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Nucleic Acids Research 2005 33(7):e68; doi:10.1093/nar/gni073
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Published online 20 April 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

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Analysis of scanning force microscopy images of protein-induced DNA bending using simulations

Remus T. Dame*, Joost van Mameren, Martijn S. Luijsterburg, Monika E. Mysiak1, Ana Janicijevic2, Grzegorz Pazdzior, Peter C. van der Vliet1, Claire Wyman2,3 and Gijs J.L. Wuite

Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081, NL-1081 HV, Amsterdam, The Netherlands 1Department of Physiological Chemistry, University Medical Center Utrecht and Centre for Biomedical Genetics Utrecht, The Netherlands 2Department of Cell Biology and Genetics, Erasmus MC PO Box 1738, 3000 DR, Rotterdam, The Netherlands 3Department of Radiation Oncology, Erasmus MC PO Box 1738, 3000 DR, Rotterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 59 87 838; Fax: +31 20 59 87 991; Email: rtdame{at}nat.vu.nl

Received December 23, 2004. Revised March 8, 2005. Accepted April 4, 2005.

Bending of DNA is a feature essential to the function of many DNA-binding proteins. Bending angles can be estimated with a variety of techniques, but most directly from images obtained using scanning force microscopy (SFM). Direct measurement of the bending angle using a tangent method often produces angles that deviate significantly from values obtained using other techniques. Here, we describe the application of SFM in combination with simulations of DNA as a means to estimate protein-induced bending angles in a reliable and unbiased fashion. In this manner, we were able to obtain accurate estimates for the bending angles induced by nuclear factor I, octamer-binding transcription factor 1, the human XPC-Rad23B complex.

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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