Methods for identifying and characterizing interactions involving RNA

Tetrahedron

Volumn 68, Issue 43, 2012, Pages 8837-8855

  Blakeley, Brett D ^a   Deporter, Sandra M ^a   Mohan, Utpal ^a   Burai, Ritwik ^a   Tolbert, Blanton S ^b   McNaughton, Brian R ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINOPURINE; ACRIDINE; AGAROSE; BIOPOLYMER; MERCAPTOETHANOL; PROFLAVINE; RNA; STREPTAVIDIN; TYROSINE; ZINOSTATIN;

ANISOTROPY; COMBINATORIAL CHEMISTRY; DISSOCIATION CONSTANT; DROSOPHILA MELANOGASTER; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GEL MOBILITY SHIFT ASSAY; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; IC 50; ISOTHERMAL TITRATION CALORIMETRY; ISOTOPE LABELING; MASS SPECTROMETRY; MICROARRAY ANALYSIS; NONHUMAN; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN DEGRADATION; REVIEW; RNA BINDING; RNA SEQUENCE; RNA STRUCTURE; SPECTROPHOTOMETER; SURFACE PLASMON RESONANCE; VIRUS REPLICATION;

EID: 84866019613     PISSN: 00404020     EISSN: 14645416     Source Type: Journal    
DOI: 10.1016/j.tet.2012.07.001     Document Type: Review

References (155)

1. J.P. Overington, B. Al-Lazikani, and A.L. Hopkins Nat. Rev. Drug Discov. 5 2006 993
2. F. Bernal, A.F. Tyler, S.J. Korsmeyer, L.D. Walensky, and G.L. Verdine J. Am. Chem. Soc. 129 2007 5298
3. B. Leader, Q.J. Baca, and D.E. Golan Nat. Rev. Drug Discov. 7 2008 21
4. G.L. Verdine, and L.D. Walensky Clin. Cancer Res. 13 2007 7264
5. A.P. Russ, and S. Lampel Drug Discov. Today 10 2005 1607
6. M.K. Sakharkar, P. Li, Z.W. Zhong, and K.R. Sakharkar Int. J. Biol. Sci. 4 2008 15
7. S.M. Hecht Bioorganic Chemistry: Nucleic Acids 1996 Oxford University Press New York, NY
8. J.H. Zhao, A. Bacolla, G.L. Wang, and K.M. Vasquez Cell Mol. Life Sci. 67 2010 43
9. D.M. Chenoweth, and P.B. Dervan J. Am. Chem. Soc. 132 2010 14521
10. A.C. Stelzer, A.T. Frank, J.D. Kratz, M.D. Swanson, M.J. Gonzalez-Hernandez, J. Lee, I. Andricioaei, D.M. Markovitz, and H.M. Al-Hashimi Nat. Chem. Biol. 7 2011 553
11. C.B. Carlson, M. Vuyisich, B.D. Gooch, and P.A. Beal Chem. Biol. 10 2003 663
12. A. Roth, and R.R. Breaker Annu. Rev. Biochem. 78 2009 305
13. T.A. Cooper, L. Wan, and G. Dreyfuss Cell 136 2009 777
14. A.C. Cheng, R.G. Coleman, K.T. Smyth, Q. Cao, P. Soulard, D.R. Caffrey, A.C. Salzberg, and E.S. Huang Nat. Biotechnol. 25 2007 71
15. T.H. Keller, A. Pichota, and Z. Yin Curr. Opin. Chem. Biol. 10 2006 357
16. A. Merino, A.K. Bronowska, D.B. Jackson, and D.J. Cahill Drug Discov. Today 15 2010 749
17. D. Fourmy, and S. Yoshizawa Wiley Interdiscip Rev RNA 3 2012 557
