Orientation dependence of current blockade in single amino acid translocation through a graphene nanopore†

Abstract

After the successful commercialization of DNA sequencing using biological nanopores, the next frontier for nanopore technology is protein sequencing, a significantly more complex task. Molecules passing through the solid-state nanopores produce current blockades that correlate linearly with their volume in the simplest model. As thinner membranes provide better volume sensitivity, 2D materials such as graphene and MoS₂ membranes have been explored. Molecular dynamics studies have primarily focused on the translocation of the homogeneous polypeptide chains through 2D membranes. In this study, we investigated the translocation of 20 single amino acids through the monolayer and bilayer graphene nanopores using the all-atom molecular dynamics. These studies were motivated by the fact that single amino acids, as fundamental units of peptide chains, provide a simpler model for understanding pore-molecule interactions during translocations by eliminating the neighbour effects found in chains. Herein, it is shown that the correlation between the ionic current blockade and the volume of single amino acids is strongly affected by their orientation at the pore, especially when the molecule is static at the pore. We explained this phenomenon by the fact that with increasing vdW volume, the amino acid in a particular orientation has a longer projection along the perpendicular direction of the pore plane. We demonstrated distinctive current and force signals for different amino-acid translocations. We observed that some of the smaller amino acids with low molecular volume produced disproportionately high current blockades in a particular orientation due to their lower structural fluctuations during translocation. We investigated how the dipole moment (of the translocating amino acids) and its alignment with the electric field in the pores were linked with our observations.