Blank M., Blind M. Aptamers as tools for target validation // Curr. Opin. Chem. Biol. 2005. V.9. P.336.
Blank M., Weinschenk T., Priemer M., Schluesener H. Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. Selective targeting of endothelial regulatory protein pigpen // J. Biol. Chem. 2001. V.276. P.16464-16468.
Blind M., Kolanus W., Famulok M. Cytoplasmic RNA modulators of an inside-out signal-transduction cascade // Proc. Natl. Acad. Sci. USA. 1999. V.96. P.3606-3610.
Blouin S., Lafontaine D.A. A loop–loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control // RNA. 2007. V.13. P.1256-1267.
Bock L.C., Griffin L.C., Latham J.A., Vermaas E.H., Toole J.J. Selection of singlestranded DNA molecules that bind and inhibit human thrombin // Nature. 1992. V.355. P.564-566.
Boese B.J., Breaker R.R. In vitro selection and characterization of cellulose-binding DNA aptamers // Nucleic Acids Research. 2007. V.35. P.6378-6388.
Bogenhagen D.F., Brown D.D. Nucleotide sequences in Xenopus 5S DNA required for transcription termination // Cell. 1981. V.24. P.261–270.
Boiziau C., Dausse E., Mishra R., Duconge F., Toulme J.J. Identification of aptamers against the DNA template for in vitro transcription of the HIV-1 TAR element // Antisense Nucleic Acid Drug Dev. 1997. V.7. P.369-380.
Boiziau C., Dausse E., Yurchenko L., Toulme J.J. DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes // J. Biol. Chem. 1999. V.274. P.12730–12737.
Bokman S.H., Ward W.W. Renaturation of Aequorea green-fluorescent protein // Biochem. Biophys. Res. Commun. 1981. V.101. P.1372-1380.
Bondensgaard K., Mollova E.T., Pardi A. The global conformation of the hammerhead ribozyme determined using residual dipolar couplings // Biochemistry. 2002. V.41. P.11532–11542.
Borer P.N. et al. // Biochemistry. 1995. V.34. P.6488.
Braasch D.A., Corey D.R. Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA // Chem. Biol. 2000. V.55. P.1–7.
Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding // Anal. Biochem. 1976. V.72. P.248–254.
Breaker R.R. In Vitro Selection of Catalytic Polynucleotides // Chem. Rev. 1997. V.97. P.371-390.
Breaker R.R. DNA aptamers and DNA enzymes // Curr. Opin. Chem. Biol. 1997. V.1. P.26–31.
Breaker R.R. Riboswitches and the RNA World // The RNA World—Gesteland RF. Cech T.R., Atkins J.F., eds. 3rd. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press, 2006.
Breaker R.R., Joyce G.F. Inventing and improving ribozyme function—rational design versus iterative selection methods // Trends Biotechnol. 1994. V.12. P.268–275.
Breaker R.R., Joyce G.F. A DNA enzyme that cleaves RNA // Chem. Biol. 1994. V.1. P.223-229.
Breaker R.R., Joyce G.F. A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity // Chem. Biol. 1995. V.2. P.655-660.
Bridonneau P., Chang Y.F., O'Connell D., Gill S.C., Snyder D.W., Johnson L., Goodson T., Jr., Herron D.K., Parma D.H. High-affinity aptamers selectively inhibit human nonpancreatic secretory phospholipase A2 (hnps-PLA2) // J. Med. Chem. 1998. V.41. P.778-786.
Brockstedt U., Uzarowska A., Montpetit A., Pfau W., Labuda D. In vitro evolution of RNA aptamers recognizing carcinogenic aromatic amines // Biochem. Biophys. Res. Commun. 2004. V.313. P.1004–1008.
Brody E.N., Gold L. Aptamers as therapeutic and diagnostic agents // J. Biotechnol. 2000. V.74. P.5–13.
Brody E.N., Willis M.C., Smith J.D., Jayasena S., Zichi D., Gold L. The use of aptamers in large arrays for molecular diagnostics // Mol. Diagn. 1999. V.4. P.381–388.
