A 'one-pot' assay for the accessibility of DNA in a nucleosome core particle

Nucleic Acids Res. 2004 Aug 25;32(15):e122. doi: 10.1093/nar/gnh121.

Abstract

The accessibility of nucleosomal DNA to transcription factors and other sequence-specific DNA binding proteins is of importance in the consideration of mechanisms of transcriptional control. Here, we report a simple novel assay which determines this accessibility at eight different rotationally equivalent sites on nucleosomal DNA and shows that linker histones and the chromosomal HMGB proteins, HMG-D and HMG-Z, have opposite effects on the accessibility of nucleosomal DNA. We compare this assay to previously described methods.

Publication types

  • Comparative Study

MeSH terms

  • Binding Sites
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Restriction Enzymes / metabolism
  • High Mobility Group Proteins / metabolism
  • Histones / metabolism
  • Kinetics
  • Nuclease Protection Assays / methods*
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism*

Substances

  • High Mobility Group Proteins
  • Histones
  • Nucleosomes
  • DNA
  • DNA Restriction Enzymes