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Hoogsteen base pairs proximal and distal to echinomycin binding sites on DNA

Mendel, David and Dervan, Peter B. (1987) Hoogsteen base pairs proximal and distal to echinomycin binding sites on DNA. Proceedings of the National Academy of Sciences of the United States of America, 84 (4). pp. 910-914. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:MENpnas87

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Abstract

Forms of the DNA double helix containing non-Watson-Crick base-pairing have been discovered recently based on x-ray diffraction analysis of quinoxaline antibiotic-oligonucleotide complexes. In an effort to find evidence for Hoogsteen base-pairing at quinoxaline-binding sites in solution, chemical "footprinting" (differential cleavage reactivity) of echinomycin bound to DNA restriction fragments was examined. We report that purines (A>G) in the first and/or fourth base-pair positions of occupied echinomycin-binding sites are hyperreactive to diethyl pyrocarbonate. The correspondence of the solid-state data and the sites of diethyl pyrocarbonate hyperreactivity suggests that diethyl pyrocarbonate may be a sensitive reagent for the detection of Hoogsteen base-pairing in solution. Moreover, a 12-base-pair segment of alternating A-T DNA, which is 6 base pairs away from the nearest strong echinomycin-binding site, is also hyperreactive to diethyl pyrocarbonate in the presence of echinomycin. This hyperreactive segment may be an altered form of right-handed DNA that is entirely Hoogsteen base-paired.


Item Type:Article
Additional Information:Copyright © 1987 by the National Academy of Sciences. Contributed by Peter B. Dervan, September 29, 1986. We are grateful to the American Cancer Society (NP428) and to the Burroughs Wellcome Company for support. 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.
Subject Keywords:diethyl pyrocarbonate-mediated DNA-cleavage patterns; DNA polymorphism; ailosteric transitions; non-Watson-Crick base pairs
Record Number:CaltechAUTHORS:MENpnas87
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:MENpnas87
Alternative URL:http://www.pnas.org/cgi/content/abstract/84/4/910
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1509
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:25 Jan 2006
Last Modified:26 Dec 2012 08:44

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