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Volume 13   Issue 2   Year 2018
Diverse RNA pseudoknots exist for short stems only

Baulin E., Korinevskaya A., Tikhonova P., Roytberg M.

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, Russia
Faculty of Innovations and High Technology, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia

 
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  and kissing loops.
 

Key words: pseudoknot, short stem, RNA secondary structure, pseudoknot signature, base pair, stem, group II intron. 

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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