Significant alteration in DNA electrophoretic translocation velocity through soft nanopores by ion partitioning

Abstract

The application of nanopores for DNA sequencing faces some challenges. The main challenge is controlling the electrophoretic translocation velocity of DNA and one remedy is covering the inner wall of the nanopore with a polyelectrolyte layer (PEL). In this study, a more realistic analytical model is presented for DNA translocation in PEL-grafted nanopores that improves the available models by considering different values for permittivity and viscosity inside and outside the PEL, taking the wall charge effects into account, and relaxing the assumption of a linear hydrodynamic drag profile inside the PEL. It is shown that ignoring the ion partitioning, arisen due to the PEL-electrolyte permittivity difference, can lead to the overestimation of the electrophoretic velocity of DNA, whereas the opposite is true when the increase in the liquid viscosity within the PEL is not accounted for. Accordingly, polyelectrolyte monomers of lower permittivities may be utilized to reduce the DNA velocity, thereby increasing the resolution of DNA sequencing. This goal may also be achieved through correctly adjusting the wall charge and the charge density of the PEL fixed ions. The details regarding the control of the DNA translocation velocity are all discussed.

Keywords: DNA sequencing; Electrophoretic translocation; Ion partitioning; Soft nanopores.