 20040110235A1 US 62754303 A US62754303 A US 62754303A US 2004110235 A1 US2004110235 A1 US 2004110235A1
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binding
aptamer
ligand
target
aptamers
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David Epstein
Charles Wilson
John Diener
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Archemix Corp
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Priority to US11/291,610 priority patent/US7960102B2/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
    • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1048—SELEX
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/66—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving blood sugars, e.g. galactose
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/16—Aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3519—Fusion with another nucleic acid
    • C—CHEMISTRY; METALLURGY
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    • C12N2320/00—Applications; Uses
    • C12N2320/50—Methods for regulating/modulating their activity

Definitions

  • the invention relates generally to the field of nucleic acids and more particularly to compositions and methods for treating diseases with regulated aptamer compositions of the present invention.
  • Aptamers are nucleic acid molecules having specific binding affinity to molecules through interactions other than classic Watson-Crick base pairing.
  • Aptamers like peptides generated by phage display or monoclonal antibodies (MAbs), are capable of specifically binding to selected targets and, through binding, block their targets' ability to function.
  • FOG. 1 random sequence oligonucleotides (FIG. 1)
  • aptamers have been generated for over 100 proteins including growth factors, transcription factors, enzymes, immunoglobulins, and receptors.
  • a typical aptamer is 10-15 kDa in size (30-45 nucleotides), binds its target with sub-nanomolar affinity, and discriminates against closely related targets (e.g., will typically not bind other proteins from the same gene family).
  • a series of structural studies have shown that aptamers are capable of using the same types of binding interactions (hydrogen bonding, electrostatic complementarity, hydrophobic contacts, steric exclusion, etc.) that drive affinity and specificity in antibody-antigen complexes.
  • Aptamers have a number of desirable characteristics for use as therapeutics including high specificity and affinity, biological efficacy, and excellent pharmacokinetic properties. In addition, they offer specific competitive advantages over antibodies and other protein biologics, for example:
  • aptamers can be administered by subcutaneous injection. This difference is primarily due to the comparatively low solubility and thus large volumes necessary for most therapeutic MAbs. With good solubility (>150 mg/ml) and comparatively low molecular weight (aptamer: 10-50 KD; antibody: 150 KD), a weekly dose of aptamer may be delivered by injection in a volume of less than 0.5 ml. Aptamer bioavailability via subcutaneous administration is >80% in monkey studies (Tucker, 1999).
  • the insulin receptor is a surface receptor and is a tetramer of 2 alpha and 2 transmembrane beta chains linked by disulfide bonds.
  • the insulin receptor which is activated by insulin, is a tyrosine kinase receptor. Its activation leads to an increase in the storage of glucose with a concomitant decrease in hepatic glucose release to the circulation.
  • the insulin receptor induces a cellular response by phosphorylating proteins on their tyrosine residues.
  • the IR is known to phosphorylate several proteins in the cytoplasm, including insulin receptor substrates (IRSs) and Shc.
  • Phosphatidylinositol 3-kinase is one signaling molecule that is activated by binding IRSs and is important in coupling the IR to glucose uptake.
  • PK13 mediates glucose uptake by the IR as well as a variety of other cellular responses by generating PI(3,4)P 2 and PI(3,4,5)P 3 .
  • PI(3,4)P 2 and PI(3,4,5)P 3 then function directly as second messengers to activate downstream signaling molecules by binding pleckstrin homology (PH) domains in these signaling molecules.
  • PH pleckstrin homology
  • the major function of insulin is to counter the concerted action of a number of hyperglycemia-generating hormones and to maintain low blood glucose levels. Because there are numerous hyperglycemic hormones, untreated disorders associated with insulin generally lead to severe hyperglycemia and shortened life span. Insulin is synthesized as a preprohormone in the b cells of the islets of Langerhans. Its signal peptide is removed in the cisternae of the endoplasmic reticulum and it is packaged into secretory vesicles in the Golgi, folded to its native structure, and locked in this conformation by the formation of 2 disulfide bonds. Specific.
  • protease activity cleaves the center third of the molecule, which dissociates as C peptide, leaving the amino terminal B peptide disulfide bonded to the carboxy terminal A peptide.
  • Insulin secretion from b cells is principally regulated by plasma glucose levels, but the precise mechanism by which the glucose signal is transduced remains unclear.
  • One possibility is that the increased uptake of glucose by pancreatic b-cells leads to a concommitant increase in metabolism. The increase in metabolism leads to an elevation in the ATP/ADP ratio. This in turn leads to an inhibition of an ATP-sensitive K + channel. The net result is a depolarization of the cell leading to Ca 2+ influx and insulin secretion.
  • epinephrine diminishes insulin secretion by a cAMP-coupled regulatory path.
  • epinephrine counters the effect of insulin in liver and peripheral tissue, where it binds to b-adrenergic receptors, induces adenylate cycles activity, increases cAMP, and activates PKA activates PKA similarly to that of glucagon.
  • epinephrine influences glucose homeostasis through interaction with a-adrenergic receptors. Insulin secreted by the pancreas is directly infused via the portal vein to the liver, where it exerts profound metabolic effects. These effects are the response of the activation of the insulin receptor which belongs to the class of cell surface receptors that exhibit intrinsic tyrosine kinase activity. With respect to hepatic glucose homeostasis, the effects of insulin receptor activation are specific phosphorylation events that lead to an increase in the storage of glucose with a concomitant decrease in hepatic glucose release to the circulation.
  • F2,6BP fructose-2,6-bisphosphate
  • F2,6BP is a potent allosteric activator of the rate limiting enzyme of glycolysis, PFK-1, and an inhibitor of the gluconeogenic enzyme, fructose-1,6-bisphosphatase.
  • phophatases specific for the phosphorylated forms of the glycolytic enzymes increase in activity under the influence of insulin. All these events lead to conversion of the glycolytic enzymes to their active forms and consequently a significant increase in glycolysis.
  • glucose-6-phosphatase activity is down-regulated.
  • the net effect is an increase in the content of hepatocyte glucose and its phosphorylated derivatives, with diminished blood glucose.
  • diminished cAMP and elevated phosphatase activity combine to convert glycogen phosphorylase to its inactive form and glycogen synthase to its active form, with the result that not only is glucose funneled to glycolytic products, but glycogen content is increased as well.
