Abstract
In recent years, both theoretical and experimental indicators have been gathering, showing that sequence effects on the physical properties of DNA molecules contribute nontrivially to the molecule's behavior. Here we present the first results of a study of sequence effects on the formation and dynamics of plectonemes, the supercoiled structures produced when the DNA is put under torsional stress. Using, for the first time in this context, a fully sequence-dependent, non-coursegrained rigid base pair model for the DNA molecule, we examined the process of sliding a formed plectoneme along a DNA molecule in its entirety as a mechanism for plectoneme transport. We were able to map out the relevant energy landscapes and we find that we can rule out sliding as the dominant transporation mechanism.
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