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Related Experiment Videos

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

J C Randell1, D M Coen

  • 1Committee on Virology and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Molecular Cell
|October 31, 2001
PubMed
Summary
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Herpes simplex virus UL42, a monomeric DNA binding protein, exhibits high affinity for dsDNA. Despite tight binding, it slides along DNA, facilitating replication alongside the polymerase catalytic subunit.

Area of Science:

  • Molecular Biology
  • Virology
  • Biochemistry

Background:

  • Oligomeric sliding clamps like PCNA associate loosely with DNA for processivity.
  • Herpes simplex virus DNA polymerase subunit UL42 is a monomer with high, sequence-independent dsDNA affinity.

Purpose of the Study:

  • To investigate the DNA translocation and sliding mechanism of the monomeric UL42 protein.
  • To compare UL42's mechanism with established oligomeric sliding clamps.

Main Methods:

  • DNase footprinting assays to observe UL42 translocation during DNA synthesis.
  • Electrophoretic mobility shift assays (EMSAs) to determine DNA binding and diffusion rates.

Main Results:

  • UL42 translocates with the catalytic subunit of the DNA polymerase during chain elongation.

Related Experiment Videos

  • UL42 demonstrates linear diffusion on dsDNA at rates of 17-47 bp/s, despite high affinity.
  • UL42 exhibits a sliding mechanism distinct from but functionally similar to PCNA.

    • Conclusions:

    • Monomeric UL42 protein utilizes a sliding mechanism for DNA processivity, independent of oligomeric clamp structure.
    • UL42's high affinity and rapid diffusion enable efficient translocation with the viral DNA polymerase.
    • This study reveals novel insights into viral DNA replication mechanisms and protein-DNA interactions.