Coarse-grained modelling of supercoiled RNA
Christian Matek, Petr Sulc, Ferdinando Randisi, Jonathan P.K. Doye, and Ard A. Louis
J. Chem. Phys. 143, 243122 (2015)
AbstractWe 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.
The full paper is available from The Journal of Chemical Physics and arXiv.org.
It appears in the JCP special issue on Coarse graining of macromolecules, biopolymers and membranes