Analysis of scanning force microscopy images of protein-induced DNA bending using simulations.
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]
Dame
Remus T
RT
Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081, NL-1081 HV, Amsterdam, The Netherlands. rtdame@nat.vu.nl
van Mameren
Joost
J
Luijsterburg
Martijn S
MS
Mysiak
Monika E
ME
Janićijević
Ana
A
Pazdzior
Grzegorz
G
van der Vliet
Peter C
PC
Wyman
Claire
C
Wuite
Gijs J L
GJ
D022762:CCAAT-Enhancer-Binding Proteins / Q000378:metabolism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D045643:DNA Repair Enzymes; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006801:Humans; D018625:Microscopy, Atomic Force; D015394:Molecular Structure; D051839:NFI Transcription Factors; D009690:Nucleic Acid Conformation; D050811:Octamer Transcription Factor-1; D014157:Transcription Factors / Q000378:metabolism
D022762:CCAAT-Enhancer-Binding Proteins; D004268:DNA-Binding Proteins; D051839:NFI Transcription Factors; D050811:Octamer Transcription Factor-1; C494165:POU2F1 protein, human; C513287:RAD23B protein, human; D014157:Transcription Factors; C086985:RAD23A protein, human; D004247:DNA; D045643:DNA Repair Enzymes