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Combinatorial Chemistry of Nucleic Acids: SELEX

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A method of irrational oligonucleotide design, SELEX, is considered. Individual SELEX products, aptamers, are small molecules (40–100 nt) that have a unique three-dimensional structure, which provides for their specific and high-affinity binding to targets varying from low-molecular-weight ligands to proteins. Thus, the sophisticated biosynthesis of recognizing protein elements, antibodies, can be emulated in vitro via selection and synthesis of principally new recognizing elements based on nucleic acids.

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REFERENCES

  1. Tuerk, C. and Gold, L., Science, 1990, vol. 249, pp. 505–510.

    PubMed  Google Scholar 

  2. Ellington, A.D. and Szostak, J.W., Nature, 1990, vol. 346, pp. 818–822.

    PubMed  Google Scholar 

  3. Burke, J.M. and Bezzal-Herranz, A., FASEB J., 1993, vol. 7, pp. 106–112.

    PubMed  Google Scholar 

  4. Klug, S.J. and Famulok, M., Mol. Biol. Rep., 1994, vol. 20, pp. 97–107.

    PubMed  Google Scholar 

  5. Breaker, R.R. and Joyce, G.F., Trends Biotechnol., 1994, vol. 12, pp. 268–275.

    PubMed  Google Scholar 

  6. Gold, L., Polisky, B., Uhlenbeck, O., and Yarus, M., Annu. Rev. Biochem., 1995, vol. 64, pp. 763–797.

    PubMed  Google Scholar 

  7. Gold, L., J. Biol. Chem., 1995, vol. 270, pp. 13581–13584.

    PubMed  Google Scholar 

  8. Iverson, B.L., Chem. Biol., 1995, vol. 2, pp. 67–70.

    PubMed  Google Scholar 

  9. Bartel, D.P. and Szostak, J.W., RNA-Protein Interactions, Nagai, K. and Mattaj, I.W., Eds., Oxford: IRL, 1996, pp. 248–268.

    Google Scholar 

  10. Eaton, B.E., Gold, L., Hicke, B.J., et al., Bioorg. Med. Chem., 1997, vol. 5, pp. 1087–1096.

    PubMed  Google Scholar 

  11. Gold, L., Brown, D., He, Y.-Y., et al., Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 59–64.

    PubMed  Google Scholar 

  12. Osborne, S.E., Matsumura, I., and Ellington, A.D., Curr. Opin. Chem. Biol., 1997, vol. 1, pp. 5–9.

    PubMed  Google Scholar 

  13. Famulok, M. and Jenne, A., Curr. Opin. Biol., 1998, vol. 2, pp. 320–327.

    Google Scholar 

  14. Famulok, M. and Mayer, G., Curr. Top. Microbiol. Immunol., 1999, vol. 243, pp. 123–136.

    PubMed  Google Scholar 

  15. Famulok, M., Curr. Opin. Struct. Biol., 1999, vol. 9, pp. 324–329.

    PubMed  Google Scholar 

  16. Kopylov, A.M., Spiridonova, V.A., and Park, K.-H., Ros. Khem. Zh., 1998, vol. 42, pp. 89–96.

    Google Scholar 

  17. Gordon, E.M., Barrett, R.W., Dower, W.J., et al., J. Med. Chem., 1994, vol. 37, pp. 1385–1401.

    PubMed  Google Scholar 

  18. Kim, I.C., Cha, J.I., Kim, J.R., et al., J. Biol. Chem., 1992, vol. 267, pp. 22108–22114.

    PubMed  Google Scholar 

  19. Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., et al., J. Biol. Chem., 1993, vol. 268, pp. 17651–17654.

