On the length scale dependence of DNA conformational change under local perturbation

Abstract

Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modeled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of conformational change in the model have been investigated and several reduced order models developed, the conformational dynamics as a function of the length of the oscillator chain is relatively less clear. To address this, we use a modified Lindstedt–Poincare method and numerical computations. We calculate a perturbation expansion of the frequency of the model’s nonzero modes, finding that approximating these modes with their unperturbed dynamics, as in a previous reduced order model, may not hold when the length of the DNA model increases. We investigate the conformational change to the local perturbation in models of varying lengths, finding that for the chosen input and parameters, there are two regions of DNA length in the model — first, where the minimum energy required to undergo the conformational change increases with the DNA length; and second, where it is almost independent of the length of the DNA model. We analyze the conformational change in these models by adding randomness to the local perturbation, finding that the tendency of the system to remain in a stable conformation against random perturbation decreases with increase in DNA length. These results should help to understand the role of the length of a DNA molecule in influencing its conformational dynamics.