A nucleotide-level coarse-grained model of RNA

Petr Šulc, Flavio Romano, Thomas E. Ouldridge, Jonathan P.K. Doye, Ard A. Louis

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Abstract

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

Original languageEnglish (US)
Article number235102
JournalJournal of Chemical Physics
Volume140
Issue number23
DOIs
StatePublished - Jun 21 2014
Externally publishedYes

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ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Šulc, P., Romano, F., Ouldridge, T. E., Doye, J. P. K., & Louis, A. A. (2014). A nucleotide-level coarse-grained model of RNA. Journal of Chemical Physics, 140(23), [235102]. https://doi.org/10.1063/1.4881424