Development of a DNA Methylation Sensor Based On Fluorescence Correlation Spectroscopy

Biomarkers based on DNA methylation patterns dictate the combined genetic (inherited) and epigenetic (environmental) manifestations of cancer risk and are highly promising to detect early-stage cancers, such as lung and prostate cancers. However, the current approaches for finding novel methylation targets and detect small changes in DNA methylation levels either do not provide sufficient resolution or are laborious to perform. We engineered a protein probe based on DNA CpG methyl-binding-domains to overcome these challenges. Coupled with the fluorescence correlation spectroscopy, the engineered protein probe can be used to detect small changes in DNA methylation level using low concentrations of chromosomal DNA, i.e., ~pM. The sensitivity and specificity of the engineered probe are characterized. Extension of this platform for in vivo detection of DNA methylation patterns will also be discussed.