Днк наномеханические роботы и вычислительные устройства

Вид материалаДокументы
Подобный материал:
1   ...   7   8   9   10   11   12   13   14   15
33. P.5482-5493.
  • Majerfeld I., Yarus M. Isoleucine:RNA sites with associated coding sequences // RNA. 1998. V.4. P.471–478.
  • Majerfeld I., Yarus M. An RNA pocket for an aliphatic hydrophobe // Nat. Struct. Biol. 1994. V.1. P.287-292.
  • Mandal M., Boese B., Barrick J.E., Winkler W.C., Breaker R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria // Cell. 2003. V.113. P.577–586.
  • Mandal M., Breaker R.R. Gene regulation by riboswitches // Nature Rev. Mol. Cell Biol. 2004. V.5. P.451–463.
  • Manimala J.C., Wiskur S.L., Ellington A.D., Anslyn E.V. Tuning the specificity of a synthetic receptor using a selected nucleic Acid receptor // J. Am. Chem. Soc. 2004. V.126. P.16515-16519.
  • Mann D., Reinemann C., Stoltenburg R., Strehlitz B. In vitro selection of DNA aptamers binding ethanolamine // Biochem. Biophys. Res. Commun. 2005. V.338. P.1928-1934.
  • Mannironi C., Di Nardo A., Fruscoloni P., Tocchini-Valentini G.P. In vitro selection of dopamine RNA ligands // Biochemistry. 1997. V.36. P.9726–9734.
  • Mannironi C., Scerch C., Fruscoloni P., Tocchini-Valentini G.P. Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif // RNA. 2000. V.6. P.520–527.
  • Marschall P., Thomson J.B., Eckstein F. // Cell. Mol. Neurobiol. 1994. V.14. P.523–538.
  • Masud M.M., Kuwahara M., Ozaki H., Sawai H. Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX // Bioorg. Med. Chem. 2004. V.12. P.1111-1120.
  • Mathews H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure // J. Mol. Biol. 1999. V.288. P.911–940.
  • Matsugami A., Kobayashi S., Ouhashi K., Uesugi S., Yamamoto R., Taira K., Nishikawa S., Kumar P.K.R., Katahira M. Structural basis of the highly efficient trapping of the HIV Tat protein by an RNA aptamer // Structure. 2003. V.11. P.533–545.
  • Mattick J.S., Mankunin I.V. Small regulatory RNAs in mammals // Hum. Mol. Genet. 2005. V.14. P.R121–R132.
  • Mayer G., Wulffen B., Huber C., Brockmann J., Flicke B., Neumann L., Hafenbradl D., Klebl B.M., Lohse M.J., Krasel C., et al. An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro // RNA. 2008. V.14. P.524-534.
  • Mayer O., Rajkowitsch L., Lorenz C., Konrat R., Schroeder R. RNA chaperone activity and RNA-binding properties of the E. coli protein StpA // Nucleic Acids Res. 2007. P.35. P.1257-1269.
  • McCall M.J., Hendry P., Mir A.A., Conaty J., Brown G., Lockett T.J. Small, efficient hammerhead ribozymes // Mol. Biotechnol. 2000. V.14. P.15–17.
  • McGregor A., Murray J.B., Adams C.J., Stockley P.G., Connolly B.A. Secondary structure mapping of an RNA ligand that has high affinity for the MetJ repressor protein and interference modification analysis of the protein-RNA complex // J. Biol. Chem. 1999. V.274. P.2255-2262.
  • Meister G., Tuschl T. Mechanisms of gene silencing by double-stranded RNA // Nature. 2004. V.431. P.343–349.
  • Meister G., Landthaler M., Dorsett Y., Tuschl T. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing // RNA. 2004. V.10. P.544–550.
  • Meli M., Vergne J., Decout J.L., Maurel M.C. Adenine–aptamer complexes: a bipartite RNA site that binds the adenine nucleic base // J. Biol. Chem. 2002. V.277. P.2104–2111.
  • Mello C.C., Conte D. Jr. Revealing the world of RNA interference // Nature. 2004. V.431. P.338–342.
  • Mendonsa S.D., Bowser M.T. In vitro evolution of functional DNA using capillary electrophoresis // J. Am. Chem. Soc. 2004. V.126. P.20-21.
  • Mescalchin A., Wunsche W., Laufer S.D., Grohmann D., Restle T., Sczakiel G.. Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules // Nucleic Acids Res. 2006. V.34. P.5631-5637.