  • Insulin therapy is the only treatment for Type 1 diabetic patients. Occasionally, Type 2 diabetic patients are also treated with insulin. Type 2 diabetic patients usually require larger doses of insulin to achieve the target blood glucose value. At present, two methods of insulin delivery are available in the USA; multiple daily insulin injections and an insulin pump. Nasal insulin therapy is currently undergoing clinical trials and is not yet approved by the FDA for general use. All insulins sold in the United States today are of U-100 strength, 100 units of insulin per cc of fluid. There are other dilutions in other countries. Dosing is at least three times a day with meals.
  • Insulin generates its intracellular effects by binding to a plasma membrane receptor, which is the same in all cells.
  • the receptor is a disulfide-bonded glycoprotein.
  • One function of insulin (aside from its role in signal transduction.) is to increase glucose transport in extrahepatic tissue is by increasing the number of glucose transport molecules in the plasma membrane.
  • Glucose transporters are in a continuous state of turnover. Increases in the plasma membrane content of transporters stem from an increase in the rate of recruitment of new transporters into the plasma membrane, deriving from a special pool of preformed transporters localized in the cytoplasm.
  • insulin stimulates lipogenesis, diminishes lipolysis, and increases amino acid transport into cells.
  • Insulin also modulates transcription, altering the cell content of numerous mRNAs. It stimulates growth, DNA synthesis, and cell replication, effects that it holds in common with the IGFs and relaxin.
  • the most common method of insulin delivery is subcutaneous injection. Another method is an insulin pump.
  • the biggest advantage of an insulin pump is greater flexibility in the timing of meals, the patient does not have to eat at a particular time as is the case with insulin injection therapy. Meals can be skipped without the fear of low blood sugar.
  • the disadvantages of insulin pump delivery are the risk of skin infection at the needle site, insulin delivery can be halted due to mechanical problems which can result in severe hyperglycemia (high blood glucose) and even diabetic ketoacidosis (a life-threatening condition), and cosmetic problems.
  • FIG. 1 shows a schematic of the SELEX method.
  • FIG. 2 shows a schematic of a glucose activated therapeutic to regulate insulin.
  • the present invention provides regulated aptamers that can be used, e.g., to treat certain diseases. More specifically, the present invention provides aptamers wherein binding of the aptamer to a second ligand is regulated, i.e., activated or suppressed, by binding to a first (or effector) ligand.
  • the present invention provides therapeutic aptamers whose binding activity is controlled by a first ligand which serves, e.g., as a disease marker.
  • the first ligand activates the binding activity of the therapeutic aptamer.
  • the present invention provides therapeutic aptamers whose binding activity is controlled by a first ligand which serves, e.g., as a disease marker.
  • the first ligand suppresses the binding activity of the therapeutic aptamer.
  • the present invention provides therapeutic aptamers that bind to the insulin receptor (thus triggering glucose uptake by cells) only after binding glucose.
  • aptamers are nucleic acid ligands which have the property of binding specifically to a desired target compound or molecule or a nucleic acid target through non-Watson-Crick base pairing.
  • a regulated aptamer is an aptamer whose binding (or other biological) activity is controlled allosterically by an effector ligand which serves, e.g., as a disease marker.
  • the effector ligand can either activate or suppress the binding (or other biological) activity of the aptamer.
  • an agonist-aptamer is an aptamer that activates the activity of a target when it binds thereto.
  • an antagonist-aptamer is an aptamer which inactivates the activity of a target when it binds thereto.
  • a suitable method for generating an aptamer to a target of interest is with the process entitled “Systematic Evolution of Ligands by EXponential Enrichment” (“SELEXTM”) depicted in FIG. 1.
  • SELEXTM Systematic Evolution of Ligands by EXponential Enrichment
  • the SELEXTM process is a method for the in vitro evolution of nucleic acid molecules with highly specific binding to target molecules and is described in, e.g., U.S. patent application Ser. No. 07/536,428, filed Jun. 11, 1990, now abandoned, U.S. Pat. No. 5,475,096 entitled “Nucleic Acid Ligands”, and U.S. Pat. No. 5,270,163 (see also WO 91/19813) entitled “Nucleic Acid Ligands”.
  • Each SELEX-identified nucleic acid ligand is a specific ligand of a given target compound or molecule.
  • the SELEXTM process is based on the unique insight that nucleic acids have sufficient capacity for forming a variety of two- and three-dimensional structures and sufficient chemical versatility available within their monomers to act as ligands (form specific binding pairs) with virtually any chemical compound, whether monomeric or polymeric. Molecules of any size or composition can serve as targets.
  • the SELEXTM method applied to the application of high affinity binding involves selection from a mixture of candidate oligonucleotides and step-wise iterations of binding, partitioning and amplification, using the same general selection scheme, to achieve virtually any desired criterion of binding affinity and selectivity.
  • the SELEXTM method includes steps of contacting the mixture with the target under conditions favorable for binding, partitioning unbound nucleic acids from those nucleic acids which have bound specifically to target molecules, dissociating the nucleic acid-target complexes, amplifying the nucleic acids dissociated from the nucleic acid-target complexes to yield a ligand-enriched mixture of nucleic acids, then reiterating the steps of binding, partitioning, dissociating and amplifying through as many cycles as desired to yield highly specific high affinity nucleic acid ligands to the target molecule.
  • SELEXTM Systematic Evolution of Ligands by Exponential Enrichment
  • SELEXTM technology is based on the fact that nucleic acids have sufficient capacity for forming a variety of two- and three-dimensional structures and sufficient chemical versatility available within their monomers to act as ligands (i.e., form specific binding pairs) with virtually any chemical compound, whether large or small in size.
  • the method involves selection from a mixture of candidates and step-wise iterations of structural improvement, using the same general selection theme, to achieve virtually any desired criterion of binding affinity and selectivity.
  • the SELEXTM method includes steps of contacting the mixture with the target under conditions favorable for binding, partitioning unbound nucleic acids from those nucleic acids which have bound to target molecules, dissociating the nucleic acid-target pairs, amplifying the nucleic acids dissociated from the nucleic acid-target pairs to yield a ligand-enriched mixture of nucleic acids, then reiterating the steps of binding, partitioning, dissociating and amplifying through as many cycles as desired.
  • a nucleic acid mixture comprising, for example a 20 nucleotide randomized segment can have 4 20 candidate possibilities. Those which have the higher affinity constants for the target are most likely to bind to the target.
