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J Biol Chem, Vol. 274, Issue 25, 17605-17611, June 18, 1999
From the Single base mispairs and small loops are
corrected by DNA mismatch repair, but little is known about the
correction of large loops. In this paper, large loop repair was
examined in nuclear extracts of yeast. Biochemical assays showed that
repair activity occurred on loops of 16, 27, and 216 bases, whereas a
G-T mispair and an 8-base loop were poorly corrected under these
conditions. Two modes of loop repair were revealed by comparison of
heteroduplexes that contained a site-specific nick or were covalently
closed. A nick-stimulated repair mode directs correction to the
discontinuous strand, regardless of which strand contains the loop. An
alternative mode is nick-independent and preferentially removes the
loop. Both outcomes of repair were largely eliminated when DNA
replication was inhibited, suggesting a requirement for repair
synthesis. Excision tracts of 100-200 nucleotides, spanning the
position of the loop, were observed on each strand under conditions of limited DNA repair synthesis. Both repair modes were independent of the
mismatch correction genes MSH2, MSH3,
MLH1, and PMS1, as judged by activity in mutant
extracts. Together the loop specificity and mutant results furnish
evidence for a large loop repair pathway in yeast that is distinct from
mismatch repair.
Correction of Large Mispaired DNA Loops by Extracts of
Saccharomyces cerevisiae
,, and§
Eppley Institute for Research in Cancer and
Allied Diseases, University of Nebraska Medical Center,
Omaha, Nebraska 68198-6805 and the § Department of
Biochemistry and Molecular Biology, University of Massachusetts Medical
Center, Worcester, Massachusetts 01655
Copyright © 1999 by The American Society for Biochemistry and Molecular Biology, Inc.
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