Coarse-grained modelling of supercoiled RNA

被引：14

作者：

Matek, Christian ^{[1
]}

Sulc, Petr ^{[2
]}

Randisi, Ferdinando ^{[1
,3
]}

Doye, Jonathan P. K. ^{[4
]}

Louis, Ard A. ^{[1
]}

机构：

[1] Univ Oxford, Rudolf Peierls Ctr Theoret Phys, 1 Keble Rd, Oxford OX1 3NP, England

[2] Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10065 USA

[3] Life Sci Interface Doctoral Training Ctr, Oxford OX1 3QU, England

[4] Univ Oxford, Dept Chem, Phys & Theoret Chem Lab, Oxford OX1 3QZ, England

来源：

JOURNAL OF CHEMICAL PHYSICS | 2015年 / 143卷 / 24期

基金：

英国工程与自然科学研究理事会;

关键词：

DOUBLE-STRANDED-RNA; THERMODYNAMIC PARAMETERS; DNA; MOLECULE; TORQUE; ELASTICITY; DYNAMICS; DUPLEXES; FORCE; TWIST;

D O I：

10.1063/1.4933066

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We study the behaviour of double-stranded RNA eunder 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. (C) 2015 AIP Publishing LLC.

引用

页数：7

共 47 条

[31] Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model [J].