  • a second nucleic acid mixture is generated, enriched for the higher binding affinity candidates. Additional rounds of selection progressively favor the best ligands until the resulting nucleic acid mixture is predominantly composed of only one or a few sequences. These can then be cloned, sequenced and individually tested for binding affinity as pure ligands.
  • the method may be used to sample as many as about 10 18 different nucleic acid species.
  • the nucleic acids of the test mixture preferably include a randomized sequence portion as well as conserved sequences necessary for efficient amplification.
  • Nucleic acid sequence variants can be produced in a number of ways including synthesis of randomized nucleic acid sequences and size selection from randomly cleaved cellular nucleic acids.
  • the variable sequence portion may contain fully or partially random sequence; it may also contain subportions of conserved sequence incorporated with randomized sequence. Sequence variation in test nucleic acids can be introduced or increased by mutagenesis before or during the selection/amplification iterations.
  • the selection process is so efficient at isolating those nucleic acid ligands that bind most strongly to the selected target, that only one cycle of selection and amplification is required.
  • Such an efficient selection may occur, for example, in a chromatographic-type process wherein the ability of nucleic acids to associate with targets bound on a column operates in such a manner that the column is sufficiently able to allow separation and isolation of the highest affinity nucleic acid ligands.
  • the target-specific nucleic acid ligand solution may include a family of nucleic acid structures or motifs that have a number of conserved sequences and a number of sequences which can be substituted or added without significantly affecting the affinity of the nucleic acid ligands to the target.
  • nucleic acid primary, secondary and tertiary structures are known to exist.
  • the structures or motifs that have been shown most commonly to be involved in non-Watson-Crick type interactions are referred to as hairpin loops, symmetric and asymmetric bulges, pseudoknots and myriad combinations of the same.
  • Almost all known cases of such motifs suggest that they can be formed in a nucleic acid sequence of no more than 30 nucleotides. For this reason, it is often preferred that SELEX procedures with contiguous randomized segments be initiated with nucleic acid sequences containing a randomized segment of between about 20-50 nucleotides.
  • SELEXTM can also be used to obtain nucleic acid ligands that bind to more than one site on the target molecule, and to nucleic acid ligands that include non-nucleic acid species that bind to specific sites on the target.
  • SELEXTM provides means for isolating and identifying nucleic acid ligands which bind to any envisionable target, including large and small biomolecules including proteins (including both nucleic acid-binding proteins and proteins not known to bind nucleic acids as part of their biological function) cofactors and other small molecules. See U.S. Pat. No. 5,580,737 for a discussion of nucleic acid sequences identified through SELEXTM which are capable of binding with high affinity to caffeine and the closely related analog, theophylline.
  • Counter-SELEXTM is a method for improving the specificity of nucleic acid ligands to a target molecule by eliminating nucleic acid ligand sequences with cross-reactivity to one or more non-target molecules.
  • Counter-SELEXTM is comprised of the steps of a) preparing a candidate mixture of nucleic acids; b) contacting the candidate mixture with the target, wherein nucleic acids having an increased affinity to the target relative to the candidate mixture may be partitioned from the remainder of the candidate mixture; c) partitioning the increased affinity nucleic acids from the remainder of the candidate mixture; d) contacting the increased affinity nucleic acids with one or more non-target molecules such that nucleic acid ligands with specific affinity for the non-target molecule(s) are removed; and e) amplifying the nucleic acids with specific affinity to the target molecule to yield a mixture of nucleic acids enriched for nucleic acid sequences with a relatively higher affinity and specificity for binding to the target molecule.
  • a heterogeneous population of oligonucleotide molecules comprising randomized sequences is generated and selected to identify a nucleic acid molecule having a binding affinity which is selective for a target molecule.
  • U.S. Pat. Nos. 5,475,096; 5,476,766; and 5,496,938 each of is incorporated herein by reference.
  • a population of 100% random oligonucleotides is screened.
  • each oligonucleotide in the population comprises a random sequence and at least one fixed sequence at its 5′ and/or 3′ end.
  • the oligonucleotide can be RNA, DNA, or mixed RNA/DNA, and can include modified or nonnatural nucleotides or nucleotide analogs.
  • the random sequence portion of the oligonucleotide is flanked by at least one fixed sequence which comprises a sequence shared by all the molecules of the oligonucleotide population.
  • Fixed sequences include sequences such as hybridization sites for PCR primers, promoter sequences for RNA polymerases (e.g., T3, T4, T7, SP6, and the like), restriction sites, or homopolymeric sequences, such as poly A or poly T tracts, catalytic cores (described further below), sites for selective binding to affinity columns, and other sequences to facilitate cloning and/or sequencing of an oligonucleotide of interest.
  • the random sequence portion of the oligonucleotide is about 15-70 (e.g., about 30-40) nucleotides in length and can comprise ribonucleotides and/or deoxyribonucleotides.
  • Random oligonucleotides can be synthesized from phosphodiester-linked nucleotides using solid phase oligonucleotide synthesis techniques well known in the art (Froehler et al., Nucl. Acid Res. 14:5399-5467 (1986); Froehler et al., Tet. Lett. 27:5575-5578 (1986)).
  • Oligonucleotides can also be synthesized using solution phase methods such as triester synthesis methods (Sood et al., Nucl. Acid Res. 4:2557 (1977); Hirose et al., Tet. Lett., 28:2449 (1978)).
  • Typical syntheses carried out on automated DNA synthesis equipment yield 10 15 -10 17 molecules. Sufficiently large regions of random sequence in the sequence design increases the likelihood that each synthesized molecule is likely to represent a unique sequence.
  • random oligonucleotides comprise entirely random sequences; however, in other embodiments, random oligonucleotides can comprise stretches of nonrandom or partially random sequences. Partially random sequences can be created by adding the four nucleotides in different molar ratios at each addition step.
  • the SELEX method encompasses the identification of high-affinity nucleic acid ligands containing modified nucleotides conferring improved characteristics on the ligand, such as improved in vivo stability or improved delivery characteristics. Examples of such modifications include chemical substitutions at the ribose and/or phosphate and/or base positions. SELEX-identified nucleic acid ligands containing modified nucleotides are described in U.S. Pat. No. 5,660,985, which describes oligonucleotides containing nucleotide derivatives chemically modified at the 5′ and 2′ positions of pyrimidines. U.S. Pat. No.
  • 5,756,703 describes oligonucleotides containing various 2′-modified pyrimidines.
