Feedback control of biological polymers in a nanopore

Noah Wilson, UC Santa Cruz

In our experiment, a single channel (pore) is formed in a lipid bilayer membrane by self-insertion of a protein into the membrane. The resulting “nanopore” is 10 nm long and 1.5-3 nm in diameter. An electric potential applied across the membrane creates a measurable ionic current that flows through the pore. The electric potential is also sufficient for capture and translocation of single stranded DNA (ssDNA) and RNA through the pore, leveraging the charged backbone of these biopolymers. As a single polymer passes through the pore, the flow of ions is obstructed and the ionic current amplitude decreases. Based on features in the attenuated current, nucleotides of translocating ssDNA and RNA polymers have been identified. Consequently, the nanopore has demonstrated great potential for high-throughput, rapid sequencing. Moreover, polymers that are bound to enzymes have been captured in the pore, with the enzyme remaining on the top side of the nanopore. In these experiments, varying the potential and measuring the ionic current allow one to probe and characterize the enzyme.

In this talk, I will briefly discuss related methods for single-molecule sensing and manipulation, some of which require feedback control.

I'll then describe the nanopore system, and recent results [1] demonstrating feedback control of individual DNA polymers in a nanopore while bound to the Klenow fragment (KF) of Escherichia coli DNA polymerase I.