Single-molecule Fluorescent Reporters for Epigenetic Marks and DNA Damage: Precise Quantitation and super-resolution Mapping

Silicon nano channel arrays with channel cross section on the order of 50-100nm are now routinely fabricated and have recently been commercialized. Such nanochannels allow stretching individual DNA molecules by applying an electric field. By attaching fluorescent reporters to genetic and epigenetic marks on the DNA molecule, the stretched DNA is visualized as a pattern of fluorescent spots along the DNA molecules. We show how physical extension of long DNA molecules in nanofluidic channels reveals this information in the form of a linear, optical “barcode”. Recent results from our lab demonstrate our ability to detect genetic structural variations (SVs), DNA repeats, and various forms of DNA epigenetic modifications. Applying super-resolution imaging techniques and accounting for DNA fluctuation dynamics allowed us to improve mapping precision 15 fold over commonly used techniques.