In vitro replication slippage by DNA polymerases from thermophilic organisms

J Mol Biol. 2001 Sep 14;312(2):323-33. doi: 10.1006/jmbi.2001.4943.


Replication slippage of DNA polymerases is a potential source of spontaneous genetic rearrangements in prokaryotic and eukaryotic cells. Here we show that different thermostable DNA polymerases undergo replication slippage in vitro, during single-round replication of a single-stranded DNA template carrying a hairpin structure. Low-fidelity polymerases, such as Thermus aquaticus (Taq), high-fidelity polymerases, such as Pyrococcus furiosus (Pfu) and a highly thermostable polymerase from Pyrococcus abyssi (Pyra exo(-)) undergo slippage. Thermococcus litoralis DNA polymerase (Vent) is also able to slip; however, slippage can be inhibited when its strand-displacement activity is induced. Moreover, DNA polymerases that have a constitutive strand-displacement activity, such as Bacillus stearothermophilus DNA polymerase (Bst), do not slip. Polymerases that slip during single-round replication generate hairpin deletions during PCR amplification, with the exception of Vent polymerase because its strand-displacement activity is induced under these conditions. We show that these hairpin deletions occurring during PCR are due to replication slippage, and not to a previously proposed process involving polymerization across the hairpin base.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artifacts
  • Base Sequence
  • DNA Replication* / drug effects
  • DNA-Binding Proteins / metabolism
  • DNA-Binding Proteins / pharmacology
  • DNA-Directed DNA Polymerase / metabolism*
  • Enzyme Stability
  • Geobacillus stearothermophilus / enzymology*
  • Humans
  • Magnesium / pharmacology
  • Models, Genetic
  • Mutagenesis / drug effects
  • Mutagenesis / genetics*
  • Nucleic Acid Conformation
  • Polymerase Chain Reaction
  • Pyrococcus / enzymology*
  • RNA, Ribosomal, 18S / chemistry
  • RNA, Ribosomal, 18S / genetics
  • Sequence Deletion / genetics
  • Templates, Genetic
  • Thermococcus / enzymology*
  • Thermus / enzymology*


  • DNA-Binding Proteins
  • RNA, Ribosomal, 18S
  • DNA-Directed DNA Polymerase
  • Magnesium