3,N(4)-ethano-2'-deoxycytidine: chemistry of incorporation into oligomeric DNA and reassessment of miscoding potential

Nucleic Acids Res. 1999 Dec 15;27(24):4725-33. doi: 10.1093/nar/27.24.4725.

Abstract

3,N(4)-Ethano-2'-deoxycytidine (ethano-dC) may be incorporated successfully into synthetic oligodeoxynucleotides by omitting the capping procedure used in the automated DNA synthetic protocols immediately after inserting the lesion and in all iterations thereafter. Ethano-dC is sensitive to acetic anhydride found in the capping reagent, and multiple oligomeric products are formed. These products were identified by examining the reaction of ethano-dC with the capping reagent, and several acetylated, ring-opened products were characterized by electrospray mass spectrometry and collision induced dissociation experiments on a tandem quadrupole mass spectrometer. A scheme for the formation of the acetylated products is proposed. In addition, the mutagenic profile of ethano-dC was re-examined and compared to that for etheno-dC. Ethano-dC is principally a blocking lesion; however, when encountered by the exo(-)Klenow fragment of DNA polymerase, dAMP (22%), TMP (16%), dGMP (5.3%) and dCMP (1.2%) were all incorporated opposite ethano-dC, along with an oligomer containing a one-base deletion (0.6%).

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acetylation
  • Automation
  • Base Sequence
  • Chromatography, High Pressure Liquid
  • DNA / chemical synthesis*
  • DNA / chemistry
  • DNA Polymerase I / metabolism
  • Deoxycytidine / analogs & derivatives
  • Deoxycytidine / pharmacology
  • Indicators and Reagents
  • Molecular Structure
  • Mutagens / chemistry
  • Mutagens / pharmacology
  • Oligodeoxyribonucleotides / chemical synthesis*
  • Oligodeoxyribonucleotides / chemistry*
  • Spectrometry, Mass, Secondary Ion

Substances

  • Indicators and Reagents
  • Mutagens
  • Oligodeoxyribonucleotides
  • Deoxycytidine
  • 3,N(4)-ethenodeoxycytidine
  • DNA
  • DNA Polymerase I