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.

Stiff filamentous virus translocations through solid-state nanopores

“…According to the conventional theoretical picture, the electrokinetic driving force 10,12,13 and stochastic thermal forces 8,9,15 are balanced by the total viscous drag on the translocating polymer. The translocation is also retarded by electro-osmotic fluid flow through the nanopore 11,31 .…”

“…It senses when a single biopolymer threads it by registering a change in its ionic conductance 1,2 . The possibility of applying nanopores to the analysis of nucleic acids, in particular DNA sequencing, has generated interest 3 , and motivated fundamental studies of the physics of nanopore translocations [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . The uses of solid-state nanopores have recently expanded to include detecting single proteins 18 , mapping structural features along RecA-bound DNA-protein complexes 19 and detecting spherical and icosahedral virus strains [20][21][22] .…”

Single Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through Nanocapillaries

“…In the case of nanopores, the electric field acting on the DNA and protein is mostly localised around the pore opening 14 . We approximate the electrostatic potential in nanopores by using…”

Probing surface hydrophobicity of individual protein at single-molecule resolution using solid-state nanopores

“…2e) is a strong evidence for real translocation behavior. Secondly, Poisson-Boltzmann formulation was used to calculate the openpore current and DNA translocation blockage in nanopores in our previous work [46]. By setting the DNA radius as 1.25 nm, due to the Stern layer effect on DNA solution interface, and associated with other original boundary condition setting, the pore-geometry-variation curves based on a specific openpore current or DNA blockage can be independently mapped.…”

“…SCIENCE CHINA Materials mulation, as previously described [46]. To determine the geometry parameters of the nanopore, we have done a series of ionic current calculations with and without the protein inside the nanopore respectively.…”