  • U.S. Pat. No. 5,580,737 describes highly specific nucleic acid ligands containing one or more nucleotides modified with 2′-amino (2′-NH 2 ), 2′-fluoro (2′-F), and/or 2′-O-methyl (2′-OMe) substituents.
  • the SELEX method encompasses combining selected oligonucleotides with other selected oligonucleotides and non-oligonucleotide functional units as described in U.S. Pat. No. 5,637,459 and U.S. Pat. No. 5,683,867.
  • the SELEX method further encompasses combining selected nucleic acid ligands with lipophilic or non-immunogenic high molecular weight compounds in a diagnostic or therapeutic complex, as described in U.S. Pat. No. 6,011,020.
  • VEGF nucleic acid ligands that are associated with a lipophilic compound, such as diacyl glycerol or dialkyl glycerol, in a diagnostic or therapeutic complex are described in U.S. Pat. No. 5,859,228.
  • VEGF nucleic acid ligands that are associated with a lipophilic compound, such as a glycerol lipid, or a non-immunogenic high molecular weight compound, such as polyalkylene glycol are further described in U.S. Pat. No. 6,051,698.
  • VEGF nucleic acid ligands that are associated with a non-immunogenic, high molecular weight compound or a lipophilic compound are further described in PCT Publication No. WO 98/18480.
  • modified oligonucleotides can be used and can include one or more substitute internucleotide linkages, altered sugars, altered bases, or combinations thereof.
  • oligonucleotides are provided in which the P(O)O group is replaced by P(O)S (“thioate”), P(S)S (“dithioate”), P(O)NR 2 (“amidate”), P(O)R, P(O)OR′, CO or CH 2 (“formacetal”) or 3′-amine (—NH—CH 2 —CH 2 —), wherein each R or R′ is independently H or substituted or unsubstituted alkyl.
  • Linkage groups can be attached to adjacent nucleotide through an —O—, —N—, or —S— linkage. Not all linkages in the oligonucleotide are required to be identical.
  • the oligonucleotides comprise modified sugar groups, for example, one or more of the hydroxyl groups is replaced with halogen, aliphatic groups, or functionalized as ethers or amines.
  • the 2′-position of the furanose residue is substituted by any of an O-methyl, O-alkyl, O-allyl, S-alkyl, S-allyl, or halo group.
  • 2-fluoro-ribonucleotide oligomer molecules can increase the sensitivity of a nucleic acid sensor molecule for a target molecule by ten- to- one hundred-fold over those generated using unsubstituted ribo- or deoxyribooligonucleotides (Pagratis, et al., Nat. Biotechnol.
  • Nucleic acid aptamer molecules are generally selected in a 5 to 20 cycle procedure. In one embodiment, heterogeneity is introduced only in the initial selection stages and does not occur throughout the replicating process.
  • the starting library of DNA sequences is generated by automated chemical synthesis on a DNA synthesizer. This library of sequences is transcribed in vitro into RNA using T7 RNA polymerase and purified. In one example, the 5′-fixed:random:3′-fixed sequence is separated by a random sequence having 30 to 50 nucleotides.
  • 5′-GCCTGTTGTGAGCCTCCTGTCGAA-(N 40 )-TTGAGCGTTTATTCTTGTCTCCCTATAGTGAGTCGTATTA -3′ is synthesized using an ABI EXPEDITETM DNA synthesizer, and purified by standard methods (N 40 denotes a random sequence of 40 nucleotides built uniquely into each aptamer). Approximately 10 15 DNA molecules with unique sequences from the template pool can be PCR amplified using the primers YW.42.30.A (5′-TAATACGACTCACTATAGGGAGACAAGAATAAACGCTCAA-3′) and YW.42.30B (5′-GCCTGTTGTGAGCCTCCTGTCGAA-3′).
  • Amplified pool PCR product is precipitated with ethanol, re-suspended in water and desalted on a Nap-5 column (Pharmacia).
  • Approximately 4 ⁇ 10 15 DNA molecules from the pool PCR amplification are transcribed in vitro using a mutant Y639F T7 RNA polymerase which accepts 2′-fluoropyrimidines (Sousa, 1999), 2′-fluoropyrimidine and 2′-OH purine NTPs, to yield ⁇ 3 ⁇ 10 16 RNA molecules with corresponding sequences.
  • Stabilized 2′-fluoro-pyrimidine pools made up of 10 14 -10 5 random sequences in a total volume of approximately 100 ⁇ l are contacted with either biotinylated target immobilized in neutravidin coated plates (Pierce) or adherent target-expressing cells immobilized in plates.
  • a typical binding buffer used for the positive and negative selection steps contains 20 mM HEPES, pH 7.4, 150 mM NaCl, 10 mM MgCl2, 1 mM EDTA, 1 mM DTT, and 0.1 mg/ml tRNA (4 mM). Following a 10 min. negative incubation step at room temperature, RNAs which bind to the target alone will be removed in this negative selection step.
  • the solution containing unbound RNA is then transferred to another identical well containing immobilized target and effector is added to the solution.
  • concentration of effector added can be adjusted to ultimately enrich molecules which respond to effector at the most appropriate concentration.
  • the effector is provided at saturating concentrations (typically millimolar for small molecule effectors such as glucose and high micromolar concentration for protein effectors) to ensure that molecules with any measure of effector dependence are isolated.
  • the effector concentration can be reduced to preferentially isolate the most effector-dependent molecules.
  • wells are rinsed with excess binding buffer (typically washing four times with 120 ul of 1 ⁇ ASB on a robotic plate washer with 30 sec. shakes).
  • RT primer 4 ⁇ M; 5 ⁇ “Thermo buffer”, 1 ⁇ ; DTT, 100 mM; mixed dNTPs, 0.2mM each; vanadate nucleotide inhibitor 200 ⁇ M; tRNA 10 g/ml; 0.51 ⁇ l Invitrogen Thermoscript Reverse Transcriptase; brought to 50 ⁇ l with water
  • RT primer 4 ⁇ M; 5 ⁇ “Thermo buffer”, 1 ⁇
  • DTT 100 mM
  • mixed dNTPs 0.2mM each
  • tRNA 10 g/ml 0.51 ⁇ l Invitrogen Thermoscript Reverse Transcriptase; brought to 50 ⁇ l with water
  • the RT reaction is diluted 10-fold into a 100 ⁇ l PCR reaction (containing 5′-primer, 1 ⁇ M; 3′-primer, 1 ⁇ M; 10 ⁇ Invitrogen supplied PCR buffer (no Mg), 1 ⁇ ; dNTPs, 0.2mM each; MgCl 2 , 3 mM; 1 ul Invitrogen Taq; 10 ⁇ l incubated RT reaction and brought to 100 ⁇ l with water) and thermocycled with the following schedule: 94° C., 1 min; 62° C., 1 min; 72° C. 3 min.
