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RESEARCH PAPER
maintains a ligatable nick during lagging-strand DNA replication
1 Department of Biochemistry, Washington University School of Medicine, St. Louis, Missouri 63110, USA; 2 Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
During each yeast cell cycle, 
100,000 nicks are generated during lagging-strand DNA replication. Efficient nick processing during Okazaki fragment maturation requires the coordinated action of DNA polymerase 
(Pol ) and the FLAP endonuclease FEN1. Misregulation of this process leads to the accumulation of double-stranded breaks and cell lethality. Our studies highlight a remarkably efficient mechanism for Okazaki fragment maturation in which Pol by default displaces 2–3 nt of any downstream RNA or DNA it encounters. In the presence of FEN1, efficient nick translation ensues, whereby a mixture of mono- and small oligonucleotides are released. If FEN1 is absent or not optimally functional, the ability of Pol to back up via its 3'–5'-exonuclease activity, a process called idling, maintains the polymerase at a position that is ideal either for ligation (in case of a DNA–DNA nick) or for subsequent engagement by FEN1 (in case of a DNA–RNA nick). Consistent with the hypothesis that DNA polymerase 
is the leading-strand enzyme, we observed no idling by this enzyme and no cooperation with FEN1 for creating a ligatable nick.
[Keywords: Okazaki fragment; DNA replication; DNA polymerase; nick translation; exonuclease]
Received August 20, 2004; revised version accepted September 20, 2004.
3 Corresponding author. E-MAIL burgers{at}biochem.wustl.edu; FAX (314) 362-7183.
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