18. S.A. Hofstadler, and R.H. Griffey Chem. Rev. 101 2001 377
19. J.R. Thomas, and P.J. Hergenrother Chem. Rev. 108 2008 1171
20. J. Gallego, and G. Varani Acc. Chem. Res. 34 2001 836
21. Q. Vicens, and E. Westhof ChemBioChem 4 2003 1018
22. M. Wanunu, and Y. Tor Methods for Studying Nucleic Acid/Drug Interactions 2011 Taylor & Francis Group Boca Raton, FL
23. P. Chomczynski, and N. Sacchi Nat. Protoc. 1 2006 581
24. J.E. Larkin, B.C. Frank, H. Gavras, R. Sultana, and J. Quackenbush Nat. Methods 2 2005 337
25. S.T. Hess, S.H. Huang, A.A. Heikal, and W.W. Webb Biochemistry-US 41 2002 697
26. D.A. Jeffery, and M. Bogyo Curr. Opin. Biotechnol. 14 2003 87
27. T. Hermann Biochimie 84 2002 869
28. D. Proudnikov, and A. Mirzabekov Nucleic Acids Res. 24 1996 4535
29. A. Richter, C. Schwager, S. Hentze, W. Ansorge, M.W. Hentze, and M. Muckenthaler Biotechniques 33 2002 620
30. R.W. Sinkeldam, N.J. Greco, and Y. Tor Chem. Rev. 110 2010 2579
31. S.G. Srivatsan, H. Weizman, and Y. Tor Org. Biomol. Chem. 6 2008 1334
32. S.G. Srivatsan, N.J. Greco, and Y. Tor Angew. Chem., Int. Ed. 47 2008 6661
33. S.G. Srivatsan, and Y. Tor Tetrahedron 63 2007 3601
34. M.K. Smalley, and S.K. Silverman Nucleic Acids Res. 34 2006 152
35. K. Yamana, H. Zako, K. Asazuma, R. Iwase, H. Nakano, and A. Murakami Angew. Chem., Int. Ed. 40 2001 1104
36. F. Wincott, A. Direnzo, C. Shaffer, S. Grimm, D. Tracz, C. Workman, D. Sweedler, C. Gonzalez, S. Scaringe, and N. Usman Nucleic Acids Res. 23 1995 2677
37. N. Kojima, T. Takebayashi, A. Mikami, E. Ohtsuka, and Y. Komatsu Bioorg. Med. Chem. Lett. 19 2009 2144
38. S.G. Srivatsan, and Y. Tor J. Am. Chem. Soc. 129 2007 2044
39. S.G. Srivatsan, and Y. Tor Nat. Protoc. 2 2007 1547
40. J.M. Jean, and K.B. Hall Proc. Natl. Acad. Sci. U.S.A. 98 2001 37
41. E.L. Rachofsky, R. Osman, and J.B.A. Ross Biochemistry-US 40 2001 946
42. M.F. Souliere, A. Haller, R. Rieder, and R. Micura J. Am. Chem. Soc. 133 2011 16161
43. R. Buscaglia, D.M. Jameson, and J.B. Chaires Nucleic Acids Res. 40 2012 4203
44. T.D. Bradrick, and J.P. Marino RNA 10 2004 1459
45. A.W. Cochrane, C.H. Chen, and C.A. Rosen Proc. Natl. Acad. Sci. U.S.A. 87 1990 1198
46. M.L. Zapp, and M.R. Green Nature 342 1989 714
47. M.H. Malim, W.W. Freimuth, J. Liu, T.J. Boyle, H.K. Lyerly, B.R. Cullen, and G.J. Nabel J. Exp. Med. 176 1992 1197
48. L. Duan, M. Zhu, I. Ozaki, H. Zhang, D.L. Wei, and R.J. Pomerantz Gene Ther. 4 1997 533
49. E.S. DeJong, C.E. Chang, M.K. Gilson, and J.P. Marino Biochemistry-US 42 2003 8035