  • PCR reactions are assayed at 10 cycles by agarose gel, and then each successive 5 cycles until defined amplification bands are visible via ethidium bromide staining.
  • Completed PCR reactions are purified using a Centri-sep column and diluted 10-fold into a 50 ⁇ transcription reaction (4 ⁇ TK Transcription buffer, 1 ⁇ ; MgCl 2 , 25 mM; NTPs 5 mM each; NEB T7 RNA polymerase 2 ul; water to 50 ⁇ l).
  • the transcription reaction is incubated overnight at 37° C. and the resulting transcription products are purified by denaturing polyacrylamide gel electrophoresis (10% gel).
  • the entire selection process is repeated until the fraction of molecules surviving both positive and negative selection increases significantly above the original na ⁇ ve pool fraction, typically >10% of the input. Typically >10 cycles of selection are required for enrichment.
  • Individual molecules within the enriched pool are isolated and characterized by subcloning the pooled template DNA using the TOPO TA cloning system (Invitrogen). Individual clones are sequenced and unique clones screened for effector dependent binding.
  • Selection method (1) can be modified as follows if the probability that molecules with both target and effector binding properties exist in the starting pool is low. Instead of selecting initially for both target binding and effector dependence, in vitro selection can be used to isolate molecules with high affinity for the target. Following an optional diversification step (wherein the selected pool of target-binding sequences is partially randomized), effector-dependent selection can be applied. To isolate target specific aptamers, the previously described selection method is applied with the following modifications: (1) target is omitted from the negative selection step, and (2) effector is omitted from the positive selection step. 5-15 rounds of selection will typically yield a pool of target binding species containing 1-1000 unique sequences. Individual clones are screened for the ability to specifically bind to the target.
  • a diversified pool of sequences with increased likelihood of effector-dependent target binding activity can be generated by a number of means including the following:
  • Selection method (1) can be modified as follows if the probability that molecules with both target and effector binding properties exist in the starting pool is low. Instead of selecting initially for both target binding and effector dependence, in vitro selection can be used to isolate molecules with high affinity for the effector. Following an optional diversification step (wherein the selected pool of effector-binding sequences is partially randomized), effector-dependent, target-binding selection can be applied as described previously. To isolate effector-specific aptamers, the first selection method is applied with the following modifications: (1) target is omitted from the negative selection step, and (2) target is omitted from the positive selection step and instead effector is immobilized to the capture solid support.
  • effectors such as glucose
  • conventional affinity chromatography using 200 ⁇ l agarose bead columns with 1-5 mM immobilized effector is the preferred immobilization format. 5-15 rounds of selection will typically yield a pool of effector binding species containing 1-1000 unique sequences. Individual clones are screened for the ability to specifically bind to the effector.
  • a sequence-diversified pool of effector-binding molecules can be generated by one of the following methods:
  • the diversified pool is subjected to selection for effector-dependent target binding as described in selection method (1).
  • Selection method (1) can be modified as follows if the probability that molecules with both target and effector binding properties exist in the starting pool is low. Instead of selecting initially for both target binding and effector dependence, in vitro selection can be used to isolate two separate pools of molecules, one with high affinity for the effector and the other with high affinity for the target. Subdomains within the two pools can be engineered to create a chimeric pool of molecules in which each molecule contains one copy of an effector-binding motif and one copy of a target binding motif. This chimeric pool is then subjected to effector-dependent, target-binding selection as described previously.
  • selection method (1) is applied with the following modifications: (1) target is omitted from the negative selection step, and (2) effector is omitted from the positive selection step.
  • the selection method (1) is applied with the following modifications: (1) target is omitted from the negative selection step, and (2) target is omitted from the positive selection step and instead effector is immobilized to the capture solid support.
  • small molecule effectors such as glucose
  • conventional affinity chromatography using 200 ⁇ l agarose bead columns with 1-5 mM immobilized effector is the preferred immobilization format.
  • functional subdomains of high affinity clones from each of the target- and effector-specific pools are used to create the chimeric pool for effector-dependent selection.
  • the functional subdomains can be identified as described previously (selection method (2)).
  • the chimeric pool can be generated by linearly concatenating the functional motifs together with an intervening random sequence domain.
  • the motifs can be combined at the secondary structure level by coupling via linking helices as described previously for effector-dependent ribozymes (Soukup, G., and Breaker, R. (1999) Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. Structure Fold Des 7 (7): 783-91).
  • Self-regulating aptamers that can functionally substitute for insulin can be created by the following method.
  • Insulin-receptor (IR) binding activity A pool of nucleic acid molecules is selected for the ability to bind to the extracellular portion of the insulin receptor using selection method (2). Previous studies have identified epitopes for IR-specific antibodies that are able to mimic the effect of insulin (Steele-Perkins, G, and Roth, R. A. (1990) Insulin-mimetic anti-insulin receptor monoclonal antibodies stimulate receptor kinase activity in intact cells. J. Biol. Chem. 265(16):9458-9463). Protein fragments containing these epitopes are suitable starting points for the isolation of aptamers with insulin-mimetic activity. Modified monomeric and dimeric forms of IR-specific aptamers can be assayed for the ability to stimulate the intrinsic receptor kinase activity of IR and thus identify molecules with intrinsic agonist activities.
  • the minimized functional domain of aptamers with insulin-like activity can be used to construct a pool of potentially glucose-dependent molecules by linear concatenation with a random sequence domain (e.g. N 20 ) and flanked by constant sequence primers to facilitate subsequent selection.
  • Selection method (2) with high (e.g. 100 mM) initial concentrations of glucose as an effector yields glucose-regulator insulin-mimetic aptamers.
  • the invention also includes pharmaceutical compositions containing regulated aptamer molecules.
  • the compositions are suitable for internal use and include an effective amount of a pharmacologically active compound of the invention, alone or in combination, with one or more pharmaceutically acceptable carriers.
  • the compounds are especially useful in that they have very low, if any toxicity.
