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 <i>p16</i> and <i>GALR2</i> in two cell lines. Methylation of <i>p16</i> was detected in both HT29 and HepG2 cell lines, whereas methylation of <i>GALR2</i> 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 <i>p16</i> and <i>GALR2</i> to be strongly inhibited. The results show that this method is sensitive to DNA methylation and is fit for evaluation of methyltransferase inhibitors