title: (1,4,7-trimethyl-1,4,7-triazacyclononane)iron (III)-mediated cleavage of DNA: detection of selected protein-DNA interactions.
abstract: A new reagent for the oxidative cleavage of DNA, (1,4,7-trimethyl-1, 4,7-triazacyclononane)iron(III) chloride was recently introduced. We have determined the utility of this reagent for detecting protein-DNA interactions within two types of complexes. Interestingly, we find that the rates of DNA cleavage by this reagent are differentially affected by the two classes of protein-DNA interactons studied. We find that the rate of DNA cleavage by this reagent is relatively unaffected by the non-sequence-specific histone-DNA interactions within a nucleosome complex. Conversely, a clear footprint pattern is obtained with two different DNA sequence-specific protein-DNA complexes. The results suggest that (1,4,7-trimethyl-1,4,7-triazacyclononane)iron(III) chloride will be a useful reagent to probe trans -acting-factor-DNA interactions within a chromatin environment. Differences between these two types of protein-DNA interactions, which might account for this observation, are discussed.
authors.affiliation: Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA.
authors.forename: A
authors.initials: A
authors.lastname: Ehmann
authors.forename: D
authors.initials: D
authors.lastname: Chafin
authors.forename: K M
authors.initials: KM
authors.lastname: Lee
authors.forename: J J
authors.initials: JJ
authors.lastname: Hayes
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D018983:DNA Footprinting / Q000379:methods*; D004265:DNA Helicases / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004492:Edetic Acid; D005290:Ferric Compounds / Q000737:chemistry*; D009707:Nucleosomes / Q000378:metabolism; D011485:Protein Binding; D012097:Repressor Proteins; D015534:Trans-Activators / Q000378:metabolism
chemical_list: C112451:(1,4,7-trimethyl-1,4,7-triazacyclononane)iron(III); D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D005290:Ferric Compounds; D009707:Nucleosomes; D012097:Repressor Proteins; D015534:Trans-Activators; C045264:replication initiator protein; C071577:dinR protein, Bacillus subtilis; D004247:DNA; D004492:Edetic Acid; D004265:DNA Helicases