Linear diffusion on DNA despite high-affinity binding by a DNA polymerase processivity factor

Mol Cell. 2001 Oct;8(4):911-20. doi: 10.1016/s1097-2765(01)00355-0.


The oligomeric "sliding clamp" processivity factors, such as PCNA, are thought to rely on a loose, topological association with DNA to slide freely along dsDNA. Unlike PCNA, the processivity subunit of the herpes simplex virus DNA polymerase, UL42, is a monomer and has an intrinsic affinity for dsDNA that is remarkably high for a sequence-independent DNA binding protein. Using a DNase footprinting assay, we demonstrate that UL42 translocates with the catalytic subunit of the polymerase during chain elongation. In addition, footprinting and electrophoretic mobility shift assays show that, despite its tight DNA binding, UL42 is capable of linear diffusion on DNA at a rate of between 17 and 47 bp/s. Our results thus suggest that, despite profound biochemical differences with the sliding clamps, UL42 can freely slide downstream with the catalytic subunit during DNA replication.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA / metabolism*
  • DNA Footprinting
  • DNA Replication / physiology*
  • DNA-Binding Proteins*
  • DNA-Directed DNA Polymerase / metabolism
  • Exodeoxyribonucleases*
  • Fungal Proteins / metabolism
  • Indicators and Reagents / metabolism
  • Models, Biological*
  • Peptide Initiation Factors / metabolism
  • Protein Binding
  • Protein Kinases / metabolism
  • Saccharomyces cerevisiae Proteins*
  • Streptavidin / metabolism
  • Viral Proteins / metabolism*


  • DNA-Binding Proteins
  • Fungal Proteins
  • Indicators and Reagents
  • Peptide Initiation Factors
  • Saccharomyces cerevisiae Proteins
  • Viral Proteins
  • DNA
  • Streptavidin
  • Protein Kinases
  • DNA-Directed DNA Polymerase
  • Exodeoxyribonucleases
  • DNA polymerase, Simplexvirus