DNA Sequencing with Protein Nanopores: A Story of Strands and Nucleotides

Protein based nanopores have shown great potential as components of DNA sequencing devices. However for commercial exploitation it is imperative that the resolution of the method is improved upon. To do so we must understand the biophysics that underpins the movement of both DNA and single nucleotides through engineered protein nanopores.Here we present a molecular modeling and simulation study of the widely studied pore-forming toxin; alpha hemolysin (aHL). We use atomistic molecular dynamics with applied electric fields to mimic the experimental conditions. Umbrella sampling has been utilized to calculate the free energy profiles of single nucleotides through the aHL pore, to pinpoint the location of the energetic barriers experienced by each of the 4 DNA bases.Our results provide insights of direct relevance to the production of commercial nanopore-based DNA sequencing devices.