A method for finding optimal RNA secondary structures using a new entropy model (vsfold)

Authors: Dawson, Wayne1; Fujiwara, Kazuya1; Kawai, Gota1; Futamura, Yasuhiro2; Yamamoto, Kenji2

Source: Nucleosides, Nucleotides & Nucleic Acids, Volume 25, Number 2, Number 2/January 2006 , pp. 171-189(19)

Publisher: Taylor and Francis Ltd

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Abstract:

We are developing a program to calculate optimal RNA secondary structures. The model uses di-nucleotide pairing energies as with most traditional approaches. However, for long-range entropy interactions, the approach uses an entropy-loss model based on the accumulated sum of the entropy of bonding between each base-pair weighted inversely by the correlation of the RNA sequence (the Kuhn length). Stiff RNA forms very different structures from flexible RNA. The results demonstrate that the long-range folding is largely governed by this entropy and the Kuhn length.

Keywords: RNA secondary structure; Free energy; Cross linking entropy; Kuhn length; Folding; Renormalization theory

Document Type: Research article

DOI: 10.1080/15257770500446915

Affiliations: 1: Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan 2: International Medical Center of Japan, Toyama, Shinjuku-ku, Tokyo, Japan

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