Bruesehoff P.J., Li J., Augustine A.J., 3rd, Lu Y. Improving metal ion specificity during in vitro selection of catalytic DNA // Comb. Chem. High Throughput Screen. 2002. V.5. P.327-335.
Brummelkamp T.R., Bernards R., Agami R. A system for stable expression of short interfering RNAs in mammalian cells // Science. 2002. V.296. P.550–553.
Bruno J.G., Kiel J.L. In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection // Biosens. Bioelectron. 1999. V.14. P.457-464.
Bryant K.F., Cox J.C., Wang H., Hogle J.M., Ellington A.D., Coen D.M. Binding of herpes simplex virus-1 US11 to specific RNA sequences // Nucleic Acids Res. 2005. V.33. P.6090-6100.
Bunka D.H.J., Mantle B.J., Morten I.J., Tennent G.A., Radford S.E., Stockley P.G. Production and Characterization of RNA Aptamers Specific for Amyloid Fibril Epitopes // J. Biol. Chem. 2007. V.282. P.34500-34509.
Bunka D.H.J., Stockley P.G. Aptamers come of age—at last! // Nat. Rev. Microbiol. 2006. V.44. P.589–596.
Burgstaller P., Famulok M. Isolation of RNA–aptamers for biological cofactors by in vitro selection // Angew. Chem. Int. Ed. Engl. 1994. V.33. P.1084–1087.
Burgstaller P., Famulok M. Structural characterization of a flavin-specific RNA aptamer by chemical probing // Bioorg. Med. Chem. Lett. 1996. V.6. P.1157-1162.
Burgstaller P., Jenne A., Blind M. Aptamers and aptazymes: accelerating small molecule drug discovery // Curr. Opin. Drug. Discov. Devel. 2002. V.5. P.690–700.
Burgstaller P., Kochoyan M., Famulok M. Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding // Nucleic Acids Res. 1995. V.23. P.4769-4776.
Burke D.H., Gold L. RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX // Nucleic Acids Res. 1997. V.25. P.2020–2024.
Burke D.H., Hoffman D.C. A novel acidophilic RNA motif that recognizes coenzyme A // Biochemistry. 1997. V.37. P.4653–4663.
Burke D.H., Hoffman D.C., Brown A., Hansen M., Pardi A., Gold L. RNA aptamers to the peptidyl transferase inhibitor chloramphenicol // Chem. Biol. 1997. V.4. P.833–843.
Burke D.H., Scates L., Andrews K., Gold L. Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase // J. Mol. Biol. 1996. V.264. P.650-666.
Burmeister J., von Kiedrowski G., Ellington A.D. Cofactor-Assisted Self-Cleavage in DNA Libraries with a 3'-5' Phosphoramidate Bond // Angew. Chem. Int. Ed. Engl. 1997. V.36. P.1321-1324.
Buskirk A.R., Kehayova P.D., Landrigan A., Liu D.R. In vivo evolution of an RNAbased transcriptional activator // Chem. Biol. 2003. V.10. P.533-540.
Buskirk A.R., Landrigan A., Liu D.R. Engineering a ligand-dependent RNA transcriptional activator // Chem. Biol. 2004. V.11. P.1157–1163.
Butcher S.E., Burke J.M. Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex // J. Mol. Biol. 1994. V.244. P.52–63.
Cai Z. et al. // Nature Struct. Biol. 1998. V.5. P.203.
Calabro V., Daugherty M.D., Frankel A.D. A single intermolecular contact mediates intramolecular stabilization of both RNA and protein // PNAS. 2005. V.102. P.6849-6854.
Carmi N., Balkhi S.R., Breaker R.R. Cleaving DNA with DNA // Proc. Natl. Acad. Sci. USA. 1998. V.95. P.2233-2237.
Carmi N., Shultz L.A., Breaker R.R. In vitro selection of self-cleaving DNAs // Chem. Biol. 1996. V.3. P.1039-1046.
Carothers J.M., Davis J.H., Chou J.J., Szostak J.W. Solution structure of an informationally complex high-affinity RNA aptamer to GTP // RNA. 2006. V.12. P.567–579.
