title: DNase I footprinting of small molecule binding sites on DNA.
abstract: 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.
authors.affiliation: INSERM U-524, Institut de Recherches sur le Cancer de Lille, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Bailly
authors.forename: Jérôme
authors.initials: J
authors.lastname: Kluza
authors.forename: Christopher
authors.initials: C
authors.lastname: Martin
authors.forename: Thomas
authors.initials: T
authors.lastname: Ellis
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Waring
mesh_terms: D001345:Autoradiography; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D018983:DNA Footprinting / Q000379:methods*; D003609:Dactinomycin / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D008969:Molecular Sequence Data
chemical_list: D003609:Dactinomycin; D004247:DNA