  • Meyer M.M., Roth A., Chervin S.M., Garcia G.A., Breaker R.R. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria // RNA. 2008. V.14. P.685-695.
  • Mi J., Zhang X., Giangrande P.H., McNamara J.O., 2nd, Nimjee S.M., Sarraf-Yazdi S., Sullenger B.A., Clary B.M. Targeted inhibition of αvβ3 integrin with an RNA aptamer impairs endothelial cell growth and survival // Biochem. Biophys. Res. Commun. 2005. V.338. P.956-963.
  • Mi J., Zhang X., Rabbani Z.N., Liu Y., Su Z., Vujaskovic Z., Kontos C.D., Sullenger B.A., Clary B.M. H1 RNA polymerase III promoter-driven expression of an RNA aptamer leads to high-level inhibition of intracellular protein activity // Nucleic Acids Res. 2006. V.34. P.3577-3584.
  • Michaud M., Jourdan E., Villet A., Ravel A., Grosset C., Peyrin E. A DNA aptamer as a new target-specific chiral selector for HPLC // J.Am.Chem.Soc. 2003. V.125. P.8672–8679.
  • Michel F., Hanna M., Green R., Bartel D.P., Szostak J.W. The guanosine binding site of the Tetrahymena ribozyme // Nature. 1989. V.342. P.391–395.
  • Miller O.J., Bernath K., Agresti J.J., Amitai G., Kelly B.T., Mastrobattista E., Taly V., Magdassi S., Tawfik D.S., Griffiths A.D. Directed evolution by in vitro compartmentalization // Nat. Methods. 2006. V.3. P.561-570.
  • Mironov A.S., Gusarov I., Rafikov R., Lopez L.E., Shatalin K., Kreneva R.A., Perumov D.A., Nudler E. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria // Cell. 2002. V.111. P.747–756.
  • Mishra R.K., Le Tinevez R., Toulme J.J. Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection // Proc. Natl. Acad. Sci. USA. 1996. V.93. P.10679-10684.
  • Misono T.S., Kumar P.K.R. Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance // Anal. Biochem. 2005. V.342. P.312–317.
  • Missailidis S., Thomaidou D., Borbas K.E., Price M.R. Selection of aptamers with high affinity and high specificity against C595, an anti-MUC1 IgG3 monoclonal antibody, for antibody targeting // J. Immunol. Methods. 2005. V.296. P.45-62.
  • Miyagishi M., Taira K. U6 promoter driven siRNAs with four uridine 3' overhangs efficiently suppress targeted gene expression in mammalian cells // Nat. Biotechnol. 2002. V.20. P.497–500.
  • Miyakawa S., Nomura Y., Sakamoto T., Yamaguchi Y., Kato K., Yamazaki S., Nakamura Y. Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G // RNA. 2008. V.14. P.1154-1163.
  • Miyakawa S., Oguro A., Ohtsu T., Imataka H., Sonenberg N., Nakamura Y. RNA aptamers to mammalian initiation factor 4G inhibit cap-dependent translation by blocking the formation of initiation factor complexes // RNA. 2006. V.12. P.1825-1834.
  • Mizuno T., Kawasaki K., Miyamoto H. Construction of a thermotaxis chamber providing spatial or temporal thermal gradients monitored by an infrared video camera system // Anal. Biochem. 1992. V.207. P.208–213.
  • Moazed D., Noller H.F. Interaction of antibiotics with functional sites in 16S ribosomal RNA // Nature. 1987. V.327. P.389-394.
  • Montange R.K., Batey R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element // Nature. 2006. V.441. P.1172–1175.
  • Moore P.B. // Annu. Rev. Biochem. 1999. V.67. P.287.
  • Moreno M., Rincón E., Piñeiro D., Fernández G., Domingo A., Jiménez-Ruíz A., Salinas M., González V.M. Selection of aptamers against KMP-11 using colloidal gold during the SELEX process // Biochem. Biophys. Res. Commun. 2003. V.308. P.214-218.
  • Morris K.N., Jensen K.B., Julin C.M., Weil M., Gold L. High affinity ligands from in vitro selection: complex targets // Proc. Natl. Acad. Sci. USA. 1998. V.95. P.2902-2907.
  • Morris K.N., Tarasow T.M., Julin C.M., Simons S.L., Hilvert D., Gold L. Enrichment for RNA molecules that bind a Diels-Alder transition state analog // Proc. Natl. Acad. Sci. USA. 1994. V.91. P.13028-13032.
