Forces affecting double-stranded DNA translocation through synthetic nanopores

Abstract

One of the recent applications of nanopores is to use them as detectors/analyzers for bio-molecules and nanopore based sequencing has been studied to quickly sequence DNA. In this paper, three categories of forces proposed in the literature to oppose the electrical driving forces in the DNA translocation process are analyzed, (1) the entropic forces of DNA uncoiling/recoiling at the pore entrance/exits, (2) the viscous drag acting on the blob like DNA outside the nanopore, and (3) the viscous drag acting on the linear DNA inside the nanopore. The magnitudes of these forces are calculated based on the parameters used in experiments and it is shown that the first two of the aforementioned categories of forces are usually small compared to the electrical driving force, while the last one is of the same order as the electrical driving force. To evaluate the viscous drag force acting on the linear DNA inside the nanopore, a hydrodynamic model based on the lubrication approximation is used to calculate the flow field and the viscous drag force acting on a DNA immobilized in a nanopore. This model is validated by good agreement with the experimental data for the tethering force used to immobilize a DNA inside the nanopore.