Implications of active site constraints on varied DNA polymerase selectivity

J Am Chem Soc. 2002 Sep 25;124(38):11230-1. doi: 10.1021/ja027060k.


DNA polymerase selectivity often varies significantly depending on the DNA polymerase. The origin of this varying error propensity is elusive. It is assumed that DNA polymerases form nucleotide binding pockets that differ in properties such as shape and tightness. We tested this prediction and studied HIV-1 RT by employment of size-augmented nucleotides and site-directed mutagenesis of the enzyme. New valuable insights into the mechanism of DNA polymerase fidelity were obtained. The presented study provides experimental evidence that variations of steric constraints within the nucleotide binding pocket of at least two DNA polymerases cause variations in nucleotide incorporation selectivity. Thus, our results support the concept of active site tightness as a causative in differential fidelity among DNA polymerases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • HIV Reverse Transcriptase / chemistry*
  • HIV Reverse Transcriptase / genetics
  • HIV Reverse Transcriptase / metabolism*
  • Kinetics
  • Mutation
  • Structure-Activity Relationship
  • Substrate Specificity
  • Thymidine / analogs & derivatives
  • Thymidine / chemistry
  • Thymidine / metabolism


  • HIV Reverse Transcriptase
  • Thymidine