FIGURE 6.

Models of FEN1 flap substrate recognition and genome protection. A, FEN1 tracking model. FEN1 identifies the single-stranded 5′ terminus of the downstream flap, tracks down the flap, and binds the base of the flap prior to cleaving the substrate. B, FEN1 threading model. FEN1 initially binds to the flap base and flap nucleotides near the base, threads the single-stranded 5′ flap through the protein, and finally cleaves the substrate. C, FEN1 Short flap processing. In the presence of short flaps, FEN1 binds to the flap base and then directly cleaves the short flap without threading. D, junction between adjacent Okazaki fragments (OF1 and OF2) has most of the elements of a 5′ flap structure. The tracking model provides template protection because FEN1 cannot track onto the template strand because of the annealed upstream Okazaki fragment (OF2). In the threading model, FEN1 binds the template strand between the Okazaki fragments, but cannot thread the template because of OF2. Therefore, the threading model also provides template strand protection.