Map of Distamycin, Netropsin, and Actinomycin Binding Sites on Heterogeneous DNA: DNA Cleavage-inhibition Patterns with Methidiumpropyl-EDTA.Fe(II)

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1982 Sep 1

PMID 6291045

Citations 85

Authors

M W Van Dyke

R P Hertzberg

P B Dervan

Affiliations

Soon will be listed here.

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.

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