Kinetics of photoinduced RNA refolding by real-time NMR spectroscopy

Angewandte Chemie - International Edition

Volumn 44, Issue 17, 2005, Pages 2600-2603

  Wenter, Philipp ^a   Fürtig, Boris ^b   Hainard, Alexandre ^a   Schwalbe, Harald ^b   Pitsch, Stefan ^a  

^a EPFL   (Switzerland)

^b GOETHE UNIVERSITY   (Germany)

Author keywords

Kinetics; NMR spectroscopy; Oligonucleotides; Photolysis; RNA structures

Indexed keywords

CHEMICAL ANALYSIS; CONFORMATIONS; GRAPH THEORY; LASER PULSES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; REACTION KINETICS; REAL TIME SYSTEMS;

GUANOSINE; PHOTOINDUCED RNA FOLDING; REFOLDING PROCESS; RNA SEQUENCES;

RNA;

RNA;

ARTICLE; CHEMISTRY; CONFORMATION; KINETICS; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; KINETICS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA;

EID: 18044387417     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/anie.200462724     Document Type: Article

References (31)

1. a) N. G. Walter, D. A. Harris, M. J. B. Pereira, D. Rueda, Biopolymers 2002, 61, 224-241;
2. b) W. C. Winkler, R. R. Breaker, ChemBioChem 2001, 2, 1024-1032;
3. c) P. Brion, E. Westhof, Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 113-137.
4. J. Pan, D. Thirumalai, S. A. Woodson, J. Mol. Biol. 1997, 273, 7-13.
5. D. K. Treiber, M. S. Rook, P. P. Zarrinkar, J. R. Williamson, Science 1998, 279, 1943-1946.
6. C. Höbartner, R. Micura, J. Mol. Biol. 2003, 325, 421-431.
7. a) P. P. Zarrinkar, J. R. Williamson, Science 1994, 265, 918-924;
8. b) X. Zhuang, L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, S. Chu, Science 2000, 288, 2048-2051 ;
9. c) B. Sclavi, M. Sullivan, M. R. Chance, M. Brenowitz, S. A. Woodson, Science 1998, 279, 1940-1943;
10. d) J. Ravetch, J. Gralla, D. M. Crothers, Nucleic Acids Res. 1974, 1, 109-127;
11. e) M. Menger, F. Eckstein, D. Porschke, Biochemistry 2000, 39, 4500-4507.
12. a) D. Pörschke, Mol. Biol. Biochem. Biophys. 1977, 24, 191-218;
13. b) D. M. Crothers, P. E. Cole, C. W. Hilbers, P. G. Shulman, J. Mol. Biol. 1974, 87, 63-88;
14. c) D. Thirumalai, S. A. Woodson, RNA 2000, 6, 790-794;
15. d) D. Thirumalai, N. Lee, S. A. Woodson, D. K. Klimov, Annu. Rev. Phys. Chem. 2001, 52, 751-762;
16. e) I. Tinoco, Jr., C. Bustamante, J. Mol. Biol. 1999, 293, 271-281.
17. a) T. C. Gluick, R. B. Gerstner, D. E. Draper, J. Mol. Biol. 1997, 270, 451-463;
18. b) D. C. Lynch, P. R. Schimmel, Biochemistry 1974, 13, 1841-1852;
19. c) D. C. Lynch, P. R. Schimmel, Biochemistry 1974, 13, 1852-1861.
20. C. Höbartner, M. O. Ebert, B. Jaun, R. Micura, Angew. Chem. 2002, 114, 619-623; Angew. Chem. Int. Ed. 2002, 41, 605-609.
21. C. Höbartner, M. O. Ebert, B. Jaun, R. Micura, Angew. Chem. 2002, 114, 619-623; Angew. Chem. Int. Ed. 2002, 41, 605-609.
22. 15N-labeled phosphoramidites is reported in b) P. Wenter, S. Pitsch, Helv. Chim. Acta 2003, 86, 3955-3974.
23. 15N-labeled phosphoramidites is reported in b) P. Wenter, S. Pitsch, Helv. Chim. Acta 2003, 86, 3955-3974.
24. 6-(2,2,2-trichloroethyl)-modified guanosine was reported by C. Höbartner, H. Mittendorfer, K. Breuker, R. Micura, Angew. Chem. 2004, 116, 4012-4015; Angew. Chem. Int. Ed. 2004, 43, 3922-3925; however, removal of the Zn-labile trichloroethyl group is much slower than RNA refolding processes and thus prevents the determination of kinetic parameters.
25. 6-(2,2,2-trichloroethyl)-modified guanosine was reported by C. Höbartner, H. Mittendorfer, K. Breuker, R. Micura, Angew. Chem. 2004, 116, 4012-4015; Angew. Chem. Int. Ed. 2004, 43, 3922-3925; however, removal of the Zn-labile trichloroethyl group is much slower than RNA refolding processes and thus prevents the determination of kinetic parameters.
26. 2O (9:1) and potassium arsenate buffer (25 mM, pH 7.0; identical results were obtained with sodium and potassium phosphate buffers in preliminary experiments). The 2D-HSQC and HNN-COSY spectra were recorded according to a) S. Mori, C. Abeygunawardana, M. O'Neil-Johnson, P. C. M. Vanzijl, J. Magn. Reson. B 1995, 108, 94-98 and b) A. J. Dingley, S. Grzesiek, J. Am. Chem. Soc. 1998, 120, 8293-8297.
27. 2O (9:1) and potassium arsenate buffer (25 mM, pH 7.0; identical results were obtained with sodium and potassium phosphate buffers in preliminary experiments). The 2D-HSQC and HNN-COSY spectra were recorded according to a) S. Mori, C. Abeygunawardana, M. O'Neil-Johnson, P. C. M. Vanzijl, J. Magn. Reson. B 1995, 108, 94-98 and b) A. J. Dingley, S. Grzesiek, J. Am. Chem. Soc. 1998, 120, 8293-8297.
28. T. Kühn, H. Schwalbe, J. Am. Chem. Soc. 2000, 122, 6169-6174.
29. H2O could influence the intensity of the exchange-induced water-imino cross-peaks in the 2D NOESY experiment; however, the ribose protons are too far away from the imino protons. Hydroxy group protons are in exchange with water and could potentially contribute to the cross-peak intensity; again, the effect is made negligible by long distance. Base protons resonate upfield and cannot contribute to the cross-peak intensity.
30. a) C. Flamm, W. Fontana, I. L. Hofacker, P. Schuster, RNA 2000, 6, 325-338;
31. b) W. Zhang, S. J. Chen, Proc. Natl. Acad. Sci. USA 2002, 99, 1931-1936.