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Sci Rep. 2016 Apr 1;6:23697. doi: 10.1038/srep23697.

Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase.

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School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
Department of Physics and Astronomy, Northwestern University, Evanston IL 60208.
Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles CA 90095-1737.
Department of Molecular Biosciences, Northwestern University, Evanston IL 60208.


DNA strand exchange by serine recombinases has been proposed to occur by a large-scale rotation of halves of the recombinase tetramer. Here we provide the first direct physical evidence for the subunit rotation mechanism for the Hin serine invertase. Single-DNA looping assays using an activated mutant (Hin-H107Y) reveal specific synapses between two hix sites. Two-DNA "braiding" experiments, where separate DNA molecules carrying a single hix are interwound, show that Hin-H107Y cleaves both hix sites and mediates multi-step rotational relaxation of the interwinding. The variable numbers of rotations in the DNA braid experiments are in accord with data from bulk experiments that follow DNA topological changes accompanying recombination by the hyperactive enzyme. The relatively slow Hin rotation rates, combined with pauses, indicate considerable rotary friction between synapsed subunit pairs. A rotational pausing mechanism intrinsic to serine recombinases is likely to be crucial for DNA ligation and for preventing deleterious DNA rearrangements.

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