  • Mulhbacher J., Lafontaine D.A. Ligand recognition determinants of guanine riboswitches // Nucleic Acids Research. 2007. V.35. P.1–13.
  • Muller M., Weigand J.E., Weichenrieder O., Suess B. Thermodynamic characterization of an engineered tetracycline-binding riboswitch // Nucleic Acids Res. 2006. V.34. P.2607-2617.
  • Murphy M.B., Fuller S.T., Richardson P.M., Doyle S.A. An improved method for the in vitro evolution of aptamers and applications in protein detection and purification // Nucleic Acids Res. 2003. V.31. P.e110.
  • Murray J.B., Collier A.K., Arnold J.R.P. A general purification procedure for chemically synthesized oligoribonucleotides // Anal. Biochem. 1994. V.218. P.177.
  • Myszka D.G., Morton T.A. CLAMP: a biosensor kinetic data analysis program // Trends Biochem. Sci. 1998. V.23. P.149–150.
  • Nagaswamy U., Larios-Sanz M., Hury J., Collins S., Zhang Z., Zhao Q., Fox G.E. NCIR: A database of non-canonical interactions in known RNA structures // Nucleic Acids Res. 2002. V.30. P.395– 397.
  • Nahvi A., Barrick J.E., Breaker R.R. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes // Nucleic Acids Res. 2004. V.32. P.143–150.
  • Nahvi A., Sudarsan N., Ebert M.S., Zou X., Brown K.L., Breaker R.R. Genetic control by a metabolite binding mRNA // Chem. Biol. 2002. V.9. P.1043–1049.
  • Najafi-Shoushtari S.H., Famulok M. Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector // RNA. 2005. V.11. P.1514-1520.
  • Najafi-Shoushtari S.H., Mayer G., Famulok M. Sensing complex regulatory networks by conformationally controlled hairpin ribozymes // Nucleic Acids Res. 2004. V.32. P.3212-3219.
  • Nazarenko I.A., Uhlenbeck O.C. Defining a smaller RNA substrate for elongation factor Tu // Biochemistry. 1995. V.34. P.2545-2552.
  • Ng E.W., Shima D.T., Calias P., Cunningham Jr. E.T., Guyer D.R., Adamis A.P. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease // Nat. Rev. Drug Discov. 2006. V.5. P.123–132.
  • Nguyen D.H., DeFina S.C., Fink W.H., Dieckmann T. Binding to an RNA aptamer changes the charge distribution and conformation of malachite green // J. Am. Chem. Soc. 2002. V.124. P.15081-15084.
  • Nickens D.G., Patterson J.T., Burke D.H. Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli // RNA. 2003. V.9. P.1029–1033.
  • Nielsen P.E. // J. Mol. Recog. 1990. V.3. P.1–25.
  • Nieuwlandt D., Wecker M., Gold L. In vitro selection of RNA ligands to substance P // Biochemistry. 1995. V.34. P.5651-5659.
  • Nieuwlandt D., West M., Cheng X., Kirshenheuter G., Eaton B.E. The First Example of an RNA Urea Synthase: Selection through the Enzyme Active Site of Human Neutrophile Elastase // ChemBioChem. 2003. V.4. P.651-654.
  • Nikonowicz E., Sirr A., Legault P., Jucker F., Baer L., Pardi A. Preparation of 13C and 15N labeled RNAs for heteronuclear multi-dimensional NMR studies // Nucleic Acids Res. 1992. V.20. P.4507– 4513.
  • Nimjee S.M., Rusconi C.P., Sullenger B.A. Aptamers: an emerging class of therapeutics // Annu. Rev. Med. 2005. V.56. P.555-583.
  • Ninichuk V., Clauss S., Kulkarni O., Schmid H., Segerer S., Radomska E., Eulberg D., Buchner K., Selve N., Klussmann S., et al. Late Onset of Ccl2 Blockade with the Spiegelmer mNOX-E36-3'PEG Prevents Glomerulosclerosis and Improves Glomerular Filtration Rate in db/db Mice // Am. J. Pathol. 2008. V.172. P.628-637.
  • Nishikawa F., Funaji K., Fukuda K., Nishikawa S. In vitro selection of RNA aptamers against the HCV NS3 helicase domain // Oligonucleotides. 2004. V.14. P.114–129.
  • Nishikawa F., Kakiuchi N., Funaji K., Fukuda K., Sekiya S., Nishikawa S. Inhibition of HCV NS3 protease by RNA aptamers in cells // Nucleic Acids Res. 2003. V.31. P.1935–1943.