  • the compounds or their pharmaceutically acceptable salts are administered in amounts which will be sufficient to induce lysis of a desired cell.
  • the active drug component can be combined with an oral, non-toxic pharmaceutically acceptable inert carrier such as ethanol, glycerol, water and the like.
  • an oral, non-toxic pharmaceutically acceptable inert carrier such as ethanol, glycerol, water and the like.
  • suitable binders, lubricants, disintegrating agents and coloring agents can also be incorporated into the mixture.
  • Suitable binders include starch, magnesium aluminum silicate, starch paste, gelatin, methylcellulose, sodium carboxymethylcellulose and/or polyvinylpyrrolidone, natural sugars such as glucose or beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth or sodium alginate, polyethylene glycol, waxes and the like.
  • Lubricants used in these dosage forms include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride, silica, talcum, stearic acid, its magnesium or calcium salt and/or polyethyleneglycol and the like.
  • Disintegrators include, without limitation, starch, methyl cellulose, agar, bentonite, xanthan gum starches, agar, alginic acid or its sodium salt, or effervescent mixtures, and the like.
  • Diluents include, e.g., lactose, dextrose, sucrose, mannitol, sorbitol, cellulose and/or glycine.
  • compositions are preferably aqueous isotonic solutions or suspensions, and suppositories are advantageously prepared from fatty emulsions or suspensions.
  • the compositions may be sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers. In addition, they may also contain other therapeutically valuable substances.
  • the compositions are prepared according to conventional mixing, granulating or coating methods, respectively, and contain about 0.1 to 75%, preferably about 1 to 50%, of the active ingredient.
  • the compounds of the invention can also be administered in such oral dosage forms as timed release and sustained release tablets or capsules, pills, powders, granules, elixers, tinctures, suspensions, syrups and emulsions.
  • Liquid, particularly injectable compositions can, for example, be prepared by dissolving, dispersing, etc.
  • the active compound is dissolved in or mixed with a pharmaceutically pure solvent such as, for example, water, saline, aqueous dextrose, glycerol, ethanol, and the like, to thereby form the injectable solution or suspension.
  • a pharmaceutically pure solvent such as, for example, water, saline, aqueous dextrose, glycerol, ethanol, and the like.
  • solid forms suitable for dissolving in liquid prior to injection can be formulated.
  • Injectable compositions are preferably aqueous isotonic solutions or suspensions.
  • the compositions may be sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers. In addition, they may also contain other therapeutically valuable substances.
  • the compounds of the present invention can be administered in intravenous (both bolus and infusion), intraperitoneal, subcutaneous or intramuscular form, all using forms well known to those of ordinary skill in the pharmaceutical arts.
  • injectables can be prepared in conventional forms, either as liquid solutions or suspensions.
  • the materials of the present invention can be delivered to the ocular cavity with the methods described below.
  • the materials of the present invention can be administered to subjects in the modalities known in the art as described below.
  • Parenteral injectable administration is generally used for subcutaneous, intramuscular or intravenous injections and infusions. Additionally, one approach for parenteral administration employs the implantation of a slow-release or sustained-released systems, which assures that a constant level of dosage is maintained, according to U.S. Pat. No. 3,710,795, incorporated herein by reference.
  • preferred compounds for the present invention can be administered in intranasal form via topical use of suitable intranasal vehicles, or via transdermal routes, using those forms of transdermal skin patches well known to those of ordinary skill in that art.
  • the dosage administration will, of course, be continuous rather than intermittent throughout the dosage regimen.
  • Other preferred topical preparations include creams, ointments, lotions, aerosol sprays and gels, wherein the concentration of active ingredient would range from 0.1% to 15%, w/w or w/v.
  • excipients include pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like may be used.
  • the active compound defined above may be also formulated as suppositories using for example, polyalkylene glycols, for example, propylene glycol, as the carrier.
  • suppositories are advantageously prepared from fatty emulsions or suspensions.
  • the compounds of the present invention can also be administered in the form of liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles and multilamellar vesicles.
  • Liposomes can be formed from a variety of phospholipids, containing cholesterol, stearylamine or phosphatidylcholines.
  • a film of lipid components is hydrated with an aqueous solution of drug to a form lipid layer encapsulating the drug, as described in U.S. Pat. No. 5,262,564.
  • the aptamer-toxin and/or riboreporter molecules described herein can be provided as a complex with a lipophilic compound or non-immunogenic, high molecular weight compound constructed using methods known in the art.
  • a lipophilic compound or non-immunogenic, high molecular weight compound constructed using methods known in the art.
  • An example of nucleic-acid associated complexes is provided in U.S. Pat. No. 6,011,020.
  • the compounds of the present invention may also be coupled with soluble polymers as targetable drug carriers.
  • soluble polymers can include polyvinylpyrrolidone, pyran copolymer, polyhydroxypropyl-methacrylamide-phenol, polyhydroxyethylaspanamidephenol, or polyethyleneoxidepolylysine substituted with palmitoyl residues.
  • the compounds of the present invention may be coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.
  • a drug for example, polylactic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydropyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels.
  • the pharmaceutical composition to be administered may also contain minor amounts of non-toxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and other substances such as for example, sodium acetate, triethanolamine oleate, etc.
  • non-toxic auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and other substances such as for example, sodium acetate, triethanolamine oleate, etc.
  • the dosage regimen utilizing the compounds is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal and hepatic function of the patient; and the particular compound or salt thereof employed.
  • An ordinarily skilled physician or veterinarian can readily determine and prescribe the effective amount of the drug required to prevent, counter or arrest the progress of the condition.
  • Oral dosages of the present invention when used for the indicated effects, will range between about 0.05 to 1000 mg/day orally.
  • the compositions are preferably provided in the form of scored tablets containing 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0, 50.0, 100.0, 250.0, 500.0 and 1000.0 mg of active ingredient.
  • Effective plasma levels of the compounds of the present invention range from 0.002 mg to 50 mg per kg of body weight per day.
  • Compounds of the present invention may be administered in a single daily dose, or the total daily dosage may be administered in divided doses of two, three or four times daily.
  • RNA aptamers are capable of inhibiting proteins with high affinity and specificity, but this effect is not readily reversible.
  • a SELEX protocol was used to raise RNA aptamers to the DNA repair enzyme, formamidopyrimidine glycosylase (Fpg), and neomycin was employed in each round to dissociate Fpg-bound RNAs.
