title: 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 ~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.
authors.affiliation: Research Organization of Science & Engineering, Ritsumeikan University, Noji-higashi 1-1-1, Kusatsu 525-8577, Japan. okushima@ike-dyn.ritsumei.ac.jp
authors.forename: Teruaki
authors.initials: T
authors.lastname: Okushima
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kuratsuji
mesh_terms: D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D043542:DNA, Z-Form / Q000737:chemistry*; D004548:Elasticity; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D012997:Solvents; D013314:Stress, Mechanical; D019415:Torque
chemical_list: D043542:DNA, Z-Form; D012997:Solvents; D004247:DNA