Ponthier J.L., Schluepen C., Chen W., Lersch R.A., Gee S.L., Hou V.C., Lo A.J., Short S.A., Chasis J.A., Winkelmann J.C., et al. Fox-2 Splicing Factor Binds to a Conserved Intron Motif to Promote Inclusion of Protein 4.1R Alternative Exon 16 // J. Biol. Chem. 2006. V.281. P.12468-12474.
Porta H., Lizardi P.M. An allosteric hammerhead ribozyme // Biotechnology. 1995. V.13. P.161–164.
Proske D., Blank M., Buhmann R., Resch A. Aptamers: Basic research, drug development, and clinical applications // Appl. Microbiol. Biotechnol. 2005. V.69. P.367–374.
Puglisi J.D., Chen L., Frankel A.D., Williamson J.R. // Proc. Natl. Acad. Sci. USA. 1993. V.90. P.3680.
Puglisi J.D., Williamson J.R. // R. F. Gesteland, T. R. Cech, J. F. Atkins, Eds. The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2nd ed., 1999. P.403-425.
Purschke W.G., Eulberg D., Buchner K., Vonhoff S., Klussmann S. An L-RNA-based aquaretic agent that inhibits vasopressin in vivo // PNAS. 2006. V.103. P.5173-5178.
Purschke W.G., Radtke F., Kleinjung F., Klussmann S. A DNA Spiegelmer to staphylococcal enterotoxin B // Nucleic Acids Res. 2003. V.31. P.3027-3032.
Purtha W.E., Coppins R.L., Smalley M.K., Silverman S.K. General Deoxyribozyme-Catalyzed Synthesis of Native 3’–5’ RNA Linkages // J. Am. Chem. Soc. 2005. V.127. P.13124-13125.
Rathbone D.A., Bruce N.C. Microbial transformation of alkaloids // Curr. Opin. Microbiol. 2002. V.5. P.274–281.
Ravelet C., Grosset C., Peyrin E. Liquid chromatography, electrochromatography and capillary electrophoresis applications of DNA and RNA aptamers // J. Chromatogr. A. 2006. V.1117. P.1-10.
Reader J.S., Joyce G.F. A ribozyme composed of only two different nucleotides // Nature. 2002. V.420. P.841-844.
Reiter N.J., Maher III L.J., Butcher S.E. DNA mimicry by a high-affinity anti-NF-{kappa}B RNA aptamer // Nucleic Acids Res. 2008. V.36. P.1227-1236.
Rentmeister A., Bill A., Wahle T., Walter J., Famulok M. RNA aptamers selectively modulate protein recruitment to the cytoplasmic domain of {beta}-secretase BACE1 in vitro // RNA. 2006. V.12. P.1650-1660.
Reynolds A., Leake D., Boese Q., Scaringe S., Marshall W.S., Khvorova A. Rational siRNA design for RNA interference // Nat. Biotechnol. 2004. V.22. P.326–330.
Rhie A., Kirby L., Sayer N., Wellesley R., Disterer P., Sylvester I., Gill A., Hope J., James W., Tahiri-Alaoui A. Characterization of 2'-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion // J. Biol. Chem. 2003. V.278. P.39697-39705.
Richards B., Karpilow J., Dunn C., Peterson I., Maxfield A., Zharkikh L., Abedi M., Hurlburt A., Hardman J., Hsu F., et al. Genetic Selection for Modulators of a Retinoic-Acid-Responsive Reporter in Human Cells // Genetics. 2003. V.163. P.1047-1060. |
Rimmele M. Nucleic acid aptamers as tools and drugs: recent developments // Chembiochem. 2003. V.4. P.963–971.
Rink S.M., Shen J.C., Loeb L.A. Creation of RNA molecules that recognize the oxidative lesion 7,8-dihydro-8-hydroxy-2'-deoxyguanosine (8-oxodG) in DNA // Proc. Natl. Acad. Sci. USA. 1998. V.95. P.11619-11624.
Robertson M.P., Ellington A.D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons // Nat. Biotechnol. 1999. V.17. P.62–66.
Robertson M.P., Ellington A.D. Design and optimization of effector-activated ribozyme ligases // Nucleic Acids Res. 2000. V.28. P.1751–1759.
