Coarse-grained modelling of supercoiled RNA
Journal of Chemical Physics American Institute of Physics 143:24 (2015) 243122
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.Simulating supercoiled nucleic acids: From single molecule modelling to genomic mechanisms
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 44 (2015) S170-S170
Characterizing the bending and flexibility induced by bulges in DNA duplexes
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The role of loop stacking in the dynamics of DNA hairpin formation.
The journal of physical chemistry. B 118:49 (2014) 14326-14335