Idling by DNA polymerase δ maintains a ligatable nick during lagging-strand DNA replication

Parie Garg, Carrie M. Stith, Nasim Sabouri, Erik Johansson, Peter M. Burgers

Research output: Contribution to journalArticlepeer-review

171 Scopus citations


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 δ (Pol δ) 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 δ 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 δ 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 åis the leading-strand enzyme, we observed no idling by this enzyme and no cooperation with FEN1 for creating a ligatable nick.

Original languageEnglish
Pages (from-to)2764-2773
Number of pages10
JournalGenes and Development
Issue number22
StatePublished - Nov 15 2004


  • DNA polymerase
  • DNA replication
  • Exonuclease
  • Nick translation
  • Okazaki fragment


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