A powerful approach for the selection of 2-aminopurine substitution sites to investigate RNA folding

Journal of the American Chemical Society

Volumn 133, Issue 40, 2011, Pages 16161-16167

  Soulière, Marie F ^a   Haller, Andrea ^a   Rieder, Renate ^a,b   Micura, Ronald ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

2-AMINOPURINE; 2-AMINOPURINE (2AP); BENZOYL CYANIDE; BIOLOGICAL SIGNIFICANCE; CLASS II; FOLDING DYNAMICS; FOLDING KINETICS; NUCLEOBASES; NUCLEOTIDE SUBSTITUTION; PRIMER EXTENSION; RIBOSWITCHES; RNA FOLDING; RNA MOLECULES; RNA STRUCTURES; SITE-SPECIFIC; STRAIGHT-FORWARD METHOD; STRUCTURAL DATA; TARGET MOLECULE; TERTIARY STRUCTURES; THREE MODELS;

CYANIDES; FLUORESCENCE; MOLECULES; NUCLEOTIDES;

RNA;

2 AMINOPURINE; ADENINE; MAGNESIUM; NUCLEOTIDE; RNA;

ACYLATION; ARTICLE; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; RNA STRUCTURE; SUBSTITUTION REACTION;

2-AMINOPURINE; BASE SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA; RNA FOLDING; SPECTROMETRY, FLUORESCENCE;

EID: 80053542128     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja2063583     Document Type: Article

References (42)

1. Strobel, S. A.; Cochrane, J. C. Curr. Opin. Chem. Biol. 2007, 11, 636-643
2. Serganov, A.; Patel, D. J. Nat. Rev. Genet. 2007, 8, 776-790
3. Nudler, E.; Mironov, A. S. Trends Biochem. Sci. 2004, 29, 11-17
4. Zhou, X.; Wang, G.; Zhang, W. Mol. Syst. Biol. 2007, 3, 103-113
5. Inui, M.; Martello, G.; Piccolo, S. Nat. Rev. Mol. Cell Biol. 2010, 11, 252-263
6. Weigand, J. E.; Suess, B. Appl. Microbiol. Biotechnol. 2009, 85, 229-236
7. Wieland, M.; Hartig, J. S. Chem B ioChem 2008, 9, 1873-1878
8. Batey, R. T.; Rambo, R. P.; Doudna, J. A. Angew. Chem., Int. Ed. Engl. 1999, 38, 2326-2343
9. Roth, A.; Breaker, R. R. Annu. Rev. Biochem. 2009, 78, 305-334
10. Schwalbe, H.; Buck, J.; Furtig, B.; Noeske, J.; Wohnert, J. Angew. Chem., Int. Ed. Engl. 2007, 46, 1212-1219
11. Jean, J. M.; Hall, K. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 37-41
12. Sinkeldam, R. W.; Greco, N.; Tor, Y. Chem. Rev. 2010, 110, 2579-2619
13. Law, S. M.; Eritja, R.; Goodman, M. F.; Breslauer, K. J. Biochemistry 1996, 35, 12329-12337
14. Sowers, L. C.; Fazakerley, G. V.; Eritja, R.; Kaplan, B. E.; Goodman, M. F. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 5434-5438
15. Means, J. A.; Simson, C. M.; Zhou, S.; Rachford, A. A.; Rack, J. J.; Hines, J. V. Biochem. Biophys. Res. Commun. 2009, 389 (4) 616-621
16. Heppell, B.; Mulhbacher, J.; Penedo, J. C.; Lafontaine, D. A. Methods Mol. Biol. 2009, 540, 25-37
17. Lang, K.; Rieder, R.; Micura, R. Nucleic Acids Res. 2007, 35, 5370-5378
18. Rieder, R.; Lang, K.; Graber, D.; Micura, R. ChemBioChem 2007, 8, 896-902
19. Rieder, U.; Kreutz, C.; Micura, R. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 10804-10809
20. Haller, A.; Rieder, U.; Aigner, M.; Blanchard, S. C.; Micura, R. Nat. Chem. Biol. 2011, 7, 393-400
21. Heppell, B.; Lafontaine, D. A. Biochemistry 2008, 47, 1490-1499
22. Gilbert, S. D; Stoddard, C. D.; Wise, S. J.; Batey, R. T. J. Mol. Biol. 2006, 359, 754-768
23. Haller, A.; Soulière, M. F.; Micura, R. Acc. Chem. Res. 2011, DOI: 10.1021/ar200035g.
24. Merino, E. J.; Wilkinson, K. A.; Coughlan, J. L.; Weeks, K. M. J. Am. Chem. Soc. 2005, 127, 4223-4231
25. Weeks, K. M.; Mauger, D. M. Acc. Chem. Res. 2011, DOI: 10.1021/ar200051h.
26. Wilkinson, K. A.; Merino, E. J.; Weeks, K. M. Nat. Protoc. 2006, 1, 1610-1616
27. Low, J. T.; Weeks, K. M. Methods 2010, 52, 150-158
28. Mortimer, S. A.; Weeks, K. M. J. Am. Chem. Soc. 2007, 129, 4144-4145
29. Watts, J. M.; Dang, K. K.; Gorelick, R. J.; Leonard, C. W.; Bess, J. W., Jr.; Swanstrom, R.; Burch, C. L.; Weeks, K. M. Nature 2009, 460, 711-716
30. Gherghe, C. M.; Shajani, Z.; Wilkinson, K. A.; Varani, G.; Weeks, K. M. J. Am. Chem. Soc. 2008, 130, 12244-12245
31. Gilbert, S. D.; Rambo, R. P.; Van Tyne, D.; Batey, R. T. Nat. Struct. Mol. Biol. 2008, 15, 177-182
32. Serganov, A.; Yuan, Y. R.; Pikovskaya, O.; Polonskaia, A.; Malinina, L.; Phan, A. T.; Höbartner, C.; Micura, R.; Breaker, R. R.; Patel, D. J. Chem. Biol. 2004, 11, 1729-1741
33. Rieder, R., Ph.D. thesis, Leopold-Franzens Universität, Innsbruck, Austria, 2008.
34. Meyer, M. M.; Roth, A.; Chervin, S. M.; Garcia, G. A.; Breaker, R. R. RNA 2008, 14, 685-695
35. Jucker, F. M.; Heus, H. A.; Yip, P. F.; Moors, E. H.; Pardi, A. J. Mol. Biol. 1996, 264, 968-980
36. Pan, T.; Loria, A.; Zhong, K. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 12510-12514
37. Pyle, A. M.; Cech, T. R. Nature 1991, 350, 628-631
38. Brunel, C; Romby, P. Methods Enzymol. 2000, 318, 3-21
39. Weeks, K. M. Curr. Opin. Struct. Biol. 2010, 20, 295-304
40. Lang, K.; Micura, R. Nat. Protoc. 2008, 3, 1457-1466
41. Rieder, R.; Höbartner, C.; Micura, R. Methods Mol. Biol. 2009, 540, 15-24
42. Höbartner, C.; Micura, R. J. Am. Chem. Soc. 2004, 126, 1141-1149