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

Nucleic Acids Res. 2005 Apr 20;33(7):e68. doi: 10.1093/nar/gni073.

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]

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • CCAAT-Enhancer-Binding Proteins / metabolism
  • Computer Simulation
  • DNA / chemistry*
  • DNA / metabolism
  • DNA / ultrastructure*
  • DNA Repair Enzymes
  • DNA-Binding Proteins / metabolism*
  • Humans
  • Microscopy, Atomic Force*
  • Molecular Structure
  • NFI Transcription Factors
  • Nucleic Acid Conformation
  • Octamer Transcription Factor-1
  • Transcription Factors / metabolism

Substances

  • CCAAT-Enhancer-Binding Proteins
  • DNA-Binding Proteins
  • NFI Transcription Factors
  • Octamer Transcription Factor-1
  • POU2F1 protein, human
  • RAD23B protein, human
  • Transcription Factors
  • RAD23A protein, human
  • DNA
  • DNA Repair Enzymes