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Modeling RNA Structure

Bio/Technology volume 2, pages 791–795 (1984)Cite this article

Abstract

RNA secondary structure can be most simply visualized on the basis of runs of complementary bases in the primary sequence. These complementary regions predict an ability of a molecule to fold back on itself to form double stranded helical regions. Computer methods which utilize energy rules to predict a secondary structure for the entire molecule have been devised. These predictions can be made to accommodate other types of chemical and genetic analysis. The limitations of the modeling methods are discussed and their use in folding several RNA molecules is demonstrated. Regulatory mechanisms which may be controlled by RNA structure and amenable to genetic analysis are also discussed.

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References

  1. Gold, L., Pribnow, D., Schneider, R., Shinedling, S., Singer, B.W. and Stormo, G. 1981. Translational initiation in prokaryotes. Ann. Rev. Microbiol. 35: 365–403.

    Article  CAS  Google Scholar 

  2. Simons, R.W. and Kleckner, N. 1983. Translational control of 1S10 transposition. Cell 34: 683–691.

    Article  CAS  PubMed  Google Scholar 

  3. Sauer, R.T., Krovatin, W., DeAnda, J., Youderian, P. and Suskind, M.M. 1983. Primary structure of the immI immunity region of bacteriophage P22. J. Mol. Biol. 168: 699–713.

    Article  CAS  PubMed  Google Scholar 

  4. Mizuno, T., Chou, M. and Inouye, M. 1984. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc. Natl. Acad. Sci USA 81: 1966–1970.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Olins, P.O. and Nomura, M. 1981. Translational regulation by ribosomal protein S8 in Escherichia coil: structural homology between rRNA binding site and feedback target on mRNA. Nucl. Acids Res. 9: 1757–1764.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Friesen, J.D., Tropak, M. and An, G., 1983. Mutations in the rplJ leader of Escherichia coli that abolish feedback regulation. Cell 32: 361–369.

    Article  CAS  PubMed  Google Scholar 

  7. von Gabain, A., Belasco, J.G., Schottel, J.L., Chang, C.Y., and Cohen, S.N. 1983. Decay of mRNA in Escherichia coli: Investigation of the fate of specific segments of transcripts. Proc. Natl. Acad. Sci USA 80: 653–657.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kolter, R. and Yanofsky, C. 1982. Attenuation in amino add biosynthetic operons. Ann. Rev. Genet. 16: 113–134.

    Article  CAS  PubMed  Google Scholar 

  9. Selzer, G., Som, T., Itoh, T. and Tomizawa, J. 1983. The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids. Cell 32: 119–129.

    Article  CAS  PubMed  Google Scholar 

  10. Masukata, H. and Tomizawa, J. 1984. Effect of point mutations on formation and structure of the RNA primer for colE1 replication. Cell 36: 513–522.

    Article  CAS  PubMed  Google Scholar 

  11. Mullin, D.A., Garcia, G.M. and Walker, J.R., 1984. An Escherichia coli DNA fragment 118 base pairs in length provides dnaY+ complementing activity. Cell (in press).

  12. Walter, P. and Bloebel, G. 1982. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 299: 691–698.

    Article  CAS  PubMed  Google Scholar 

  13. Cech, T.R., Tanner, N.K., Tinoco, I.Jr., Weir, B.R., Zuker, M. and Perlman, P.S. 1983. Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: Structural homology with fungal mitochondrial intervening sequences. Proc. Natl. Acad. Sci. USA 80: 3903–3907.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zuker, M. and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Adds Res. 9: 133–148.

    Article  CAS  Google Scholar 

  15. Jacobson, A.B., Good, L., Simonetti, J. and Zuker, M. 1984. Some simple computational methods to improve the folding of large RNAs. Nucl. Acids Res. 12: 45–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Comay, E., Nussinov, R. and Comay, O. 1984. An accelerated algorithm for calculating the secondary structure of single stranded RNAs. Nucl. Acids Res. 12: 53–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Martinez, H.M. 1984. An RNA folding rule. Nucl. Acids Res. 12: 323–334.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Papanicolaou, C., Gouy, M. and Ninio, J. 1984. An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. Nucl. Acids Res. 12: 31–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Goad, W.B. and Kanehisa, M.I. 1982. Pattern recognition in nucleic acid sequences, I. A general method for finding local homologies arid symmetries. Nucl. Acids Res. 10: 247–263.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Kanehisa, M.I. and Goad, W.B. 1982. Pattern recognition in nucleic-acid sequences, II. An efficient method for finding locally stable secondary structures. Nucl. Adds Res. 10: 265–278.

    Article  CAS  Google Scholar 

  21. Hogeweg, P. and Hesper, B. 1984. Energy directed folding of RNA sequences. Nucl. Acids Res. 12: 67–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Shapiro, B.A., Maizel, J., Lipkin, L.E., Currey, K. and Whitney, C. 1984. Generating non-overlapping displays of nucleic acid secondary structure. Nucl. Adds Res. 12: 75–88.

