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Nucleic Acids Research 2006 34(6):1711-1720; doi:10.1093/nar/gkl076
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Published online 23 March 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Protein assembly and DNA looping by the FokI restriction endonuclease

Lucy E. Catto, Sumita Ganguly, Susan E. Milsom, Abigail J. Welsh and Stephen E. Halford*

Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk Bristol BS8 1TD, UK

*To whom correspondence should be addressed. Tel: +44 117 928 7429; Fax: +44 117 928 8274; Email: s.halford{at}bristol.ac.uk

Received February 3, 2006. Revised March 3, 2006. Accepted March 3, 2006.

The FokI restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands at fixed positions upstream of the site. The sequence is contacted by a single monomer of the protein, but the monomer has only one catalytic centre and forms a dimer to cut both strands. FokI is also known to cleave DNA with two copies of its site more rapidly than DNA with one copy. To discover how FokI acts at a single site and how it acts at two sites, its reactions were examined on a series of plasmids with either one recognition site or with two sites separated by varied distances, sometimes in the presence of a DNA-binding defective mutant of FokI. These experiments showed that, to cleave DNA with one site, the monomer bound to that site associates via a weak protein–protein interaction with a second monomer that remains detached from the recognition sequence. Nevertheless, the second monomer catalyses phosphodiester bond hydrolysis at the same rate as the DNA-bound monomer. On DNA with two sites, two monomers of FokI interact strongly, as a result of being tethered to the same molecule of DNA, and sequester the intervening DNA in a loop.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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