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Open AccessArticle

Theoretical Search for RNA Folding Nuclei

Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
Author to whom correspondence should be addressed.
Academic Editor: Kevin H. Knuth
Entropy 2015, 17(11), 7827-7847;
Received: 30 April 2015 / Revised: 5 November 2015 / Accepted: 17 November 2015 / Published: 23 November 2015
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
The functions of RNA molecules are defined by their spatial structure, whose folding is regulated by numerous factors making RNA very similar to proteins. Prediction of RNA folding nuclei gives the possibility to take a fresh look at the problems of the multiple folding pathways of RNA molecules and RNA stability. The algorithm previously developed for prediction of protein folding nuclei has been successfully applied to ~150 various RNA structures: hairpins, tRNAs, structures with pseudoknots, and the large structured P4-P6 domain of the Tetrahymena group I intron RNA. The calculated Φ-values for tRNA structures agree with the experimental data obtained earlier. According to the experiment the nucleotides of the D and T hairpin loops are the last to be involved in the tRNA tertiary structure. Such agreement allowed us to do a prediction for an example of large structured RNA, the P4-P6 RNA domain. One of the advantages of our method is that it allows us to make predictions about the folding nucleus for nontrivial RNA motifs: pseudoknots and tRNA. View Full-Text
Keywords: RNA domain; phi value; RNA folding; mutant; pseudoknot; hairpin; stability RNA domain; phi value; RNA folding; mutant; pseudoknot; hairpin; stability
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Pereyaslavets, L.B.; Galzitskaya, O.V. Theoretical Search for RNA Folding Nuclei. Entropy 2015, 17, 7827-7847.

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