The kinetics and magnesium requirements for the folding of antigenomic δ ribozymes

Biochemical and Biophysical Research Communications

Volumn 270, Issue 2, 2000, Pages 600-607

  Ananvoranich, Sirinart ^a   Perreault, Jean Pierre ^a  

^a UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

Folding; Kinetics; Native structure; ribozyme

Indexed keywords

MAGNESIUM ION; OLIGONUCLEOTIDE; RIBOZYME;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME KINETICS; HYBRIDIZATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION; TRANSACTIVATION;

EID: 0034643251     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1006/bbrc.2000.2465     Document Type: Article

References (26)

1. Narlikar G. J, Herschlag D. Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem. 66:1997;19-59.
2. Turner, P. C. 1997, Methods in Molecular Biology: Ribozyme Protocols, Vol, 74, Humana Press, Totowa, NJ.
3. Pley H. W., Flaherty K. M., McKay D. B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-113.
4. Pley H. W., Lindes D. S., DeLuca-Flaherty C., McKay D. B. Crystals of a hammerhead ribozyme. J. Biol. Chem. 268:1993;19656-19658.
5. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
6. Scott W. G., Murray J. B., Arnold J. R. P., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme. Science. 274:1996;2065-2069.
7. Walter F., Murchie A. I. H., Lilley D. M. J. Folding of the four-way RNA junction of the hairpin ribozyme. Biochemistry. 37:1998;17629-17636.
8. Bassi G. S., Murchie A. I. H., Walter F., Clegg R. M., Lilley D. M. J. Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study. EMBO J. 16:1997;7481-7489.
9. Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
10. Zarrinkar P. P., Wang J., Williamson J. R. Slow folding kinetics of RNase P RNA. RNA. 2:1996;564-573.
11. Ferre-D'Amare A. R., Zhou K. Crystal structure of a hepatitis delta virus ribozyme. Nature. 395:1998;567-574.
12. Wadkins T. S., Perrotta A. T., Ferre-D'Amare A. R., Doudna J. A., Been M. D. A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA. 5:1999;720-727.
13. Nishikawa F., Nishikawa S. Requirement for canonical base pairing in the short pseudoknot structure of genomic hepatitis delta virus ribozyme. Nucleic Acids Res. 28:2000;925-931.
14. Murray J. B., Seyhan A. A., Walter N. G., Burke J. M., Scott W. G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5:1998;587-595.
15. Wu H.-Y., Lai M. M. RNA conformational requirements of self-cleavage of hepatitis delta virus RNA. Mol. Cell. Biol. 10:1990;5575-5579.
16. Gottlieb P. A., Prasad Y., Smith J. B., Williams A. P., Dinter-Gottlieb G. Evidence that alternate foldings of the hepatitis delta RNA confer varying rates of self-cleavage. Biochemistry. 33:1994;2802-2808.
17. Wu H.-N., Lee J.-Y., Ping Y.-H., Wang C.-N. The effect of Lp3 enlargement on the folding and catalysis of hepatitis delta virus cis-cleaving ribozyme. FEBS Lett. 439:1998;312-316.
18. Ananvoranich S., Perreault J. P. Substrate specificity of delta ribozyme cleavage. J. Biol. Chem. 273:1998;13182-13188.
19. Perrotta A. T., Shih I. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science. 286:1999;123-126.
20. Fauzi H., Kawakami J., Nishikawa F. Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme. Nucleic Acids Res. 25:1997;3124-3130.
21. Puglisi J. D., Wyatt J. R., Tinoco I. Jr. Conformation of an RNA pseudoknot. J. Mol. Biol. 214:1990;437-453.
22. Jeoung Y. H., Kumar P. K., Suh Y. A., Taira K., Nishikawa S. Identification of phosphate oxygens that are important for self-cleavage activity of the HDV ribozyme by phosphorothioate substitution interference analysis. Nucleic Acids Res. 22:1994;3722-3727.
23. Pan, T., Long, D. M., and Uhlenbeck, O. C.1993InThe RNA World (Gesteland, R. F., and Atkins, J. F., Eds.), pp. 371-302. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
24. Lafontaine, D. A., Ananvoranich, S., and Perreault, J. P.1999 Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme Nucleic Acids Res.27, 3236-3243.
25. Mercure S., Lafontaine D., Ananvoranich S., Perreault J. P. Kinetic analysis of delta ribozyme cleavage. Biochemistry. 37:1998;16975-16982.
26. Been M. D., Perrotta A. T., Rosenstein S. P. Secondary structure of the self-cleaving RNA of hepatitis delta virus: Applications to catalytic RNA design. Biochemistry. 31:1992;11843-11852.