Robertson M.P., Ellington A.D. In vitro selection of nucleoprotein enzymes // Nat. Biotechnol. 2001. V.19. P.650–655.
Rogers J., Chang A.H., von Ahsen U., Schroeder R., Davies J. // J. Mol. Biol. 1996. V.259. P.916.
Rogers J., Joyce G.F. A ribozyme that lacks cytidine // Nature. 1999. V.402. P.323-325.
Rogers J., Joyce G.F. The effect of cytidine on the structure and function of an RNA ligase ribozyme // RNA. 2001. V.7. P.395-404.
Romero-Lopez C., Barroso-delJesus A., Puerta-Fernandez E., Berzal-Herranz A. Interfering with hepatitis C virus IRES activity using RNA molecules identified by a novel in vitro selection method // Biol. Chem. 2005. V.386. P.183-190.
Rosenstein S.P., Been M.D. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions // Biochemistry. 1990. V.29. P.8011–8016.
Roth A., Breaker R.R. An amino acid as a cofactor for a catalytic polynucleotide // Proc. Natl. Acad. Sci. USA. 1998. V.95. P.6027-6031.
Rowsell S., Stonehouse N.J., Convery M.A., Adams C.J., Ellington A.D., Hirao I., Peabody D.S., Stockley P.G., Phillips S.E.V. Crystal structures of a series of RNA aptamers complexed to the same protein target // Nature Struct. Biol. 1998. V.5. P.970-975.
Roychowdhury-Saha M., Lato S.M., Shank E.D., Burke D.H. Flavin recognition by an RNA aptamer targeted toward FAD // Biochemistry. 2002. V.41. P.2492-2499.
Ruckman J., Green L.S., Beeson J., Waugh S., Gillette W.L., Henninger D.D., Claesson-Welsh L., Janjic N. 2'-Fluoroprymidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165) // J. Biol. Chem. 1998. V.273. P.20556–20567.
Rusconi C.P., Roberts J.D., Pitoc G.A., Nimjee S.M., White R.R., Quick G. Jr., Scardino E., Fay W.P., Sullenger B.A. Antidote-mediated control of an anticoagulant aptamer in vivo // Nat. Biotechnol. 2004. V.22. P.1423-1428.
Rusconi C.P., Scardino E., Layzer J., Pitoc G.A., Ortel T.L., Monroe D., Sullenger B.A. RNA aptamers as reversible antagonists of coagulation factor IXa // Nature. 2002. V.419. P.90–94.
Rusconi C.P., Yeh A., Lyerly H.K., Lawson J.H., Sullenger B.A. Blocking the initiation of coagulation by RNA aptamers to factor VIIa // Thromb. Haemost. 2000. V.84. P.841-848.
Russell R., Zhuang X., Babcock H.P., Millett I.S., Doniach S., Chu S., Herschlag D. Exploring the folding landscape of a structured RNA // Proc. Natl Acad. Sci. USA. 2002. V.99. P.155–160.
Sabeti P.C., Unrau P.J., Bartel D.P. Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool // Chem. Biol. 1997. V.4. P.767–774.
Saha S., Ansari A.Z., Jarrell K.A., Ptashne M. RNA sequences that work as transcriptional activating regions // Nucleic Acids Res. 2003. V.31. P.1565-1570.
Saito H., Kourouklis D., Suga H. An in vitro evolved precursor tRNA with aminoacylation activity // EMBO J. 2001. V.20. P.1797-1806.
Saito H., Suga H. Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme // Nucleic Acids Res. 2002. V.30. P.5151-5159.
Sakamoto T., Oguro A., Kawai G., Ohtsu T., Nakamura Y. NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A // Nucleic Acids Res. 2005. V.33. P.745-754.
Salehi-Ashtiani K., Szostak J.W. In vitro evolution suggests multiple origins for the hammerhead ribozyme // Nature. 2001. V.414. P.82–84.
Sandy P., Ventura A., Jacks T. Mammalian RNAi: A practical guide // Biotechniques. 2005. V.39. P.215–224.
