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Published March 1, 1986 | Published
Journal Article Open

A mammalian high mobility group protein recognizes any stretch of six A·T base pairs in duplex DNA


α-Protein is a high mobility group protein originally purified from African green monkey cells based on its affinity for the 172-base-pair repeat of monkey α-satellite DNA. We have used DNase I footprinting to identify 50 α-protein binding sites on simian virus 40 DNA and thereby to determine the DNA binding specificity of this mammalian nuclear protein. α-Protein binds with approximately equal affinity to any run of six or more A·T base pairs in duplex DNA, to many, if not all, runs of five A·T base pairs, and to a small number of other sequences within otherwise (A+T)-rich regions. Unlike well characterized sequence-specific DNA binding proteins such as bacterial repressors, α-protein makes extensive contacts within the minor groove of B-DNA. These and related findings indicate that, rather than binding to a few specific DNA sequences, α-protein recognizes a configuration of the minor groove characteristic of short runs of A·T base pairs. We discuss possible functions of α-protein and the similarities in DNA recognition by α-protein and the antibiotic netropsin.

Additional Information

© 1986 by the National Academy of Sciences. Communicated by John M. Buchanan, October 23, 1985. We thank John McCartney, Lawrence Peck, and especially Daniel Finley for helpful discussions and comments on the manuscript. We also thank Barbara Doran for secretarial assistance. This work was supported by grants to A.V. from the National Cancer Institute (CA30367) and from the National Institute of General Medical Sciences (GM33401). M.S. was supported by a predoctoral fellowship from the National Science Foundation. F.S. was supported by the Centre National de la Recherche Scientifique (France) and by a Fogarty International Fellowship from the National Institutes of Health. 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.

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