Coarse-grained modelling of supercoiled RNA

TL;DR

This paper uses a coarse-grained RNA model to study supercoiling behavior, reproducing experimental extension curves and predicting bubble formation and plectoneme localization in supercoiled RNA.

Contribution

The study introduces explicit salt dependence into the oxRNA model, enabling accurate simulation of supercoiling phenomena and comparison with experimental data.

Findings

Reproduces extension curves with twist and force

Predicts denaturation bubbles in plectoneme end-loops

Shows positive twist-stretch coupling consistent with experiments

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.