Helicase mediated active DNA unwinding in a stochastic field

The mechanism of unwinding of DNA by a class of motor proteins called helicase, in contact with a thermal bath, is theoretically investigated. The dynamic simulations, incorporating the considerations of externally applied unwinding forces as well as stochastically fluctuating Langevin interactions, are utilized to calculate the critical force required for the base pair opening, which comes out to be in close agreement with the experimentally obtained results. The simulation predictions effectively demonstrate how the thermal stochasticities can be overridden by directional openings, as an extended viewpoint of the classical Peyrard-Bishop [Phys. Rev. Lett. 62, 2755 (1989)] model. (c) 2006 American Institute of Physics.