Coarse-grained modelling of supercoiled RNA

Christian Matek, Petr Šulc, Ferdinando Randisi, Jonathan P.K. Doye, Ard A. Louis

Research output: Contribution to journalArticle

6 Scopus citations

Abstract

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.

Original languageEnglish (US)
Article number243122
JournalJournal of Chemical Physics
Volume143
Issue number24
DOIs
StatePublished - Dec 28 2015
Externally publishedYes

ASJC Scopus subject areas

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

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    Matek, C., Šulc, P., Randisi, F., Doye, J. P. K., & Louis, A. A. (2015). Coarse-grained modelling of supercoiled RNA. Journal of Chemical Physics, 143(24), [243122]. https://doi.org/10.1063/1.4933066