Russian version English version
Volume 13   Issue 2   Year 2018
Baulin E., Korinevskaya A., Tikhonova P., Roytberg M.

Diverse RNA pseudoknots exist for short stems only

Mathematical Biology & Bioinformatics. 2018;13(2):526-533.

doi: 10.17537/2018.13.533.

References

 

  1. Marzluff W.B. Twenty years of RNA: reflections on post-transcriptional regulation. RNA (New York, NY). 2015;21(4):687-689. doi: 10.1261/rna.050997.115
  2. Eiring A.M., Harb J.G., Neviani P., Garton Ch., Oaks J.J., Spizzo R., Liu Sh., Schwind S., Santhanam R., Hickey Ch.J. et al. miR-328 Functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts. Cell. 2010;140(5):652-665. doi: 10.1016/j.cell.2010.01.007
  3. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215-233. doi: 10.1016/j.cell.2009.01.002
  4. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermüller J., Hofacker I.L. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316(5830):1484-1488. doi: 10.1126/science.1138341
  5. Shapiro B.A., Yingling Ya.G., Kasprzak W., Bindewald E. Bridging the gap in RNA structure prediction. Current opinion in structural biology. 2007;17(2):157-165. doi: 10.1016/j.sbi.2007.03.001
  6. Rastogi T., Beattie T.L., Olive J.E., Collins R.A. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. The EMBO journal. 1996;15(11):2820. doi: 10.1002/j.1460-2075.1996.tb00642.x
  7. Ke A., Zhou K., Ding F., Cate J.H., Doudna J.A. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 2004;429:201-205. doi: 10.1038/nature02522
  8. Adams P.L., Stahley M.R., Kosek A.B., Wang J., Strobel S.A. Crystal structure of a self-splicing group I intron with both exons. Nature. 2004;430:45-50. doi: 10.1038/nature02642
  9. Theimer C.A., Blois C.A., Feigon J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Molecular cell. 2005;17(5):671-682. doi: 10.1016/j.molcel.2005.01.017
  10. Condon A., Davy B., Rastegari B., Zhao Sh., Tarrant F. Classifying RNA pseudoknotted structures. Theoretical Computer Science. 2004;320(1):35-50. doi: 10.1016/j.tcs.2004.03.042
  11. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic acids research. 2003;31(13):3406-3415. doi: 10.1093/nar/gkg595
  12. Reeder J., Höchsmann M., Rehmsmeier M., Voss B., Giegerich R. Beyond Mfold: recent advances in RNA bioinformatics. Journal of biotechnology. 2006;124(1):41-55. doi: 10.1016/j.jbiotec.2006.01.034
  13. Rivas E., Eddy S.R. A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of molecular biology. 1999;285(5):2053-2068. doi: 10.1006/jmbi.1998.2436
  14. Lyngsø R.B., Pedersen C.N.S. Pseudoknots in RNA secondary structures. In: Proceedings of the fourth annual international conference on Computational molecular biology. ACM. 2000:201-209. doi: 10.1145/332306.332551
  15. Lyngsø R.B., Pedersen C.N.S. RNA pseudoknot prediction in energy-based models. Journal of computational biology. 2000;7(3-4):409-427. doi: 10.1089/106652700750050862
  16. Tan Z., Zhang W., Shi Ya., Wang F. RNA folding: structure prediction, folding kinetics and ion electrostatics. In: Advance in Structural Bioinformatics. Springer Netherlands, 2015:143-183. doi: 10.1007/978-94-017-9245-5_11
  17. Xia T., SantaLucia J. Jr., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox Ch., Turner D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson − Crick base pairs. Biochemistry. 1998;37(42):14719-14735. doi: 10.1021/bi9809425
  18. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of molecular biology. 1999;288(5):911-940. doi: 10.1006/jmbi.1999.2700
  19. Baulin E., Yacovlev V., Khachko D., Spirin S., Roytberg M. URS DataBase: universe of RNA structures and their motifs. Database. 2016;2016. Article No. baw085. doi: 10.1093/database/baw085
  20. Zuker M., Mathews D.H., Turner D.H. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: RNA biochemistry and biotechnology. Springer Netherlands, 1999:11-43. doi: 10.1007/978-94-011-4485-8_2
  21. Andersen J.E., Penner R.C., Reidys C.M., Waterman M.S. Topological classification and enumeration of RNA structures by genus. Journal of mathematical biology. 2013;67(5):1261-1278. doi: 10.1007/s00285-012-0594-x
  22. Bon M., Vernizzi G., Orland H., Zee A.Topological classification of RNA structures. Journal of molecular biology. 2008;379(4):900-911. doi: 10.1016/j.jmb.2008.04.033
  23. Rødland E.A. Pseudoknots in RNA secondary structures: representation, enumeration, and prevalence. Journal of Computational Biology. 2006;13(6):1197-1213. doi: 10.1089/cmb.2006.13.1197
  24. Reidys C.M., Huang F.W.D., Andersen J.E., Penner R.C., Stadler P.F., Nebel M.E. Topology and prediction of RNA pseudoknots. Bioinformatics. 2011;27(8):1076-1085. doi: 10.1093/bioinformatics/btr090
  25. Chiu J.K.H., Chen Y.P.P. Conformational features of topologically classified RNA secondary structures. PloS one. 2012;7(7). Article No. e39907. doi: 10.1371/journal.pone.0039907
  26. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic acids research. 2000;28(1):235-242. doi: 10.1093/nar/28.1.235
  27. Leontis N. B., Zirbel C. L. Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking. RNA 3D structure analysis and prediction. Springer Berlin Heidelberg, 2012:281-298. doi: 10.1007/978-3-642-25740-7_13
Table of Contents Original Article
Math. Biol. Bioinf.
2018;13(2):526-533
doi: 10.17537/2018.13.533
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References
Supplementary data Translation into English
Math. Biol. Bioinf.
2019;14(S):t37-t43
doi: 10.17537/2019.14.t37

Full text (eng., pdf)

 

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