The mammalian 5-to 3-exonuclease/endonuclease, called RAD2 homologue 1 or flap endonuclease 1, has a unique cleavage activity, dependent on specific substrate structure. On a primer-template, in which the primer has an unannealed 5-tail, endonucleolytic cleavage near the annealing point releases the tail intact. Entering at the 5-end, the nuclease tracks along the entire tail to the point of cleavage. Genetic analyses suggest that this nuclease removes DNA adducts in vivo (Sommers, C. H., Miller, E. J., Dujon, B., Prakash, S., and Prakash, L. (1995) J. Biol. Chem. 270, 4193-4196). Micrococcal nuclease footprinting shows that after tracking the nuclease protects a region of the tail 25 nucleotides long, adjacent to the cleavage site.Substrates with adducts at specific locations were used to assess the mechanism of RAD2 homologue 1 nuclease tracking and its ability to cleave modified DNA. Either a conventional cis-diamminedichloroplatinum (II) (CDDP) or a bulky CDDP derivative was placed within or beyond the region protected by the nuclease. The nuclease cleaved the tail of both substrates. In contrast, a CDDP adduct just adjacent to the expected cleavage point was inhibitory. A CDDP adduct at the very 5-end of the tail was also cleaved. The nuclease could remove tails containing adducts on the sugarphosphate backbone. Apparently, the nuclease is designed to slide over various types of damage on single stranded DNA and then cut past the damaged site.Many of the reactions that occur at the mammalian DNA replication fork have been reconstituted in vitro using purified enzymes, as reviewed by Bambara and Huang (1). We have studied the processing of Okazaki fragments during lagging strand DNA replication using reconstitution reactions with purified calf enzymes. We found that the initiator RNA primers were removed by the combined action of two nucleases, RNase H1 and a 5Ј-to 3Ј-exonuclease (2). RNase H1 cleaves the initiator RNA 1 residue upstream of the RNA-DNA junction, leaving a single 5Ј-terminal ribonucleotide. This remaining RNA residue is removed by the 5Ј-to 3Ј-exonuclease. Following RNA removal, the exonuclease works coordinately with any polymerase in a nick translation reaction (3) followed by ligation (4). We also found that this nuclease removes unannealed 5Ј-tails of primers on templates through endonucleolytic cleavage (5).The mammalian 5Ј-to 3Ј-exonuclease/endonuclease has been purified and examined by several groups. The calf enzyme was first described as a double strand specific exonuclease stimulated by synthesis from an upstream primer (3). The homologous murine enzyme was isolated and named circle closing activity exonuclease (cca exonuclease) or flap endonuclease 1 (FEN1) 1 (6, 7). Several groups have purified the human homologue from HeLa cells (8 -11). This enzyme was named maturation factor I (9) or DNase IV (8, 10). The yeast homologue has been purified from Saccharomyces cerevisiae and named RAD2 homologue 1 (RTH1) (12, 13). Analysis indicates that RTH1 shares homology with the RAD2 gene pro...