Effective driving force applied on DNA inside a solid-state nanopore

Abstract

A detailed understanding of the origin of the electrophoretic force on DNA molecules in a solid-state nanopore is important for the development of nanopore-based sequencing technologies. Because of the discrepancies between recent attempts to predict this force and both direct and indirect experimental measurements, this topic has been the focus of much recent discussion. We show that the force is predictable to very good accuracy if all of the experimental conditions are accounted for properly. To resolve this issue, we compare the calculation efficiency and accuracy of numerical solutions of Poisson-Boltzmann and Poisson-Nernst-Planck descriptions of electrolyte behavior in the nanopore in the presence of DNA molecules. Two geometries--axially symmetric and cross-sectional--are compared and shown to be compatible. Numerical solutions are carried out on a sufficiently fine mesh to evaluate the viscous drag force acting on DNA inside a silicon nitride nanopore. By assuming the DNA is immobilized in the axial center of the nanopore, the calculation result of this viscous drag force is found to be rather larger than the experimental result. Because the viscous drag force decreases if DNA is closer to the surface of the nanopore, however, the relevant effective driving force is the average over all possible positions of the DNA in the nanopore. When this positional uncertainty is taken into account, the effective driving force acting on DNA inside the nanopore is found to agree very well with the experimental results.