Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 May 25;11(10):3363–3373. doi: 10.1093/nar/11.10.3363

Melting of local ordered structures in yeast 5S ribosomal RNA in aqueous salts.

S Ohta, S Maruyama, K Nitta, S Sugai
PMCID: PMC325969  PMID: 6344010

Abstract

Equilibrium and kinetics of thermal melting of yeast 5S ribosomal RNA in aqueous NaCl with or without Mg2+ were investigated by differential thermal melting and temperature jump methods. Two peaks (1 and 2) and a shoulder were observed in each of melting curves at ionic strength I=0.002-0.5 and linearity between each of melting temperatures T1m and T2m and log I was found at I=0.01-0.5 in the Mg2+-free solution. The local structures were found to be stabilized considerably by Mg2+. The temperature jump measurements gave the kinetic melting curve of the structure 1 at I=0.03 without Mg2+ or with 0.5 mM Mg2+. The kinetic Tm coincided well with the corresponding static Tm. For the structure 1, various parameters were calculated from the kinetic data, which indicated a double helical character of the structure 1. In terms of the values of Tm, G-C content, and enthalpy change of the transition of the structure 1 or 2, appropriateness of each of the secondary structure models of eukaryotic 5S RNA proposed previously was discussed.

Full text

PDF
3363

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Burns P. D., Luoma G. A., Marshall A. G. Evaluation of base-pairing schemes for E. coli 5S RNA by 400 MHz proton nuclear magnetic resonance spectroscopy. Biochem Biophys Res Commun. 1980 Sep 30;96(2):805–811. doi: 10.1016/0006-291x(80)91426-6. [DOI] [PubMed] [Google Scholar]
  2. Chen M. C., Giegé R., Lord R. C., Rich A. Raman spectra of ten aqueous transfer RNAs and 5S RNA. Conformational comparison with yeast phenylalanine transfer RNA. Biochemistry. 1978 Jul 25;17(15):3134–3138. doi: 10.1021/bi00608a030. [DOI] [PubMed] [Google Scholar]
  3. Cole P. E., Yang S. K., Crothers D. M. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry. 1972 Nov 7;11(23):4358–4368. doi: 10.1021/bi00773a024. [DOI] [PubMed] [Google Scholar]
  4. Coutts S. M., Gangloff J., Dirheimer G. Conformational transitions in tRNA Asp (brewer's yeast). Thermodynamic, kinetic, and enzymatic measurements on oligonucleotide fragments and the intact molecule. Biochemistry. 1974 Sep 10;13(19):3938–3948. doi: 10.1021/bi00716a019. [DOI] [PubMed] [Google Scholar]
  5. Coutts S. M. Thermodynamics and kinetics of G-C base pairing in the isolated extra arm of serine-specific transfer RNA from yeast. Biochim Biophys Acta. 1971 Feb 25;232(1):94–106. doi: 10.1016/0005-2787(71)90494-1. [DOI] [PubMed] [Google Scholar]
  6. Crothers D. M., Cole P. E., Hilbers C. W., Shulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol. 1974 Jul 25;87(1):63–88. doi: 10.1016/0022-2836(74)90560-9. [DOI] [PubMed] [Google Scholar]
  7. Dourlent M., Yaniv M., Hélène C. Temperature-jump relaxation studies on transfer ribonucleic acids. Valine and tyrosine-specific tRNAs from Escherichia coli. Eur J Biochem. 1971 Mar 1;19(1):108–114. doi: 10.1111/j.1432-1033.1971.tb01293.x. [DOI] [PubMed] [Google Scholar]
  8. Erdmann V. A., Huysmans E., Vandenberghe A., De Wachter R. Collection of published 5S and 5.8S ribosomal RNA sequences. Nucleic Acids Res. 1983 Jan 11;11(1):r105–r133. [PMC free article] [PubMed] [Google Scholar]
  9. Erdmann V. A. Structure and function of 5S and 5.8 S RNA. Prog Nucleic Acid Res Mol Biol. 1976;18:45–90. [PubMed] [Google Scholar]
  10. Garrett R. A., Noller H. F. Structures of complexes of 5S RNA with ribosomal proteins L5, L18 and L25 from Escherichia coli: identification of kethoxal-reactive sites on the 5S RNA. J Mol Biol. 1979 Aug 25;132(4):637–648. doi: 10.1016/0022-2836(79)90379-6. [DOI] [PubMed] [Google Scholar]
  11. Gralla J., Crothers D. M. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J Mol Biol. 1973 Feb 5;73(4):497–511. doi: 10.1016/0022-2836(73)90096-x. [DOI] [PubMed] [Google Scholar]
