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

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.

9 pages, 4 figures

References in corpus (4)

• Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy
• Discontinuities at the DNA supercoiling transition
• Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects
• DNA as a one-dimensional chiral material: Application to the structural transition between B form and Z form

Cited by in corpus (1)

• Mechanical response to tension and torque of molecular chains via statistically interacting particles associated with extension, contraction, twist, and supercoiling