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

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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 produce...

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Detalles Bibliográficos
Autores principales: Dame, Remus T., van Mameren, Joost, Luijsterburg, Martijn S., Mysiak, Monika E., Janićijević, Ana, Pazdzior, Grzegorz, van der Vliet, Peter C., Wyman, Claire, Wuite, Gijs J.L.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Methods Online
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1083423/
https://www.ncbi.nlm.nih.gov/pubmed/15843682
http://dx.doi.org/10.1093/nar/gni073
Descripción
Sumario: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.

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