Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 124

SBM DNA target faced repulsive potential due to same-charge. DNA flux and
average translocation time was explained with the help of diffusion molecular
transport theory and nearest neighbor thermodynamics calculations [ 59 - 62 ].
It was proven that the nanopore channels provided repulsive potential to the
SBM DNA target, which caused its translocation time to increase and gave lesser
flux compared with PC DNA target. The magnitude of repulsive potential for the
SBM target was larger than attractive potential offered to PC DNA targets.
Due to single-base-mismatch, the value of

DG SBM was greater in comparison to

that for PC DNA target.
Energy-based mesoscale DNA translocation model was also developed by Liu
and Iqbal [ 63 ] for optimizing the experimental parameters. Hairpin loop DNAs
were modeled as independent potential wells inside the nanopore. When PC
DNA passes through the functionalized nanopore, the hybridization lowers the
potential of the well which facilitates the translocation of PC DNA through
the nanopore. But the SBM DNA faces repulsive force from the constant potential
well. Translocation kinetics of DNA were shown to largely depend on the applied
potential. At lower applied electric field, the hybridization dominates the trans-
location process of PC DNA, while at higher applied potential, the electric field
dominates the translocation process. In the case of SBM DNA, at lower applied
potential the DNA can not pass through the nanopore due to repulsion from
the potential wells, while at higher potential, the external force dominates the
repulsive force and facilitates the DNA translocation process. So at higher
applied potential (

200 mV), the single base selectivity of DNA diminishes and
both types of DNA (PC and SBM DNAs) translocate with almost same speed.
The model describes nonlinear behavior between the translocation speed and
applied potential in the case of PC DNA. The model predicts blocking behavior
at lower potential and direct pass behavior at higher potential during SBM
DNA translocation. The model describes that at lower applied electric field,
although the translocation velocity of PC DNA is significantly more than the
SBM DNA but the output signal strength would be small. At higher applied
potential, there would not be significant velocity difference. The model was opti-
mized for electric field strength to obtain clear and distinctive signal for PC and
SBM DNA during translocation. The model suggested that the applied potential
in the range of 2.5-5 mV/nm would be ideal for this type of nanopore sensing
setup. The output of the model agreed with the previous experimental results.

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5.5 Biological Applications

At present we don't have ultimate knowledge about the self assembled monolayer
(SAM) density, orientation and degree of order. In that respect protein functiona-
lized nanopores are preferable because the single target attachment at desired
location is achievable through mutagenesis. In a number of reports, nanocapillary
array membranes (NCAMs) having arrays of nanopores ranging from 100 nm