Capture and Translocation of a Rod-like dsDNA by a Nanopore:~A Lattice Boltzmann Simulation Study

Short dsDNA, viruses like the tobacco mosaic virus and filamentous bacteriophages can be considered as a rigid rods. We previously argued that the field-driven orientation of a rod-like object will impact its capture by a nanopore because both its translational diffusion coefficient D and electrophoretic mobility μ vary with orientation. We also introduced a critical orientational capture radius to describe this effect. In this talk, we investigate this problem further using a coarse-grained (CG) model of a charged double-stranded DNA where the hydrodynamic interactions are added by coupling the CG DNA with a lattice-Boltzmann fluid via a raspberry approach. The electrostatic interactions with the salt ions are modeled with the P3M algorithm. We also discuss the capture of modified DNAs, including partially charged and branched DNAs. In all cases, we examine how molecular orientation affect capture and entry into the pore.