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Nucleic Acids Research Advance Access originally published online on December 20, 2007
Nucleic Acids Research 2008 36(4):1120-1128; doi:10.1093/nar/gkm1125
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Nucleic Acids Research, 2008, Vol. 36, No. 4 1120-1128
© 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.

Structural Biology

Kinking the double helix by bending deformation

Quan Du, Alexander Kotlyar and Alexander Vologodskii*

Department of Chemistry, New York University, New York, NY 10003, USA

*To whom correspondence should be addressed. Tel: 212 998 3599; Fax: 212 260 7905; Email: alex.vologodskii{at}nyu.edu

Received October 24, 2007. Revised November 30, 2007. Accepted December 3, 2007.

DNA bending and torsional deformations that often occur during its functioning inside the cell can cause local disruptions of the regular helical structure. The disruptions created by negative torsional stress have been studied in detail, but those caused by bending stress have only been analyzed theoretically. By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm. First, we developed an efficient method to obtain covalently closed DNA minicircles. To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases. The data showed that the regular DNA structure is disrupted by bending deformation in the 64–65-bp minicircles, but not in the 85–86-bp minicircles. Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.


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