![]() ![]() ![]() The torsional stress in a supercoiled DNA loop is distributed between untwisting and writhing, with conversion between the two being crucial for genetic regulation ( 2). Prokaryotes store their DNA as negatively supercoiled plectonemes bound to nucleoid associated proteins (NAPs) ( 2). Eukaryotic DNA is condensed into chromatin, which is made up of units of 146 bp of DNA wrapped 1.6 times around each histone octamer to form the nucleosome complex ( 1). These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA.ĭNA rarely exists as a relaxed linear molecule in the cell. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. 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 over the same MD timescales. 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. 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. 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. ![]()
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