Quantification of Global DNA Methylation by Capillary Electrophoresis and Mass Spectrometry

Two approaches for the evaluation of the relative degree of global DNA methylation through the quantification of 2′ deoxynucleosides are described. Detection and quantification of 5-methyl 2′-deoxycytidine in genomic DNA is performed using both high-performance capillary electrophoresis (HPCE) with UV–Vis detection or liquid chromatography with electrospray ionization mass spectrometric detection (LC-ESI/MS). Treatment of genomic DNA with a ribonuclease and generation of nucleosides through enzymatic hydrolysis notably increases the specificity of both techniques. Both approaches have been demonstrated to be highly specific and sensitive, being useful for the rapid quantification of the degree of global DNA methylation and its exploitation for the analysis of poorly purified and/or concentrated DNA samples, such as tumor biopsies.