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End joining of HO endonuclease-cleaved DNA. The 4-bp complementary ends can be ligated, which is an efficient process, or can be joined by NHEJ mechanisms that are inefficient. If the bases marked “f” pair, fill-in synthesis will generate a 3-bp insertion. If the bases marked “d” pair and the short tails are clipped off, a 3-bp deletion can result. Other, much larger deletions can occur in the same fashion, using bases exposed by the 5′-to-3′ resection of the DSB ends.
