Twisting and bending stress in DNA minicircles

Abstract

The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with ∼100 base pairs, is addressed. Three minicircles with different radii and almost equal contents of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of 66 bps whose bending angle is ∼6°. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at T = 315 K. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.