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Nucleic Acids Research Advance Access originally published online on March 20, 2009
Nucleic Acids Research 2009 37(10):3165-3176; doi:10.1093/nar/gkp165
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Nucleic Acids Research, 2009, Vol. 37, No. 10 3165-3176
© 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

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling

Giuseppe Sicoli1, Gérald Mathis2, Samia Aci-Sèche3, Christine Saint-Pierre2, Yves Boulard3, Didier Gasparutto2,* and Serge Gambarelli1,*

1Laboratoire de Résonance Magnétique, 2Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E n°3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9 and 3Laboratoire de Biologie Intégrative, Service de Biologie Intégrative et Génétique Moléculaire, Institut de Biologie et de Technologies de Saclay; CEA-Saclay, F-91191, Gif-sur-Yvette Cedex, France

**To whom the correspondence should be addressed. Tel: +33-4-38-78-39-40; Fax: +33-4-38-78-50-90; Email: serge.gambarelli{at}cea.fr Correspondence may also be addressed to Didier Gasparutto. Tel: +33-4-38-78-45-58; Fax: +33-4-38-78-50-90; Email: didier.gasparutto{at}cea.fr

Received November 25, 2008. Revised February 5, 2009. Accepted March 1, 2009.

Double electron-electron resonance (DEER) was applied to determine nanometre spin–spin distances on DNA duplexes that contain selected structural alterations. The present approach to evaluate the structural features of DNA damages is thus related to the interspin distance changes, as well as to the flexibility of the overall structure deduced from the distance distribution. A set of site-directed nitroxide-labelled double-stranded DNA fragments containing defined lesions, namely an 8-oxoguanine, an abasic site or abasic site analogues, a nick, a gap and a bulge structure were prepared and then analysed by the DEER spectroscopic technique. New insights into the application of 4-pulse DEER sequence are also provided, in particular with respect to the spin probes’ positions and the rigidity of selected systems. The lesion-induced conformational changes observed, which were supported by molecular dynamics studies, confirm the results obtained by other, more conventional, spectroscopic techniques. Thus, the experimental approaches described herein provide an efficient method for probing lesion-induced structural changes of nucleic acids.

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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