Label-free real-time detection of DNA methylation based on quartz crystal microbalance measurement

DNA methylation plays an important role in the regulation of gene transcription, chromatin compaction, genome imprinting, and X-chromosome inactivation. DNA methyltransferase is considered a potential target for anticancer drug design. It is important to locate aberrantly methylated sequences on the human genome that are linked to specific diseases and to discover new low-toxic methylation inhibitors for medical treatments. We developed a DNA methylation detection method using a quartz crystal microbalance (QCM). We applied this method to assay genes p16 and GALR2 in two cell lines. Methylation of p16 was detected in both HT29 and HepG2 cell lines, whereas methylation of GALR2 was detected only in the HT29 cell line. We also used this method to evaluate the effect of 5-aza-2'-deoxycytidine (decitabine), a methyltransferase inhibitor used in clinical treatment. We found methylation of genes p16 and GALR2 to be strongly inhibited. The results show that this method is sensitive to DNA methylation and is fit for evaluation of methyltransferase inhibitors.