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arXiv · 1506.02539

Coarse-grained modelling of supercoiled RNA

Christian Matek·Petr Šulc·Ferdinando Randisi·Jonathan P. K. Doye·Ard A. Louis
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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.

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Christian Matek, Petr Šulc, Ferdinando Randisi, Jonathan P. K. Doye, Ard A. Louis. 2015-06-08. Coarse-grained modelling of supercoiled RNA. https://doi.org/10.1063/1.4933066

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