Matematicheskaya Biologiya i Bioinformatika
RUS  ENG    JOURNALS   PEOPLE   ORGANISATIONS   CONFERENCES   SEMINARS   VIDEO LIBRARY   PACKAGE AMSBIB  
General information
Latest issue
Archive
Impact factor

Search papers
Search references

RSS
Latest issue
Current issues
Archive issues
What is RSS



Mat. Biolog. Bioinform.:
Year:
Volume:
Issue:
Page:
Find






Personal entry:
Login:
Password:
Save password
Enter
Forgotten password?
Register


Matematicheskaya Biologiya i Bioinformatika, 2019, Volume 14, Issue Suppl., Pages t37–t43
DOI: https://doi.org/10.17537/2019.14.t37
(Mi mbb415)
 

Translations of Published Articles

Diverse RNA pseudoknots exist for short stems only

E. F. Baulina, A. V. Korinevskayab, P. O. Tikhonovab, M. A. Roitbergac

a Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
b Faculty of Computer Science, National Research University Higher School of Economics, Moscow 101000, Russia
c Faculty of Innovations and High Technology, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141700, Russia
References:
Abstract: RNA secondary structure prediction including pseudoknotted structures of arbitrary types is a well-known NP-hard problem of computational biology. By limiting the possible types of pseudoknots the problem can be solved in polynomial time. According to the empirical thermodynamic parameters, the formation of a stem starts to decrease free energy of the structure only after the formation of the third stack of base pairs. Thus, the short stems may be unstable and provide a limited contribution to the overall free energy of a folded RNA molecule. Therefore, detailed analysis of stems in pseudoknots could facilitate reducing pseudoknots complexity. In this paper, we show that the pseudoknots from experimentally determined RNA spatial structures are primarily formed by short stems of 2–3 base pairs. The short stems tend to avoid hairpins and prefer internal loops that indicates that they could be energetically insignificant. An exclusion of short stems reduces the diversity of pseudoknots to two basic types which are H-knots (signature abAB) and kissing loops (signature abAcBC). The only exception is a pseudoknot formed by 12–13 stems that was found in group II intron molecule from Oceanobacillus iheyensis only in the presence of exon segment IBS1. In the absence of IBS1 the pseudoknot is reduced to kissing loops type.
Key words: pseudoknot, short stem, RNA secondary structure, pseudoknot signature, base pair, stem, group II intron.
Funding agency Grant number
Russian Foundation for Basic Research 16-04-01640
This work was supported by the Russian Foundation for Basic Research [grant number 16-04-01640].
Received 16.06.2019, Published 18.07.2019
Document Type: Article
UDC: 577.214.5
Language: English
Citation: E. F. Baulin, A. V. Korinevskaya, P. O. Tikhonova, M. A. Roitberg, “Diverse RNA pseudoknots exist for short stems only”, Mat. Biolog. Bioinform., 14, Suppl. (2019), t37–t43
Citation in format AMSBIB
\Bibitem{BauKorTik19}
\by E.~F.~Baulin, A.~V.~Korinevskaya, P.~O.~Tikhonova, M.~A.~Roitberg
\paper Diverse RNA pseudoknots exist for short stems only
\jour Mat. Biolog. Bioinform.
\yr 2019
\vol 14
\pages t37--t43
\issueinfo Suppl.
\mathnet{http://mi.mathnet.ru/mbb415}
\crossref{https://doi.org/10.17537/2019.14.t37}
Linking options:
  • https://www.mathnet.ru/eng/mbb415
  • https://www.mathnet.ru/eng/mbb/v14/i3/p37
    Translation
    Citing articles in Google Scholar: Russian citations, English citations
    Related articles in Google Scholar: Russian articles, English articles
     
      Contact us:
     Terms of Use  Registration to the website  Logotypes © Steklov Mathematical Institute RAS, 2024