Unzipping Dynamics of Long DNAs

TL;DR

This paper investigates the dynamics of DNA unzipping and rezipping under force, highlighting the effects of velocity, torque, and sequence, and explaining deviations from equilibrium behavior observed in experiments.

Contribution

It provides a comprehensive analysis of unzipping dynamics incorporating rotational viscous drag and sequence effects, extending previous models to higher velocities.

Findings

At low velocities, equilibrium theory applies.

High velocities cause torque buildup, affecting unzipping force.

Sequence influences unzipping and rezipping behavior.

Abstract

The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For unzipping of 50 kilobase DNAs at less than about 1000 bases per second, thermal equilibrium-based theory applies. However, for higher unzipping velocities, rotational viscous drag creates a buildup of elastic torque to levels above kBT in the dsDNA region, causing the unzipping force to be well above or well below the equilibrium unzipping force during respectively unzipping and rezipping, in accord with recent experimental results of Thomen et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect of sequence on unzipping and rezipping, and the transient delay in buildup of the unzipping force due to the approach to the steady state.