50. D.L. Boger, B.E. Fink, S.R. Brunette, W.C. Tse, and M.P. Hedrick J. Am. Chem. Soc. 123 2001 5878
51. B.C. Baguley, W.A. Denny, G.J. Atwell, and B.F. Cain J. Med. Chem. 24 1981 520
52. S.T. Meyer, and P.J. Hergenrother Org. Lett. 11 2009 4052
53. A.J. Cross, and G.R. Fleming Biophys. J. 46 1984 45
54. M. Tramier, and M. Coppey-Moisan Methods Cell Biol. 85 2008 395
55. A. Schmidt, T. Schwerd, W. Hamm, J.C. Hellmuth, S. Cui, M. Wenzel, F.S. Hoffmann, M.C. Michallet, R. Besch, K.P. Hopfner, S. Endres, and S. Rothenfusser Proc. Natl. Acad. Sci. U.S.A. 106 2009 12067
56. X.S. Shi, and D. Herschlag Methods Enzymol. 469 2009 287
57. J.A. Cruz-Aguado, and G. Penner Anal. Chem. 80 2008 8853
58. W. Li, K.M. Wang, W.H. Tan, C.B. Ma, and X.H. Yang Analyst 132 2007 107
59. N.W. Luedtke, Q. Liu, and Y. Tor Biochemistry-US 42 2003 11391
60. W.C. Winkler, and R.R. Breaker Anal. Biochem. 59 2005 487
61. J. Martinez, A. Patkaniowska, H. Urlaub, R. Luhrmann, and T. Tuschl Cell 110 2002 563
62. K. Okamura, A. Ishizuka, H. Siomi, and M.C. Siomi Genes Dev. 18 2004 1655
63. J.A. Doudna, and T.R. Cech Nature 418 2002 222
64. C.H.T. Webb, N.J. Riccitelli, D.J. Ruminski, and A. Luptak Science 326 2009 953
65. R.M. Clegg Curr. Opin. Biotechnol. 6 1995 103
66. P.R. Selvin Nat. Struct. Biol. 7 2000 730
67. Y. Xie, T. Maxson, and Y. Tor J. Am. Chem. Soc. 132 2010 11896
68. D.J. Brooks, J.R. Fresco, A.M. Lesk, and M. Singh Mol. Biol. Evol. 19 2002 1645
69. A. Yonath Annu. Rev. Biochem. 74 2005 649
70. R. Green, and H.F. Noller Annu. Rev. Biochem. 66 1997 679
71. T. Hermann Biochimie 88 2006 1021
72. S.N. Hobbie, S.K. Kalapala, S. Akshay, C. Bruell, S. Schmidt, S. Dabow, A. Vasella, P. Sander, and E.C. Bottger Nucleic Acids Res. 35 2007 6086
73. Y. Xie, A.V. Dix, and Y. Tor Chem. Commun. 2010 5542
74. C.H. Fan, K.W. Plaxco, and A.J. Heeger J. Am. Chem. Soc. 124 2002 5642
75. M. Torimura, S. Kurata, K. Yamada, T. Yokomaku, Y. Kamagata, T. Kanagawa, and R. Kurane Anal. Sci. 17 2001 155
76. A.I.H. Murchie, B. Davis, C. Isel, M. Afshar, M.J. Drysdale, J. Bower, A.J. Potter, I.D. Starkey, T.M. Swarbrick, S. Mirza, C.D. Prescott, P. Vaglio, F. Aboul-ela, and J. Karn J. Mol. Biol. 336 2004 625
77. B.P. Davies, and C. Arenz Bioorg. Med. Chem. 16 2008 49
78. H.D. Zhang, F.A. Kolb, L. Jaskiewicz, E. Westhof, and W. Filipowicz Cell 118 2004 57
79. D. Kosman, C.M. Mizutani, D. Lemons, W.G. Cox, W. McGinnis, and E. Bier Science 305 2004 846
80. C.H. Wong, M. Hendrix, D.D. Manning, C. Rosenbohm, and W.A. Greenberg J. Am. Chem. Soc. 120 1998 8319
