Equilibrium unfolding (folding) pathway of a model H-type pseudoknotted RNA: The role of magnesium ions in stability

Biochemistry

Volumn 37, Issue 46, 1998, Pages 16116-16129

  Nixon, Paul L ^a   Giedroc, David P ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM; MESSENGER RNA; NUCLEOTIDE; RNA;

ARTICLE; BASE PAIRING; ENTHALPY; GENE; MODEL; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; RNA STRUCTURE;

BASE PAIRING; DNA-BINDING PROTEINS; MAGNESIUM; MODELS, MOLECULAR; MUTATION; MYOVIRIDAE; NUCLEIC ACID CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; RNA, MESSENGER; RNA, VIRAL; THERMODYNAMICS; VIRAL PROTEINS;

EID: 0032542051     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi981726z     Document Type: Article

References (34)

1. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golder, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. (1996) Science 273, 1678-1685.
2. Strobel, S. A., and Doudna, J. A. (1997) Trends Biochem. Sci. 22, 262-266.
3. Kolk, M. H., van der Graf, M., Wijmenga, S. S., Pleij, C. W. A., Heus, H. A., and Hilbers, C. W. (1998) Science 280, 343-438.
4. Shen, L. X., and Tinoco, I., Jr. (1995) J. Mol. Biol. 247, 963-978.
5. Mujeeb, A., Clever, J. L., Billeci, T. M., James T. L., and Parslow, T. G. (1998) Nat. Struct. Biol. 5, 432-435.
6. Philippe, C., Bénard, L., Portier, C., Westhof E., Ehresmann, B., and Ehresmann, C. (1995) Nucleic Acids Res. 23, 18-28.
7. McPheeters, D. S., Stormo, G. D., and Gold, L. (1988) J. Mol. Biol. 201, 517-535.
8. Bravo, C., Lescure, F., Laugâa, P., Fourrey, J.-L., and Favre, A. (1996) Nucleic Acids Res. 24, 1351-1359
9. Chen, X., Kang, H., Shen, L. X., Chamorro, M. Varmus, H. E., and Tinoco, I., Jr. (1996) J. Mol. Biol. 260, 479-483.
10. Shi, P. Y., Brinton, M. A., Veal, J. M., Zhong, Y. Y., and Wilson, W. D. (1996) Biochemistry 35, 4222-4230.
11. McDowell, J. A., He, L., Chen, X., and Turner, D. H. (1997) Biochemistry 36, 8030-8038.
12. Kim, J., Walter, A. E., and Turner, D. H. (1996) Biochemistry 35, 13753-13761.
13. Morse, S. E., and Draper, D. E. (1995) Nucleic Acids Res. 23, 302-306.
14. Turner, D. H. (1996) Curr. Opin. Struct. Biol. 6, 299-304.
15. Draper, D. E. (1996) Trends Biochem. Sci. 21, 145-149.
16. Laing, L. G., and Draper, D. E. (1994) J. Mol. Biol. 237, 560-576.
17. Gluick, T. C., and Draper, D. E. (1994) J. Mol. Biol. 241, 246-262.
18. Gluick, T. C., Wills, N. M., Gesteland, R. F., and Draper, D. E. (1997) Biochemistry 36, 16173-16186.
19. Michel, F., and Westhof, E. (1996) Science 273, 1676-1677.
20. Theimer, C. A., Wang, Y., Hoffman, D. W., Krisch, H. M., and Giedroc, D. P. (1998) J. Mol. Biol. 279, 545-564.
21. Shamoo, Y., Tam, A., Konigsberg, W. H., and Willilams, K. R. (1993) J. Mol. Biol. 232, 89-104.
22. Qiu, H., Kaluarachchi, K., Du, Z., Hoffman, D. W., and Giedroc, D. P. (1996) Biochemistry 35, 4176-4186.
23. Du, Z., Giedroc, D. P., and Hoffman, D. W. (1996) Biochemistry 35, 4187-4198.
24. Holland, J. A., Hansen, M. R., Du, Z., and Hoffman, D. W. (1998) RNA 4 (in press).
25. Stein, A., and Crothers, D. M. (1976) Biochemistry 15, 160-168.
26. Laing, L. G., Gluick, T. C., and Draper, D. E. (1994) J. Mol. Biol. 237, 577-587.
27. Schellman, J. A. (1975) Biopolymers 14, 999-1018.
28. Hill, T. L. (1957) J. Polym. Sci. 23, 549-562.
29. Wyman, J., and Gill, S. J. (1990) in Binding and Linkage. Functional Chemistry of Biological Macromolecules, University Science Books, Mill Valley, CA.
30. Turner, D. H., Sugimoto, N., and Freier, S. M. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 167-192.
31. Fresco, J. R., Klotz, L. C., and Richards, E. G. (1963) Cold Spring Harbor Symp. Quant. Biol. 28, 83-90.
32. Record, M. T., Jr., Lohman, T. M., and de Haseth, P. (1976) J. Mol. Biol. 107, 145-158.
33. Crothers, D. M., Cole, P. E., Hilbers, C. W., and Shulman, R. G. (1974) J. Mol. Biol. 87, 63-88.
34. Wyatt J. R., Puglisi, J. D., and Tinoco, I., Jr. (1990) J. Mol. Biol. 214, 455-470.