DNA methylation often reflects epigenetic changes that affect oncogenesis and normal cell functions. Current methods for assessing DNA methylation, however, are labor intensive, technically complicated, and often ambiguous.

A novel microarray-based technique for the quantification of DNA methylation has been developed. The microarray uses methyl binding domain proteins to recognize CpGs with high specificity both in vivo and in vitro. The two step process hybridizes the DNA to an array of oligonucleotide probes and then exposes the DNA to fluorescently labeled methyl binding proteins. Analysis of the binding kinetics provides information of the methylation level at each addressable spot with increased specificity. This technique dramatically simplifies quantification of methylated DNA, increases accuracy, and avoids limitations associated with prior methods.