Oligonucleotide Synthesis pp 319-342

Part of the Methods in Molecular Biology book series (MIMB, volume 288)

DNase I Footprinting of Small Molecule Binding Sites on DNA

  • Christian Bailly
  • Jérôme Kluza
  • Christopher Martin
  • Thomas Ellis
  • Michael J. Waring


Nuclease footprinting techniques were initially developed to investigate protein-deoxyribonucleic acid (DNA) interactions but these tools of molecular biology have also become instrumental for probing sequence-selective binding of small molecules to DNA. Here, the method is described and technical details are given for performing deoxyribonuclease (DNase) I footprinting with DNA-binding drugs. An example is presented where DNase I is used (as well as DNase II and micrococcal nuclease) to probe the patterns of sequence-selective recognition of DNA by the anticancer antibiotic actinomycin D. DNase I is a convenient endonuclease for detecting and locating the position of actinomycin-binding sites within GC-rich sequences.

Key Words

Nuclease DNase I footprinting DNA-binding drugs DNase I DNase II micrococcal nuclease anticancer antibiotic actinomycin D endonuclease electrophoresis polyacrylamide gels echinomycin cooperativity drug-DNA recognition reverse transcriptase DNA polymerase I diaminopurine, inosine electroelution dimethylsulfate densitometric analysis capillary electrophoresis sequence selectivity DNA recognition 


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Copyright information

© Humana Press Inc. 2005

Authors and Affiliations

  • Christian Bailly
    • 1
  • Jérôme Kluza
    • 2
  • Christopher Martin
    • 3
  • Thomas Ellis
    • 3
  • Michael J. Waring
    • 3
  1. 1.INSERM U-524Institut de Recherches sur le Cancer de LilleLilleFrance
  2. 2.INSERM U-524Génétique Moléculaire et Approches Thérapeutiques de éopathies MalignesLilleFrance
  3. 3.Department of PharmacologyUniversity of CambridgeCambridgeUK

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