A Sequential Folding Model Predicts Length-Independent Secondary Structure Properties of Long ssRNA

TitleA Sequential Folding Model Predicts Length-Independent Secondary Structure Properties of Long ssRNA
Publication TypeJournal Article
Year of Publication2011
AuthorsL. T. Fang, A. M. Yoffe, W. M. Gelbart and A. Ben-Shaul
Refereed DesignationRefereed
Journal TitleJournal of Physical Chemistry B
Volume115
Issue2
Pages3193-3199
Start Page3193
Date Published03/2011
KeywordsMODEL, RNA, ssRNA, theory
Abstract

We consider the force acting on a polymer part of whose length is configurationally confined in a tube and the rest of which is free. This situation arises in many different physical contexts, including a flexible synthetic polymer partially confined in a nanopore and a stiff viral genome partially ejected from its capsid. In both cases the force acting to pull the chain molecule out of its confinement is argued to be constant once a few persistence lengths are “free”/“outside”. We present Brownian dynamics simulations that confirm the constancy of the force for different chain lengths and illustrate the dependence of the force on the strength of tube confinement. Experimental results are reported for genome ejection from viral capsids, from which we estimate the pulling force to be a few tenths of a piconewton.

URLhttp://dx.doi.org/10.1021/jp110680e
DOI10.1021/jp110680e