A recommended workflow for DNase I footprinting using a capillary electrophoresis genetic analyzer

Anal Biochem. 2015 Jul 15:481:1-3. doi: 10.1016/j.ab.2015.04.013. Epub 2015 Apr 20.

Abstract

Fragment analysis was developed to determine the sizes of DNA fragments relative to size standards of known lengths using a capillary electrophoresis genetic analyzer. This approach has since been adapted for use in DNA footprinting. However, DNA footprinting requires accurate determination of both fragment length and intensity, imposing specific demands on the experimental design. Here we delineate essential considerations involved in optimizing the fragment analysis workflow for use in DNase I footprinting to ensure that changes in DNase I cleavage patterns may be reliably identified.

Keywords: Capillary electrophoresis; DNase I footprinting; Fragment analysis; Single hit.

Publication types

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

MeSH terms

  • Binding Sites
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism*
  • DNA Footprinting / methods*
  • Deoxyribonuclease I / metabolism*
  • Electrophoresis, Capillary / methods*
  • Promoter Regions, Genetic
  • Streptomyces coelicolor / chemistry
  • Streptomyces coelicolor / genetics
  • Streptomyces coelicolor / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Workflow

Substances

  • Transcription Factors
  • DNA
  • Deoxyribonuclease I