Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates

J Am Chem Soc. 2012 Jul 25;134(29):11840-3. doi: 10.1021/ja3017889. Epub 2012 Apr 11.


The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • DNA Polymerase I / chemistry*
  • DNA Polymerase I / metabolism
  • Models, Molecular
  • Polyphosphates / chemistry
  • Polyphosphates / metabolism
  • Protein Binding
  • Protein Conformation
  • Purine Nucleosides / chemistry*
  • Purine Nucleosides / metabolism
  • Purines / chemistry
  • Purines / metabolism
  • Pyrimidine Nucleosides / chemistry*
  • Pyrimidine Nucleosides / metabolism
  • Thermus / chemistry
  • Thermus / enzymology*


  • 7-deazapurine
  • Polyphosphates
  • Purine Nucleosides
  • Purines
  • Pyrimidine Nucleosides
  • DNA Polymerase I
  • triphosphoric acid