    Article  CAS  Google Scholar 

  23. Quigley, G.J., Gehrke, E., Rothe, D.A. and Auron, P.E. 1984. Computer-aided- nucleic acid secondary structure modeling incorporating enzymatic digestion data. Nucl. Acids Res. 12: 347–366.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yamamoto, K., Kitamura, Y. and Yoshikura, H. 1984. Computation of statistical secondary structure of nucleic acids. Nucl. Acids Res. 12: 335–346.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Auron, P.E., Rindone, W.P., Vary, P.H., Celentano, J.J. and Vournakis, J.N. 1982. Computer aided prediction of RNA secondary structure. Nucl. Acids Res. 10: 403–419.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Needleman, S.B. and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino add sequences of two proteins.J. Mol. Biol. 48: 443–453.

    Article  CAS  PubMed  Google Scholar 

  27. Smith, T.F. and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147: 195–197.

    Article  CAS  PubMed  Google Scholar 

  28. Martinez, H. 1983. An efficient method for finding repeals in molecular sequences. Nucl. Acids Res. 11: 4629–4634.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Woese, C.R., Magrum, L.J., Gupta, R., Siegel, R.B., Stahl, D.A., Kop, J., Crawford, N., Brosius, J., Gutell, R., Hogan, J.J. and Noller, H.F. 1980. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical data. Nucl. Acids Res. 8: 2275–2293.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Swerdlow, H. and Guthrie, C. 1984. Structure homology of introncontaining tRNA precursors. J. Biol. Chem. 259: 5197–5207.

    CAS  PubMed  Google Scholar 

  31. Gauss, D.H. and Sprinzl, M. 1984. Compilation of tRNA sequences. Nucl. Acids Res. 12: rl–r58.

    Google Scholar 

  32. Haseloff, J., Mohamed, N.A. and Symons, R.H., 1982. RNAs of cadang-cadang disease of coconuts. Nature 299: 316–321.

    Article  CAS  Google Scholar 

  33. Delilas, N. and Andersen, J. 1982. Generalized structures of the 5S ribosomal RNA's. Nucl. Acids Res. 10: 7323–7344.

    Article  Google Scholar 

  34. Erdmann, V.A., Wolters, J., Huysmans, E., Vandenberghe, A. and De Wachter, R.D., 1984. Collection of published 5S and 5.8S ribosomal RNA sequences. Nucl. Acids Res. 12: rl33–rl66.

    Article  Google Scholar 

  35. Maizel, J.V. and Lenk, R.P. 1981. Proc. Natl. Acad. Sci. USA 12: 7665–7669.

    Article  Google Scholar 

  36. Mount, D.W. and Conrad, B. 1984. Microcomputer programs for graphic analysis of nucleic acids and proteins. Nucl. Acids Res. 12: 811–818.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Gross, H.J., Domdey, H., Lossow, C., Jank, P., Raba, M. and Alberty, H. 1978. Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature 273: 203–208.

    Article  CAS  PubMed  Google Scholar 

  38. Tinoco, I., Borer, P.N., Dengler, B., Levine, M.D., Uhlenbeck, O.C., Crothers, D.M., and Gralla, J. 1973. Improved estimation ot secondary structure in ribonucleic acids. Nature New Biol. 246: 40–42.

    Article  CAS  PubMed  Google Scholar 

  39. Borer, P.N., Dengler, B., Tinoco, I. and Uhlenbech, O.C. 1974. Stability of riboriucleic acid double-stranded helices. J. Mol. Biol. 86: 843–853.

    Article  CAS  PubMed  Google Scholar 

  40. Salser, W. 1977. Globin rnRNA sequences: Analysis of base pairing and evolutionary implications. Cold Spring Harbor Symp. Quant. Biol. 62: 985–1002.

    Google Scholar 

  41. Fitch, W.M. 1983. Calculating the expected frequencies of potential secondary structure in nucleic acids as a function of stem length, loop size, base composition and nearest neighbor frequencies. Nucl. Acids Res. 13: 4655–4663.

    Article  Google Scholar 

  42. Beck, E. and Bremer, E. 1980. Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12. Nucl. Acids Res. 8: 3011–3024.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Inokuchi, K., Mutoh, N., Matsuyama, S. and Mizushima, S. 1982. Primary structure of the ompF gene that codes for a major outer membrane protein of Escherichia coli K-12. Nucl. Acids Res. 10: 6957–6968.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Author notes

  1. David W. Mount: On leave from Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143

    David W. Mount

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Mount, D. Modeling RNA Structure. Nat Biotechnol 2, 791–795 (1984). https://doi.org/10.1038/nbt0984-791

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