title: Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II).
abstract: We report a direct technique for determining the binding sites of small molecules on naturally occurring heterogeneous DNA. Methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II) cleaves double helical DNA with low sequence specificity. Using a combination of MPE.Fe(II) cleavage of drug-protected DNA fragments and Maxam-Gilbert gel methods of sequence analysis, we have determined the preferred binding sites on a Rsa I-EcoRI restriction fragment from pBR322 for the intercalator actinomycin D and the minor groove binders netropsin and distamycin A. Netropsin and distamycin A gave identical DNA cleavage-inhibition patterns and bound preferentially to A+T-rich regions with a minimal protected site of four base pairs. We were able to observe the effect of increasing concentration on site selection by netropsin and distamycin A. Actinomycin D afforded a completely different cleavage-inhibition pattern, with 4- to 16-base-pair-long protected regions centered around one or more G.C base pairs.
mesh_terms: D055598:Chemical Phenomena; D002621:Chemistry; D004269:DNA, Bacterial; D003609:Dactinomycin; D003630:Daunorubicin; D004214:Distamycins; D004926:Escherichia coli; D006146:Guanidines; D009429:Netropsin; D010957:Plasmids; D011758:Pyrroles; D013329:Structure-Activity Relationship
chemical_list: D004269:DNA, Bacterial; D004214:Distamycins; D006146:Guanidines; D011758:Pyrroles; D003609:Dactinomycin; D009429:Netropsin; C030000:stallimycin; D003630:Daunorubicin