    PubMed  Google Scholar 

  20. Tsiang, M., Gibbs, C.S., Griffin, L.C., et al., J. Biol. Chem., 1995, vol. 270, pp. 19370–19376.

    PubMed  Google Scholar 

  21. Drolet, D.W., Jenison, R.D., Smith, D.E., et al., Comb. Chem. High Throughput Screen., 1999, vol. 2, pp. 271–278.

    PubMed  Google Scholar 

  22. Patel, D.J., Curr. Opin. Chem. Biol., 1997, vol. 1, pp. 32–46.

    PubMed  Google Scholar 

  23. Hermann, T. and Patel, D.J., Science, 2000, vol. 287, pp. 820–825.

    PubMed  Google Scholar 

  24. Hermann, T. and Patel, D.J., Struct. Fold Des., 2000, vol. 15, pp. 47–54.

    Google Scholar 

  25. Pace, N., Thomas, B.C., and Woese, C.R., The RNA World, Gesteland, R.F., Cech, T.R., and Atkins, J.F., Eds., New York: CHSL, 1999, pp. 113–141.

    Google Scholar 

  26. Moore, P., The RNA World, Gesteland, R.F., Cech, T.R., and Atkins, J.F., Eds., New York: CHSL, 1999, pp. 381–401.

    Google Scholar 

  27. McGregor, A., Murray, J.B., Adams, C.J., et al., J. Biol. Chem., 1999, vol. 274, pp. 2256–2262.

    Google Scholar 

  28. Wang, K.Y., Swaminathan, S., and Bolton, P.H., Biochemistry, 1994, vol. 33, pp. 7517–7527.

    PubMed  Google Scholar 

  29. Willis, M.C., Hicke, B.J., Uhlenbeck, O.C., et al., Science, 1993, vol. 262, pp. 1255–1257.

    PubMed  Google Scholar 

  30. Hicke, B.J., Willis, M.C., Koch, T.H., and Cech, T.R., Biochemistry, 1994, vol. 33, pp. 3364–3373.

    PubMed  Google Scholar 

  31. Cantor, C. and Shimmel, P., Biophysical Chemistry. Translated under the titile Biofizicheskaya khimiya, Moscow: Mir, 1984, vol. 1, pp. 287–294.

