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Nucleic Acids Research Advance Access originally published online on July 8, 2009
Nucleic Acids Research 2009 37(16):5568-5577; doi:10.1093/nar/gkp556
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Nucleic Acids Research, 2009, Vol. 37, No. 16 5568-5577
© 2009 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.

Structural Biology

In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form

Graham L. Randall1, Lynn Zechiedrich1,2,3,4,* and B. Montgomery Pettitt1,5,*

1Program in Structural and Computational Biology and Molecular Biophysics, 2Department of Molecular Virology and Microbiology, 3Verna and Marrs McLean Department of Biochemistry and Molecular Biology, 4Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030-3498, USA and 5Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA

*To whom correspondence should be addressed. Tel: +1 713 798 5126; Fax: +1 713 798 7375; Email: elz{at}bcm.edu Correspondence may also be addressed to B. Montgomery Pettitt. Tel: +1 713 743 3263; Email: pettitt{at}uh.edu

Received April 28, 2009. Revised June 12, 2009. Accepted June 15, 2009.

To understand how underwinding and overwinding the DNA helix affects its structure, we simulated 19 independent DNA systems with fixed degrees of twist using molecular dynamics in a system that does not allow writhe. Underwinding DNA induced spontaneous, sequence-dependent base flipping and local denaturation, while overwinding DNA induced the formation of Pauling-like DNA (P-DNA). The winding resulted in a bimodal state simultaneously including local structural failure and B-form DNA for both underwinding and extreme overwinding. Our simulations suggest that base flipping and local denaturation may provide a landscape influencing protein recognition of DNA sequence to affect, for examples, replication, transcription and recombination. Additionally, our findings help explain results from single-molecule experiments and demonstrate that elastic rod models are strictly valid on average only for unstressed or overwound DNA up to P-DNA formation. Finally, our data support a model in which base flipping can result from torsional stress.


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