The Computer Simulation of RNA Folding Pathways Using a Genetic Algorithm

A procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as disruption of temporarily formed structures, the folding of a molecule during its synthesis and pseudoknot...

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Bibliographic Details
Published in:Journal of molecular biology 1995-06, Vol.250 (1), p.37-51
Main Authors: Gultyaev, Alexander P., van Batenburg, F.H.D., Pleij, Cornelis W.A.
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
Computer Simulation
genetic algorithm
Introns
Kinetics
metastable structures
Molecular Sequence Data
Nucleic Acid Conformation
Phylogeny
RNA - chemistry
RNA folding pathway
RNA Precursors - chemistry
RNA pseudoknots
RNA structure prediction
RNA, Ribosomal - chemistry
RNA, Ribosomal, 16S - chemistry
RNA, Viral - chemistry
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Summary:A procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as disruption of temporarily formed structures, the folding of a molecule during its synthesis and pseudoknot formation. The simulations are able to predict functional metastable foldings and kinetically driven transitions to more stable structures. The analysis of free energies for intermediate foldings allows estimation of the ranges of kinetic refolding barriers and suggests that in some RNAs the selective evolutionary pressure suppresses the possibilities for alternative structures that could form in the course of transcription. It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions. This suggest that suggest that RNA folding kinetics is very important for the formation of functional RNA structures. Therefore, apart from its value for predictions RNA structures, the proposed computer stimulations can be a powerful tool in the studies of RNA folding features.f2f2Abbreviations used: GA, genetic algorithm; STNV, satellite tobacco necrosis virus; UTR, untranslated region; CaMV, cauliflower mosaic virus; CERV, carnation etched ring virus; FMV, figwort mosaic virus; MNV11, minivariant; SV11, salt-resistant variant.
ISSN:0022-2836
1089-8638
DOI:10.1006/jmbi.1995.0356