    Google Scholar 

  32. Ni, J., Pomerantz, S.C., Rozenski, J., et al., Anal. Chem., 1996, vol. 68, pp. 1989–1999.

    PubMed  Google Scholar 

  33. Porter, K.W., Tomasz, J., Huang, F., et al., Biochemistry, 1995, vol. 34, pp. 11963–11969.

    PubMed  Google Scholar 

  34. Dewey, T.M., Mundt, A., Crouch, G.J., et al., J. Am. Chem. Soc., 1995, vol. 117, pp. 8474–8475.

    Google Scholar 

  35. Eaton, B.E., Curr. Opin. Chem. Biol., 1997, vol. 1, pp. 10–16.

    PubMed  Google Scholar 

  36. Eaton, B.E. and Pieken, W.A., Annu. Rev. Biochem., 1995, vol. 64, pp. 837–863.

    PubMed  Google Scholar 

  37. Latham, J.A., Johnson, R., and Toole, J.J., Nucleic Acids Res., 1994, vol. 22, pp. 2817–2822.

    PubMed  Google Scholar 

  38. Crouch, G.J. and Eaton, B.E., Nucleosides Nucleotides, 1994, vol. 13, pp. 939–944.

    Google Scholar 

  39. Dewey, T.M., Zyzniewski, M.C., and Eaton, B.E., Nucleosides Nucleotides, 1996, vol. 15, pp. 1611–1617.

    Google Scholar 

  40. Tu, C., Keane, C., and Eaton, B.E., Nucleosides Nucleotides, 1995, vol. 14, pp. 1631–1638.

    Google Scholar 

  41. Sebesta, D.P., O'Rourke, S.S., Martinez, R.L., et al., Tetrahedron, 1996, vol. 52, pp. 14 385–14 402.

    Google Scholar 

  42. McGee, D.P.C., Sebesta, D.P., O'Rourke, S.S., and Martinez, R.L., Tetrahedron Lett., 1996, vol. 37, pp. 1995–1998.

    Google Scholar 

  43. McGee, D.P.C., Vaughn-Settle, A., Vargeese, C., and Zhai, Y., J. Org. Chem., 1996, vol. 61, pp. 781–785.

    PubMed  Google Scholar 

  44. Bridonneau, P., Bunch, S., Tengler, R., et al., J. Chromatogr. B. Biomed. Sci. Appl., 1999, vol. 726, pp. 237–247.

    PubMed  Google Scholar 

  45. Limbach, P.A., Crain, P.F., and McCloskey, J.A., Nucleic Acids Res., 1994, vol. 22, pp. 2183–2196.

    PubMed  Google Scholar 

  46. Felden, B., Hanawa, K., Atkins, J.F., et al., EMBO J., 1998, vol. 17, pp. 3188–3196.

    PubMed  Google Scholar 

  47. McCloskey, J.A., Whitehill, A.B., Rozenski, J., et al., Nucleosides Nucleotides, 1999, vol. 18, pp. 1549–1553.

    PubMed  Google Scholar 

  48. Green, L.S., Jellinek, D., Bell, C., et al., Chem. Biol., 1995, vol. 2, pp. 683–695.

    PubMed  Google Scholar 

  49. Osborne, S.E., Volker, J., Stevens, S.Y., et al., J. Am. Chem. Soc., 1996, vol. 118, pp. 11993–12003.

    Google Scholar 

  50. Ferentz, A.E. and Verdine, G.L., J. Am. Chem. Soc., 1991, vol. 113, pp. 4000–4002.

    Google Scholar 

  51. Gao, H., Yang, M., and Cook, A., Nucleic Acids Res., 1995, vol. 23, pp. 285–292.

    PubMed  Google Scholar 

  52. Cain, R.J., Zuiderweg, E.R.P., and Glik, G.D., Nucleic Acids Res., 1995, vol. 23, pp. 2153–2160.

    PubMed  Google Scholar 

  53. Goodwin, J.T. and Glik, G.D., Tetrahedron Lett., 1994, vol. 35, pp. 1647–1650.

    Google Scholar 

  54. Goodwin, J.T., Osborn, S.E., Swanson, P.C., and Glik, G.D., Tetrahedron Lett., 1994, vol. 35, pp. 4527–4530.

    Google Scholar 

  55. Salunke, M., Wu, T., and Letsinger, R.L., J. Am. Chem. Soc., 1992, vol. 114, pp. 8768–8772.

    Google Scholar 

  56. Cowart, M. and Benkovic, S.J., Biochemistry, 1991, vol. 30, pp. 788–796.

    PubMed  Google Scholar 

  57. Pieles, U., Sproat, B.S., Neuner, P., and Cramer, F., Nucleic Acids Res., 1989, vol. 17, pp. 8967–8978.

    PubMed  Google Scholar 

  58. Durand, M., Peloille, S., Thuong, N.T., and Maurizot, J.C., Biochemistry, 1992, vol. 31, pp. 9197–9204.

    PubMed  Google Scholar 

  59. Rumney, S. and Kool, E.T., Angew Chem. Int. Ed. Engl., 1992, pp. 1617–1619.

  60. Rumney, S. and Kool E.T., J. Am. Chem. Soc., 1992, vol. 117, pp. 5635–5646.

    Google Scholar 

  61. Ma, M.Y.-X., Reid, L.S., Clime, S.C., et al., Biochemistry, 1993, vol. 32, pp. 1751–1758.

    PubMed  Google Scholar 

  62. Ma, M.Y.-X., McCallum, K., Clime, S.C., et al., Nucleic Acids Res., 1993, vol. 21, pp. 2585–2589.

    PubMed  Google Scholar 

  63. Letsinger, R.L. and Wu, T., J. Am. Chem. Soc., 1995, vol. 117, pp. 7323–7328.

    Google Scholar 

  64. Nelson, J. S., Giver, L., Ellington, A.D., and Letsinger, R.L., Biochemistry, 1996, vol. 35, pp. 5339–5344.

    PubMed  Google Scholar 

  65. Jensen, K.B., Atkinson, B.L., Wills, M.C., et al., Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 12220–12224.

    PubMed  Google Scholar 

  66. Stump, W.T. and Hall, K.B., RNA, 1995, vol. 1, pp. 55–63.

    PubMed  Google Scholar 

  67. Tuerk, C., MacDougal, S., Hertz, G., and Gold, L., The Polymerase Chain Reaction, Ferre, R., Mullis, K., Gibbs, R., and Ross, A., Eds., New York: Birkhauser, 1993, pp. 233–243.

    Google Scholar 

  68. Tuerk, C. and MacDougal-Waugh, S., Gene, 1993, vol. 137, pp. 33–39.

    PubMed  Google Scholar 

  69. Jensen, K.B., Green, L., MacDougal-Waugh, S., and Tuerk, C., J. Mol. Biol., 1994, vol. 235, pp. 237–247.

    PubMed  Google Scholar 

  70. Bartel, D., Zapp, M., Green, M., Szostak, J.W., Cell, 1991, vol. 67, pp. 529–536.

    PubMed  Google Scholar 

  71. Giver, L., Bartel, D., Zapp, M., et al., Nucleic Acids Res., 1993, vol. 21, pp. 5509–5516.

    PubMed  Google Scholar 

  72. Foote, J. and Eisen, H.N., Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 1254–1256.

    PubMed  Google Scholar 

  73. Lin, Y., Nieuwlandt, D., Magallanez, A., et al., Nucleic Acids Res., 1996, vol. 24, pp. 3407–3414.

    PubMed  Google Scholar 

  74. Drolet, D.W., Moon-Dermott, L., and Romig, T.S., Nat. Biotechnol., 1996, vol. 14, pp. 1021–1025.

    PubMed  Google Scholar 

  75. Davis, K.A., Abrams, B., Lin, Y., and Jayasena, S.D., Nucleic Acids Res., 1996, vol. 24, pp. 702–706.

    PubMed  Google Scholar 

  76. Hicke, B.J., Watson, S.R., Koenig, A., et al., J. Clin. Invest., 1996, vol. 98, pp. 2688–2692.

    PubMed  Google Scholar 

  77. Conrad, R. and Ellington, A.D., Anal. Biochem., 1996, vol. 242, pp. 261–265.

    PubMed  Google Scholar 

  78. Dougan, H., Hobbs, J.B., Weitz, J.I., and Lyster, D.M., Nucleic Acids Res., 1997, vol. 25, pp. 2897–2901.

    PubMed  Google Scholar 

  79. Davis, K.A., Lin, Y., Abrams, B., and Jayasena, S.D., Nucleic Acids Res., 1998, vol. 26, pp. 3915–3924.

    PubMed  Google Scholar 

  80. Potyrailo, R.A., Conrad, R.C., Ellington, A.D., and Hieftje, G.M., Anal. Chem., 1998, vol. 70, pp. 3419–3425.

    PubMed  Google Scholar 

  81. Brody, E.N., Willis, M.C., Smith, J.D., et al., Mol. Diagn., 1999, vol. 4, pp. 381–388.

    PubMed  Google Scholar 

  82. Jellinek, D., Green, L.S., Bell, C., and Janjic, N., Biochemistry, 1994, vol. 33, pp. 10450–10456.

    PubMed  Google Scholar 

  83. Jellinek, D., Linott, C.K., Rifkin, D.B., and Janjic, N., Proc. Natl. Acad. Sci. USA, 1993, vol. 90, pp. 11227–11231.