  • Fpg formamidopyrimidine glycosylase
  • neomycin was employed in each round to dissociate Fpg-bound RNAs.
  • Fpg activity is recovered by the addition of neomycin.
  • LIRAs ligand-regulated aptamers
  • RNA aptamers are capable of inhibiting proteins with high affinity and specificity, but this effect is not readily reversible.
  • a SELEX protocol was used to raise RNA aptamers to the DNA repair enzyme, formamidopyrimidine glycosylase (Fpg), and neomycin was employed in each round to dissociate Fpg-bound RNAs.
  • Fpg formamidopyrimidine glycosylase
  • neomycin was employed in each round to dissociate Fpg-bound RNAs.
  • Fpg activity is recovered by the addition of neomycin.
  • LIRAs ligand-regulated aptamers
  • RNA aptamer approach One potential drawback of the RNA aptamer approach described above is that once the aptamer is expressed in the cell and the target protein is inhibited, activity can no longer be precisely controlled. Tight temporal regulation of protein activity may be desired in certain instances when the timing of events is critical, such as during the cell cycle or in early development. (McCollum, D., and Gould, K. L. Trends Cell Biol. 11, 89-95 (2001); Ambros, V. Curr. Opin. Genet. Dev. 10, 428-433 (2000); Lee, R. C., and Ambros, V. Science 294, 862-864 (2001)).
  • RNA aptamer whose binding to the protein was itself regulated by an organic small molecule.
  • a selected RNA could bind and inhibit the target protein.
  • addition of the small molecule would disrupt the RNA-protein complex, leading to the functional protein.
  • Our approach was to employ a small molecule in an elution step during the SELEX protocol, leading to the amplification of RNAs that bind a target protein but dissociate from it in the presence of a small molecule. (See FIG. 2, Vuyisich and Beal, Chem.
  • RNAs ligand-regulated aptamers
  • LIRAs ligand-regulated aptamers
  • a functional protein can be inhibited for a specific period of time as the inhibition is temporally controlled by adding the inducer.
  • RNA structures should be capable of performing such tasks.
  • in vitro selected RNAs are capable of recognizing small organic molecules with high affinity and specificity. (Wilson, D. S., and Szostak, J. W., Annu. Rev. Biochem. 66, 611-647 (1999); Hermann, T., and Patel, D. J., Science 287, 820-825 (2000); Jenison, R. D., et al., Science 263, 1425-1429 (1994)).
  • ribozymes whose activity can be regulated by the presence of small molecules called effectors.
  • effectors Soukup, G. A., and Breaker, R. R., Proc Natl. Acad. Sci. USA 96, 3584- 3589 (1999); Robertson, M. P., and Ellington, A. D., Nucleic Acids Res. 28, 1751-1759 (2000); Piganeau, N., et al., Angew Chem. Int. Ed. 39, 4369-4373 (2000); Hartig, J. S., et al., Nat. Biotechnol. 20, 717-722 (2002)).
  • neomycin belongs to the aminoglycoside class of antibiotics. These molecules have been shown to bind many naturally occurring RNA ligands. (Moazed, D., and Noller, H. F. Nature 327, 389-394 (1987); Yoshizawa, S., et al., Biochemistry 41, 6263-6270 (2002); Carter, A. P., et al.
  • neomycin was used as a SELEX target and shown to bind a specific sequence motif in RNA. (Wallis, M. G., et al., Chem. Biol. 2, 543-552 (1995)).
  • RNA library was allowed to bind Fpg in solution followed by separation of free RNA from the Fpg-bound species using filter paper.
  • a nonspecific urea buffer was used for elutions of Fpg-bound RNAs.
  • the RNA pool was split and used for two parallel selections. In the N selection, neomycin was used in the elution step.
  • RNAs that bound Fpg but dissociated in the presence of the aminoglycoside were collected and amplified.
  • urea continued to be used in the elution step, selecting any RNA structure with affinity for Fpg.
  • RNA pool from the 23 rd N selection was tested the ability of the RNA pool from the 23 rd N selection to inhibit Fpg in the presence of neomycin.
  • RNA pool from the fourteenth round of the U selection was indeed more sensitive to neomycin (by an order of magnitude) than the U selection pool, which was never pressured to dissociate from Fpg in the presence of the aminoglycoside.
  • U aptamers were more sensitive to neomycin than U selection aptamers.
  • FIG. 9 shows cleavage of N1 aptamer by S1 and V1 ribonucleases under native conditions.
  • Major cleavage sites on the RNA are mapped onto the predicted secondary structure of the aptamer.
  • FIG. 5B Vuyisich and Beal, Chem. & Biol. 9: 907-913 (2002).
  • the mapping also includes the major cleavage sites of T1 ribonuclease digest under native conditions, which are shown in FIG. 6A, lane 4 of Vuyisich and Beal, Chem. & Biol. 9: 907-913 (2002).
  • the reactivity observed with the different ribonucleases agrees with the predicted secondary structure.
  • cleavage protection assays were performed.
  • Lanes 14-19 show a decrease in T1 cleavage from G27 to G35 in response to increasing amounts of Fpg.
  • Fpg and neomycin bind the N1 aptamer at apparently overlapping sites at the junction between a stem structure and a single-stranded loop near the center of the RNA strand.
  • FIG. 6B Vuyisich and Beal, Chem. & Biol. 9: 907-913 (2002).
  • the data can be fitted using a single-site binding equation, which results in a K d of 0.94 ⁇ 0.06 ⁇ M.
  • FIG. 6C Vuyisich and Beal, Chem. & Biol. 9: 907-913 (2002)).
  • RNA aptamers that bind the DNA repair protein formamidopyrimidine glycosylase, Fpg. (Wilson, D. S., and Szostak, J. W., Annu. Rev. Biochem. 66, 611-647 (1999)).
  • Fpg DNA repair protein formamidopyrimidine glycosylase
  • the 5′-GU-3′ step which is present in N1 aptamer as G27 and U28, has recently been shown to bind the aminoglycoside deoxystreptamine ring.
  • neomycin binding aptamers contain G-rich regions adjacent to a bulge, which is similar to the 5′ end of N1 aptamer.
  • the method developed here for discovering a LIRA small molecule pair is potentially general for any target protein or protein domain.
  • Such inhibitor/inducer pairs could be used to inhibit proteins in vivo, then relieve the inhibition at desired points in time. This would be valuable for the study of cellular phenomena in which the timing of molecular events is critical, such as in cell cycle regulation, circadian clocks, or controlling cell fates during early development.
