Nucleic Acids Research Advance Access originally published online on November 5, 2007
Nucleic Acids Research 2008 36(1):21-29; doi:10.1093/nar/gkm891
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. 1 21-29
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
1School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT,UK, 2School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK and 3Department of Mathematics, University of Bristol, Bristol, BS8 1TW
*To whom correspondence should be addressed: Tel: +44 (0)113 343 3816; Fax: +44 (0)113 343 3900; Email: s.a.harris{at}leeds.ac.uk
Received May 17, 2007. Revised September 24, 2007. Accepted October 3, 2007.
We have investigated the effects of duplex length, sequence, salt concentration and superhelical density on the conformation of DNA nanocircles containing up to 178 base pairs using atomistic molecular dynamics simulation. These calculations reveal that the partitioning of twist and writhe is governed by a delicate balance of competing energetic terms. We have identified conditions which favour circular, positively or negatively writhed and denatured DNA conformations. Our simulations show that AT-rich DNA is more prone to denaturation when subjected to torsional stress than the corresponding GC containing circles. In contrast to the behaviour expected for a simple elastic rod, there is a distinct asymmetry in the behaviour of over and under-wound DNA nanocircles. The most biologically relevant negatively writhed state is more elusive than the corresponding positively writhed conformation, and is only observed for larger circles under conditions of high electrostatic screening. The simulation results have been summarised by plotting a phase diagram describing the various conformational states of nanocircles over the range of circle sizes and experimental conditions explored during the study. The changes in DNA structure that accompany supercoiling suggest a number of mechanisms whereby changes in DNA topology in vivo might be used to influence gene expression.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. L. Randall, L. Zechiedrich, and B. M. Pettitt In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form Nucleic Acids Res., September 1, 2009; 37(16): 5568 - 5577. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Lavery, M. Moakher, J. H. Maddocks, D. Petkeviciute, and K. Zakrzewska Conformational analysis of nucleic acids revisited: Curves+ Nucleic Acids Res., September 1, 2009; 37(17): 5917 - 5929. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Curuksu, M. Zacharias, R. Lavery, and K. Zakrzewska Local and global effects of strong DNA bending induced during molecular dynamics simulations Nucleic Acids Res., June 1, 2009; 37(11): 3766 - 3773. [Abstract] [Full Text] [PDF]
|
|