Santoro S.W., Joyce G.F. A general purpose RNA-cleaving DNA enzyme // Proc. Natl. Acad. Sci. USA. 1997. V.94. P.4262–4266.
Santoro S.W., Joyce G.F., Sakthivel K., Gramatikova S., Barbas C.F. III. RNA cleavage by a DNA enzyme with extended chemical functionality // J. Am. Chem. Soc. 2000. V.122. P.2433-2439.
Santulli-Marotto S., Nair S.K., Rusconi C., Sullenger B., Gilboa E. Multivalent RNA aptamers that inhibit CTLA-4 and enhance tumor immunity // Cancer Res. 2003. V.63. P.7483-7489.
Saran D., Frank J., Burke D.H. The tyranny of adenosine recognition among RNA aptamers to coenzyme A // BMC Evol. Biol. 2003. V.3. P.26.
Sassanfar M., Szostak J.W. An RNA motif that binds ATP // Nature. 1993. V.364. P.550–553.
Sayer N.M., Cubin M., Rhie A., Bullock M., Tahiri-Alaoui A., James W. Structural determinants of conformationally selective, prion-binding aptamers // J. Biol. Chem. 2004. V.279. P.13102-13109.
Sazani P.L., Larralde R., Szostak J.W. A small aptamer with strong and specific recognition of the triphosphate of ATP // J. Am. Chem. Soc. 2004. V.126. P.8370-8371.
Scarabino D., Crisari A., Lorenzini S., Williams K., Tocchini-Valentini G.P. tRNA prefers to kiss // EMBO J. 1999. V.18. P.4571-4578.
Scaringe S.A., Wincott F.E., Caruthers M.H. Novel RNA synthesis method using 5'-O-silyl-2'-O-orthoester protecting groups // J. Am. Chem. Soc. 1998. V.120. P.11820–11821.
Schlatterer J.C., Stuhlmann F., Jäschke A. Stereoselective synthesis using immobilized Diels-Alderase ribozymes // Chembiochem. 2003. V.4. P.1089–1092.
Schlosser K., Lam J.C.F., Li Y. Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection // Nucleic Acids Res. 2006. V.34. P.2445-2454.
Schmidt K.S., Borkowski S., Kurreck J., Stephens A.W., Bald R., Hecht M., Friebe M., Dinkelborg L., Erdmann V.A. Application of locked nucleic acids to improve aptamer in vivo stability and targeting function // Nucleic Acids Research. 2004. V.32. P.5757-5765.
Schneider D., Tuerk C., Gold L. Selection of high affinity RNA ligands to the bacteriophage R17 coat protein // J. Mol. Biol. 1992. V.228. P.862-869.
Schubert S., Gul D.C., Grunert H.P., Zeichhardt H., Erdmann V.A., Kurreck J. RNA leaving ‘10–23’ DNAzymes with enhanced stability and activity // Nucleic Acids Res. 2003. V.31. P.5982–5992.
Schultes E.A., Bartel D.P. One sequence, two ribozymes: implications for the emergence of new ribozyme folds // Science. 2000. V.289. P.448-452.
Schultes E.A., Spasic A., Mohanty U., Bartel D.P. Compact and ordered collapse of randomly generated RNA sequences // Nat. Struct. Mol. Biol. 2005. V.12. P.1130–1136.
Schultze P., Macaya R.F., Feigon J. Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) // J. Mol. Biol. 1994. V.235. P.1532-1547.
Schwalbe H, Buck J, Furtig B, Noeske J, Wohnert J. Structures of RNA switches: insight into molecular recognition and tertiary structure // Angew. Chem. Int. Ed. Engl. 2007. V.46. P.1212–1219.
Sclavi B., Sullivan M., Chance M.R., Brenowitz M., Woodson S.A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting // Science. 1998. V.279. P.1940–1943.
Scott W.G., Finch J.T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage // Cell. 1995. V.81. P.991–1002.
Seelig B., Jäschke A. A small catalytic RNA motif with Diels-Alderase activity // Chem. Biol. 1999. V.6. P.167-176.
Seelig B., Keiper S., Stuhlmann F., Jäschke A. Enantioselective Ribozyme Catalysis of a Bimolecular Cycloaddition Reaction // Angew. Chem. Int. Ed. 2000. V.39. P.4576-4579.
Seetharaman S., Zivarts M., Sudarsan N., Breaker R.R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures // Nat. Biotechnol. 2001. V.19. P.336–341.
Sekiya S., Noda K., Nishikawa F., Yokoyama T., Kumar P.K.R., Nishikawa S. Characterization and Application of a Novel RNA Aptamer against the Mouse Prion Protein // Journal of Biochemistry. 2006. V.139. P.383-390.
Sekkai D., Dausse E., Di Primo C., Darfeuille F., Boiziau C., Toulme J.J. In vitro selection of DNA aptamers against the HIV-1 TAR RNA hairpin // Antisense Nucleic Acid Drug Dev. 2002. V.12. P.265-274.
Sengle G., Eisenführ A., Arora P.S., Nowick J.S., Famulok M. Novel RNA catalysts for the Michael reaction // Chem. Biol. 2001. V.8. P.459-473.
SenGupta D.J., Zhang B., Kraemer B., Pochart P., Fields S., Wickens M. A three-hybrid system to detect RNA–protein interactions in vivo // Proc. Natl. Acad. Sci. 1996. V.93. P.8496–8501.
SenGupta D.J., Wickens M., Fields S. Identification of RNAs that bind to a specific protein using the yeast three-hybrid system // RNA. 1999. V.5. P.596–601.
Septak M. Kinetic studies on depurination and detritylation of CPG-bound intermediates during oligonucleotide synthesis // Nucleic Acids Res. 1996. V.24. P.3053–3058.
Serganov A., Keiper S., Malinina L., Tereshko V., Skripkin E., Höbartner C., Polonskaia A., Phan A.T., Wombacher R., Micura R., Dauter Z., Jäschke A., Patel D.J. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation // Nat. Struct. Mol. Biol. 2005. V.12. P.218-224.
Serganov A., Polonskaia A., Phan A.T., Breaker R.R., Patel D.J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch // Nature. 2006. V.441. P.1167–1171.
Serganov A., Yuan Y.R., Pikovskaya O., Polonskaia A., Malinina L., Phan A.T., Hobartner C., Micura R., Breaker R.R., et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs // Chem. Biol. 2004. V.11. P.1729–1741.
Sevilimedu A., Shi H., Lis J.T. TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages // Nucleic Acids Res. 2008. V.36. P.3118-3127.
Shangguan D., Cao Z.C., Li Y., Tan W. Aptamers Evolved from Cultured Cancer Cells Reveal Molecular Differences of Cancer Cells in Patient Samples // Clin. Chem. 2007. V.53. P.1153-1155.
Shangguan D., Li Y., Tang Z., Cao Z.C., Chen H.W., Mallikaratchy P., Sefah K., Yang C.J., Tan W. Aptamers evolved from live cells as effective molecular probes for cancer study // Proc. Natl. Acad. Sci. USA. 2006. V.103. P.11838-11843.
Sheppard T.L., Ordoukhanian P., Joyce G.F. A DNA enzyme with N-glycosylase activity // Proc. Natl. Acad. Sci. USA. 2000. V.97. P.7802-7807.
Shi H., Fan X., Sevilimedu A., Lis J.T. RNA aptamers directed to discrete functional sites on a single protein structural domain // Proc. Natl. Acad. Sci. USA. 2007. V.104. P.3742-3746.
Shikamoto Y., Morita T., Fujimoto A., Mizuno H. Crystal structure of Mg2+ and Ca2+-bound Gla domain of factor IX complexed with binding protein // J. Biol. Chem. 2003. V.278. P.24090–24094.
Shimada T., Fujita N., Maeda M., Ishihama A. Systematic search for the Cra-binding promoters using genomic SELEX system // Genes Cells. 2005. V.10. P.907-918.
Shu D., Guo P. A viral RNA that binds ATP and contains a motif similar to an ATP-binding aptamer from SELEX // J. Biol. Chem. 2003. V.278. P.7119–7125.
Sidorov A.V., Grasby J.A., Williams D.M. Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities // Nucleic Acids Res. 2004. V.32. P.1591-1601.
