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. 1986 Feb 11;14(3):1365–1378. doi: 10.1093/nar/14.3.1365

Secondary structure of Tetrahymena thermophilia 5S ribosomal RNA as revealed by enzymatic digestion and microdensitometric analysis.

B Sneath, C Vary, G Pavlakis, J Vournakis
PMCID: PMC339510  PMID: 3005972

Abstract

The secondary structure of [32P] end-labeled 5S rRNA from Tetrahymena thermophilia (strain B) has been investigated using the enzymes S1 nuclease, cobra venom ribonuclease and T2 ribonuclease. The results, analyzed by scanning microdensitometry and illustrated by three-dimensional computer graphics, support the secondary structure model of Curtiss and Vournakis for 5S rRNA. Aberrent mobility of certain RNA fragments on sequencing gels was observed as regions of band compression. These regions are postulated to be caused by stable internal base-pairing. The molecule was probed with T2 RNase in neutral (pH 7.5) and acidic (pH 4.5) buffers and only minor structural differences were revealed. One of the helices was found to be susceptible to enzymatic attack by both the single-strand and double-strand specific enzymes. These observations are evidence for the existence of dynamic structural equilibria in 5S rRNA.

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Selected References

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

  1. Andersen J., Delihas N., Hanas J. S., Wu C. W. 5S RNA structure and interaction with transcription factor A. 2. Ribonuclease probe of the 7S particle from Xenopus laevis immature oocytes and RNA exchange properties of the 7S particle. Biochemistry. 1984 Nov 20;23(24):5759–5766. doi: 10.1021/bi00319a014. [DOI] [PubMed] [Google Scholar]
  2. Auron P. E., Weber L. D., Rich A. Comparison of transfer ribonucleic acid structures using cobra venom and S1 endonucleases. Biochemistry. 1982 Sep 14;21(19):4700–4706. doi: 10.1021/bi00262a028. [DOI] [PubMed] [Google Scholar]
  3. Böhm S., Venyaminov SYu, Fabian H., Filimonov V. V., Welfle H. Conserved unpaired adenine residues are important for ordered structures of 5S ribosomal RNA. An infrared study of the secondary and tertiary structure of Thermus thermophilus 5S rRNA. Eur J Biochem. 1985 Mar 15;147(3):503–510. doi: 10.1111/j.0014-2956.1985.00503.x. [DOI] [PubMed] [Google Scholar]
  4. Curtiss W. C., Vournakis J. N. Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure. J Mol Evol. 1984;20(3-4):351–361. doi: 10.1007/BF02104741. [DOI] [PubMed] [Google Scholar]
  5. De Wachter R., Chen M. W., Vandenberghe A. Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable. Biochimie. 1982 May;64(5):311–329. doi: 10.1016/s0300-9084(82)80436-7. [DOI] [PubMed] [Google Scholar]
  6. De Wachter R., Chen M. W., Vandenberghe A. Equilibria in 5-S ribosomal RNA secondary structure. Bulges and interior loops in 5-S RNA secondary structure may serve as articulations for a flexible molecule. Eur J Biochem. 1984 Aug 15;143(1):175–182. doi: 10.1111/j.1432-1033.1984.tb08356.x. [DOI] [PubMed] [Google Scholar]
  7. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Erdmann V. A., Wolters J., Huysmans E., Vandenberghe A., De Wachter R. Collection of published 5S and 5.8S ribosomal RNA sequences. Nucleic Acids Res. 1984;12 (Suppl):r133–r166. doi: 10.1093/nar/12.suppl.r133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Kumazaki T., Hori H., Osawa S., Mita T., Higashinakagawa T. The nucleotide sequences of 5S rRNAs from three ciliated protozoa. Nucleic Acids Res. 1982 Jul 24;10(14):4409–4412. doi: 10.1093/nar/10.14.4409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lockard R. E., Kumar A. Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom. Nucleic Acids Res. 1981 Oct 10;9(19):5125–5140. doi: 10.1093/nar/9.19.5125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Solie T. N., Schellman J. A. The interaction of nucleosides in aqueous solution. J Mol Biol. 1968 Apr 14;33(1):61–77. doi: 10.1016/0022-2836(68)90281-7. [DOI] [PubMed] [Google Scholar]
  13. Troutt A., Savin T. J., Curtiss W. C., Celentano J., Vournakis J. N. Secondary structure of Bombyx mori and Dictyostelium discoideum 5S rRNA from S1 nuclease and cobra venom ribonuclease susceptibility, and computer assisted analysis. Nucleic Acids Res. 1982 Jan 22;10(2):653–664. doi: 10.1093/nar/10.2.653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Uchida T. Purification and properties of RNase T2. J Biochem. 1966 Aug;60(2):115–132. doi: 10.1093/oxfordjournals.jbchem.a128410. [DOI] [PubMed] [Google Scholar]
  15. Uhlenbeck O. C., Borer P. N., Dengler B., Tinoco I., Jr Stability of RNA hairpin loops: A 6 -C m -U 6 . J Mol Biol. 1973 Feb 5;73(4):483–496. doi: 10.1016/0022-2836(73)90095-8. [DOI] [PubMed] [Google Scholar]
  16. Vary C. P., Vournakis J. N. RNA structure analysis using T2 ribonuclease: detection of pH and metal ion induced conformational changes in yeast tRNAPhe. Nucleic Acids Res. 1984 Sep 11;12(17):6763–6778. doi: 10.1093/nar/12.17.6763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Vournakis J. N., Celantano J., Finn M., Lockard R. E., Mitra T., Pavlakis G., Troutt A., van den Berg M., Wurst R. M. Sequence and structure analysis of end-labeled RNA with nucleases. Gene Amplif Anal. 1981;2:267–298. [PubMed] [Google Scholar]
  18. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Wurst R. M., Vournakis J. N., Maxam A. M. Structure mapping of 5'-32P-labeled RNA with S1 nuclease. Biochemistry. 1978 Oct 17;17(21):4493–4499. doi: 10.1021/bi00614a021. [DOI] [PubMed] [Google Scholar]

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