Functional nucleic acids in high throughput screening and drug discovery

Combinatorial Chemistry and High Throughput Screening

Volumn 10, Issue 8, 2007, Pages 698-705

  Srivatsan, Seergazhi G ^a   Famulok, Michael ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF BONN   (Germany)

Author keywords

Allostery; Aptamer displacement assays; Aptamers; Aptazymes; in vitro selection; Riboswitches; Ribozymes; Signaling aptamers

Indexed keywords

APTAMER; MICRORNA; NUCLEIC ACID; RIBOZYME; RNA;

ALLOSTERISM; COMBINATORIAL CHEMISTRY; DRUG RESEARCH; DRUG SCREENING; FLUORESCENCE POLARIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; FUNCTIONAL GENOMICS; HIGH THROUGHPUT SCREENING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; STRUCTURAL GENOMICS;

ALLOSTERIC REGULATION; APTAMERS, NUCLEOTIDE; BIOSENSING TECHNIQUES; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; MODELS, MOLECULAR; NUCLEIC ACIDS; RIBOSOMES; RNA, CATALYTIC; SIGNAL TRANSDUCTION;

EID: 36048969852     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: 10.2174/138620707782507359     Document Type: Review

References (90)

1. Kozlowski, M. High Throughput Screening: Methods and Protocols, Janzen, W.P., Ed.; Humana Press: Towata, New Jersey, 2002.
2. Devlin, J.P. High Throughput Screening: The Discovery of Bioactive Substances, CRC Press, 1997.
3. Wu, G.; Doberstein, S.K. Drug Discov. Today, 2006, 11, 718.
4. Famulok, M. Curr. Opin. Mol. Ther., 2005, 7, 137.
5. Nimjee, S.M.; Rusconi, C.P.; Sullenger, B.A. Annu. Rev. Med., 2005, 56, 555.
6. Mayer, G.; Jenne, A. Biodrugs, 2004, 18, 351.
7. Nutiu, R.; Mei, S.; Liu, Z.; Li, Y. Pure Appl. Chem., 2004, 76, 1547.
8. Burgstaller, P.; Girod, A.; Blind, M. Drug Discov. Today, 2002, 7, 1221.
9. Rajendran, M.; Ellington, A.D. Comb. Chem. High Throughput Screen., 2002, 5, 263.
10. Williamson, J.R. Nat. Struct. Biol., 2000, 7, 834.
11. Yang, Y.; Kochoyan, M.; Burgstaller, P.; Westhof, E.; Famulok, M. Science, 1996, 272, 1343.
12. Ellington, A.D.; Szostak, J.W. Nature, 1990, 346, 818.
13. Robertson, D.L.; Joyce, G.F. Nature, 1990, 344, 467.
14. Tuerk, C.; Gold, L. Science, 1990, 249, 505.
15. Lee, S.W.; Sullenger, B.A. Nat. Biotechnol., 1997, 15, 41.
16. Soukup, G.A.; Breaker, R.R. Trends Biotechnol., 1999, 17, 469.
17. Mei, H.-Y.; Cui, M.; Sutton, S.T.; Truong, H.N.; Chung, F.Z.; Czarnik, A.W. Nucleic Acids Res., 1996, 24, 5051.
18. Foloppe, N.; Chen, I.-J.; Davis, B.; Hold, A.; Morley, D.; Howes, R. Bioorg. Med. Chem., 2004, 12, 935.
19. Klostermeier, D.; Sears, P.; Wong, C.-H.; Millar, D.P.; Williamson, J.R. Nucleic Acids Res., 2004, 32, 2707.
20. Mei, H.-Y.; Mack, D.P.; Galan, A.A.; Halim, N.S.; Heldsinger, A.; Loo, J.A.; Moreland, D.W.; Sannes-Lowery, K.A.; Sharmeen, L.; Truong, H.N.; Czarnik, A.W. Bioorg. Med. Chem., 1997, 5, 1173.
21. Winkler, W.C.; Breaker, R.R. Chembiochem, 2003, 4, 1024.
22. Barrick, J.E.; Corbino, K.A.; Winkler, W.C.; Nahvi, A.; Mandal, M.; Collins, J.; Lee, M.; Roth, A.; Sudarsan, N.; Jona, I.; Wickiser, J.K.; Breaker, R.R. Proc. Natl. Acad. Sci. USA, 2004, 101, 6421.
23. Owicki, J.C. J. Biomol. Screen., 2000, 5, 297.
24. Hertzberg, R.P.; Pope, A.J. Curr. Opin. Chem. Biol., 2000, 4, 445.
25. Liu, B.; Li, S.; Hu, J. Am. J. Pharmacogenomics, 2004, 4, 263.
26. Hamaguchi, N.; Ellington, A.; Stanton, M. Anal. Biochem., 2001, 294, 126.
27. Yamamoto, R.; Baba, T.; Kumar, P.K. Genes Cells, 2000, 5, 389.
28. Rist, M.J.; Marino, J.P. Curr. Org. Chem., 2002, 6, 775.
29. Kirk, S.R.; Luedtke, N.W.; Tor, Y. Bioorg. Med. Chem., 2001, 9, 2295.
30. Jhaveri, S.; Kirby, R.; Conrad, R.; Maglott, E.; Bowser, M.; Kennedy, R.T.; Glick, G.; Ellington, A.D. J. Am. Chem. Soc., 2000, 122, 2469.
31. Menger, M.; Tuschl. T.; Eckstein, F.; Porschke, D. Biochemistry, 1996, 35, 14710.
32. Huizenga, D.E.; Szostak, J.W. Biochemistry, 1995, 34, 656.
33. Nutiu, R.; Li, Y. J. Am. Chem. Soc., 2003, 125, 4771.
34. Nutiu, R.; Yu, J.M.Y.; Li, Y. Chembiochem, 2004, 5, 1139.
35. Aldrich, M.B.; Blackburn, M.R.; Kellems, R.E. Biochem. Biophys. Res. Commun., 2000, 272, 311.
36. Elowe, N.H.; Nutiu, R.; Allali-Hassani, A.; Cechetto, J.D.; Hughes, D.W.; Li, Y.; Brown, E.D. Angew. Chem. Int. Ed. Engl., 2006, 45, 5648.
37. Green, L.S.; Bell, C.; Janjic, N. Biotechniques, 2001, 30, 1094.
38. Green, L.S.; Jellinek, D.; Jenison, R.; Ostman, A.; Heldin, C.H.; Janjic, N. Biochemistry, 1996, 35, 14413.
39. Katilius, E.; Katiliene, Z.; Woodbury, N.W. Anal. Chem., 2006, 78, 6484.
40. Rachofsky, E.L.; Osman, R.; Ross, J.B.A. Biochemistry, 2001, 40, 946.
41. Hafner, M.; Schmitz, A.; Grune, I.; Srivatsan, S.G.; Paul, B.; Kolanus, W.; Quast, T.; Kremmer, E.; Bauer, I.; Famulok, M. Nature, 2006, 444, 941.
42. Mayer, G.; Blind, M.; Nagel, W.; Böhm, T.; Knorr, T.; Jackson, C.L.; Kolanus, W.; Famulok, M. Proc. Natl. Acad. Sci. USA, 2001, 98, 4961.
43. Biddinger, S.B.; Kahn, C.R. Annu. Rev. Physiol., 2006, 68, 123.
44. Fuss, B.; Becker, T.; Zinke, I.; Hoch, M. Nature, 2006, 444, 945.
45. Burgstaller, P.; Kochoyan, M.; Famulok, M. Nucleic Acids Res., 1995, 23, 4769.
46. Jiang, F.; Kumar, P.A.; Jones, R.A.; Patel, D.J. Nature, 1996, 382, 183.
47. Tang, J.; Breaker, R.R. Chem. Biol., 1997, 4, 453.
48. Tang, J.; Breaker, R.R. Nucleic Acids Res., 1998, 26, 4214.
49. Najafi-Shoushtari, S.H.; Mayer, G.; Famulok, M. Nucleic Acids Res., 2004, 32, 3212.
50. Koizumi, M.; Soukop, G.A.; Kerr, J.Q.; Breaker, R.R. Nat. Struct. Biol., 1999, 6, 1062.
51. Piganeau, N.; Jenne, A.; Thuillier, V.; Famulok, M. Angew. Chem. Int. Ed. Engl., 2000, 39, 4369.
52. Piganeau, N.; Thuillier, V.; Famulok, M. J. Mol. Biol., 2001, 312, 1177.
53. Robertson, M.P.; Ellington, A.D. Nat. Biotechnol., 2001, 19, 650.
54. Robertson, M.P.; Knudsen, S.M.; Ellington, A.D. RNA, 2004, 10, 114.
55. Soukup, G.A.; Breaker, R.R. Proc. Natl. Acad. Sci. USA, 1999, 96, 3584.
56. Araki, M.; Okuno, Y.; Hara, Y.; Sugiura, Y. Nucleic Acids Res., 1998, 26, 3379.
57. Jenne, A.; Gmelin, W.; Raffler, N.; Famulok, M. Angew. Chem. Int. Ed., 1999, 38, 1300.
58. Hartig, J.S.; Najafi-Shoushtari, S.H.; Grune, I.; Yan, A.; Ellington, A.D.; Famulok, M. Nat. Biotechnol., 2002, 20, 717.
