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Published June 15, 1989 | public
Journal Article

DNA-binding properties of the Hin recombinase


The recombinase of the Salmonella inversion system, Hin, mediates site-specific recombination between two 26 base pairs (bp) inverted repeat sequences (hixL and hixR) which flank a 993-bp DNA segment. We have investigated Hin recognition of, and association with, the hix recombination sites. Nuclease and chemical protection studies with linear and supercoiled DNA substrates demonstrate that Hin initially binds hixL and hixR independently of binding of the other protein components of the inversion system, Fis and HU. DNA-binding assays with mutant recombination sites and methylation interference experiments indicate that the critical bases for Hin recognition of its DNA-binding site are within an 8-bp sequence covering adjacent major and minor grooves of the DNA helix in each of the 12-bp half-sites of the hix recombination sites. The nature of the Hin-hix complexes in these binding studies and the results of gel filtration assays with purified Hin suggests that Hin binds the recombination sites as a dimer. The implications of the nature of the interactions of Hin with its recombination sites on the mechanism of the recombination reaction and on the novel features of DNA recognition by Hin are discussed.

Additional Information

© 1989 by The American Society for Biochemistry and Molecular Biology, Inc. Received for publication, November 18, 1988. This work was supported in part by a grant from the National Science Foundation (to M. I. S.) and from Defense Advanced Research Project Agency Grant N00014-86K-0755. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. Supported by a postdoctoral fellowship from the National Institutes of Health. We thank Carol Lee for technical assistance and Ryn Miake-Lye, Kathy Borkovich, Kelly Hughes, Bob Bourret, and Reid Johnson for helpful discussions and critical reading of this manuscript. We also thank Howard Nash for his advice and the use of his facilities for performing the indirect end-labeled supercoiled DNA methylation protection experiments.

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