DNA-protein interactions: methods for detection and analysis

Mol Cell Biochem. 2012 Jun;365(1-2):279-99. doi: 10.1007/s11010-012-1269-z. Epub 2012 Mar 8.

Abstract

DNA-binding proteins control various cellular processes such as recombination, replication and transcription. This review is aimed to summarize some of the most commonly used techniques to determine DNA-protein interactions. In vitro techniques such as footprinting assays, electrophoretic mobility shift assay, southwestern blotting, yeast one-hybrid assay, phage display and proximity ligation assay have been discussed. The highly versatile in vivo techniques such as chromatin immunoprecipitation and its variants, DNA adenine methyl transferase identification as well as 3C and chip-loop assay have also been summarized. In addition, some in silico tools have been reviewed to provide computational basis for determining DNA-protein interactions. Biophysical techniques like fluorescence resonance energy transfer (FRET) techniques, FRET-FLIM, circular dichroism, atomic force microscopy, nuclear magnetic resonance, surface plasmon resonance, etc. have also been highlighted.

Publication types

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

MeSH terms

  • Animals
  • Calorimetry
  • Chromatin Immunoprecipitation / methods
  • Circular Dichroism
  • Computer Simulation
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Footprinting
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Electrophoretic Mobility Shift Assay
  • Fluorescence Resonance Energy Transfer
  • Humans
  • Magnetic Resonance Spectroscopy
  • Microscopy, Atomic Force
  • Models, Molecular
  • Peptide Library
  • Protein Binding
  • Software
  • Surface Plasmon Resonance
  • Two-Hybrid System Techniques

Substances

  • DNA-Binding Proteins
  • Peptide Library
  • DNA