59. Hartig, J.S.; Famulok, M. Angew. Chem. Int. Ed. Engl., 2002, 41, 4263.
60. Giedroc, D.P.; Theimer, C.A.; Nixon, P.L. J. Mol. Biol., 2000, 298, 167.
61. Ben-Asouli, Y.; Banai, Y.; Pel-Or, Y.; Shir, A.; Kaempfer, R. Cell, 2002, 108, 221.
62. Yamazaki, S.; Tan, L.; Mayer, G.; Hartig, J. S.; Song, J.-N.; Reuter, S.; Restle, T.; Laufer, S. D.; Grohmann, D.; Kräusslich, H.-G.; Bajorath, J.; Famulok, M. Chem. Biol., 2007, 14, 804.
63. Giver, L.; Bartel, D.; Zapp, M.; Pawul, A.; Green, M.; Ellington, A.D. Nucleic Acids Res., 1993, 21, 5509.
64. Esteban, J.A.; Banerjee, A.R.; Burke, J.M. J. Biol. Chem., 1997, 272, 13629.
65. 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. Chem. Biol., 2004, 11, 499.
66. Hermann, T. Angew. Chem. Int. Ed. Engl., 2000, 39, 1890.
67. Afshar, M.; Prescott, C.D.; Varani, G. Curr. Opin. Biotech., 1999, 10, 59.
68. Tor, Y. Angew. Chem. Int. Ed. Engl., 1999, 38, 1579.
69. Hermann, T.; Westhof, E. Comb. Chem. High Throughput Screen., 2000, 3, 219.
70. Blount, K.; Breaker, R. Nat. Biotechnol., 2006, 12, 1558.
71. Winkler, W.C. Curr. Opin. Chem. Biol., 2005, 9, 594.
72. Nahvi, A.; Sudarsan, N.; Ebert, M.S.; Zou, X.; Brown, K.L.; Breaker, R.R. Chem. Biol., 2002, 9, 1043.
73. Winkler, W.; Nahvi, A.; Breaker, R.R. Nature, 2002, 419, 952.
74. Mandal, M.; Boese, B.; Barrick, J.E.; Winkler, W.C.; Breaker, R.R. Cell, 2003, 113, 577.
75. Mironov, A.S.; Gusarov, I.; Rafikov, R.; Lopez, L.E.; Shatalin, K.; Kreneva, R.A.; Perumov, D.A.; Nudler, E. Cell, 2002, 111, 747.
76. McDaniel, B.A.; Grundy, F.J.; Artsimovitch, I.; Henkin, T.M. Proc. Natl. Acad. Sci. USA, 2003, 100, 3083.
77. Schwalbe, H.; Buck, J.; Fürtig, B.; Noeske, J. Wöhnert, J. Angew. Chem. Int. Ed. Engl., 2007, 46, 1212.
78. Mayer, G.; Famulok, M. Chembiochem, 2006, 7, 602.
79. Winkler, W.C.; Nahvi, A.; Roth, A.; Collins, J.A.; Breaker, R.R. Nature, 2004, 428, 281.
80. Blount, K.; Puskarz, I.; Penchovsky, R.; Breaker, R. RNA Biol., 2006, 3, 77.
81. Sudarsan, N.; Cohen-Chalamish, S.; Nakamura, S.; Emilsson, G.M.; Breaker, R.R. Chem. Biol., 2005, 12, 1325.
82. Sudarsan, N.; Wickiser, J.K.; Nakamura, S.; Ebert, M.S.; Breaker, R.R. Genes Dev., 2003, 17, 2688.
83. Mayer, G.; Raddatz, M.-S.; Grunwald, J. D.; Famulok, M. Angew. Chem. Int. Ed. Engl., 2007, 46, 557.
84. Sontheimer, E.J.; Carthew, R.W. Cell, 2005, 122, 9.
85. Croce, C.M.; Calin, G.A. Cell, 2005, 122, 6.
86. Voorhoeve, P.M.; le Sage, C.; Schrier, M.; Gillis, A.J.; Stoop, H.; Nagel, R.; Liu, Y.P.; van Duijse, J.; Drost, J.; Griekspoor, A.; Zlotorynski, E.; Yabuta, N.; De Vita, G.; Nojima, H.; Looijenga, L.H.; Agami, R. Cell, 2006, 124, 1169.
87. Yanaihara, N.; Caplen, N.; Bowman, E.; Seike, M.; Kumamoto, K.; Yi, M.; Stephens, R.M.; Okamoto, A.; Yokota, J.; Tanaka, T.; Calin, G.A.; Liu, C.G.; Croce, C.M.; Harris, C.C. Cancer Cell, 2006, 9, 189.
88. Czech, M.P. N. Engl. J. Med., 2006, 354, 1194.
89. Davies, B.P.; Arenz, C. Angew. Chem. Int. Ed. Engl., 2006, 45, 5550.
90. Hutvagner, G.; McLachlan, J.; Pasquinelli, A.E.; Balint, E.; Tuschl, T.; Zamore, P.D. Science, 2001, 293, 834.