RNA tetraloop folding reveals tension between backbone restraints and molecular interactions

Journal of the American Chemical Society

Volumn 132, Issue 36, 2010, Pages 12679-12689

  Mohan, Srividya ^a   Hsiao, Chiaolong ^a   Bowman, Jessica C ^a   Wartell, Roger ^a   Williams, Loren Dean ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY STRATEGIES; HYDROGEN BONDING INTERACTIONS; IRREVERSIBLE THERMODYNAMICS; PAIRING INTERACTIONS; RNA MOTIFS; ROTAMERS; STRUCTURAL ELEMENTS; TETRALOOPS; TORSION ANGLE; TORSIONAL ENERGIES; TRIMETHYLENE;

ACTIVE NETWORKS; EVOLUTIONARY ALGORITHMS; HYDROGEN; HYDROGEN BONDS; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE;

RNA;

ADENINE; CYCLOPROPANE DERIVATIVE; GUANINE; PHOSPHATE; PURINE; RIBOSE;

3' UNTRANSLATED REGION; ARTICLE; ENERGY; ENTHALPY; GEOMETRY; HYDROGEN BOND; MOLECULAR INTERACTION; MOLECULAR MODEL; RNA STRUCTURE; TENSION; THERMODYNAMICS;

MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS;

EID: 77956431277     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja104387k     Document Type: Article

References (64)