Carothers J.M., Oestreich S.C., Davis J.H., Szostak J.W. Informational complexity and functional activity of RNA structures // J. Am. Chem. Soc. 2004. V.126. P.5130–5137.
Carothers J.M., Oestreich S.C., Szostak J.W. Aptamers selected for higher-affinity binding are not more specific for the target ligand // J. Am. Chem. Soc. 2006. V.128. P.7929-7937.
Carothers J.M., Szostak J.W. In vitro selection of functional oligonucleotides and the origins of biochemical activity // S. Klussmann, Ed. Aptamers and synthetic catalytically active oligonucleotides: Identification and applications. Wiley-VCH, Berlin, Germany, 2006. P.3-28.
Cassiday L.A., Maher L.J. In vivo recognition of an RNA aptamer by its transcription factor target // Biochemistry. 2001. V.40. P.2433–2438.
Cassiday L.A., Maher L.J. Yeast genetic selections to optimize RNA decoys for transcription factor NF- B // Proc. Natl. Acad. Sci. 2003. V.100. P.3930–3935.
Caughey B., Brown K., Raymond G.J., Katzenstein G.E., Thresher W. Binding of the protease-sensitive form of PrP (prion protein) to sulfated glycosaminoglycan and congo red // J. Virol. 1994. V.68. P.2135–2141.
Cech T.R. Fostering Innovation and Discovery in Biomedical Research // JAMA. 2005. V.294. P.1390-1393.
Cech T.R. Self-splicing of group I introns // Annu. Rev. Biochem. 1990. V.59. P.543–568.
Cerchia L., Duconge F., Pestourie C., Boulay J., Aissouni Y., Gombert K., Tavitian B., de Franciscis V., Libri D. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase // PLoS Biol. 2005. V.3. P.e123.
Cerchia L., Hamm J., Libri D., Tavitian B., de Franciscis V. Nucleic acid aptamers in cancer medicine // FEBS Lett. 2002. V.528. P.12-16.
Chapman K.B., Szostak J.W. Isolation of a ribozyme with 5'-5' ligase activity // Chem. Biol. 1995. V.2. P.325–333.
Chapple K.E., Bartel D.P., Unrau P.J. Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme // RNA. 2003. V.9. P.1208-1220.
Charlton J., Kirschenheuter G.P., Smith D. Highly potent irreversible inhibitors of neutrophil elastase generated by selection from a randomized DNA-valine phosphonate library // Biochemistry. 1997. V.36. P.3018-3026.
Charlton J., Sennello J., Smith D. In vivo imaging of inflammation using an aptamer inhibitor of human neutrophil elastase // Chem. Biol. 1997. V.4. P.809–816.
Cheah M.T., Wachter A., Sudarsan N., Breaker R.R. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches // Nature. 2007. V.447. P.497–500.
Chen C.H., Chernis G.A., Hoang V.Q., Landgraf R. Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3 // Proc. Natl. Acad. Sci. USA. 2003. V.100. P.9226-9231.
Chen X., McDowell J.A., Kierzek R., Krugh T.R., Turner D.H. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G·U pairs: One hydrogen bond for each G·U pair in r(GGCGUGCC)(2) and two for each G·U pair in r(GAGUGCUC)(2) // Biochemistry. 2000. V.39. P.8970–8982.
Childs-Disney J.L., Disney M.D. A simple ligation-based method to increase the information density in sequencing reactions used to deconvolute nucleic acid selections // RNA. 2008. V.14. P.390-394.
Chinnapen D.J., Sen D. Hemin-stimulated docking of cytochrome c to a hemin-DNA aptamer complex // Biochemistry. 2002. V.41. P.5202-5212.
Chinnapen D.J., Sen D. A deoxyribozyme that harnesses light to repair thymine dimers in DNA // Proc. Natl. Acad. Sci. USA. 2004. V.101. P.65-69.
Chiu Y.L., Ali A., Chu C.Y., Cao H., Rana T.M. Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells // Chem. Biol. 2004. V.11. P.1165–1175.