  • Nix J., Sussman D., Wilson C. The 1.3 Å crystal structure of a biotin-binding pseudoknot and the basis for RNA molecular recognition // J. Mol. Biol. 2000. V.296. P.1235-1244.
  • Noeske J., Buck J., Furtig B., Nasiri H.R., Schwalbe H., Wohnert J. Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch // Nucleic Acids Res. 2007. V.35. P.572-583.
  • Nolte A., Klussmann S., Bald R., Erdmann V.A., Furste J.P. Mirror-design of L-oligonucleotide ligands binding to L-arginine // Nat Biotechnol. 1996. V.14. P.1116–1119.
  • Nonin S., Jiang F., Patel D.J. Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex // J. Mol. Biol. 1997. V.268. P.359-374.
  • Nonin-Lecomte S., Lin C.H., Patel D.J. Additional hydrogen bonds and base-pair kinetics in the symmetrical AMP-DNA aptamer complex // Biophys. J. 2001. V.81. P.3422-3431.
  • Nowakowski J., Shim P.J., Prasad G.S., Stout C.D., Joyce G.F. Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme // Nat. Struct. Biol. 1999. V.6. P.151-156.
  • Noyes M.B., Meng X., Wakabayashi A., Sinha S., Brodsky M.H., Wolfe S.A. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system // Nucleic Acids Res. 2008. V.36. P.2547-2560.
  • Nudler E., Mironov A.S. The riboswitch control of bacterial metabolism // Trends Biochem. Sci. 2004. V.29. P.11–17.
  • Nutiu R., Li Y. Structure-switching signaling aptamers // J. Am. Chem. Soc. 2003. V.125. P.4771–4778.
  • Nutiu R., Li Y.F. In vitro selection of structure-switching signaling aptamers // Angew. Chem. Int. Ed. Engl. 2005. V.44. P.1061–1065.
  • Nutiu R., Mei S., Liu Z.J., Li Y.F. Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties // Pure Appl. Chem. 2004. V.76. P.1547–1561.
  • O'Connell D., Koenig A., Jennings S., Hicke B., Han H.L., Fitzwater T., Chang Y.F., Varki N., Parma D., Varki A. Calcium-dependent oligonucleotide antagonists specific for L-selectin // Proc. Natl. Acad. Sci. USA. 1996. V.93. P.5883-5887.
  • Ohuchi S.P., Ohtsu T., Nakamura Y. Selection of RNA aptamers against recombinant transforming growth factor-β type III receptor displayed on cell surface // Biochimie. 2006. V.88. P.897-904.
  • Ordoukhanian P., Joyce G.F. A molecular description of the evolution of resistance // Chem. Biol. 1999. V.6. P.881-889.
  • Osborne S.E., Ellington A.D. Nucleic Acid Selection and the Challenge of Combinatorial Chemistry // Chem. Rev. 1997. V.97. P.349-370.
  • Osborne S.E., Matsumura I., Ellington A.D. Aptamers as therapeutic and diagnostic reagents: problems and prospects // Curr. Opin. Chem. Biol. 1997. V.1. P.5–9.
  • O'Sullivan C.K. Aptasensors--the future of biosensing? // Anal. Bioanal. Chem. 2002. V.372. P.44–48.
  • Ottink O.M., Rampersad S.M., Tessari M., Zaman G.J.R., Heus H.A., Wijmenga S.S. Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined–induced fit mechanism // RNA. 2007. V.13. P.2202-2212.
  • Padmanabhan K., Padmanabhan K.P., Ferrara J.D., Sadler J.E., Tulinsky A. The structure of α-thrombin inhibited by a 15-mer single-stranded DNA aptamer // J. Biol. Chem. 1993. V.268. P.17651-17654.
  • Padmanabhan K., Tulinsky A. An ambiguous structure of a DNA 15-mer thrombin complex // Acta Crystallogr. D. 1996. V.52. P.272-282.
  • Pagratis N.C., Bell C., Chang Y.F., Jennings S., Fitzwater T., Jellinek D., Dang C. Potent 2'-amino-, and 2'-fluoro-2'-deoxyribonucleotide RNA inhibitors of keratinocyte growth factor // Nat. Biotechnol. 1997. V.15. P.68-73.
  • Pakleza C., Cognet J.A.H. Biopolymer Chain Elasticity: a novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances // Nucleic Acids Res. 2003. V.31. P.1075-1085.
  • Pan J., Thirumalai D., Woodson S.A. Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics and kinetics // Proc. Natl Acad. Sci. USA. 1999. V.96. P.6149–6154.
