Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation

J Mol Biol. 2020 Dec 4;432(24):166698. doi: 10.1016/j.jmb.2020.10.032. Epub 2020 Nov 4.


More than a million Okazaki fragments are synthesized, processed and joined during replication of the human genome. After synthesis of an RNA-DNA oligonucleotide by DNA polymerase α holoenzyme, proliferating cell nuclear antigen (PCNA), a homotrimeric DNA sliding clamp and polymerase processivity factor, is loaded onto the primer-template junction by replication factor C (RFC). Although PCNA interacts with the enzymes DNA polymerase δ (Pol δ), flap endonuclease 1 (FEN1) and DNA ligase I (LigI) that complete Okazaki fragment processing and joining, it is not known how the activities of these enzymes are coordinated. Here we describe a novel interaction between Pol δ and LigI that is critical for Okazaki fragment joining in vitro. Both LigI and FEN1 associate with PCNA-Pol δ during gap-filling synthesis, suggesting that gap-filling synthesis is carried out by a complex of PCNA, Pol δ, FEN1 and LigI. Following ligation, PCNA and LigI remain on the DNA, indicating that Pol δ and FEN1 dissociate during 5' end processing and that LigI engages PCNA at the DNA nick generated by FEN1 and Pol δ. Thus, dynamic PCNA complexes coordinate Okazaki fragment synthesis and processing with PCNA and LigI forming a terminal structure of two linked protein rings encircling the ligated DNA.

Keywords: DNA flap cleavage; DNA ligation; DNA replication; DNA synthesis; DNA-protein complex.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / biosynthesis
  • DNA / genetics
  • DNA Ligase ATP / genetics*
  • DNA Ligases / genetics
  • DNA Polymerase I / genetics
  • DNA Polymerase III / genetics*
  • DNA Replication / genetics
  • Flap Endonucleases / genetics*
  • Genome, Human / genetics
  • Holoenzymes / genetics
  • Humans
  • Multiprotein Complexes / genetics
  • Multiprotein Complexes / ultrastructure
  • Proliferating Cell Nuclear Antigen / genetics*
  • Protein Binding / genetics
  • Replication Protein C / genetics


  • Holoenzymes
  • Multiprotein Complexes
  • Okazaki fragments
  • Proliferating Cell Nuclear Antigen
  • DNA
  • DNA Polymerase I
  • DNA Polymerase III
  • Flap Endonucleases
  • FEN1 protein, human
  • Replication Protein C
  • DNA Ligases
  • DNA Ligase ATP