Unzipping dynamics of long DNAs

The two strands of the DNA double helix can be “unzipped” by the application of [formula presented] force. We analyze the dynamics of unzipping and rezipping for the case where the molecule ends are separated and reapproached 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 [formula presented] in the double-stranded DNA 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.