(1,4,7-trimethyl-1,4,7-triazacyclononane)iron (III)-mediated cleavage of 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 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.