Faculty Advisor: David Schwartz
My postdoctoral research is focused on human genome mapping with nanocoding in nanoslit microfluidic devices. The Optical Mapping System has emerged as a unique approach for the discovery and characterization of structural variants . It is a high throughput system that constructs whole genome physical maps through the acquisition and analysis of large datasets comprising restriction maps created from individual DNA molecules (~500 kb). Such analysis creates scaffolds for sequence assembly and more importantly, reveals structural variation not discernable by other means. The Optical Mapping System relies on stretching out long individual DNA molecules from their random coil conformation, normally assumed in solution, where a molecule’s apparent length is approaching its polymer contour length. Several approaches for the stretching and presentation of large DNA molecules have been explored and developed in to practical systems for genome analysis. The first one is immobilization of DNA molecules on glass surfaces under capillary flow. It was pioneered in our laboratory, greatly advanced over the course of 15 years and to date is the workhorse of optical mapping systems.
The second method is to electrophoretically drive DNA molecules into nanoslits with at least one dimension being on the order of DNA molecule persistence length . It has been shown both theoretically and experimentally that at such conditions with low ionic strength buffer a nearly 100% DNA elongation is possible. Very importantly the DNA elongations obtained within nanoslits are expected theoretically and have been shown experimentally to have narrower distribution than elongations obtained for DNA molecules immobilized on the surface. This fundamentally improves the precision of DNA optical mapping technology. Previous work included largely manual Mesoplasma florum (793 kb) genome mapping. In the next step we will improve and automate this new system to allow rapid human genome analysis.
In addition, I will also conduct research on electronic detection of DNA which allows for sensitive detection of charges in the vicinity of the measuring device. Exploring sensitivity limit of electronic detection and its applicability to the analysis of long DNA molecule will be the focus of this part of my research.