Quantification of DNA damage products resulting from deamination, oxidation and reaction with products of lipid peroxidation by liquid chromatography isotope dilution tandem mass spectrometry

Nat Protoc. 2008;3(8):1287-98. doi: 10.1038/nprot.2008.119.


The analysis of damage products as biomarkers of inflammation has been hampered by a poor understanding of the chemical biology of inflammation, the lack of sensitive analytical methods and a focus on single chemicals as surrogates for inflammation. To overcome these problems, we developed a general and sensitive liquid chromatographic tandem mass spectrometry (LC/MS-MS) method to quantify, in a single DNA sample, the nucleoside forms of seven DNA lesions reflecting the range of chemistries associated with inflammation: 2'-deoxyuridine, 2'-deoxyxanthosine and 2'-deoxyinosine from nitrosative deamination; 8-oxo-2'-deoxyguanosine from oxidation; and 1,N(2)-etheno-2'-deoxyguanosine, 1,N(6)-etheno-2'-deoxyadenosine and 3,N(4)-etheno-2'-deoxycytidine arising from reaction of DNA with lipid peroxidation products. Using DNA purified from cells or tissues under conditions that minimize artifacts, individual nucleosides are purified by HPLC and quantified by isotope-dilution, electrospray ionization LC/MS-MS. The method can be applied to other DNA damage products and requires 4-6 d to complete depending upon the number of samples.

Publication types

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

MeSH terms

  • Animals
  • Biomarkers / analysis
  • Calibration
  • Chromatography, High Pressure Liquid / methods*
  • DNA / chemistry*
  • DNA Adducts / chemistry
  • DNA Damage*
  • Deamination
  • Humans
  • Hydrolysis
  • Lipid Peroxidation
  • Mice
  • Oxidation-Reduction
  • Phosphorylation
  • Tandem Mass Spectrometry / methods*


  • Biomarkers
  • DNA Adducts
  • DNA