Nanopore Sensing and Sequencing Insights from Molecular Dynamics

Over the past decades nanopore technology has emerged as a cheap , fast , single-molecule , label-free alternative to standard analysis techniques of biological samples. This technique was already successfully employed for DNA sequencing [1]. The further development of nanopore based fluidic devices for molecular characterization would have relevant consequences in biosciences and energy applications [2]. A first mandatory requirment for an effective nanopore based sequencing system is that the single residues have to be associated to different current levels [3]. In our recent works, using all-atom molecular dynamics simulations , we investigated the theoretical blockage of small homopeptides and other chemicals (related to sulfur-based batteries) in α-Hemolysin nanopore. In the first we estimated the hindrance associated to different homopeptides , one for each standard amino acid [4], showing that current blockage is affected by amino acid volume, hydrophobicity and net charge. In the second we demonstrate that supramolecular polysulfide/cyclodextrin complexes only differing by one sulfur can be discriminated at the single molecule level [5]. Our findings offer molecular insights into protein sequencing , and innovative perspectives to use nanopores as electrolyte sensors for designing new generation lithium-sulfur batteries .