DNA as a one-dimensional chiral material. II. Dynamics of the structural transition between B form and Z form

TL;DR

This study models the dynamics of DNA structural transitions between B and Z forms under external torque, revealing different transition mechanisms such as nucleation and spinodal-like processes depending on torque strength.

Contribution

The paper introduces a Langevin equation-based model to simulate DNA B-Z transition dynamics, highlighting the transition mechanisms under varying external torques.

Findings

Slow relaxation dynamics following sudden torque changes

Transition mechanism shifts from nucleation to spinodal-like with increasing torque

Qualitative understanding via simple phenomenological arguments

Abstract

We analyze the dynamics of structural transitions between normal right-handed B form and unusual left-handed Z form for a linear DNA molecule. The dynamics under the external torque in physiological buffer is modeled by a Langevin equation, with the potential term given by the authors previously [Phys. Rev. E 84, 021926 (2011)]. With this model, we first simulate the relaxation processes around B-form structure after sudden changes of the external torques, where slow relaxation $\sim t^{-1/2}$ as a function of the elapsed time $t$ is observed. Then, the dynamics of structural transition from Z form to B form is computed under various external torque strength. For small external torques, the transition proceeds via nucleation and the growth, while for higher torques, Z-form structure becomes unstable, and the transition mechanism is switched to a spinodal-like process. These numerical results are qualitatively understood by simple phenomenological arguments.