Mean bubble formation time in DNA denaturation
School of Physics, University of Hyderabad, Central University P.O. - Hyderabad 500 046, Andhra Pradesh, India
2 Theoretical Soft Matter and Biophysics, Institute of Complex Systems, Forschungszentrum Jülich Jülich, Germany, EU
Accepted: 3 November 2011
Using the Poland-Scheraga free energy of the bubble size in a double-stranded DNA we propose a discrete stochastic dynamics for the number of base pairs N of an unzipped bubble. We derive a universal subdiffusive growth TN∼A/Γ(b+2)N1+b for the mean formation time (MBFT) TN of a bubble of size N. The amplitude A is determined by the bubble initiation rate and time spent in the denaturated state. We examine critically the significance of these results for experiments. We find: i) Our results provide a new method to determine whether the order of the denaturation transition is discontinuous (b>2) or not. ii) The asymptotic growth law of TN is reached with 10% precision already for small bubbles of sizes >20. However, the amplitude is very sensitive to modeling details for small bubbles. iii) In an equilibrium sample of bubbles up to size N the averaged MBFT grows diffusively, TN*∝N2, irrespective of b.
PACS: 87.15.H- – Dynamics of biomolecules / 87.14.gk – DNA / 05.40.Fb – Random walks and Levy flights
© EPLA, 2011