Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA.

ABSTRACT: Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp

SUBMITTER: Mitchell JS 

PROVIDER: S-EPMC3089460 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature