How helix-coil transition influences translocation of a single-stranded DNA and kinetics of its fluctuation inside the channel

Department of Physics, Indian Institute of Technology - Bombay, Powai, Mumbai-400 076, India

^(a) kulveersingh85@gmail.com
^(b) asain@phy.iitb.ac.in

Received: 10 August 2013
Accepted: 14 October 2013

Abstract

Many biopolymers like proteins, RNA, single-stranded DNA form secondary structures, namely helices and loops. These polymers often get transported from one compartment of the cell to another through narrow protein channels. Motivated by recent experimental results on translocation of polymers through channels and helix-coil transition inside the channel, we have constructed a two-dimensional toy model to study how secondary structures influence such processes. Through a Langevin dynamics simulation we investigated the statistics of translocation as well as how channel width, force and temperature affect the helix-coil transition inside a channel. Our results are in qualitative agreement with experimental data.