RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNAAsp transcripts

Journal of the American Chemical Society

Volumn 127, Issue 13, 2005, Pages 4659-4667

  Wilkinson, Kevin A ^a   Merino, Edward J ^a   Weeks, Kevin M ^a  

^a University of North Carolina at Chapel Hill   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACYLATION; ESTERS; ION EXCHANGE; PROTEINS; REACTION KINETICS; STRUCTURE (COMPOSITION);

HYDROGEN EXCHANGE; NUCLEOTIDES; RNA FOLDING; TERTIARY STRUCTURES;

RNA;

ACID ANHYDRIDE; ASPARTIC ACID TRANSFER RNA; HYDROXYL GROUP; N METHYLISATOIC ANHYDRIDE; UNCLASSIFIED DRUG;

ACYLATION; ANTICODON; ARTICLE; CONFORMATIONAL TRANSITION; DENATURATION; HYDROLYSIS; MELTING POINT; RNA STRUCTURE; TEMPERATURE DEPENDENCE;

ACYLATION; ANHYDRIDES; ANTHRANILIC ACIDS; BASE SEQUENCE; KINETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, TRANSFER, ASP; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE;

EID: 16344370497     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0436749     Document Type: Article

References (34)

1. (a) Brion, P.; Westhof, E. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 113-137.
2. (b) Tinoco, I.; Bustamante, C. J. Mol. Biol. 1999, 293, 271-281.
3. Gesteland, R. F.; Cech, T. R.; Atkins, J. F. The RNA World, 2 ed.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1999.
4. (a) LeCuyer, K. A.; Crothers, D. M. Biochemistry 1993, 32, 5301-5311.
5. (b) Gluick, T. C.; Draper, D. E. J. Mol. Biol. 1994, 241, 246-262.
6. (c) Wu, M.; Tinoco, I. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 11555-11560.
7. (a) Levitt, M. Nature 1969, 224, 759-763.
8. (b) Nissen, P.; Ippolito, J. A.; Ban, N.; Moore, P. B.; Steitz, T. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4899-4903.
9. (c) Leontis, N. B.; Stombaugh, J.; Westhof, E. Nucleic Acids Res. 2002, 30, 3497-3531.
10. Englander, S. W.; Kallenbach, N. R. Q. Rev. Biophys. 1983, 16, 521-655.
11. Englander, S. W. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 213-238.
12. Merino, E. J.; Wilkinson, K. A.; Coughlan, J. L.; Weeks, K. M. J. Am. Chem. Soc. 2005, 127, accepted for publication.
13. (a) Moorman, A. R.; Abeles, R. H. J. Am. Chem. Soc. 1982, 104, 6785-6786.
14. (b) Hiratsuka, T. Biochim. Biophys. Acta 1983, 742, 496-508.
15. Snoussi, K.; Leroy, J.-L. Biochemistry 2001, 40, 8898-8904.
16. Spies, M. A.; Schowen, R. L. J. Am. Chem. Soc. 2002, 124, 14049-14053.
17. Jean, J. M.; Hall, K. B. Biochemistry 2004, 43, 10277-10284.
18. (a) Decatur, W. A.; Fournier, M. J. J. Biol. Chem. 2003, 278, 695-698.
19. (b) Agris, P. F. Nucleic Acids Res. 2004, 32, 223-238.
20. (a) Westhof, E.; Dumas, P.; Moras, D. J. Mol. Biol. 1985, 184, 119-145.
21. (b) Westhof, E.; Dumas, P.; Moras, D. Acta Crystallogr. A 1988, 44, 112-123.
22. (a) Romby, P.; Moras, D.; Dumas, P.; Ebel, J. P.; Giege, R. J. Mol. Biol. 1987, 195, 193-204.
23. (b) Perret, V.; Garcia, A.; Puglisi, J.; Grosjean, H.; Ebel, J. P.; Florentz, C.; Giege, R. Biochimie 1990, 72, 735-743.
24. Chamberlin, S. I.; Weeks, K. M. J. Am. Chem. Soc. 2000, 122, 216-224.
25. (a) Perret, V.; Garcia, A.; Grosjean, H.; Ebel, J. P.; Florentz, C.; Giege, R. Nature 1990, 344, 787-789.
26. (b) Sissler, M.; Eriani, G.; Martin, F.; Giege, R.; Florentz, C. Nucleic Acids Res. 1997, 25, 4899-4906.
27. (a) Jaeger, J. A.; Turner, D. H.; Zuker, M. Methods Enzymol. 1990, 183, 281-306.
28. (b) Xia, T.; SantaLucia, J. J.; Burkard, M. E.; Kierzek, R.; Schroeder, S. J.; Jiao, X.; Cox, C.; Turner, D. H. Biochemistry 1998, 37, 14719-14735.
29. Mathews, D. H.; Disney, M. D.; Childs, J. L.; Schroeder, S. J.; Zuker, M.; Turner, D. H. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7287-7292.
30. (a) Walter, A. E.; Turner, D. H.; Kim, J.; Lyttle, M. H.; Muller, P.; Mathews, D. H.; Zuker, M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 9218-9222.
31. (b) Draper, D. E.; Gluick, T. C. Methods Enzymol. 1995, 259, 281-305.
32. Das, R.; Laederach, A.; Pearlman, S.; Herschlag, D.; Altman, R. B. SAFA: Semi-automated Footprinting Analysis Software for High-Throughput Quantification of Nucleic Acid Footprinting Experiments. RNA 2005, 11, 344-354.
33. Chambers, J. M.; Cleveland, W. S.; Kleiner, B.; Tukey, P. A. Graphical Methods for Data Analysis; Wadsworth International Group: Belmont, CA, 1983; pp 91-104.
34. John, D. M.; Weeks, K. M. Protein Sci. 2000, 9, 1416-1419.