Resolution of AP sites via the multiple-nucleotide patch replacement pathway

While the single nucleotide replacement pathway appears to facilitate the repair of most damaged bases, an alternative BER pathway is evoked when the structure of the 5'-terminal sugar phosphate is such that it cannot be cleaved through the AP lyase activity of DNA polymerase beta (POLB). Under these circumstances, a short stretch of residues containing the abasic site is excised and replaced. Following DNA glycosylase-mediated cleavage of the damaged base, the endonuclease APEX1 is recruited to the site of damage where it cleaves the 5' side of the abasic deoxyribose residue, as in the single nucleotide replacement pathway. However, POLB then synthesizes the first replacement residue without prior cleavage of the 5'-terminal sugar phosphate, hence displacing this entity. Long-patch BER can be completed by continued POLB-mediated DNA strand displacement synthesis in the presence of PARP1 or PARP2, FEN1 and DNA ligase I (LIG1). When the PCNA-containing replication complex is available, as is the case with cells in the S-phase of the cell cycle, DNA strand displacement synthesis is catalyzed by DNA polymerase delta (POLD) or DNA polymerase epsilon (POLE) complexes, in the presence of PCNA, RPA, RFC, APEX1, FEN1 and LIG1. In both POLB-dependent and PCNA-dependent DNA displacement synthesis, the displaced DNA strand containing the abasic sugar phosphate creates a flap structure that is recognized and cleaved by the flap endonuclease FEN1. The replacement residues added by POLB or POLD/POLE are then ligated by the DNA ligase I (LIG1).

Summary from Reactome (R-HSA-110373), read 2026-09-23.