The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine

The electronic detection and characterization of individual polynucleotides driven through a single protein nanopore holds promise for rapid and low-cost DNA sequencing. A variation on reading DNA in a ticker tape fashion was recently proposed. The pore would electrically detect single nucleotides that are cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We will present the results of an analytical and computational study of this scheme. The analysis examines the effects of diffusive motion on the capture probability for each nucleotide. The capture probability increases with the applied transmembrane potential, but this is offset by the reduction in the residence time of each nucleotide in the pore. The theoretical results demonstrate that these two effects limit the capability of a cleavage-based nanopore sequencing engine. We will discuss these constraints and speculate on how the system could be improved.