DNA Footprinting

  • M. Stacey Ricci
  • Wafik S. El-Deiry
Part of the Methods in Molecular Biology™ book series (MIMB, volume 223)

Abstract

The classic paper by Schmitz and Galas (1) established the usefulness of footprinting analysis for identifying protein-bound sites on DNA. The basis of the footprinting technique is that DNA-bound proteins protect the phosphodiester backbone of DNA from modification or cleavage by external agents, such as deoxyribonuclease. The technique is used most commonly to identify protected DNA sequences that are binding sites for transcription factors or other proteins involved in transcription initiation. When used in combination with other methods that confirm high-affinity protein-DNA interactions, such as electrophoretic mobility shift assay or chromatin immunoprecipitation, footprinting adds important evidence that delineates the residues critical for protein binding.

Keywords

Glycerol Phenol EDTA Dimethyl Adenine 

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Copyright information

© Humana Press Inc. 2003

Authors and Affiliations

  • M. Stacey Ricci
    • 1
    • 2
    • 3
  • Wafik S. El-Deiry
    • 4
    • 5
    • 6
  1. 1.Howard Hughes Medical Institute, Department of MedicineUniversity of Pennsylvania School of MedicinePhiladelphia
  2. 2.Howard Hughes Medical Institute, Department of GeneticsUniversity of Pennsylvania School of MedicinePhiladelphia
  3. 3.Howard Hughes Medical Institute, Department of PharmacologyUniversity of Pennsylvania School of MedicinePhiladelphia
  4. 4.Department of MedicineUniversity of Pennsylvania School of MedicinePhiladelphia
  5. 5.Department of GeneticsUniversity of Pennsylvania School of MedicinePhiladelphia
  6. 6.Department of PharmacologyUniversity of Pennsylvania School of MedicinePhiladelphia

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