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.
@article{arxiv.1506.02539,
title = {Coarse-grained modelling of supercoiled RNA},
author = {Christian Matek and Petr Šulc and Ferdinando Randisi and Jonathan P. K. Doye and Ard A. Louis},
journal= {arXiv preprint arXiv:1506.02539},
year = {2016}
}