    PubMed  Google Scholar 

  84. Jellinek, D., Green, L.S., Bell, C., et al., Biochemistry, 1995, vol. 34, pp. 11363–11372.

    PubMed  Google Scholar 

  85. Conrad, R., Keranen, L.M., Ellington, A.D., and Newton, A.C., J. Biol. Chem., 1994, vol. 269, pp. 32051–32054.

    PubMed  Google Scholar 

  86. Schneider, D.J., Feigon, J., Hostomsky, Z., and Gold, L., Biochemistry, 1995, vol. 34, pp. 9599–9610.

    PubMed  Google Scholar 

  87. Tasset, D.M., Kubik, M.F., and Steiner, W., J. Mol. Biol., 1997, vol. 272, pp. 688–698.

    PubMed  Google Scholar 

  88. Kubik, M.F., Stephens, A.W., Schneider, D., et al., Nucleic Acids Res., 1994, vol. 22, pp. 2619–2626.

    PubMed  Google Scholar 

  89. Block, L.C., Griffin, L.C., Latham, J.A., et al., Nature, 1992, vol. 355, pp. 564–566.

    PubMed  Google Scholar 

  90. Griffin, L.C., Tidmarsh, G.F., Bock, L.C., et al., Blood, 1993, vol. 81, pp. 3271–3276.

    PubMed  Google Scholar 

  91. Smith, D., Kischenheuter, G.P., Charlton, J., et al., Chem. Biol., 1995, vol. 2, pp. 741–750.

    PubMed  Google Scholar 

  92. Wiegand, T.W., Williams, P.B., Dreskin, S.C., et al., Immunology, 1996, vol. 157, pp. 221–230.

    Google Scholar 

  93. Pagratis, N.C., Bell, C., Chang, Y.-C., et al., Nat. Biotechnol., 1997, vol. 15, pp. 68–73.

    PubMed  Google Scholar 

  94. Pan, W., Craven, R.C., Qiu, Q., et al., Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 11509–11513.

    PubMed  Google Scholar 

  95. Lin, Y., Qiu, Q., Gill, S.C., and Jayasena, S.D., Nucleic Acids Res., 1994, vol. 22, pp. 5229–5234.

    PubMed  Google Scholar 

  96. Tam, R.C., Wu-Pong, S., Pai, B., et al., Antisense Nucleic Acid Drug Dev., 1999, vol. 9, pp. 289–300.

    PubMed  Google Scholar 

  97. Pieken, W.A., Olsen, D.B., Benseler, F., et al., Science, 1991, vol. 253, pp. 314–317.

    PubMed  Google Scholar 

  98. Willis, M.C., Collins, B.D., Zhang, T., et al., Bioconjug. Chem., 1998, vol. 9, pp. 573–582.

    PubMed  Google Scholar 

  99. Biesecker, G., Dihel, L., Enney, K., and Bendele, R.A., Immunopharmacology, 1999, vol. 42, pp. 219–230.

    PubMed  Google Scholar 

  100. Bell, C., Lynam, E., Landfair, D.J., et al., In Vitro Cell Dev. Biol. Anim., 1999, vol. 35, pp. 533–542.

    PubMed  Google Scholar 

  101. Williams, K.P., Liu, X.H., Schumacher, T.H., et al., Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 11285–11290.

    PubMed  Google Scholar 

  102. Reyderman, L. and Stavchansky, S., Pharm. Res., 1998, vol. 15, pp. 904–910.

    PubMed  Google Scholar 

  103. Tucker, C.E., Chen, L.S., Judkins, M.B., et al., J. Chromatogr. B Biomed. Sci. Appl., 1999, vol. 732, pp. 203–212.

    PubMed  Google Scholar 

  104. Konopka, K., Duzgunes, N., Rossi, J., and Lee, N.S., J. Drug Target, 1998, vol. 5, pp. 247–259.

    PubMed  Google Scholar 

  105. Lebruska, L.L. and Maher, J. III, Biochemistry, 1999, vol. 38, pp. 3168–3174.

    PubMed  Google Scholar 

  106. Lee, T.C., Sullenger, B.A., Gallardo, H.F., et al., New Biol., 1993, vol. 4, pp. 66–74.

    Google Scholar 

  107. Lee, S.W., Gallardo, H.F., Gilboa, E., and Smith, C., J. Virol., 1995, vol. 68, pp. 8254–8264.

    Google Scholar 

  108. Chen, H., McBroom, D.G., Zhu, Y.Q., et al., Biochemistry, 1996, vol. 35, pp. 6923–6930.

    PubMed  Google Scholar 

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Kopylov, A.M., Spiridonova, V.A. Combinatorial Chemistry of Nucleic Acids: SELEX. Molecular Biology 34, 940–954 (2000). https://doi.org/10.1023/A:1026696330245

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