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Volumn 31, Issue 1, 2007, Pages 11-35

A mathematical analysis of SELEX

Author keywords

Aptamer; Mathematical analysis; SELEX

Indexed keywords

BIOCHEMISTRY; ENZYME KINETICS; NUCLEIC ACIDS; NUMERICAL ANALYSIS;

EID: 33846889052     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2006.10.002     Document Type: Article
Times cited : (58)

References (44)
  • 1
    • 0023147228 scopus 로고    scopus 로고
    • Selection of DNA binding sites by regulatory proteins: statistical mechanical theory and application to operators and promoters
    • Berg O.G., and von Hippel P.H. Selection of DNA binding sites by regulatory proteins: statistical mechanical theory and application to operators and promoters. J. Mol. Biol. 193 (1996) 723-750
    • (1996) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 2
    • 0026575221 scopus 로고
    • Selection of single-stranded DNA molecules that bind and inhibit human thrombin
    • Bock L.C., Griffen L.C., Latham J.A., Vermass E.H., and Toole J.J. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355 (1992) 564-566
    • (1992) Nature , vol.355 , pp. 564-566
    • Bock, L.C.1    Griffen, L.C.2    Latham, J.A.3    Vermass, E.H.4    Toole, J.J.5
  • 3
    • 31144443492 scopus 로고    scopus 로고
    • Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex
    • Boyce M., Scott F., Guogas L.M., and Gehrke L. Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex. J. Mol. Recognit. 19 (2006) 68-78
    • (2006) J. Mol. Recognit. , vol.19 , pp. 68-78
    • Boyce, M.1    Scott, F.2    Guogas, L.M.3    Gehrke, L.4
  • 6
    • 0041923790 scopus 로고    scopus 로고
    • Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3
    • Chen C.H., Chernis G.A., Hoang V.Q., and 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. U.S.A. 100 (2003) 9226-9231
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 9226-9231
    • Chen, C.H.1    Chernis, G.A.2    Hoang, V.Q.3    Landgraf, R.4
  • 7
    • 0028609357 scopus 로고
    • Isozyme-specific inhibition of protein kinase C by RNA aptamers
    • Conrad R., Keranen L.M., Ellington A.D., and Newton A.C. Isozyme-specific inhibition of protein kinase C by RNA aptamers. J. Biol. Chem. 269 (1994) 32051-32054
    • (1994) J. Biol. Chem. , vol.269 , pp. 32051-32054
    • Conrad, R.1    Keranen, L.M.2    Ellington, A.D.3    Newton, A.C.4
  • 8
    • 11144285441 scopus 로고    scopus 로고
    • Selection of stable RNA molecules that can regulate the channel-opening equilibrium of the membrane-bound gamma-aminobutyric acid receptor
    • Cui Y., Rajasethupathy P., and Hess G.P. Selection of stable RNA molecules that can regulate the channel-opening equilibrium of the membrane-bound gamma-aminobutyric acid receptor. Biochemistry 43 (2004) 16442-16449
    • (2004) Biochemistry , vol.43 , pp. 16442-16449
    • Cui, Y.1    Rajasethupathy, P.2    Hess, G.P.3
  • 9
    • 31544465220 scopus 로고    scopus 로고
    • Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity
    • DeStefano J.J., and Cristofaro J.V. Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity. Nucleic Acids Res. 34 (2006) 130-139
    • (2006) Nucleic Acids Res. , vol.34 , pp. 130-139
    • DeStefano, J.J.1    Cristofaro, J.V.2
  • 10
    • 33645542019 scopus 로고    scopus 로고
    • Quantitative modeling and data analysis of SELEX experiments
    • Djordjevic M., and Sengupta A.M. Quantitative modeling and data analysis of SELEX experiments. Phys. Biol. 3 13 (2006) 13-28
    • (2006) Phys. Biol. , vol.3 , Issue.13 , pp. 13-28
    • Djordjevic, M.1    Sengupta, A.M.2
  • 11
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific nucleic acids
    • Ellington A.D., and Szostak J.W. In vitro selection of RNA molecules that bind specific nucleic acids. Nature 346 (1990) 818-822
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 12
    • 26644468823 scopus 로고    scopus 로고
    • Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonis
    • Eulberg D., Buchner K., Maasch C., and Klussmann S. Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonis. Nucleic Acids Res. 22 (2005) e45
    • (2005) Nucleic Acids Res. , vol.22
    • Eulberg, D.1    Buchner, K.2    Maasch, C.3    Klussmann, S.4
  • 13
    • 2342585280 scopus 로고    scopus 로고
    • Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes
    • Fan X., Shi H., Adelman K., and Lis J.T. Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 6934-6939
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 6934-6939
    • Fan, X.1    Shi, H.2    Adelman, K.3    Lis, J.T.4
  • 14
    • 33646901906 scopus 로고    scopus 로고
    • RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa
    • Gening L.V., Klincheva S.A., Reshetnjak A., Grollman A.P., and Miller H. RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa. Nucleic Acids Res. 34 (2006) 2579-2586
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2579-2586
    • Gening, L.V.1    Klincheva, S.A.2    Reshetnjak, A.3    Grollman, A.P.4    Miller, H.5
  • 15
    • 0032214640 scopus 로고    scopus 로고
    • Aptamers as nucleic acids in affinity probe capillary electrophoresis
    • German I., Buchanan D.D., and Kennedy R.T. Aptamers as nucleic acids in affinity probe capillary electrophoresis. Anal. Chem. 70 (1998) 4540-4545
    • (1998) Anal. Chem. , vol.70 , pp. 4540-4545
    • German, I.1    Buchanan, D.D.2    Kennedy, R.T.3
  • 16
    • 33644597254 scopus 로고    scopus 로고
    • An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion
    • Gopinath S.C., Misono T.S., Kawasaki K., Mizuno T., Imai M., Odagiri T., and Kumar P.K. An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J. Gen. Virol. 87 (2006) 479-487
    • (2006) J. Gen. Virol. , vol.87 , pp. 479-487
    • Gopinath, S.C.1    Misono, T.S.2    Kawasaki, K.3    Mizuno, T.4    Imai, M.5    Odagiri, T.6    Kumar, P.K.7
  • 17
    • 0026325728 scopus 로고
    • SELEXION, systematic evolution of nucleic acids by exponential enrichment with integrated optimization by non-linear analysis
    • Irvine D., Tuerk C., and Gold L. SELEXION, systematic evolution of nucleic acids by exponential enrichment with integrated optimization by non-linear analysis. J. Mol. Biol. 222 (1991) 739-761
    • (1991) J. Mol. Biol. , vol.222 , pp. 739-761
    • Irvine, D.1    Tuerk, C.2    Gold, L.3
  • 18
    • 0642334595 scopus 로고    scopus 로고
    • Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX
    • Jarosch K., Buchner S., and Klussmann. Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX. Nucl. Acids Res. 31 (2004) e130
    • (2004) Nucl. Acids Res. , vol.31
    • Jarosch, K.1    Buchner, S.2    Klussmann3
  • 19
    • 0037427530 scopus 로고    scopus 로고
    • Specific modulation of the anti-DNA autoantibody-nucleic acids interaction by the high affinity RNA aptamer
    • Kim Y.M., Choi K.H., Jang Y.J., Yu J., and Jeong S. Specific modulation of the anti-DNA autoantibody-nucleic acids interaction by the high affinity RNA aptamer. Biochem. Biophys. Res. Commun. 300 (2003) 516-523
    • (2003) Biochem. Biophys. Res. Commun. , vol.300 , pp. 516-523
    • Kim, Y.M.1    Choi, K.H.2    Jang, Y.J.3    Yu, J.4    Jeong, S.5
  • 20
    • 11244328059 scopus 로고    scopus 로고
    • Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB
    • Kulbachinskiy A., Feklistov A., Krasheninnikov I., Goldfarb A., and Nikiforov V. Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. Eur. J. Biochem. 271 (2004) 4921-4931
    • (2004) Eur. J. Biochem. , vol.271 , pp. 4921-4931
    • Kulbachinskiy, A.1    Feklistov, A.2    Krasheninnikov, I.3    Goldfarb, A.4    Nikiforov, V.5
  • 21
    • 11144223772 scopus 로고    scopus 로고
    • An RNA aptamer that binds to the beta-catenin interaction domain of TCF-1 protein
    • Lee S.K., Park M.W., Yang E.G., Yu J., and Jeong S. An RNA aptamer that binds to the beta-catenin interaction domain of TCF-1 protein. Biochem. Biophys. Res. Commun. 327 (2005) 294-299
    • (2005) Biochem. Biophys. Res. Commun. , vol.327 , pp. 294-299
    • Lee, S.K.1    Park, M.W.2    Yang, E.G.3    Yu, J.4    Jeong, S.5
  • 22
    • 4344676879 scopus 로고    scopus 로고
    • In vitro selection and characterization of TCF-1 binding RNA aptamers
    • Lee S.Y., and Jeong S. In vitro selection and characterization of TCF-1 binding RNA aptamers. Mol. Cells 17 (2004) 174-179
    • (2004) Mol. Cells , vol.17 , pp. 174-179
    • Lee, S.Y.1    Jeong, S.2
  • 23
    • 0002635393 scopus 로고    scopus 로고
    • Models and search strategies for applied molecular evolution
    • Levitan B. Models and search strategies for applied molecular evolution. Annu. Rep. Comb. Chem. Mol. Div. 1 (1997) 1-72
    • (1997) Annu. Rep. Comb. Chem. Mol. Div. , vol.1 , pp. 1-72
    • Levitan, B.1
  • 26
    • 11144319427 scopus 로고    scopus 로고