  • 16. T. Pan, Curr. Opin. Chem. Biol. 1, 17 (1997).
  • Pan T., Uhlenbeck O.C. A small metalloribozyme with a two-step mechanism // Nature. 1992. V.358. P.560-563.
  • Pan T., Uhlenbeck O.C. In vitro selection of RNAs that undergo autolytic cleavage with Pb2+ // Biochemistry. 1992. V.31. P.3887-3895.
  • Pan Q., Zhang X.-L., Wu H.-Y., He P.-W., Wang F., Zhang M.-S., Hu J.-M., Xia B., Wu J. Aptamers That Preferentially Bind Type IVB Pili and Inhibit Human Monocytic-Cell Invasion by Salmonella enterica Serovar Typhi // Antimicrob. Agents Chemother. 2005. V.49. P.4052-4060.
  • Pan W., Craven R.C., Qiu Q., Wilson C.B., Wills J.W., Golovine S., Wang J.F. Isolation of virus-neutralizing RNAs from a large pool of random sequences // Proc. Natl. Acad. Sci. USA. 1995. V.92. P.11509-11513.
  • Patel D.J. // Curr. Opin. Struct. Biol. 1999. V.9. P.74.
  • Patel D.J., Suri A.K. Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics // J. Biotechnol. 2000. V.74. P.39–60.
  • Patel D.J., Suri A.K., Jiang F., Jiang L., Fan P., Kumar R.A., Nonin S. Structure, recognition and adaptive binding in RNA aptamer complexes // J. Mol. Biol. 1997. V.272. P.645–664.
  • Paul N., Springsteen G., Joyce G.F. Conversion of a ribozyme to a deoxyribozyme through in vitro evolution // Chem. Biol. 2006. V.13. P.329-338.
  • Pearson N.D., Prescott C.D. RNA as a drug target // Chem. Biol. 1997. V.4. P.409–414.
  • Peeters E., Wartel C., Maes D., Charlier D. Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing // Nucleic Acids Res. 2007. V.35. P.623-633
  • Pei D.H., Ulrich H.D., Schultz P.G. A combinatorial approach toward DNA recognition // Science. 1991. V.253. P.1408-1411.
  • Penchovsky R., Breaker R.R. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes // Nat. Biotechnol. 2005. V.23. P.1424-1433.
  • Peng C.G., Damha M.J. G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA) // Nucleic Acids Res. 2007. V.35. P.4977-4988.
  • Peracchi A., Beigelman L., Usman N., Herschlag D. Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases // Proc. Natl Acad. Sci. USA. 1996. V.93. P.11522–11527.
  • Perrin D.M., Garestier T., Helene C. Bridging the Gap between Proteins and Nucleic Acids: A Metal-Independent RNAseA Mimic with Two Protein-Like Functionalities // J. Am. Chem. Soc. 2001. V.123. P.1556-1563.
  • Pestourie C., Tavitian B., Duconge F. Aptamers against extracellular targets for in vivo applications // Biochimie. 2005. V.87. P.921-930.
  • Petersen M., Wengel J. LNA: a versatile tool for therapeutics and genomics // Trends Biotechnol. 2003. V.21. P.74–81.
  • Pieken W.A., Olsen D.B., Benseler F., Aurup H., Eckstein F. Kinetic characterization of ribonuclease-resistant 2'-modified hammerhead ribozymes // Science. 1991. V.253. P.314–317.
  • Piganeau N., Jenne A., Thuillier V., Famulok M. An Allosteric Ribozyme Regulated by Doxycycline // Angew. Chem. Int. Ed. 2000. V.39. P.4369-4373.
  • Piganeau N., Schroeder R. Aptamer structures. A preview into regulatory pathways? // Chem. Biol. 2003. V.10. P.103–104.
  • Piganeau N., Thuillier V., Famulok M. In vitro selection of allosteric ribozymes: theory and experimental validation // J. Mol. Biol. 2001. V.312. P.1177-1190.
  • Pileur F., Andreola M.L., Dausse E., Michel J., Moreau S., Yamada H., Gaidamakov S.A., Crouch R.J., Toulme J.J., Cazenave C. Selective inhibitory DNA aptamers of the human RNase H1 // Nucleic Acids Res. 2003. V.31. P.5776-5788.
  • Plummer K.A., Carothers J.M., Yoshimura M., Szostak J.W., Verdine G.L. In vitro selection of RNA aptamers against a composite small molecule-protein surface // Nucleic Acids Res. 2005. V.