Monte Carlo Simulation of the Unwinding of a DNA-like Helix. II. The Effect of Interstrand Forces

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Abstract
A Monte Carlo technique is used to simulate the kinetics of the unwinding of DNA. Use is made of a high-speed computer to solve the equations of motion for the elements of a macromolecule originally set in a helical configuration. Suitable boundary conditions help simulate excluded volume and van der Waals interactions between opposite strands. The results show an exponential relaxation unwinding process with a terminal relaxation time preceded by a short-lived transient. The model of unwinding shows a rapid end unwinding followed by a progressive unwinding inward from the outer portions of the original helix. The unwinding time is seen to be critically dependent upon the interstrand potential energy.

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