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Nucleic Acids Research Advance Access originally published online on February 11, 2009
Nucleic Acids Research 2009 37(6):2026-2036; doi:10.1093/nar/gkp038
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Nucleic Acids Research, 2009, Vol. 37, No. 6 2026-2036
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4

Kirk Tevebaugh Ehmsen1 and Wolf-Dietrich Heyer1,2,*

1Department of Microbiology and 2Department of Molecular and Cellular Biology, University of California, Davis CA 95616-8665, USA

*To whom correspondence should be addressed. Tel: +1 530 752 3001; Fax: +1 530 752 3011; Email: wdheyer{at}ucdavis.edu

Received December 5, 2008. Revised January 6, 2009. Accepted January 8, 2009.

The DNA structure-selective endonuclease Mus81-Mms4/Eme1 incises a number of nicked joint molecule substrates in vitro. 3'-flaps are an excellent in vitro substrate for Mus81-Mms4/Eme1. Mutants in MUS81 are synthetically lethal with mutations in the 5'-flap endonuclease FEN1/Rad27 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Considering the possibility for isoenergetic interconversion between 3'- and 5'- flaps, these data are consistent with the hypothesis that Mus81-Mms4/Eme1 acts on 3'-flaps in vivo. FEN1/Rad27 prefers dually flapped substrates and cleaves in a way that allows direct ligation of the resulting nick in the product duplex. Here we test the activity of Mus81-Mms4 on dually flapped substrates and find that in contrast to FEN1/Rad27, Mus81-Mms4 activity is impaired on such substrates, resulting in cleavage products that do not allow direct religation. We conclude that Mus81-Mms4, unlike FEN1/Rad27, does not prefer dually flapped substrates and is unlikely to function as a 3'-flapase counterpart to the 5'-flapase activity of FEN1/Rad27. We further find that joint molecule incision by Mus81-Mms4 occurs in a fashion determined by the branch point, regardless of the position of an upstream duplex end. These findings underscore the significance of a nick adjacent to a branch point for Mus81-Mms4 incision.


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