Chiu Y.L., Dinesh C.U., Chu C.Y., Ali A., Brown K.M., Cao H., Rana T.M. Dissecting RNA-interference pathway with small molecules // Chem. Biol. 2005. V.12. P.643–648.
Chiu Y.L., Rana T.M. RNAi in human cells. Basic structural and functional features of small interfering RNA // Mol. Cell. 2002. V.10. P.549–561.
Chiu Y.L., Rana T.M. siRNA function in RNAi: A chemical modification analysis // RNA. 2003. V.9. P.1034–1048.
Chiuman W., Li Y. Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates // Nucleic Acids Res. 2007. V.35. P.401-405.
Cho J., Hamasaki K., Rando R.R. The binding site of a specific aminoglycoside binding RNA molecule // Biochemistry. 1998. V.37. P.4985–4992.
Cho S., Kim J.-E., Lee B.-R., Kim J.-H., Kim B.-G. Bis-aptazyme sensors for hepatitis C virus replicase and helicase without blank signal // Nucleic Acids Res. 2005. V.33. P.e177-e177.
Choi K.H., Park M.W., Lee S.Y., Jeon M.-Y., Kim M.Y., Lee H.K., Yu J., Kim H.-J., Han K., Lee H., et al. Intracellular expression of the T-cell factor-1 RNA aptamer as an intramer // Mol. Cancer Ther. 2006. V.5. P.2428-2434.
Chu T.C., Marks J.W. III., Lavery L.A., Faulkner S., Rosenblum M.G., Ellington A.D., Levy M. Aptamer: Toxin conjugates that specifically target prostate tumor cells // Cancer Res. 2006. V.66. P.5989–5992.
Chu T.C., Twu K.Y., Ellington A.D., Levy M. Aptamer mediated siRNA delivery // Nucleic Acids Res. 2006. V.34. P.e73.
Chun S.-M., Jeong S., Kim J.-M., Chong B.-O., Park Y.-K., Park K., Yu J. Cholesterol Esterase Activity by in Vitro Selection of RNA against a Phosphate Transition-State Analogue // J. Am. Chem. Soc. 2006. V.121. P.10844-10845.
Ciesiolka J., Gorski J., Yarus M. Selection of an RNA domain that binds Zn2+ // RNA. 1995. V.1. P.538-550.
Ciesiolka J., Illangasekare M., Majerfeld I., Nickles T., Welch M., Yarus M., Zinnen S. Affinity selection-amplification from randomized ribooligonucleotide pools // Methods Enzymol. 1996. V.267. P.315-335.
Ciesiolka J., Yarus M. Small RNA-divalent domains // RNA. 1996. V.2. P.785-793.
Clark S. L., Remcho V. T. Aptamers as analytical reagents // Electrophoresis. 2002. V.23. P.1335–1340.
Clery A., Bourguignon-Igel V., Allmang C., Krol A., Branlant C. An improved definition of the RNA-binding specificity of SECIS-binding protein 2, an essential component of the selenocysteine incorporation machinery // Nucleic Acids Res. 2007. V.35. P.1868-1884.
Collett J.R., Cho E.J., Ellington A.D. Production and processing of aptamer microarrays // Methods. 2005. V.37. P.4–15.
Collin D., van Heijenoort C., Boiziau C., Toulme J.J., Guittet E. NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer // Nucleic Acids Res. 2000. V.28. P.3386-3391.
Conn M.M., Prudent J.R., Schultz P.G. Porphyrin Metalation Catalyzed by a Small RNA Molecule // J. Am. Chem. Soc. 1996. V.118. P.7012-7013.
Connell G.J., Illangesekare M., Yarus M. Three small ribooligonucleotides with specific arginine sites // Biochemistry. 1993. V.32. P.5497-5502.
Connell G.J., Yarus M. RNAs with dual specificity and dual RNAs with similar specificity // Science. 1994. V.264. P.1137-1141.
Conrad R., Keranen L.M., Ellington A.D., Newton A.C. Isozyme-specific inhibition of protein kinase C by RNA aptamers // J. Biol. Chem. 1994. V.269. P.32051-32054.