  12. Hori H., Osawa S. Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species. Proc Natl Acad Sci U S A. 1979 Jan;76(1):381–385. doi: 10.1073/pnas.76.1.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kao T. H., Crothers D. M. A proton-coupled conformational switch of Escherichia coli 5S ribosomal RNA. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3360–3364. doi: 10.1073/pnas.77.6.3360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kuwajima K., Sugai S. Equilibrium and kinetics of the thermal unfolding of alpha-lactalbumin. The relation to its folding mechanism. Biophys Chem. 1978 Jul;8(3):247–254. doi: 10.1016/0301-4622(78)87006-9. [DOI] [PubMed] [Google Scholar]
  15. Luoma G. A., Burns P. D., Bruce R. E., Marshall A. G. Melting of Saccharomyces cerevisiae 5S ribonucleic acid: ultraviolet absorption, circular dichroism, and 360-MHz proton nuclear magnetic resonance spectroscopy. Biochemistry. 1980 Nov 11;19(23):5456–5462. doi: 10.1021/bi00564a047. [DOI] [PubMed] [Google Scholar]
  16. Luoma G. A., Marshall A. G. Lasar Raman evidence for a new cloverleaf secondary structure for eucaryotic 5 S RNA. J Mol Biol. 1978 Oct 15;125(1):95–105. doi: 10.1016/0022-2836(78)90256-5. [DOI] [PubMed] [Google Scholar]
  17. Luoma G. A., Marshall A. G. Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4901–4905. doi: 10.1073/pnas.75.10.4901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978 May;11(2):179–246. doi: 10.1017/s0033583500002031. [DOI] [PubMed] [Google Scholar]
  19. Maruyama S., Sugai S. Folding of yeast 5S ribosomal RNA induced by magnesium binding. J Biochem. 1980 Jul;88(1):151–158. [PubMed] [Google Scholar]
  20. Maruyama S., Tatsuki T., Sugai S. Equilibrium and kinetics of the thermal unfolding of yeast 5S ribosomal RNA. J Biochem. 1979 Nov;86(5):1487–1494. doi: 10.1093/oxfordjournals.jbchem.a132667. [DOI] [PubMed] [Google Scholar]
  21. Nishikawa K., Takemura S. Structure and function of 5S ribosomal ribonucleic acid from Torulopsis utilis. IV. Detection of exposed guanine residues by chemical modification with kethoxal. J Biochem. 1978 Aug;84(2):259–266. doi: 10.1093/oxfordjournals.jbchem.a132126. [DOI] [PubMed] [Google Scholar]
  22. Reid B. R. NMR studies on RNA structure and dynamics. Annu Rev Biochem. 1981;50:969–996. doi: 10.1146/annurev.bi.50.070181.004541. [DOI] [PubMed] [Google Scholar]
  23. Riesner D., Römer R., Maass G. Kinetic study of the three conformational transitions of alanine specific transfer RNA from yeast. Eur J Biochem. 1970 Jul;15(1):85–91. doi: 10.1111/j.1432-1033.1970.tb00979.x. [DOI] [PubMed] [Google Scholar]
  24. Steger G., Müller H., Riesner D. Helix-coil transitions in double-stranded viral RNA. Fine resolution melting and ionic strength dependence. Biochim Biophys Acta. 1980 Feb 29;606(2):274–284. doi: 10.1016/0005-2787(80)90037-4. [DOI] [PubMed] [Google Scholar]
  25. Studnicka G. M., Eiserling F. A., Lake J. A. A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes. Nucleic Acids Res. 1981 Apr 24;9(8):1885–1904. doi: 10.1093/nar/9.8.1885. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Stulz J., Ackermann T., Appel B., Erdmann V. A. Determination of base pairing in yeast 5S and 5.8S RNA infrared spectroscopy. Nucleic Acids Res. 1981 Aug 11;9(15):3851–3861. doi: 10.1093/nar/9.15.3851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Vigne R., Jordan B. R. Partial enzyme digestion studies on Escherichia coli, Pseudomonas, Chlorella, Drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models. J Mol Evol. 1977 Sep 20;10(1):77–86. doi: 10.1007/BF01796136. [DOI] [PubMed] [Google Scholar]
  28. Willick G. E., Nazar R. N., Van N. T. Physicochemical studies on the 5S ribonucleic acid-protein complex from a eucaryote, Saccharomyces cerevisiae. Biochemistry. 1980 Jun 10;19(12):2738–2742. doi: 10.1021/bi00553a031. [DOI] [PubMed] [Google Scholar]
  29. Wong Y. P., Kearns D. R., Reid B. R., Shulman R. G. The extent of base pairing in 5 s RNA. Yeast 5 s RNA. J Mol Biol. 1972 Dec 30;72(3):741–749. doi: 10.1016/0022-2836(72)90188-x. [DOI] [PubMed] [Google Scholar]
  30. Wool I. G. The structure and function of eukaryotic ribosomes. Annu Rev Biochem. 1979;48:719–754. doi: 10.1146/annurev.bi.48.070179.003443. [DOI] [PubMed] [Google Scholar]
  31. Wrede P., Erdmann V. A. Escherichia coli 5S RNA binding proteins L18 and L25 interact with 5.8S RNA but not with 5S RNA from yeast ribosomes. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2706–2709. doi: 10.1073/pnas.74.7.2706. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES