Analysis and suppression of DNA polymerase pauses associated with a trinucleotide consensus

Nucleic Acids Res. 1996 Jul 15;24(14):2774-81. doi: 10.1093/nar/24.14.2774.


We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist that make it difficult to incorporate nucleotides at these positions. We believe that these pauses result from constraints that make the conformation change involved in nucleotide selection more difficult. These pauses can obscure parts of DNA sequencing ladders and prevent DNA amplification by the polymerase chain reaction. The addition of betaine, and some related compounds, relieves these pauses.

Publication types

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

MeSH terms

  • Bacteriophage T7 / enzymology
  • Base Sequence
  • Betaine / pharmacology
  • Consensus Sequence*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism*
  • DNA-Directed DNA Polymerase / drug effects
  • DNA-Directed DNA Polymerase / metabolism*
  • Enzyme Stability
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Synthesis Inhibitors
  • Sarcosine / pharmacology


  • DNA, Bacterial
  • Nucleic Acid Synthesis Inhibitors
  • Betaine
  • DNA-Directed DNA Polymerase
  • Sarcosine