Conrad R.C., Giver L., Tian Y., Ellington A.D. In vitro selection of nucleic acid aptamers that bind proteins // Methods Enzymol. 1996. V.267. P.336-367.
Convery M.A., Stonehouse N.J., Rowsell S., Ellington A.D., Hirao I., Adams C.J., Peabody D.S., Phillips S.E.V., Stockley P.G. Crystal structure of an RNA-aptamer complex at 2.8A resolution. //Nat. Struct. Biol. 1998. V.5. P.133–139.
Coppins R.L., Silverman S.K. A Deoxyribozyme That Forms a Three-Helix-Junction Complex with Its RNA Substrates and Has General RNA Branch-Forming Activity // J. Am. Chem. Soc. 2005. V.127. P.2900-2907.
Cox J.C., Ellington A.D. Automated selection of anti-protein aptamers // Bioorg. Med. Chem. 2001. V.9. P.2525–2531.
Cox J.C., Hayhurst A., Hesselberth J., Bayer T.S., Georgiou G., Ellington A.D. Automated selection of aptamers against protein targets translated in vitro: From gene to aptamer // Nucleic Acids Res. 2002. V.30. P.e108.
Cox J.C., Rajendran M., Riedel T., Davidson E.A., Sooter L.J., Bayer T.S., Schmitz-Brown M., Ellington A.D. Automated acquisition of aptamer sequences // Comb. Chem. High Throughput Screen. 2002. V.5. P.289-299.
Crinelli R., Bianchi M., Gentillini L., Magnani M. Design and characterization of decoy oligonucleotides containing locked nucleic acids // Nucleic Acids Res. 2002. V.30. P.2435–2443.
Cuenoud B., Szostak J.W. A DNA metalloenzyme with DNA ligase activity // Nature. 1995. V.375. P.611-614.
Cummins L.L., Owens S.R., Risen L.M., Lesnik E.A., Freier S.M., McGee D., Guinosso C.J., Cook P.D. Characterization of fully 2'-modified oligonucleotide hetero- and homoduplex hybridization and nuclease sensitivity // Nucleic Acids Res. 1995. V.23. P.2019–2024.
Curtis E.A., Bartel D.P. New catalytic structures from an existing ribozyme // Nat. Struct. Mol. Biol. 2005. V.12. P.994-1000.
Da Rocha Gomes S., Dausse E., Toulme J.J. Determinants of apical loop-internal loop RNA-RNA interactions involving the HCV IRES // Biochem. Biophys. Res. Commun. 2004. V.322. P.820-826.
Daniels D.A., Chen H., Hicke B.J., Swiderek K.M., Gold L. A tenascin-C aptamer identified by tumor cell Selex: systematic evolution of ligands by exponential enrichment // Proc. Natl Acad. Sci. USA. 2003. V.100. P.15416–15421.
Daniels D.A., Sohal A.K., Rees S., Grisshammer R. Generation of RNA aptamers to the G-protein-coupled receptor for neurotensin, NTS-1 // Anal. Biochem. 2002. V.305. P.214-226.
Darfeuille F., Hansen J.B., Orum H., Di Primo C., Toulme J.J. LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1 // Nucleic Acids Res. 2004. V.32. P.3101–3107.
Das S.R., Piccirilli J.A. General acid catalysis by the hepatitis delta virus ribozyme // Nat. Chem. Biol. 2005. V.1. P.45-52.
Davis J.T. G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry // Angew. Chem. Int. Ed. Engl. 2004. V.43. P.668–698.
Davis J.P., Janjic N., Javornik B.E., Zichi D.A. Identifying consensus patterns and secondary structure in SELEX sequence sets // Methods Enzymol. 1996. V.267. P.302-314.
Davis K.A., Lin Y., Abrams B., Jayasena S.D. Staining of cell surface human CD4 with 2'-F-pyrimidine-containing RNA aptamers for flow cytometry // Nucleic Acids Res. 1998. V.26. P.3915–3924.
Davis J.H., Szostak J.W. Isolation of high-affinity GTP aptamers from partially structured RNA libraries // Proc. Natl Acad. Sci. USA. 2002. V.