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Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA·Fe(II)

Van Dyke, Michael W. and Hertzberg, Robert P. and Dervan, Peter B. (1982) Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA·Fe(II). Proceedings of the National Academy of Sciences of the United States of America, 79 (18). pp. 5470-5474. ISSN 0027-8424. PMCID PMC346925.

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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.

Item Type:Article
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Additional Information:© 1982 the National Academy of Sciences. Communicated by John J. Hopfield, May 24, 1982. We are grateful to the National Institutes of Health for grant support (GM 27681) and a National Research Service Award (GM 07616) to M.W.V. and R.P.H. The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact.
Funding AgencyGrant Number
NIH Predoctoral FellowshipGM-07616
Subject Keywords:DNA sequence determination, intercalation, minor groove binding, daunomycin
PubMed Central ID:PMC346925
Record Number:CaltechAUTHORS:VANpnas82
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1402
Deposited By: Tony Diaz
Deposited On:17 Jan 2006
Last Modified:09 May 2016 18:06

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