81. J.L. Childs-Disney, M.L. Wu, A. Pushechnikov, O. Aminova, and M.D. Disney ACS Chem. Biol. 2 2007 745
82. M. Uttamchandani, D.P. Walsh, S.Q. Yao, and Y.T. Chang Curr. Opin. Chem. Biol. 9 2005 4
83. M. Schena, D. Shalon, R.W. Davis, and P.O. Brown Science 270 1995 467
84. Y. Lee, E.K. Lee, Y.W. Cho, T. Matsui, I.C. Kang, T.S. Kim, and M.H. Han Proteomics 3 2003 2289
85. D. Pinkel, R. Seagraves, D. Sudar, S. Clark, I. Poole, D. Kowbel, C. Collins, W.L. Kuo, C. Chen, Y. Zhai, S.H. Dairkee, B.M. Ljung, J.W. Gray, and D.G. Albertson Nat. Genet. 20 1998 207
86. L. Cheng, Q.Y. Ge, B.L. Sun, P.F. Yu, X.Y. Ke, and Z.H. Lu J. Biomed. Nanotechnol. 5 2009 542
87. M. Cretich, G. di Carlo, R. Longhi, C. Gotti, N. Spinella, S. Coffa, C. Galati, L. Renna, and M. Chiari Anal. Chem. 81 2009 5197
88. I. Barbulovic-Nad, M. Lucente, Y. Sun, M. Zhang, A.R. Wheeler, and M. Bussmann Crit. Rev. Biotechnol. 2006 237
89. A.N. Koehler, A.F. Shamji, and S.L. Schreiber J. Am. Chem. Soc. 125 2003 8420
90. E. van Rooij, L.B. Sutherland, X.X. Qi, J.A. Richardson, J. Hill, and E.N. Olson Science 316 2007 575
91. Q.H. Jiang, Y.D. Wang, Y.Y. Hao, L.R. Juan, M.X. Teng, X.J. Zhang, M.M. Li, G.H. Wang, and Y.L. Liu Nucleic Acids Res. 37 2009 D98
92. O. Slaby, M. Svoboda, P. Fabian, T. Smerdova, D. Knoflickova, M. Bednarikova, R. Nenutil, and R. Vyzula Oncology-Basel 72 2007 397
93. S. Horvath, B. Zhang, M. Carlson, K.V. Lu, S. Zhu, R.M. Felciano, M.F. Laurance, W. Zhao, S. Qi, Z. Chen, Y. Lee, A.C. Scheck, L.M. Liau, H. Wu, D.H. Geschwind, P.G. Febbo, H.I. Kornblum, T.F. Cloughesy, S.F. Nelson, and P.S. Mischel Proc. Natl. Acad. Sci. U.S.A. 103 2006 17402
94. I. Heo, C. Joo, J. Cho, M. Ha, J.J. Han, and V.N. Kim Mol. Cells 32 2008 276
95. S. Chirayil, R. Chirayil, and K.J. Luebke Nucleic Acids Res. 37 2009 5486
96. M.M. Lee, J.L. Childs-Disney, A. Pushechnikov, J.M. French, K. Sobczak, C.A. Thornton, and M.D. Disney J. Am. Chem. Soc. 131 2009 17464
97. M.M. Lee, A. Pushechnikov, and M.D. Disney ACS Chem. Biol. 4 2009 345
98. M.D. Disney, M.M. Lee, A. Pushechnikov, and J.L. Childs-Disney ChemBioChem 11 2010 375
99. S. Tochitani, and Y. Hayashizaki Mol. Biosyst. 3 2007 195
100. L.M. Mayr E Schering Res Fdn W 58 2006 111
101. A. Anwar, N. Ali, R. Tanveer, and A. Siddiqui J. Biol. Chem. 275 2000 34231
102. A.A. Haller, and P. Sarnow Proc. Natl. Acad. Sci. U.S.A. 94 1997 8521
103. K.M. Brown, and G.M. Gilmartin Mol. Cells 12 2003 1467
104. H.J. Kim, M. Kwon, and J. Yu Bioorg. Med. Chem. 15 2007 7688
