(1,4,7-TRIMETHYL-1,4,7-TRIAZACYCLONONANE)IRON (III)-MEDIATED CLEAVAGEOF DNA - DETECTION OF SELECTED PROTEIN-DNA INTERACTIONS

A new reagent for the oxidative cleavage of DNA, (1,4,7-trimethyl-1,4, 7-triazacyclononane)iron(III) chloride was recently introduced. We hav e determined the utility of this reagent for detecting protein-DNA int eractions within two types of complexes. Interestingly, we find that t he rates of DNA cleavage by this reagent are differentially affected b y 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 com plex. Conversely, a clear footprint pattern is obtained with two diffe rent 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 with in a chromatin environment. Differences between these two types of pro tein-DNA interactions, which might account for this observation, are d iscussed.