    • High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation
    • Mochizuki K., Oguro A., Ohtsu T., Sonenberg N., and Nakamura Y. High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation. RNA 11 (2005) 77-89
    • (2005) RNA , vol.11 , pp. 77-89
    • Mochizuki, K.1    Oguro, A.2    Ohtsu, T.3    Sonenberg, N.4    Nakamura, Y.5
  • 28
    • 11344278689 scopus 로고    scopus 로고
    • RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family
    • Mori T., Oguro A., Ohtsu T., and Nakamura Y. RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family. Nucl. Acids Res. 32 (2003) 6120-6128
    • (2003) Nucl. Acids Res. , vol.32 , pp. 6120-6128
    • Mori, T.1    Oguro, A.2    Ohtsu, T.3    Nakamura, Y.4
  • 29
    • 3042636195 scopus 로고    scopus 로고
    • Aptamer selection for the inhibition of cell adhesion with fibronectin as target
    • Ogawa A., Tomita N., Kikuchi N., Sando S., and Aoyama Y. Aptamer selection for the inhibition of cell adhesion with fibronectin as target. Bioorg. Med. Chem. Lett. 4 (2004) 4001-4004
    • (2004) Bioorg. Med. Chem. Lett. , vol.4 , pp. 4001-4004
    • Ogawa, A.1    Tomita, N.2    Kikuchi, N.3    Sando, S.4    Aoyama, Y.5
  • 31
    • 58949087398 scopus 로고    scopus 로고
    • Generation and use of combinatorial libraries
    • Ausubel G., Brent F.M., Kingston R., Moore, R.E., Seidman D.D., Smith, J.G., and Struhl K. (Eds), Greene Publishing Associates, John Wiley Liss & Sons, Inc., New York, NY, USA pp. 24.21.21-24.25.34
    • Pollard J., Bell S.D., and Ellington A.D. Generation and use of combinatorial libraries. In: Ausubel G., Brent F.M., Kingston R., Moore, R.E., Seidman D.D., Smith, J.G., and Struhl K. (Eds). Current Protocols in Molecular Biology, vol. 4 (2000), Greene Publishing Associates, John Wiley Liss & Sons, Inc., New York, NY, USA pp. 24.21.21-24.25.34
    • (2000) Current Protocols in Molecular Biology, vol. 4
    • Pollard, J.1    Bell, S.D.2    Ellington, A.D.3
  • 34
    • 0026077562 scopus 로고
    • Specificity of the mnt protein determined by binding to randomized operators
    • Stormo G.D., and Yoshioka M. Specificity of the mnt protein determined by binding to randomized operators. Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 5699-5703
    • (1991) Proc. Natl. Acad. Sci. U.S.A. , vol.88 , pp. 5699-5703
    • Stormo, G.D.1    Yoshioka, M.2
  • 35
    • 0029868473 scopus 로고    scopus 로고
    • A mathematical analysis of in vitro molecular selection-amplification
    • Sun F., Galas D., and Waterman M.S. A mathematical analysis of in vitro molecular selection-amplification. J. Mol. Biol. 258 4 (1996) 650-660
    • (1996) J. Mol. Biol. , vol.258 , Issue.4 , pp. 650-660
    • Sun, F.1    Galas, D.2    Waterman, M.S.3
  • 38
    • 0025194307 scopus 로고
    • Systematic evolution of nucleic acids by exponential enrichment: RNA nucleic acids to bacteriophage T4 DNA polymerase
    • Tuerk C., and Gold L. Systematic evolution of nucleic acids by exponential enrichment: RNA nucleic acids to bacteriophage T4 DNA polymerase. Science 249 (1990) 505-510
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 39
    • 0037444390 scopus 로고    scopus 로고
    • Identification of RNA ligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates
    • Vo N.V., Oh J.W., and Lai M.M. Identification of RNA ligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates. Virology 307 (2003) 301-316
    • (2003) Virology , vol.307 , pp. 301-316
    • Vo, N.V.1    Oh, J.W.2    Lai, M.M.3
  • 43
    • 33646905186 scopus 로고    scopus 로고
    • RNA aptamers targeting the cell death inhibitor CED-9 induce cell killing in Caenorhabditis elegans
    • Yang C., Yan N., Parish J., Wang X., Shi Y., and Xue D. RNA aptamers targeting the cell death inhibitor CED-9 induce cell killing in Caenorhabditis elegans. J. Biol. Chem. 281 (2006) 9137-9144
    • (2006) J. Biol. Chem. , vol.281 , pp. 9137-9144
    • Yang, C.1    Yan, N.2    Parish, J.3    Wang, X.4    Shi, Y.5    Xue, D.6
  • 44
    • 33746910190 scopus 로고    scopus 로고
    • Pegaptanib for the treatment of age-related macular degeneration
    • Zhou B., and Wang B. Pegaptanib for the treatment of age-related macular degeneration. Exp. Eye Res. 83 (2006) 615-619
    • (2006) Exp. Eye Res. , vol.83 , pp. 615-619
    • Zhou, B.1    Wang, B.2


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