Optical and electrical sensing for epigenetic analysis

Introduction: The information content of the genome extends beyond the base sequence of DNA in the form of chemical modifications such as DNA methylation or DNA damage lesions.

Materials and Methods: We show how DNA processing enzymes may be utilized to fluorescently label various genetic and epigenetic marks on DNA. By introducing chemically modified cofactors, the enzymes are "tricked" into incorporating optical and electrical contrast agents on the DNA backbone. We use single-molecule fluorescence detection and nanopore sequencing in order to gain access to the structural variation and long range patterns of genetic and epigenetic information.

Results: We demonstrate how the physical extension of long DNA molecules on surfaces, in nanofluidic channels, and in nanopores, reveals patterns of DNA modifications in the form of a linear, “barcode”, like beads threaded on a string, where each bead represents a distinct type of observable. Recent results from our lab demonstrate our ability to detect the epigenetic mark 5-methylcytosine, 5-hydroxymethylcytosine and various forms of DNA damage on individual genomic DNA molecules.