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Surface Charge Density-Dependent DNA Capture through Polymer Planar Nanopores
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posted on 2018-10-29, 00:00 authored by Zheng Jia, Junseo Choi, Sunggook ParkSurface
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.
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nanopore mouthPolymer Planar Nanopores Surface charge densityF EP10 nm equivalent diameterF EOFnanopore devices10 nm diameter nanoporethreshold surface charge densitySurface Charge Density-Dependent DNA Captureσ thresholdsurface charge densityσ threshold valueTEdsDNA translocation experimentsnanopore wallssurface charge densities
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