Elizabeth Koch: Feedback Control of DNA Hairpin Molecules in a Nanopore

Under direction of Bill Dunbar, Elizabeth Koch worked on experiments controlling single DNA molecules driven through biological nanopores. In these experiments, an electric charge draws single-stranded DNA through tiny protein channels (nanopores) and analysis of the resulting current gives information about the structure and position of the DNA blocking the nanopore. This process could yield a low-cost method of rapid DNA sequencing, a great benefit for genetic research and personalized medical care.

The nanopore project is a collaboration between biomolecular and computer engineers; feedback control of biological components relies heavily on logic programmed in a piece of reprogrammable hardware. This hardware, an FPGA, performs real-time monitoring of the system to detect characteristic current levels corresponding to molecular complexes blocking the nanopore. The FPGA allows dynamic voltage application that quickly reacts to very fast DNA movements. Ongoing research with nanopores explores the interaction between DNA and Klenow Fragment, part of an enzyme active in DNA replication, which can help distinguish bases in single-stranded DNA and thus holds great potential for sequencing capability. Elizabeth worked with data from these experiments and wrote programs to easily extract statistics and information to make patterns and trends more visible.