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Proc Natl Acad Sci U S A. 2011 May 3;108(18):7419-24. doi: 10.1073/pnas.1018436108. Epub 2011 Apr 18.

Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase.

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Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.


Structural and topological data suggest that serine site-specific DNA recombinases exchange duplex DNAs by rigid-body relative rotation of the two halves of the synapse, mediated by a flat protein-protein interaction surface. We present evidence for this rotational motion for a simple serine recombinase, the Bxb1 phage integrase, from a single-DNA-based supercoil-release assay that allows us to follow crossover site cleavage, rotation, religation, and product release in real time. We have also used a two-DNA braiding-relaxation experiment to observe the effect of synapse rotation in reactions on two long molecules. Relaxation and unbraiding are rapid (averaging 54 and 70 turns/s, respectively) and complete, with no discernible pauses. Nevertheless, the molecular friction associated with rotation is larger than that of type-I topoisomerases in a similar assay. Surprisingly we find that the synapse can stay rotationally "open" for many minutes.

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