Genomic analysis in a solid state nanopore device using single-strand binding proteins

The goal of this project is to develop a rapid genomics platform using solid state nanopores to detect denatured AT-rich sites on DNA. Using single strand binding protein, we aim to locate the binding sites on each DNA molecule passing through the nanopore by reading the current drop due to the protein. The nanopores used are created using controlled dielectric breakdown of a silicon nitride membrane with a 4M LiCl buffer solution to produce pores between 5 and 20nm for our experiments, and DNA is translocated through the pore by electrophoresis. Previously, we showed selective single strand protein binding to the ends of DNA molecules in a 30 nm pore with a noisy amplifier. In this work we have improved the sensitivity of the device and decreased the size of the pores to allow more precise measurements, and explored a wider parameter space to facilitate binding to sequence specific denaturation bubbles.