The internal equilibrium of the hairpin ribozyme: Temperature, ion and pH effects

Journal of Molecular Biology

Volumn 286, Issue 4, 1999, Pages 1009-1024

  Nesbitt, Steven M ^a   Erlacher, Heidi A ^a   Fedor, Martha J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Hairpin ribozyme; Metal dependence of RNA catalysis; Ribozyme thermodynamics; RNA catalysis

Indexed keywords

DIVALENT CATION; MONOVALENT CATION; RIBOZYME; SODIUM CHLORIDE;

ARTICLE; CONTROLLED STUDY; ELECTRIC FIELD; ENTHALPY; ENTROPY; PH; PRIORITY JOURNAL; RNA STRUCTURE; TEMPERATURE; THERMODYNAMICS;

EID: 0033525467     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2543     Document Type: Article

References (57)

1. Anderson C. F., Record M. T. Jr. Salt-nucleic acid interactions. Annu. Rev. Phys. Chem. 46:1995;657-700.
2. Bruening G., Passmore B. K., van Tol H., Buzayan J. M., Feldstein P. A. Replication of a plant virus satellite RNA: evidence favors transcription of circular templates of both polarities. Mol. Plant Microbe Interact. 4:1991;219-225.
3. Bukhman Y. V., Draper D. E. Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. J. Mol. Biol. 273:1997;1020-1031.
4. Burke J. M., Butcher S. E., Sargueil B. Structural analysis and modifications of the hairpin ribozyme. Eckstein F., Lilley D. M. J. Catalytic RNA. 1996;129-143 Springer-Verlag, Berlin.
5. Buzayan J. M., Gerlach W. L., Bruening G. Nonenzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature. 323:1986;349-353.
6. Buzayan J. M., Feldstein P. A., Bruening G., Eckstein F. RNA mediated formation of a phosphorothioate diester bond. Biochem. Biophys. Res. Commun. 156:1988;340-347.
7. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.
8. Chowrira B. H., Burke J. M. Binding and cleavage of nucleic acids by the "hairpin" ribozyme. Biochemistry. 30:1991;8518-8522.
9. Chowrira B. M., Berzal-Herranz A., Burke J. M. Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry. 32:1993;1088-1095.
10. Conn G. L., Draper D. E. RNA structure. Curr. Opin. Struct. Biol. 8:1998;278-285.
11. 2+(aq) binding sites. J. Inorg. Biochem. 49:1993;171-175.
12. Craig M. E., Crothers D. M., Doty P. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62:1971;383-401.
13. Dahm S. C., Uhlenbeck O. C. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry. 30:1991;9464-9469.
14. Dahm S. C., Derrick W. B., Uhlenbeck O. C. Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry. 32:1993;13040-13045.
15. Donahue C. P., Fedor M. J. Kinetics of hairpin ribozyme cleavage in yeast. RNA. 3:1997;961-973.
16. Earnshaw D. J., Gait M. J. Progress toward the structure and therapeutic use of the hairpin ribozyme. Antisense Nucl. Acid Drug Dev. 7:1997;403-411.
17. Earnshaw D. J., Gait M. J. Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucl. Acids Res. 26:1998;5551-5561.
18. Feldstein P. A., Bruening G. Catalytically active geometry in the reversible circularization of 'mini-monomer' RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA. Nucl. Acids Res. 21:1993;1991-1998.
19. Forster A. C., Jeffries A. C., Sheldon C. C., Symons R. H. Structural and ionic requirements for self-cleavage of virusoid RNAs and trans self-cleavage of viroid RNA. Cold Spring Harbor Symp. Quant. Biol. 52:1987;249-259.
20. Freier S., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA. 83:1986;9373-9377.
21. Gerlt J. A., Westheimer F. H., Sturtevant J. M. The enthalpies of hydrolysis of acyclic, monocyclic, and glycoside cyclic phosphate diesters. J. Biol. Chem. 250:1975;5059-5067.
22. +on an equilibrium between alternative conformations of an RNA pseudoknot. J. Mol. Biol. 270:1997a;451-463.
23. Gluick T. C., Wills N. M., Gesteland R. F., Draper D. E. Folding of an mRNA pseudoknot required for stop codon readthrough: effects of mono- and divalent ions on stability. Biochemistry. 36:1997b;16173-16186.
24. Hampel A., Cowan J. A. A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem. Biol. 4:1997;513-517.
