Sequence-dependent folding and unfolding of ligand-bound purine riboswitches

Biopolymers

Volumn 91, Issue 11, 2009, Pages 953-965

  Prychyna, Oksana ^a   Dahabieh, Michael S ^a   Chao, Jay ^a   O'Neill, Melanie A ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

2 aminopurine; Mutagenesis; Riboswitches; RNA folding; Time resolved fluorescence

Indexed keywords

2-AMINOPURINE; BACILLUS SUBTILIS; FLUORESCENCE LIFETIMES; FOLDED STATE; LIGAND BINDING; LIGAND BINDING AFFINITY; LOOP INTERACTION; REGULATORY MECHANISM; RIBOSWITCHES; RNA DYNAMICS; RNA FOLDING; SEQUENCE-DEPENDENT; TIME-RESOLVED FLUORESCENCE;

BACTERIOLOGY; BINDING ENERGY; BIOCHEMISTRY; FLUORESCENCE; GENE EXPRESSION; LAWS AND LEGISLATION; MUTAGENESIS; NUCLEIC ACIDS; RNA;

LIGANDS;

BACTERIAL RNA; MAGNESIUM; 2 AMINOPURINE; GUANINE; MAGNESIUM ION;

ARTICLE; BACILLUS SUBTILIS; BINDING AFFINITY; CONTROLLED STUDY; GENE MUTATION; GENE SEQUENCE; LIGAND BINDING; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; QUORUM SENSING; REGULATORY MECHANISM; RIBOSWITCH; RNA FOLDING; SENSITIVITY ANALYSIS; SEQUENCE HOMOLOGY; ENZYME KINETICS; FLUORESCENCE; GENE CONTROL; GENE EXPRESSION; GENE INTERACTION; PROTEIN FOLDING; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY;

5' UNTRANSLATED REGIONS; APTAMERS, NUCLEOTIDE; BACILLUS SUBTILIS; BASE SEQUENCE; GENES, BACTERIAL; KINETICS; LIGANDS; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; MUTAGENESIS, SITE-DIRECTED; NUCLEIC ACID CONFORMATION; PURINES; RNA, BACTERIAL; RNA, MESSENGER; SPECTROMETRY, FLUORESCENCE; UDPGLUCOSE 4-EPIMERASE;

BACILLUS SUBTILIS;

EID: 70350149960     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21283     Document Type: Article

References (58)

