Active DNA unwinding dynamics during processive DNA replication

Proc Natl Acad Sci U S A. 2012 May 22;109(21):8115-20. doi: 10.1073/pnas.1204759109. Epub 2012 May 9.


Duplication of double-stranded DNA (dsDNA) requires a fine-tuned coordination between the DNA replication and unwinding reactions. Using optical tweezers, we probed the coupling dynamics between these two activities when they are simultaneously carried out by individual Phi29 DNA polymerase molecules replicating a dsDNA hairpin. We used the wild-type and an unwinding deficient polymerase variant and found that mechanical tension applied on the DNA and the DNA sequence modulate in different ways the replication, unwinding rates, and pause kinetics of each polymerase. However, incorporation of pause kinetics in a model to quantify the unwinding reaction reveals that both polymerases destabilize the fork with the same active mechanism and offers insights into the topological strategies that could be used by the Phi29 DNA polymerase and other DNA replication systems to couple unwinding and replication reactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacillus Phages / genetics*
  • DNA Helicases / genetics*
  • DNA Helicases / metabolism
  • DNA Replication / genetics*
  • DNA, Viral / chemistry
  • DNA, Viral / genetics*
  • DNA-Directed DNA Polymerase / genetics*
  • DNA-Directed DNA Polymerase / metabolism
  • Gene Expression Regulation, Viral / physiology
  • Molecular Motor Proteins / physiology
  • Nucleic Acid Conformation
  • Stress, Mechanical
  • Viral Proteins / genetics
  • Viral Proteins / metabolism


  • DNA, Viral
  • Molecular Motor Proteins
  • Viral Proteins
  • DNA-Directed DNA Polymerase
  • DNA Helicases