A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4)

Nucleic Acids Res. 2006 Feb 1;34(3):785-95. doi: 10.1093/nar/gkj479. Print 2006.


Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607-4616]. Our goal is to elucidate on a structural level how AAF-dG can be harbored in the Dpo4 active site opposite an incoming dCTP, using molecular modeling and molecular dynamics simulations, since AAF-dG prefers the syn glycosidic torsion. Both anti and syn conformations of the templating AAF-dG in a Dpo4 ternary complex were investigated. All four dNTPs were studied. We found that an anti glycosidic torsion with C1'-exo deoxyribose conformation allows AAF-dG to be Watson-Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting. The AAF is situated in the Dpo4 major groove open pocket with fluorenyl rings 3'- and acetyl 5'-directed along the modified strand, irrespective of dNTP. With AAF-dG syn, the fluorenyl rings are in the small minor groove pocket and the active site region is highly distorted. The anti-AAF-dG conformation with C1'-exo sugar pucker can explain the preferential incorporation of dC by Dpo4. Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 2-Acetylaminofluorene / analogs & derivatives*
  • 2-Acetylaminofluorene / chemistry
  • Base Pairing
  • Binding Sites
  • DNA Adducts / chemistry*
  • DNA Polymerase beta / chemistry*
  • DNA Replication
  • Deoxyadenine Nucleotides / chemistry
  • Deoxycytosine Nucleotides / chemistry
  • Deoxyguanosine / analogs & derivatives*
  • Deoxyguanosine / chemistry
  • Hydrogen Bonding
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Sulfolobus solfataricus / enzymology*


  • DNA Adducts
  • Deoxyadenine Nucleotides
  • Deoxycytosine Nucleotides
  • 2'-deoxycytidine 5'-triphosphate
  • N-(deoxyguanosin-8-yl)acetylaminofluorene
  • 2-Acetylaminofluorene
  • DNA Polymerase beta
  • Deoxyguanosine
  • 2'-deoxyadenosine triphosphate