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 language | English (US) |
---|---|
Article number | 243122 |
Journal | Journal of Chemical Physics |
Volume | 143 |
Issue number | 24 |
DOIs | |
State | Published - Dec 28 2015 |
Externally published | Yes |
ASJC Scopus subject areas
- General Physics and Astronomy
- Physical and Theoretical Chemistry