1. Woese, C. R., Winker, S., and Gutell, R. R. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 8467
2. Woese, C. R., Gutell, R., Gupta, R., and Noller, H. F. Microbiol. Rev. 1983, 47, 621
3. Klein, D. J., Schmeing, T. M., Moore, P. B., and Steitz, T. A. EMBO J. 2001, 20, 4214
4. Martin, F. H., Uhlenbeck, O. C., and Doty, P. J. Mol. Biol. 1971, 57, 201
5. Uhlenbeck, O. C., Martin, F. H., and Doty, P. J. Mol. Biol. 1971, 57, 217
6. Basu, S., Rambo, R. P., Strauss-Soukup, J., Cate, J. H., Ferre-D'Amare, A. R., Strobel, S. A., and Doudna, J. A. Nat. Struct. Biol. 1998, 5, 986
7. Batey, R. T., Rambo, R. P., and Doudna, J. A. Angew. Chem., Int. Ed. 1999, 38, 2326
8. Moore, P. B. Annu. Rev. Biochem. 1999, 68, 287
9. Leontis, N. B. and Westhof, E. Curr. Opin. Struct. Biol. 2003, 13, 300
10. Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A. Science 2000, 289, 905
11. Selmer, M., Dunham, C. M., Murphy, F. V. t., Weixlbaumer, A., Petry, S., Kelley, A. C., Weir, J. R., and Ramakrishnan, V. Science 2006, 313, 1935
12. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. Cell 2001, 107, 679
13. Schuwirth, B. S., Borovinskaya, M. A., Hau, C. W., Zhang, W., Vila-Sanjurjo, A., Holton, J. M., and Cate, J. H. Science 2005, 310, 827
14. Woese, C. R., Magrum, L. J., Gupta, R., Siegel, R. B., Stahl, D. A., Kop, J., Crawford, N., Brosius, J., Gutell, R., Hogan, J. J., and Noller, H. F. Nucleic Acids Res. 1980, 8, 2275
15. Noller, H. F., Kop, J., Wheaton, V., Brosius, J., Gutell, R. R., Kopylov, A. M., Dohme, F., Herr, W., Stahl, D. A., Gupta, R., and Waese, C. R. Nucleic Acids Res. 1981, 9, 6167
16. Isaksson, J. and Chattopadhyaya, J. Biochemistry 2005, 44, 5390
17. Mohan, S., Hsiao, C., VanDeusen, H., Gallagher, R., Krohn, E., Wartell, R., and Williams, L. D. J. Phys. Chem. B 2009, 113, 2614
18. Hsiao, C., Mohan, S., Kalahar, B. K., and Williams, L. D. Mol. Biol. Evol. 2009, 26, 2415
19. Tuerk, C., Gauss, P., Thermes, C., Groebe, D. R., Gayle, M., Guild, N., Stormo, G., d'Aubenton-Carafa, Y., Uhlenbeck, O. C., Tinoco, I., Jr., Brody, E. N., and Gold, L. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 1364
20. Keating, K. S., Toor, N., and Pyle, A. M. J. Mol. Biol. 2008, 383, 475
21. Butcher, S. E., Dieckmann, T., and Feigon, J. J. Mol. Biol. 1997, 268, 348
22. Wu, H., Yang, P. K., Butcher, S. E., Kang, S., Chanfreau, G., and Feigon, J. EMBO J. 2001, 20, 7240
23. Gutell, R. R., Cannone, J. J., Konings, D., and Gautheret, D. J. Mol. Biol. 2000, 300, 791
24. Lee, J. C., Cannone, J. J., and Gutell, R. R. J. Mol. Biol. 2003, 325, 65
25. Cheong, C., Varani, G., and Tinoco, I., Jr. Nature 1990, 346, 680
26. Varani, G., Cheong, C., Tinoco, I., Jr., and Wimberly, B. Biochemistry 1991, 30, 3280
27. Antao, V. P. and Tinoco, I., Jr. Nucleic Acids Res. 1992, 20, 819
28. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. Science 1996, 273, 1678
29. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Szewczak, A. A., Kundrot, C. E., Cech, T. R., and Doudna, J. A. Science 1996, 273, 1696
30. Batey, R. T., Rambo, R. P., Lucast, L., Rha, B., and Doudna, J. A. Science 2000, 287, 1232
31. Selinger, D., Liao, X., and Wise, J. A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5409
32. Michel, F. and Westhof, E. J. Mol. Biol. 1990, 216, 585
33. Jaeger, L., Michel, F., and Westhof, E. J. Mol. Biol. 1994, 236, 1271
34. Puglisi, J. D., Tan, R. Y., Calnan, B. J., Frankel, A. D., and Williamson, J. R. Science 1992, 257, 76
35. Qin, P. Z., Butcher, S. E., Feigon, J., and Hubbell, W. L. Biochemistry 2001, 40, 6929
36. Hsiao, C., Mohan, S., Hershkovitz, E., Tannenbaum, A., and Williams, L. D. Nucleic Acids Res. 2006, 34, 1481
37. Correll, C. C. and Swinger, K. RNA 2003, 9, 355
38. Elbashir, S. M., Lendeckel, W., and Tuschl, T. Genes Dev. 2001, 15, 188
39. Quigley, G. J. and Rich, A. Science 1976, 194, 796
40. Acharya, P., Acharya, S., Cheruku, P., Amirkhanov, N. V., Foldesi, A., and Chattopadhyaya, J. J. Am. Chem. Soc. 2003, 125, 9948
41. Romaniuk, P. J., Hughes, D. W., Gregoire, R. J., Neilson, T., and Bell, R. A. J. Am. Chem. Soc. 1978, 100, 3971
42. Freier, S. M., Alkema, D., Sinclair, A., Neilson, T., and Turner, D. H. Biochemistry 1985, 24, 4533
43. Sugimoto, N., Kierzek, R., and Turner, D. H. Biochemistry 1987, 26, 4554
44. O'Toole, A. S., Miller, S., and Serra, M. J. RNA 2005, 11, 512
45. Ohmichi, T., Nakano, S., Miyoshi, D., and Sugimoto, N. J. Am. Chem. Soc. 2002, 124, 10367
46. Burkard, M. E., Kierzek, R., and Turner, D. H. J. Mol. Biol. 1999, 290, 967
47. Santa Lucia, J., Jr., Kierzek, R., and Turner, D. Science 1992, 256, 217
48. Marky, L. A. and Breslauer, K. J. Biopolymers 1987, 26, 1601
49. Puglisi, J. D. and Tinoco, I., Jr. Methods Enzymol. 1989, 180, 304
50. Lu, X. J. and Olson, W. K. Nucleic Acids Res. 2003, 31, 5108
51. Zuker, M. Nucleic Acids Res. 2003, 31, 3406
52. Blose, J. M., Proctor, D. J., Veeraraghavan, N., Misra, V. K., and Bevilacqua, P. C. J. Am. Chem. Soc. 2009, 131, 8474
53. Batey, R. T., Sagar, M. B., and Doudna, J. A. J. Mol. Biol. 2001, 307, 229
54. Serra, M. J. and Turner, D. H. In Energetics of Biological Macromolecules; Abelson, J. N., Simon, M. I., Johnson, M. L., and Ackers, G. K., Eds.; Methods in Enzymology 259; Acedemic Press: San Diego, CA, 1995; p 242.
55. Moody, E. M. and Bevilacqua, P. C. J. Am. Chem. Soc. 2004, 126, 9570
56. Moody, E. M., Feerrar, J. C., and Bevilacqua, P. C. Biochemistry 2004, 43, 7992
57. Murray, L. J., Arendall, W. B., III, Richardson, D. C., and Richardson, J. S. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13904
58. Hershkovitz, E., Tannenbaum, E., Howerton, S. B., Sheth, A., Tannenbaum, A., and Williams, L. D. Nucleic Acids Res. 2003, 31, 6249
59. Rich, A. Nat. Struct. Mol. Biol. 2003, 10, 247
60. Sundaralingam, M. Biopolymers 1969, 7, 821
61. Kim, S. H., Sussman, J. L., Suddath, F. L., Quigley, G. J., McPherson, A., Wang, A. H., Seeman, N. C., and Rich, A. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 4970
62. Freier, S. M., Burger, B. J., Alkema, D., Neilson, T., and Turner, D. H. Biochemistry 1983, 22, 6198
63. Freier, S. M., Sugimoto, N., Sinclair, A., Alkema, D., Neilson, T., Kierzek, R., Caruthers, M. H., and Turner, D. H. Biochemistry 1986, 25, 3214
64. Bevington, P. R. Data Reduction and Error Analysis for the Physical Sciences; McGraw-Hill: New York, 1969.