Probing mechanism and transition state of RNA refolding

ACS Chemical Biology

Volumn 5, Issue 8, 2010, Pages 753-765

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

^a GOETHE UNIVERSITY   (Germany)

^b EPFL   (Switzerland)

^c MAX F PERUTZ LABORATORIES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; SPERMIDINE;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CIRCULAR DICHROISM; GENE STRUCTURE; KINETICS; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL;

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

EID: 77955917180     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb100025a     Document Type: Article

References (46)

1. Zarrinkar, P. P. and Williamson, J. R. (1994) Kinetic intermediates in RNA folding Science 265, 918-924
2. Schwalbe, H., Buck, J., Furtig, B., Noeske, J., and Wohnert, J. (2007) Structures of RNA switches: insight into molecular recognition and tertiary structure Angew. Chem., Int. Ed. 46, 1212-1219
3. Wong, T. N., Sosnick, T. R., and Pan, T. (2007) Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures Proc. Natl. Acad. Sci. U.S.A. 104, 17995-18000
4. Rajkowitsch, L. and Schroeder, R. (2007) Dissecting RNA chaperone activity RNA 13, 2053-2060
5. Furtig, B., Buck, J., Manoharan, V., Bermel, W., Jaschke, A., Wenter, P., Pitsch, S., and Schwalbe, H. (2007) Time-resolved NMR studies of RNA folding Biopolymers 86, 360-383
6. Leontis, N. B. and Westhof, E. (2003) Analysis of RNA motifs Curr. Opin. Struct. Biol. 13, 300-308
7. Westhof, E. and Fritsch, V. (2000) RNA folding: beyond Watson-Crick pairs Structure 8, R55-65
8. Misra, V. K. and Draper, D. E. (1998) On the role of magnesium ions in RNA stability Biopolymers 48, 113-135
9. Bai, Y., Greenfeld, M., Travers, K. J., Chu, V. B., Lipfert, J., Doniach, S., and Herschlag, D. (2007) Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids J. Am. Chem. Soc. 129, 14981-14988
10. Bloomfield, V. A., Crothers, D. M., and Tinoco, I. (2000) Nucleic Acids: Structures, Properties and Functions, University Science Books, Sausalito.
11. Heilman-Miller, S. L., Thirumalai, D., and Woodson, S. A. (2001) Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations J. Mol. Biol. 306, 1157-1166 (Pubitemid 33030011)
12. Bloomfield, V. A. (1997) DNA condensation by multivalent cations Biopolymers 44, 269-282
13. Porschke, D. (1984) Dynamics of DNA condensation Biochemistry 23, 4821-4828
14. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing Science 273, 1678-1685
15. Cole, P. E., Yang, S. K., and Crothers, D. M. (1972) Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams Biochemistry 11, 4358-4368
16. Pyle, A. M. (1993) Ribozymes: a distinct class of metalloenzymes Science 261, 709-714
17. Anderson, J. W., Jirsch, J. D., and Fedida, D. (1995) Cation regulation of anion current activated by cell swelling in two types of human epithelial cancer cells J. Physiol. 483 (Pt 3) 549-557
18. Manning, G. S. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Q. Rev. Biophys. 11, 179-246
19. Tabor, C. W. and Tabor, H. (1984) Polyamines Ann. Rev. Biochem. 53, 749-790
20. Rubin, R. L. (1977) Spermidine-deoxyribonucleic acid interaction in vitro and in Escherichia coli J. Bacteriol. 129, 916-925
21. Williams, L. J., Barnett, G. R., Ristow, J. L., Pitkin, J., Perriere, M., and Davis, R. H. (1992) Ornithine decarboxylase gene of Neurospora crassa: isolation, sequence, and polyamine-mediated regulation of its mRNA Mol. Cell. Biol. 12, 347-359
22. Kusama-Eguchi, K., Watanabe, S., Irisawa, M., Watanabe, K., and Igarashi, K. (1991) Correlation between spermine stimulation of rat liver Ile-tRNA formation and structural change of the acceptor stem by spermine Biochem. Biophys. Res. Commun. 177, 745-750
23. Veress, I., Haghighi, S., Pulkka, A., and Pajunen, A. (2000) Changes in gene expression in response to polyamine depletion indicates selective stabilization of mRNAs Biochem. J. 346 (Pt 1) 185-191
