Helix untwisting and bubble formation in circular DNA
Biomolecules
2013-05-30 v1 Soft Condensed Matter
Biological Physics
Chemical Physics
Abstract
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.
Cite
@article{arxiv.1305.4051,
title = {Helix untwisting and bubble formation in circular DNA},
author = {Marco Zoli},
journal= {arXiv preprint arXiv:1305.4051},
year = {2013}
}
Comments
The Journal of Chemical Physics, vol. 138 (2013), in press