Serial intermediates with a 1 nt 3′-flap and 5′ variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases

Flap endonuclease-1 (FEN-1) plays important roles with DNA polymerases in DNA replication, repair and recombination. FEN-1 activity is elevated by the presence of a 1 nucleotide expansion at the 3′ end in the upstream primer of substrates called “structures with a 1 nt 3′-flap”, which appear to be the most preferable substrates for FEN-1; however, it is unclear how such substrates are generated in vivo. Here, we show that substrate production occurred by the cooperative function of FEN-1(phFEN-1) and Pyrococcus horikoshii DNA polymerase B (phPol B) or D (phPol D). Using various substrates, the activities of several phFEN-1 F79 mutants were compared with those of the wild type. Analysis of the activity profiles of these mutants led us to discriminate “structures with a 1 nt 3′-flap” from substrates with a 3′ -projection longer than 2 nt or from those without a 3′-projection. When phFEN-1 processed a gap substrate with phPol B or phPol D, “structures with a 1 nt 3′-flap” were assumed the reaction intermediates. Furthermore, the phFEN-1 cleavage products with phPol B or D were from 1mer to 7mer, corresponding to the sizes of the strand-displacement products of these polymerases. This suggests that a series of 1 nt 3′-flap with 5′-variable length-flap configurations were generated as transient intermediates, in which the length of the 5′-flaps depended on the displacement distance of the downstream strand by phPol B or D. Therefore, phFEN-1 might act successively on displaced 5′-variable flaps.