1. Serganov, A.; Patel, D. J. Nat Rev 2007, 8, 776-790.
2. Winkler, W. C.; Breaker, R. R. Annu Rev Microbiol 2005, 59, 487-517.
3. Vitreschak, A. G.; Rodionow, D. A.; Mironov, A. A.; Gelfand, M. S. Rev Trends Genet 2004, 20, 44-50.
4. Batey, R. T. Curr Opin Struct Biol 2006, 16, 299-306.
5. Schwalbe, H.; Buck, J.; Fürtig, B.; Noeske, J.; Wöhnert, J. Angew Chem Int Ed 2007, 46, 1212-1219.
6. Sudarsan, N.; Barrick, J. E.; Breaker, R. R. RNA 2003, 9, 644-647.
7. Cheah, M. T.; Wachter, A.; Sudarsan, N.; Breaker, R. R. Nature 2007, 447, 497-501.
8. Thore, S.; Leibundgut, M.; Ban, N. N. Science 2006, 312, 1208-1211.
9. Croft, M. T.; Moulin, M.; Webb, M. E.; Smith, A. G. Proc Natl Acad Sci USA 2007, 104, 20770-20775.
10. Mironov, A. S.; Gusarov, I.; Rafikov, R.; Lopez, L. E.; Shatalin, K.; Kreneva, R. A.; Perumov, D. A.; Nudler, E. Cell 2002, 111, 747-756.
11. Wickiser, J. K.; Winkler, W. C.; Breaker, R. R.; Crothers, D. M. Mol Cell 2005, 18, 49-60.
12. Wickiser, J. K.; Cheah, M. T.; Breaker, R. R.; Crothers, D. M. Biochemistry 2005, 44, 13404-13414.
13. Sudarsan, N.; Chalamish-Cohen, S.; Nakamura, S.; Emilsson, G. M.; Breaker, R. R. Chem Biol 2005, 12, 1325-1335.
14. Gilbert, S. D.; Mediatore S. J.; Batey, R. T. J Am Chem Soc 2006, 128, 14214-14215.
15. Mandal, M.; Boese, B.; Barrick, J. E.; Winkler, W. C.; Breaker, R. R. Cell 2003, 113, 577-586.
16. Mandal, M.; Breaker, R. R. Nat Struct Mol Biol 2004, 11, 29-35.
17. Johansen, L. E.; Nygaard, P.; Lassen, C.; Agerso, Y.; Saxlid, H. H. J Bacteriol 2003, 185, 5200-5209.
18. Nygaard, P.; Saxlid, H. H. J Bacteriol 2005, 187, 791-794.
19. Batey, R. T.; Gilbert, S. D.; Montange, R. K. Nature 2004, 432, 411-415.
20. Serganov, A.; Yuan, Y. R.; Pikovskaya, O.; Polonskaia, A.; Malinina, L.; Phan, A.T.; Hobartner, C.; Micura, R.; Breaker, R. R.; Patel, D. Chem Biol 2004, 11, 1729-1741.
21. Noeske, J.; Richter, C.; Grundl, M. A.; Nasiri, H. R.; Schwalbe, H.; Wöhnert, J. Proc Natl Acad Sci USA 2005, 102, 1372-1377.
22. Gilbert, S. D.; Stoddard, C. D.; Wise, S. J.; Batey, R. T. J Mol Biol 2006, 359, 754-768.
23. Gilbert, S. D.; Love, C. E.; Edwards, A. L.; Batey, R. T. Biochemistry 2007, 46, 13297-13309.
24. Lemay, J. F.; Lafontaine, D. A. RNA 2007, 13, 339-350.
25. Mulhbacher, J.; Lafontaine, D. A. Nucleic Acids Res 2007, 35, 5568-5580.
26. Lemay, J. F.; Penedo, J. C.; Tremblay, R.; Lilley, D. M.; Lafontaine, D. A. Chem Biol 2006, 13, 857-868.
27. Rieder, R.; Lang, K.; Graber, D.; Micura, R. Chem Bio Chem 2007, 8, 896-902.
28. Noeske, J.; Buck, J.; Furtig, B.; Nasiri, H. R.; Schwalbe, H.; Wöhnert, J. Nucleic Acids Res 2007, 35, 572-583.
29. hnert, J. Nucleic Acids Res 2007, 35, 5262-5273.
30. Buck, J.; Furtig, B.; Noeske, J.; Wöhnert, J.; Schwalbe, H. Proc Natl Acad Sci USA 2007, 104, 15699-15704.
31. Ottink, O. M.; Rampersad, S. M.; Tessari, M.; Zaman, G. J. R.; Heus, H. A.; Wijmenga, S. S. RNA 2007, 13, 2202-2212.
32. Eskandari, S.; Prychyna, O.; Leung, J.; Avdic, D.; O'Neill, M. A. J Am Chem Soc 2007, 129, 11308-11309.
33. Lakowicz, J. R. Principles of Fluorescence Spectroscopy, 2nd ed.; Springer Science: New York, 2004; pp 303-310.
34. Greenleaf, W. J.; Frieda, K. L.; Foster, D. A. N.; Woodside, M. T.; Block, S. M. Science 2008, 319, 630-633.
35. Yamauchi, T.; Miyoshi, D.; Kubodera, T.; Nishimura, A.; Nakai, S.; Sugimoto, N. FEBS Lett 2005, 579, 2583-2588.
36. Heilan-Miller, S. L.; Thirumalai, D.; Woodson, S. A. J Mol Biol 2001, 306, 1157-1166.
37. Draper, D. E. RNA 2004, 10, 335-343.
38. Misra, V. K.; Draper, D. E. J Mol Biol 2002, 317, 507-521.
39. Das, R.; Travers, K. J.; Bai, Y.; Herschlag, D. J Am Chem Soc 2005, 127, 8272-8273.
40. Pan, J.; Thirumalai, D.; Woodson, S. A. Proc Natl Acad Sci USA 1999, 96, 6149-6154.
41. Stoddard, C. D.; Gilbert, S. D.; Batey, R. T. RNA 2008, 14, 675-684.
42. Lin, J. C.; Thirumalai, D. J Am Chem Soc 2008, 130, 14080-14081.
43. Guest, C. R.; Hochstrasser, R. A.; Sower, L. C.; Millar, D. P. Biochemistry 1991, 30, 3271-3279.
44. Williamson, J. R. Nat Struct Biol 2000, 7, 834-837.
45. Leulliot, N.; Varani, G. Biochemistry 2001, 40, 7947-7956.
46. Celander, D. W.; Cech, T. R. Science 1991, 51, 401-407.
47. Jucker, F. M.; Phillips, R. M.; McCallum, S. A.; Pardi, A. Biochemistry 2003, 42, 2560-2567.
48. Lipfert, J.; Das, R.; Chu, V. B.; Kudaravalli, M.; Boyd, N.; Herschlag, D.; Doniach, S. J Mol Biol 2007, 365, 1393-1406.
49. Pitt, S. W.; Zhang, Q.; Patel, D. T.; Al-Hashimi, H. M. Angew Chem Int Ed Engl 2005, 44, 3412-3415.
50. Casiano-Negroni, A.; Sun, X.; Al-Hashimi, H. M. Biochemistry 2007, 46, 6525-6535.
51. Whitford, P. C.; Schug, A.; Saunders, J.; Hennelly, S. P.; Onuchic, J. N.; Sanbonmatsu, K. Y. Biophys J Biophys Lett 2009, 96, L7-L9.
52. Woodson, S. A. Curr Opin Chem Biol 2005, 9, 104-109.
53. Brion, P.; Westhof, E. Annu Rev Biophys Biomol Struct 1997, 26, 113-137.
54. Rieder, R.; Höbartner, C.; Micura, R. Methods Mol Biol 2009, 540, 15-24.
55. Lang, K.; Rieder, R.; Micura, R. Nucleic Acids Res 2007, 35, 5730-5738.
56. Hampel, K. J.; Tinsely, M. M. Biochemistry 2006, 45, 7861-7871.
57. Tinsely, R. A.; Furchak, J. R. W.; Walter, N. G. RNA 2007, 13, 468-477.
58. Gosavi, S.; Chavez, L. L.; Jennings, P. A.; Onuchic, J. N. J Mol Biol 2006, 357, 986-996.