Recently, we found an interaction between adenomatous polyposis coli (APC) and DNA polymerase β (pol-β) and showed that APC blocks strand-displacement synthesis of long-patch base excision repair (LP-BER) however, the mechanism is not clear. Using an in vivo LP-BER assay system, we now show that the LP-BER is higher in APC −/− cells than in APC +/+ cells. In addition to pol-β, the pull-down experiments showed that the full-length APC also interacted with flap endonuclease 1 (Fen-1). To further characterize the interaction of APC with pol-β and Fen-1, we performed a domainmapping of APC and found that both pol-β and Fen-1 interact with a 138-amino acids peptide from the APC at the DRI-domain. Our functional assays showed that APC blocks pol-β-mediated 1-nucleotide (1-nt) as well as strand-displacement synthesis of reduced abasic, nicked-, or 1-nt gapped-DNA substrates. Our further studies demonstrated that APC blocks 5′-flap endonuclease as well as 5′-3′ exonuclease activity of Fen-1 resulting in the blockage of LP-BER. From these results we concluded that APC can have three different effects in the LP-BER pathway. First, APC can block pol-β-mediated 1-nt incorporation and strand-displacement synthesis. Second, APC can block LP-BER by blocking coordinated formation and removal of the strand-displaced flap. Third, APC can block LP-BER by blocking "Hit and Run" synthesis. These studies will have important implications of APC in DNA damage-induced carcinogenesis and chemoprevention.The genomic stability of an organism is dependent upon numerous DNA metabolic proteins. These proteins coordinate in a very orderly fashion to ensure that DNA repair, replication and recombination occur with high fidelity. However, many proteins involved in DNA metabolism have been linked with human diseases including cancer (1), premature aging syndrome (2), Huntington's disease, Friederich's ataxia and myotonic dystrophy (3). The modification or loss of DNA bases can alter the coding specificity leading to mutations, which are a vital source for genetic variations and major cause of human diseases. To deal with this type of situation, biological systems have evolved DNA repair mechanisms to protect genetic stability and integrity for the survival of organisms. DNA repair systems efficiently remove damaged DNA via several different pathways. Abasic DNA lesions account for a large proportion of the total damage and are mainly corrected by the base excision repair (BER) pathway. BER is mediated through two sub-pathways depending upon the size of the repair gap and the enzymes involved. In mammalian cells, single base lesions are repaired by "single-nucleotide base excision repair" † The financial support for these studies was provided to Satya Narayan by the grants from