Sievers A., Beringer M., Rodnina M.V., Wolfenden R. The ribosome as an entropy trap // Proc. Natl. Acad. Sci. USA. 2004. V.101. P.7897-7901.
Silverman S.K. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA // Nucleic Acids Res. 2005. V.33. P.6151-6163.
Silverman S.K. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA // RNA. 2003. V.9. P.377-383.
Silverman S.K. Artificial functional nucleic acids: Aptamers, ribozymes, and deoxyribozymes identified by in vitro selection // Y. Lu and Y. Li, Eds. Functional Nucleic Acids for Sensing and Other Analytical Applications. Springer: New York, 2007. P.1-38.
Siolas D., Lerner C., Burchard J., Ge W., Linsley P.S., Paddison P.J., Hannon G.J., Cleary M.A. Synthetic shRNAs as potent RNAi triggers // Nat. Biotechnol. 2005. V.23. P.227–231.
Skehel J.J., Wiley D.C. Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin // Annu. Rev. Biochem. 2000. V.69. P.531–569.
Smith D., Kirschenheuter G.P., Charlton J., Guidot D.M., Repine J.E. In vitro selection of RNA-based irreversible inhibitors of human neutrophil elastase // Chem. Biol. 1995. V.2. P.741-750.
Soller M., White K. ELAV // Curr. Biol. 2004. V.14. P.R53.
Sooter L.J., Riedel T., Davidson E.A., Levy M., Cox J.C., Ellington A.D. Toward automated nucleic acid enzyme selection // Biol. Chem. 2001. V.382. P.1327-1334.
Soukup G.A., DeRose E.C., Koizumi M., Breaker R.R. Generating new ligandbinding RNAs by affinity maturation and disintegration of allosteric ribozymes // RNA. 2001. V.7. P.524-536.
Soukup G.A., Ellington A.D., Maher L.J. 3rd. Selection of RNAs that bind to duplex DNA at neutral pH // J. Mol. Biol. 1996. V.259. P.216-228.
Soukup G.A., Emilsson G.A.M., Breaker R.R. Altering molecular recognition of RNA aptamers by allosteric selection // J. Mol. Biol. 2000. V.298. P.623–632.
Sreedhara A., Li Y., Breaker R.R. Ligating DNA with DNA // J. Am. Chem. Soc. 2004. V.126. P.3454-3460.
Srinivasan J., Cload S.T., Hamaguchi N., Kurz J., Keene S., Kurz M., Boomer R.M., Blanchard J., Epstein D., Wilson C., Diener J.L. ADP-specific sensors enable universal assay of protein kinase activity // Chem. Biol. 2004. V.11. P.499-508.
Srisawat C., Engelke D.R. Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins // RNA. 2001. V.7. P.632-641.
Stanlis K.K.H., McIntosh R. Single-strand DNA Aptamers as Probes for Protein Localization in Cells // Journal of Histochemistry and Cytochemistry. 2003. V. 51. P.797-808.
Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F.H., Goehler H., Stroedicke M., Zenkner M., Schoenherr A., Koeppen S., et al. A human protein–protein interaction network: A resource for annotating the proteome // Cell. 2005. V.122. P.957–968.
Stojanovic M.N., de Prada P., Landry D.W. Aptamer-based folding fluorescent sensor for cocaine // J. Am. Chem. Soc. 2001. V.123. P.4928–4931.
Stojanovic M.N., Landry D.W. Aptamer-based colorimetric probe for cocaine // J. Am. Chem. Soc. 2002. V.124. P.9678-9679.
Stoltenburg R., Reinemann C., Strehlitz B. FluMag-SELEX as an advantageous method for DNA aptamer selection // Anal. Bioanal. Chem. 2005. V.383. P.83-91.
Stormo G.D., Ji Y. Do mRNAs act as direct sensors of small molecules to control their expression? // PNAS. 2001. V.98. P.9465-9467.
5. Storz G. An expanding universe of noncoding RNAs // Science. 2002. V.296. P.1260–1263.
Striggles J.C., Martin M.B., Schmidt F.J. Frequency of RNA-RNA interaction in a model of the RNA World // RNA. 2006. V.