A comparison of enzymatic digestion for the quantitation of an oligonucleotide by liquid chromatography-isotope dilution mass spectrometry

J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Mar 25;817(2):173-82. doi: 10.1016/j.jchromb.2004.11.058.


DNA is a universal analyte found in almost every organism. It is the code that dictates our genetic make-up and it provides a vast library of information. DNA sequences can indicate genetic modification of foodstuffs, how we may metabolise pharmaceuticals and the likelihood of suffering particular diseases. The basis for many of these genetic tests would benefit greatly from procedures that can accurately quantitate DNA in an absolute manner. This would then provide a sound and universally consistent foundation for regulatory and diagnostic decision making. This work compares two different enzymatic digestion systems as precursor steps to high accuracy isotope dilution mass spectrometry (IDMS) quantitation of a 20mer oligonucleotide. In the first approach, snake venom phosphodiesterase (SVP) digests the oligonucleotide to its constituent deoxynucleotides (dNMPs), followed by liquid chromatography-IDMS (LC-IDMS) quantitation. The second enzyme digestion approach used a combination of snake venom phosphodiesterase and shrimp alkaline phosphatase (SAP) which reduces the oligonucleotide to its constituent deoxynucleosides (dNs). This was then followed by an alternative LC separation and equivalent IDMS measurements. Total phosphorous content of the 20mer oligonucleotide was measured by inductively coupled plasma optical emission spectroscopy (ICP-OES). This provided independent data for comparison with the two enzyme digestion-IDMS based procedures. The most appropriate method of quantitation was found to be the combined SVP and SAP digestion. This approach negates the need to consider and/or account for the lack of a 5' terminal phosphate residue. It also enables the use of positive ion mass spectrometry which simplifies the chromatographic requirements. Based on the exact matched IDMS of the adenine deoxynucleoside, the concentration of the original 20mer oligonucleotide was found to be 110+/-9 microg g(-1). This showed good agreement with the ICP-OES data based on the measurement of phosphorus which gave an equivalent value for the original 20mer oligonucleotide of 108+/-5microg g(-1) (uncertainties at the 95% confidence interval). It is intended that this high accuracy methodology should be used to produce high calibre reference standards. These, in turn, could then be used to underpin the quality and consistency of routine measurements involving a variety of more commonly encountered methodologies. It should be noted that the IDMS procedures are equally applicable to both sequenced and non-sequenced oligonucleotide materials.

Publication types

  • Comparative Study

MeSH terms

  • Alkaline Phosphatase / metabolism*
  • Chromatography, Liquid / methods*
  • Mass Spectrometry / methods*
  • Oligonucleotides / analysis*
  • Oligonucleotides / metabolism
  • Phosphoric Diester Hydrolases / metabolism*


  • Oligonucleotides
  • Alkaline Phosphatase
  • Phosphoric Diester Hydrolases