Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot

Journal of Molecular Biology

Volumn 270, Issue 3, 1997, Pages 451-463

  Gluick, Thomas C ^a   Gerstner, Resi B ^a   Draper, David E ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Cooperativity; Ion binding; Kinetics; RNA folding; RNA tertiary structure

Indexed keywords

MAGNESIUM ION; MESSENGER RNA; POTASSIUM ION; PROTON; RIBOSOME PROTEIN; TRANSFER RNA; BACTERIAL RNA; CATION; MAGNESIUM SULFATE; POTASSIUM CHLORIDE;

ARTICLE; CHEMICAL REACTION KINETICS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; EQUILIBRIUM CONSTANT; ESCHERICHIA COLI; GEL ELECTROPHORESIS; INTRON; MOLECULAR DYNAMICS; PH; PRIORITY JOURNAL; RNA CONFORMATION; CHEMISTRY; CONFORMATION; DNA DENATURATION; KINETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ESCHERICHIA COLI;

BASE SEQUENCE; CATIONS; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; KINETICS; MAGNESIUM SULFATE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; POTASSIUM CHLORIDE; RNA, BACTERIAL; RNA, MESSENGER;

EID: 0031577194     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1119     Document Type: Article

References (43)

1. Asp. Biochemistry. 35:1996;10493-10505.
2. 2. Biochemistry. 15:1976;3912-3917.
3. 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.
4. Coetzee T., Herschlag D., Belfort M. Escherichia coliin vitro. Genes Dev. 8:1994;1575-1588.
5. Cole P. E., Crothers D. M. Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli. Biochemistry. 11:1972;4368-4374.
6. Cole P. E., Yang S. K., Crothers D. M. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry. 11:1972;4358-4368.
7. Craig M. E., Crothers D. M., Doty P. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62:1971;383-401.
8. Deckman I. C., Draper D. E., Thomas M. S. S4-α mRNA translation regulation complex I. Thermodynamics of formation. J. Mol. Biol. 196:1987;313-322.
9. 3+. Biophys. Chem. 21:1985;91-101.
10. Gardiner K. J., Marsh T. L., Pace N. R. Ion dependence of theBacillus subtilis. J. Biol. Chem. 260:1985;5415-5419.
11. Gluick T. C., Draper D. E. Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241:1994;246-262.
12. Grosshans C. A., Cech T. R. Metal ion requirements for sequence-specific endoribonuclease activity of theTetrahymena. Biochemistry. 28:1989;6888-6894.
13. Herschlag D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270:1995;20871-20874.
14. Herschlag D., Khosla M., Tsuchihashi Z., Karpel R. L. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J. 13:1994;2913-2924.
15. Phe. Nucl. Acids Res. 4:1977;2811-2820.
16. 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.
17. Kao T. H., Crothers D. M. A proton-coupled conformational switch ofEscherichia coli. Proc. Natl Acad. Sci. USA. 77:1980;3360-3364.
18. Leu. J. Mol. Biol. 97:1975;519-532.
19. Krakauer H. A thermodynamic analysis of the influence of simple mono- and divalent cations on the conformational transitions of polynucleotide complexes. Biochemistry. 13:1974;2579-2589.
20. Laggerbauer B., Murphy F. L., Cech T. R. Two major tertiary folding transitions of theTetrahymena. EMBO J. 13:1994;2669-2676.
21. Laing L. G., Draper D. E. Thermodynamics of RNA folding in a highly conserved ribosomal RNA domain. J. Mol. Biol. 237:1994;560-576.
22. 2+. J. Mol. Biol. 237:1994;577-587.
23. Lecanidou R., Richards E. G. The thermodynamics and kinetics of conformational changes in 5-S RNA fromEscherichia coli. Eur. J. Biochem. 57:1975;127-133.
24. 13. J. Am. Chem. Soc. 116:1994;8390-8391.
25. Lynch D. C., Schimmel P. R. Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe. Biochemistry. 13:1974a;1841-1852.
26. 2+. Biochemistry. 13:1974b;1852-1861.
27. Macaya R., Wang E., Schultze P., Sklenár V., Feigon J. Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex. J. Mol. Biol. 225:1992;755-773.
28. Monod J., Wyman J., Changeaux J.-P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:1965;88-118.
29. Puglisi J. D., Wyatt J. D., I. Tinoco J. Solution conformation of an RNA hairpin loop. Biochemistry. 29:1990;4215-4226.
30. +2+. Biopolymers. 14:1975;2137-2158.
31. Record M. T., Lohman T. M., Haseth P. d. Ion effects on ligand-nucleic acid interactions. J. Mol. Biol. 107:1976;145-158.
32. Schellman J. A. Macromolecular binding. Biopolymers. 14:1975;999-1018.
33. Singer P., Nomura M. Stability of ribosomal protein mRNA and translational feedback regulation inEscherichia coli. Mol. Gen. Genet. 199:1985;543-546.
34. Spedding G. S., Draper D. E. Allosteric mechanism for translational repression in the E. coli. Proc. Natl Acad. Sci. USA. 90:1993;4399-4403.
35. Stein A., Crothers D. M. Conformational changes of transfer RNA. The role of magnesium(II). Biochemistry. 15:1976a;160-167.
36. fMet. Biochemistry. 15:(1976b;157-160.
37. Tang C. K., Draper D. E. An unusual mRNA pseudoknot structure is recognized by a protein translational repressor. Cell. 57:1989;531-536.
38. Thomas M., Bedwell D. M., Nomura M. Regulation of α operon gene expression inEscherichia coli. J. Mol. Biol. 196:1987;333-345.
39. Traub P., Nomura M. Structure and function ofEscherichia coliin vitro. J. Mol. Biol. 40:1969;391-413.
40. Phe. Eur. J. Biochem. 55:1975;439-444.
41. Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 265:1994;918-924.
42. Zarrinkar P. P., Wang J., Williamson J. R. Slow folding kinetics of RNase P RNA. RNA. 2:1996;564-583.
43. Zhang F., Ramsay E. S., Woodson S. A. In vivoTetrahymenaEscherichia coli. RNA. 1:1995;284-292.