Abstract
Recombination between moderately divergent DNA sequences is impaired compared with identical sequences. In yeast, an HO endonuclease-induced double-strand break can be repaired by single-strand annealing (SSA) between flanking homologous sequences. A 3% sequence divergence between 205-bp sequences flanking the double-strand break caused a 6-fold reduction in repair compared with identical sequences. This reduction in heteroduplex rejection was suppressed in a mismatch repair-defective
msh6
Δ strain and partially suppressed in an
msh2
separation-of-function mutant. In
mlh1
Δ strains, heteroduplex rejection was greater than in
msh6
Δ strains but less than in wild type. Deleting
PMS1, MLH2
,or
MLH3
had no effect on heteroduplex rejection, but a
pms1
Δ
mlh2
Δ
mlh3
Δ triple mutant resembled
mlh1
Δ. However, correction of the mismatches within heteroduplex SSA intermediates required
PMS1
and
MLH1
to the same extent as
MSH2
and
MSH6
. An SSA competition assay in which either diverged or identical repeats can be used for repair showed that heteroduplex DNA is likely to be unwound rather than degraded. This conclusion is supported by the finding that deleting the
SGS1
helicase also suppressed heteroduplex rejection.