25. Hampel A., Tritz R. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry. 28:1989;4929-4933.
26. Hegg L. A., Fedor M. J. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry. 34:1995;15813-15828.
27. Hertel K. J., Uhlenbeck O. C. The internal equilibrium of the hammerhead ribozyme reaction. Biochemistry. 34:1995;1744-1749.
28. Hertel K. J., Herschlag D., Uhlenbeck O. C. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry. 33:1994;3374-3385.
29. Jack A., Ladner J. E., Rhodes D., Brown R. S., Klug A. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111:1977;315-328.
30. Jencks W. P. Catalysis in Chemistry and Enzymology. 1969;Dover PublicationsInc, New York. p. 313-317.
31. Kao T. H., Crothers D. M. A proton-coupled conformational switch of Escherichia coli 5S ribosomal RNA. Proc. Natl Acad. Sci. USA. 77:1980;3360-3364.
32. 3by cationic metal complexes. J. Mol. Biol. 97:1975;519-532.
33. 2+binding. Biochemistry. 30:1991;5145-5150.
34. Komatsu Y., Koizumi M., Sekiguchi A., Ohtsuka E. Cross-ligation and exchange reactions catalyzed by hairpin ribozymes. Nucl. Acids Res. 21:1993;185-190.
35. Laing L. G., Gluick T. C., Draper D. E. Stabilization of RNA structure by Mg ions. Specific and non-specific effects. J. Mol. Biol. 237:1994;577-587.
36. Levy J., Rialdi G., Biltonen R. Thermodynamic studies of transfer ribonucleic acids. II. Characterization of the thermal unfolding of yeast phenylalanine-specific transfer ribonucleic acid. Biochemistry. 11:1972;4138-4144.
37. Long D. M., Uhlenbeck O. C. Self-cleaving RNA. FASEB J. 7:1993;25-30.
38. Long D. M., LaRiviere F. J., Uhlenbeck O. C. Divalent metal ions and the internal equilibrium of the hammerhead ribozyme. Biochemistry. 34:1995;14435-14440.
39. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 11:1978;179-246.
40. Milligan J. F., Uhlenbeck O. C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180:1989;51-62.
41. Mohr S. C., Thach R. E. Application of ribonuclease T1 to the synthesis of oligoribonucleotides of defined base sequence. J. Biol. Chem. 244:1969;6566-6576.
42. Murchie A. I., Thomson J. B., Walter F., Lilley D. M. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell. 1:1998;873-881.
43. 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.
44. Nesbitt S., Hegg L. A., Fedor M. J. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol. 4:1997;619-630.
45. Pan T., Long D. M., Uhlenbeck O. C. Divalent metal ions in RNA folding and catalysis. Gesteland R., Atkins J. The RNA World. 1993;271-302 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
46. Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 372:1994;68-74.
47. Pyle A. M. Ribozymes: a distinct class of metalloenzymes. Science. 261:1993;709-714.
48. Record M. T. Jr, Zhang W., Anderson C. F. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Advan. Protein Chem. 51:1998;281-353.
49. Rudolph S. A., Johnson E. M., Greengard P. The enthalpy of hydrolysis of various 3′,5′- and 2′,3′-cyclic nucleotides. J. Biol. Chem. 246:1971;1271-1273.
50. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
51. Sargueil B., Pecchia D. B., Burke J. M. An improved version of the hairpin ribozyme functions as a ribonucleoprotein complex. Biochemistry. 34:1995;7739-7748.
52. 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.
53. Slim G., Gait M. J. Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucl. Acids Res. 19:1991;1183-1188.
54. Phe(yeast): kinetics and electrostatic repulsion. Eur. J. Biochem. 55:1975;439-444.
55. Walter N. G., Burke J. M. The hairpin ribozyme: structure, assembly and catalysis. Curr. Opin. Chem. Biol. 2:1998;24-30.
56. Walter N. G., Hampel K. J., Brown K. M., Burke J. M. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J. 17:1998;2378-2391.
57. Young K. J., Gill F., Grasby J. A. Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucl. Acids Res. 25:1997;3760-3766.