Surface Charge Density-Dependent DNA Capture through Polymer Planar Nanopores

Abstract

Surface charge density of nanopore walls plays a critical role in DNA capture in nanopore-based sensing platforms. This paper studied the effect of surface charge density on the capture of double-stranded (ds) DNA molecules into a polymer planar nanopore numerically and experimentally. First, we simulated the effective driving force (Feff) for the translocation of a dsDNA through a planar nanopore with different sizes and surface charge densities. Focus was given on the capture stage from the nanopore mouth into the nanopore by placing a rodlike DNA at the nanopore mouth rather than inside the nanopore. For negatively charged DNA and nanopore walls, electrophoretic driving force (FEP) under an electric field is opposed by the viscous drag force by electroosmotic flow (FEOF). As the surface charge density of the nanopore wall becomes more negative, FEOF exceeds FEP beyond a threshold surface charge density, σthreshold, where DNA molecules cannot be driven through the nanopore via electrophoretic motion. For a 10 nm diameter nanopore filled with 1× TE buffer, σthreshold was determined to be −50 mC/m2. The simulation results were verified by performing dsDNA translocation experiments using a planar nanopore with 10 nm equivalent diameter imprinted on three polymer substrates with different surface charge densities. Both fluorescence observation and ionic current measurement confirmed that only nanopore devices with the surface charge density less negative than σthreshold allowed DNA translocation, indicating that the simulated σthreshold value can be used as a parameter to estimate the translocation of biopolymers in the design of nanopore devices