  • a system that includes neomycin as the inducer is probably not suitable for a cell biology application due to its toxicity. (Leach, B. E., et al., J. Am. Chem. Soc. 73, 2797-2800 (1951)).
  • RNA inhibitors of protein function can be discovered through in vitro evolution and are released from their targets in the presence of specific small molecules (inducers). This allows for greater temporal control of the targeted protein activity, as it can be reactivated upon addition of the inducer at a specific time point.
  • This method should prove particularly useful in defining the function of gene products involved in phenomena where the timing of events is critical, such as the cell cycle, circadian clocks, or embryonic development.
  • in-depth studies of ligand-regulated aptamers like those described here will identify features of protein-RNA complexes that make them susceptible to regulation by small molecules.
  • a Molecular Dynamics STORM 840 was used to obtain all data from phosphorimaging plates.
  • E. coli Fpg was overexpressed and purified as previously described. (Boiteux, S., et al., J. Biol. Chem. 265, 3916-3922 (1990); Leipold, M. D., et al., Biochemistry 39, 14984-14992 (2000); Zharkov, D. O., et al., J. Biol. Chem. 272, 5335-5342 (1997)). We estimated that the enzyme was 70% active.
  • a 105 nt DNA oligonucleotide (0.2 nmol) was used as the template for a three-cycle PCR reaction, which yielded a 130 bp dsDNA product consisting of a T7 promoter and a 60-mer random region flanked by EcoRl and Hindlll cloning sites. Transcription from this DNA generated a 105-nt-long random RNA pool. (Abelson, J. N. Methods Enzymol. 267, 291-335 (1996)).
  • RNA pool was denatured at 95° C. in 0.5 ml of the selection buffer (1 ⁇ SB: 10 mM Tris-HCI, 50 mM NaCI, 2.5 mM MgCI 2 (pH 7.0]) and allowed to slowly cool to room temperature.
  • a single 13 mm filter paper disc (HAWPO1300, Millipore) was added to the RNA pool, and the tube was gently mixed for 20 min. This step excluded filter paper binding RNAs.
  • the RNA pool was then transferred to a tube with 0.3 nmol of Fpg and allowed to bind for 20 min with gentle mixing.
  • RNA-protein complexes were washed with 1 ml of 1 ⁇ SB to remove weakly binding RNAs.
  • RNAs were eluted with 0.2 ml of urea elution buffer (100 mM Na citrate, 7 M urea, 10 mM EDTA [pH 5.2]) which was preheated to 65° C.
  • the eluted RNAs were washed three times with 0.5 ml water in a YM-10 microcon concentrator (Millipore), then treated with 5 units of RNase-free DNase I (Promega) for 3 hr at 37° C. Access RT-PCR kit (Promega) was used to amplify RNA winners from each round. After six rounds, the RNA pool was divided and used for two parallel selections.
  • One selection utilized the same urea elution step as before and was performed for an additional eight rounds.
  • the other selection employed elution buffer that consisted of 1 ⁇ SB supplied with neomycin. The number of rounds in this selection (including the initial six rounds) was 23.
  • cDNA from final rounds of each selection was digested with EcoRl and HindIII (NEB), then cloned into pUC-19 vector and transformed into E. coil XL-1 Blue cells. Plasmids coding for individual RNA clones were isolated, sequenced, and used for production of aptamers. (Sambrook, J., et al., Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, NY; Cold Spring Harbor Laboratory Press) (1989)).
  • Fpg activity assays were carried out at room temperature in 1 ⁇ SB under steady-state conditions with 1 nM Fpg.
  • An 18-mer dsDNA was used as the Fpg substrate.
  • the 8-oxo-dG-containing strand was 5′ labeled and had the following sequence; d(5′-TCATGG GTC(8-oxo-G)TCGGTATA-3′), and the complementary strand contained a cytidine opposite 8-oxo-dG.
  • Reaction components were mixed in 18 ⁇ l and incubated for 12 min, followed by the addition of 2 ⁇ l of 200 nM DNA substrate (20 nM final). After 7 min, reactions were quenched with 15 ⁇ l of 95° C.
  • Footprints for both Fpg and neomycin were obtained using T1 RNase under native conditions. The reactions were performed in 1 ⁇ SB at room temperature with 10 ⁇ g/ml of tRNA Phe . Increasing amounts of Fpg or neomycin were incubated with 10 nM labeled aptamer for 10 min, followed by a 10 min enzyme digest. The reactions were quenched with 15 ⁇ l of stop solution, heat denatured, and 5 ⁇ l of each was resolved on 10% denaturing PAGE. After phosphorimaging the gel, the cleavage efficiency at G27 was calculated by subtracting the background band in the control lane and normalizing for the different loading per lane.
  • the cleavage data were converted into binding data for neomycin, assuming that the maximum cleavage corresponds to 0% occupancy by neomycin and that the minimum cleavage corresponds to 100% occupancy by neomycin.
  • Glucose causes an insulin receptor agonist aptamer to become activated, binding the insulin receptor target and triggering glucose uptake by cells.
  • a method of preparing a glucose regulated aptamer includes the following steps: 1) separately isolate aptamers with insulin receptor agonist activity and glucose binding activity using SELEX, 2) engineer a diverse sequence pool of molecules that contains both functional motifs, and 3) select for aptamers whose receptor binding activity is dependent upon the presence of glucose.
  • a pool of nucleic acid molecules is selected for the ability to bind to the extracellular portion of the insulin receptor using selection method (2).
  • Selection method (2) Previous studies have identified epitopes for IR-specific antibodies that are able to mimic the effect of insulin (Steele-Perkins, 1990). Protein fragments containing these epitopes are suitable starting points for the isolation of aptamers with insulin-mimetic activity. Modified monomeric and dimeric forms of IR-specific aptamers can be assayed for the ability to stimulate the intrinsic receptor kinase activity of IR and thus identify molecules with intrinsic agonist activities.
  • the minimized functional domain of aptamers with insulin-like activity can be used to construct a pool of potentially glucose-dependent molecules by linear concatenation with a random sequence domain (e.g. N 20 ) and flanked by constant sequence primers to facilitate subsequent selection.
  • Selection method (2) with high (e.g. 100 mM) initial concentrations of glucose as an effector yields glucose-regulator insulin-mimetic aptamers.

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