105. H.R. Hoogenboom, A.P. de Bruine, S.E. Hufton, R.M. Hoet, J.W. Arends, and R.C. Roovers Immunotechnology 4 1998 1
106. E. Koivunen, W. Arap, D. Rajotte, J. Lahdenranta, and R. Pasqualini J. Nucl. Med. 40 1999 883
107. R.C. Ladner, A.K. Sato, J. Gorzelany, and M. de Souza Drug Discov. Today 9 2004 525
108. S.S. Sidhu Curr. Opin. Biotechnol. 11 2000 610
109. D.J. Rodi, A.S. Soares, and L. Makowski J. Mol. Biol. 322 2002 1039
110. W. Li, and N.B. Caberoy Appl. Microbiol. Biotechnol. 85 2010 909
111. B. Dreier, G. Mikheeva, N. Belousova, P. Parizek, E. Boczek, I. Jelesarov, P. Forrer, A. Pluckthun, and V. Krasnykh J. Mol. Biol. 405 2011 410
112. T. Clackson, and H.B. Lowman Phage Display Vol. 266 2004 Oxford University Press New York, NY
113. C.F. Barbas III, D.R. Burton, J.K. Scott, and G.J. Silverman Phage Display: A Laboratory Manual 2001 Cold Spring Harbor Laboratory Cold Spring Harbor, NY
114. J. Dietz, J. Koch, A. Kaur, C. Raja, S. Stein, M. Grez, A. Pustowka, S. Mensch, J. Ferner, L. Moller, N. Bannert, R. Tampe, G. Divita, Y. Mely, H. Schwalbe, and U. Dietrich ChemMedChem 3 2008 749
115. K.J. Gregory, Y. Sun, N.G. Chen, and V. Golovlev Anal. Biochem. 408 2011 226
116. T.N. Lamichhane, N.D. Abeydeera, A.C.E. Duc, P.R. Cunningham, and C.S. Chow Molecules 16 2011 1211
117. S. Ladame Org. Biomol. Chem. 6 2008 219
118. A.M. Belenguer, T. Friscic, G.M. Day, and J.K.M. Sanders Chem. Sci. 2 2011 696
119. B.R. McNaughton, and B.L. Miller Org. Lett. 8 2006 1803
120. A.V. Gromova, J.M. Ciszewski, and B.L. Miller Chem. Commun. 2012 2131
121. C. Karan, and B.L. Miller J. Am. Chem. Soc. 123 2001 7455
122. B.R. McNaughton, P.C. Gareiss, and B.L. Miller J. Am. Chem. Soc. 129 2007 11306
123. P.C. Gareiss, K. Sobczak, B.R. McNaughton, P.B. Palde, C.A. Thornton, and B.L. Miller J. Am. Chem. Soc. 130 2008 16254
124. P.B. Palde, L.O. Ofori, P.C. Gareiss, J. Lerea, and B.L. Miller J. Med. Chem. 53 2010 6018
125. L.O. Ofori, J. Hoskins, M. Nakamori, C.A. Thornton, and B.L. Miller Nucleic Acids Res. 2012
126. B. Cheng, and D.H. Price Nucleic Acids Res. 2008 36
127. L.M. Hellman, and M.G. Fried Nat. Protoc. 2 2007 1849
128. L.D. Kerr Oncogene Tech. 254 1995 619
129. M. Zimmer, B.L. Ebert, C. Neil, K. Brenner, L. Papaioannou, A. Melas, N. Tolliday, J. Lamb, K. Pantopoulos, T. Golub, and O. Iliopoulos Mol. Cells 32 2008 838
130. S. Yamazaki, L. Tan, G. Mayer, J.S. Hartig, J.N. Song, S. Reuter, T. Restle, S.D. Laufer, D. Grohmann, H.G. Krausslich, J. Bajorath, and M. Famulok Chem. Biol. 14 2007 804
131. S.R. Kirk, N.W. Luedtke, and Y. Tor J. Am. Chem. Soc. 122 2000 980
