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Oxford University Press, Nucleic Acids Research, 7(33), p. e68-e68, 2005

DOI: 10.1093/nar/gni073

Oxford University Press, Nucleic Acids Research, 8(33), p. 2767-2767, 2005

DOI: 10.1093/nar/gki577

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

Journal article published in 2005 by Remus T., Dame R. T., Joost van Mameren ORCID, Martijn S. Luijsterburg, Monika E. Mysiak, Ana Janićijević, Grzegorz Pazdzior, Peter C. van der Vliet, Claire Wyman, Gijs J. L. Wuite, Remus T. Dame
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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 and integration host factor [correction]