Towards Nanopore Sequencing: In-Silico Studies on the Interactions between Alpha-Hemolysin and SS DNA Molecules

Nanopore sequencing is a recently emerged approach and is an alternative to a classic and next generation genome sequencing techniques. Its main advantage over the others is the potential for achieving high-throughput sequencing with low material cost and high processing speed. On the basis of nanopore sequencing technique are the interactions between a nanopore and a single stranded (ss) DNA molecule. Therefore better understanding of those interactions' nature will greatly support the development of this new approach. In the current study we performed all-atom Molecular Dynamics (MD) simulations to examine the specific interactions of mutant alpha-hemolysin (αHl) nanopore with ss DNA, and Brownian Dynamics (Bromoc) simulations to measure ion currents, to study long-time DNA dynamics and to test a specific case earlier reported in the literature.