24. Davis, R. H., Morris, D. R., and Coffino, P. (1992) Sequestered end products and enzyme regulation: the case of ornithine decarboxylase Microbiol. Rev. 56, 280-290
25. Watanabe, S., Kusama-Eguchi, K., Kobayashi, H., and Igarashi, K. (1991) Estimation of polyamine binding to macromolecules and ATP in bovine lymphocytes and rat liver J. Biol. Chem. 266, 20803-20809
26. Heilman-Miller, S. L., Pan, J., Thirumalai, D., and Woodson, S. A. (2001) Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics J. Mol. Biol. 309, 57-68 (Pubitemid 32553507)
27. Micura, R. and Hobartner, C. (2003) On secondary structure rearrangements and equilibria of small RNAs ChemBioChem 4, 984-990
28. Furtig, B., Wenter, P., Reymond, L., Richter, C., Pitsch, S., and Schwalbe, H. (2007) Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy J. Am. Chem. Soc. 129, 16222-16229
29. Wenter, P., Furtig, B., Hainard, A., Schwalbe, H., and Pitsch, S. (2005) Kinetics of photoinduced RNA refolding by real-time NMR spectroscopy Angew. Chem., Int. Ed. 44, 2600-2603
30. Wenter, P., Furtig, B., Hainard, A., Schwalbe, H., and Pitsch, S. (2006) A caged uridine for the selective preparation of an RNA fold and determination of its refolding kinetics by real-time NMR ChemBioChem 7, 417-420
31. Wirmer, J., Kuhn, J., and Schwalbe, H. (2001) Millisecond time resolved photo-CIDNP NMR reveals a non-native folding intermediate on the ion-induced refolding pathway of bovine alpha-lactalbumin Angew. Chem., Int. Ed. 40, 4248-4251
32. Kuhn, T. and Schwalbe, H. (2000) Monitoring the kinetics of ion-dependent protein folding by time-resolved NMR spectroscopy at atomic resolution J. Am. Chem. Soc. 122, 6169-6174
33. Kohlrausch, R. (1854) Theorie des elektrischen Rückstandes in der Leidner Flasche Poggendorff 91 (56-82) 179-213
34. Allen, F. S., Gray, D. M., and Ratliff, R. L. (1984) On the first-neighbor analysis of nucleic acid CD spectra: the definitive T-matrix and considerations of various methods Biopolymers 23, 2639-2659
35. Riazance, J. H., Baase, W. A., Johnson, W. C., Hall, K., Cruz, P., and Tinoco, I. (1985) Evidence for Z-form RNA by vacuum UV circular-dichroism Nucleic Acids Res. 13, 4983-4989
36. Gueron, M. and Leroy, J. L. (1995) Studies of base pair kinetics by NMR measurement of proton exchange Methods Enzymol. 261, 383-413
37. Laing, L. G., Gluick, T. C., and Draper, D. E. (1994) Stabilization of RNA structure by Mg ions-specific and nonspecific effects J. Mol. Biol. 237, 577-587
38. Wyatt, J. R., Puglisi, J. D., and Tinoco, I. (1990) RNA pseudoknots-stability and loop size requirements J. Mol. Biol. 214, 455-470
39. Jonikas, M. A., Radmer, R. J., and Altman, R. B. (2009) Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models Bioinformatics 25, 3259-3266
40. Jonikas, M. A., Radmer, R. J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., and Altman, R. B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters RNA 15, 189-199
41. Walter, F., Murchie, A. I., Thomson, J. B., and Lilley, D. M. (1998) Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions Biochemistry 37, 14195-14203
42. Chadalavada, D. M., Senchak, S. E., and Bevilacqua, P. C. (2002) The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots J. Mol. Biol. 317, 559-575
43. Shcherbakova, I. and Brenowitz, M. (2005) Perturbation of the hierarchical folding of a large RNA by the destabilization of its scaffold's tertiary structure J. Mol. Biol. 354, 483-496
44. Rook, M. S., Treiber, D. K., and Williamson, J. R. (1998) Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape J. Mol. Biol. 281, 609-620
45. Wenter, P., Reymond, L., Auweter, S. D., Allain, F. H. T., and Pitsch, S. (2006) Short, synthetic and selectively C-13-labeled RNA sequences for the NMR structure determination of protein-RNA complexes Nucleic Acids Res. 34
46. Sklenar, V. and Bax, A. (1987) A new water suppression technique for generating pure-phase spectra with equal excitation over a wide bandwidth J. Magn. Reson. 75, 378-383