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Surface Charge Density-Dependent DNA Capture through Polymer Planar Nanopores

By Zheng Jia (1861600), Junseo Choi (5957801) and Sunggook Park (5957804)

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 (<i>F</i><sub>eff</sub>) 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 (<i>F</i><sub>EP</sub>) under an electric field is opposed by the viscous drag force by electroosmotic flow (<i>F</i><sub>EOF</sub>). As the surface charge density of the nanopore wall becomes more negative, <i>F</i><sub>EOF</sub> exceeds <i>F</i><sub>EP</sub> beyond a threshold surface charge density, σ<sub>threshold</sub>, where DNA molecules cannot be driven through the nanopore via electrophoretic motion. For a 10 nm diameter nanopore filled with 1× TE buffer, σ<sub>threshold</sub> was determined to be −50 mC/m<sup>2</sup>. 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 σ<sub>threshold</sub> allowed DNA translocation, indicating that the simulated σ<sub>threshold</sub> value can be used as a parameter to estimate the translocation of biopolymers in the design of nanopore devices

Topics: Biophysics, Physiology, Biotechnology, Plant Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, nanopore mouth, Polymer Planar Nanopores Surface charge density, F EP, 10 nm equivalent diameter, F EOF, nanopore devices, 10 nm diameter nanopore, threshold surface charge density, Surface Charge Density-Dependent DNA Capture, σ threshold, surface charge density, σ threshold value, TE, dsDNA translocation experiments, nanopore walls, surface charge densities
Year: 2018
DOI identifier: 10.1021/acsami.8b14423.s004
OAI identifier: oai:figshare.com:article/7334234
Provided by: FigShare
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