title: Coarse-grained modelling of supercoiled RNA.
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.
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom.
authors.forename: Christian
authors.initials: C
authors.lastname: Matek
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA.
authors.forename: Petr
authors.initials: P
authors.lastname: Šulc
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom.
authors.forename: Ferdinando
authors.initials: F
authors.lastname: Randisi
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom.
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
mesh_terms: D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry*
chemical_list: D012330:RNA, Double-Stranded