132. K. Ruscher, M. Reuter, D. Kupper, G. Trendelenburg, U. Dirnagl, and A. Meisel J. Biotechnol. 78 2000 163
133. M. Pellecchia, D.S. Sem, and K. Wuthrich Nat. Rev. Drug. Discov. 1 2002 211
134. M. Pellecchia, I. Bertini, D. Cowburn, C. Dalvit, E. Giralt, W. Jahnke, T.L. James, S.W. Homans, H. Kessler, C. Luchinat, B. Meyer, H. Oschkinat, J. Peng, H. Schwalbe, and G. Siegal Nat. Rev. Drug Discov. 7 2008 738
135. R. Hansel, S. Foldynova-Trantirkova, F. Lohr, J. Buck, E. Bongartz, E. Bamberg, H. Schwalbe, V. Dotsch, and L. Trantirek J. Am. Chem. Soc. 131 2009 15761
136. L.P. Yu, T.K. Oost, J.M. Schkeryantz, J.G. Yang, D. Janowick, and S.W. Fesik J. Am. Chem. Soc. 125 2003 4444
137. K. Pervushin, B. Vogeli, and A. Eletsky J. Am. Chem. Soc. 124 2002 12898
138. M. Mayer, and B. Meyer Angew. Chem., Int. Ed. 38 1999 1784
139. C. Dalvit, P. Pevarello, M. Tato, M. Veronesi, A. Vulpetti, and M. Sundstrom J. Biomol. NMR 18 2000 65
140. M. Mayer, and T.L. James J. Am. Chem. Soc. 126 2004 4453
141. E.C. Johnson, V.A. Feher, J.W. Peng, J.M. Moore, and J.R. Williamson J. Am. Chem. Soc. 125 2003 15724
142. B.P. Nelson, T.E. Grimsrud, M.R. Liles, R.M. Goodman, and R.M. Corn Anal. Chem. 73 2001 1
143. J. Homola Chem. Rev. 108 2008 462
144. F.A. Tanious, B. Nguyen, and W.D. Wilson Biophysical Tools for Biologists: Vol. 1 in Vitro Techniques Vol. 84 2008 Academic Press in Salt Lake City UT p 53
145. B. Nguyen, and W.D. Wilson J. Phys. Chem. B 113 2009 14329
146. R.E. Moellering, M. Cornejo, T.N. Davis, C. Del Bianco, J.C. Aster, S.C. Blacklow, A.L. Kung, D.G. Gilliland, G.L. Verdine, and J.E. Bradner Nature 462 2009 182
147. M. Hendrix, E.S. Priestley, G.F. Joyce, and C.H. Wong J. Am. Chem. Soc. 119 1997 3641
148. A.L. Feig Biopolymers 87 2007 293
149. S.D. Gilbert, and R.T. Batey Methods Mol. Biol. 540 2009 97
150. S. Melo, A. Villanueva, C. Moutinho, V. Davalos, R. Spizzo, C. Ivan, S. Rossi, F. Setien, O. Casanovas, L. Simo-Riudalbas, J. Carmona, J. Carrere, A. Vidal, A. Aytes, S. Puertas, S. Ropero, R. Kalluri, C.M. Croce, G.A. Calin, and M. Esteller Proc. Natl. Acad. Sci. U.S.A. 108 2011 4394
151. S.D. Gilbert, C.D. Stoddard, S.J. Wise, and R.T. Batey J. Mol. Biol. 359 2006 754
152. C. Boozer, G. Kim, S.X. Cong, H.W. Guan, and T. Londergan Curr. Opin. Biotechnol. 17 2006 400
153. M. Wanunu, S. Bhattacharya, Y. Xie, Y. Tor, A. Aksimentiev, and M. Drndic ACS Nano. 5 2011 9345
154. M.D. Burke, and S.L. Schreiber Angew. Chem., Int. Ed. 43 2004 46
155. X. Li, and D.R. Liu Angew. Chem., Int. Ed. 43 2004 4848