Figure 7: Tolerance for mismatched and damaged ends in patching and ligation for NHEJ. Black text shows sequences of ends prior to joining, while blue text shows fill-in of bases by DNA polymerase λ. Lines above and below the text represent the DNA backbone, triangles show sites of ligation by X4L4, and red bars between the bases show mismatches. All sequences read 5′→3′ in the top strand and 3′→5′ in the bottom strand. (a) Cohesive overhangs with an unpaired 3′-flap, ligated by X4L4 alone [19]. (b) Completely mismatched overhangs ligated in one strand only, by purified X4L4 plus Ku, DNA-PKcs, and XLF in vitro [20]. (c) Patching and ligation of annealed overhangs of two I-SceI-induced DSBs in hamster cells, despite an internal A-A mismatch, inferred from sequencing of repair joints [21]. (d) Ligation of a mismatched duplex resulting from error-prone fill-in in HeLa cell extracts supplemented with X4L4 and a highly error-prone mutant of polymerase λ [22]. The single dash in the top strand sequence indicates a single-base deletion. (e) Patching and ligation of partially complementary overhangs, one of which contains a 3′-terminal 8-oxoG, in X4L4-supplemented HeLa nuclear extracts [23]. (f) Patching and ligation of partially complementary overhangs in one strand, despite persistence of a 3′-PG-terminated break in the opposite strand, also in X4L4-supplemented HeLa nuclear extracts [24].