Fig 6. Pathways leading to mismatch correction of heteroduplex DNA formed during SSA.

A. Heteroduplex DNA between the F and A variants has six single base-pair differences (F/A) and an insertion (*) that lies in a run of 12 Ts. Strand annealing is followed by Rad1-Rad10 clipping of 3’-ended nonhomologous tails. The 3’ ends can then be used as primers for Polδ DNA polymerase to fill in the gaps. B. In some cases Polδ’s 3’ to 5’ proofreading exonuclease activity may be stimulated to chew back the 3’ end and remove heterologies as far as 40 nt from the end. Filling in by the same polymerase would lead to apparent mismatch correction of the terminal heterologies. C. Mismatches close to the 3’ end might also be excised by Rad1-Rad10 if the 3’ end is not firmly paired to its complementary strand. D. Mismatch repair performed by MutSα and MutLα is likely biased to remove mismatches on the strand containing the filled-in (and perhaps not yet ligated) strand, creating an opposite gradient of repair near each end.