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Nucleic Acids Research Advance Access originally published online on March 12, 2009
Nucleic Acids Research 2009 37(9):2882-2893; doi:10.1093/nar/gkp137
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Nucleic Acids Research, 2009, Vol. 37, No. 9 2882-2893
© 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

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

Davide Demurtas1, Arnaud Amzallag2, Eric J. Rawdon3, John H. Maddocks4, Jacques Dubochet5 and Andrzej Stasiak1,*

1Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 2School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland, 3Department of Mathematics, University of St. Thomas, St Paul, MN 55105, USA, 4Laboratory for Computation and Visualization in Mathematics and Mechanics, EPFL FSB IMB, Ecole Polytechnique Fédérale de Lausanne and 5Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland

*To whom correspondence should be addressed. Tel: 41 21 692 4282; Fax: 41 21 692 4105; Email: andrzej.stasiak{at}unil.ch

Received November 19, 2008. Revised February 18, 2009. Accepted February 18, 2009.

We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary bending can be redistributed and accomplished within the limits of the elastic, standard model of DNA flexibility. By comparing the shapes of covalently closed, nicked and gapped DNA minicircles, we conclude that 94-bp-long covalently closed and nicked DNA minicircles do not show sharp kinks while gapped DNA molecules, containing very flexible single-stranded regions, do show sharp kinks. We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircles.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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