Solid-State Nanopore Sensors for Nucleic Acid Analysis - Nanopores: Sensing and Fundamental Biological Interactions - page 23

1.3.6.1 Surface Enhanced DNA Transport Through Al 2 O 3 Nanopores

More and more evidence is emerging supporting the notion that nanopore surface
interactions play an integral role in determining the dynamics of DNA transport.
Nanopore surface characteristics including stoichiometry, morphology, surface
charge density, charge polarity, cone angle and rms roughness are all expected to
factor into this argument. In fact, we recently reported that surface interactions can
help enhance the detection capabilities of solid-state nanopore sensors [ 90 ]. In
experiments involving the electrophoretic transport of 5 kbp dsDNA through 7 nm
diameter nanocrystalline Al 2 O 3 nanopores, mean dwell-times at 100 mV yielded
a translocation velocity of ~1.4 nucleotides/ m s, more than an order of magnitude

slower than dsDNA transport through Si 3 N 4 nanopores (~30 nucleotides/ m

s)
at similar biases [ 26 ], but an order of magnitude faster than single stranded DNA
translocation through a -hemolysin [ 14 , 15 ].
Figure 1.8 illustrates the voltage dependent transport of dsDNA through a 7 nm
nanocrystalline Al 2 O 3 nanopore. Two distinct timescales are observed in the
translocation time histograms of Fig. 1.8 , summarized in Fig. 1.8d [ 90 ]. The shorter
timescale exhibited strong voltage dependence and was associated with fast poly-
mer transport through the nanopore with minimal DNA-nanopore interactions.
Such fast translocations are indeed probable in large 7 nm pores via translocation
through the central pore region where the effects of surface binding sites and
surface charge are significantly screened. Fast translocation events were not
observed in smaller ~5 nm Al 2 O 3 nanopores suggesting that pore size and Debye
layer thickness indeed play an important role in regulating the velocity of DNA
transport [ 89 ]. The longer timescale observed was associated with DNA
translocations involving significant interactions with the nanopore. The origins of
these interactions are hydrophobic and/or electrostatic in nature and are dependent
partially on the material properties of the pore (stoichiometry, morphology and
surface roughness). As previously discussed, materials analysis confirmed the
formation of hetero-phase crystalline domains (in particular phase Al 2 O 3 )

of varying bond lengths and coordinations in the nanopore region, resulting in non-
uniform distributions of exposed Al-O groups at the pore surface. In a hydrated
nanopore, these surface sites react with adsorbed water to form protonated hydroxyl
groups at pH 7.5, resulting in a net positive, non-homogeneous surface charge
density across the pore. These positively charged nanocrystalline domains are
expected to interact strongly with anionic DNA. In fact, modeling results by Kejian
et al. confirmed that polymer translocation velocities in a solid-state nanopore are
heavily dependent on zeta potential and surface charge [ 44 ]. Alterations to pore
stoichiometry due to the preferential desorption of O and the aggregation of Al is
also expected to result in a distribution of equilibrium constants (pK's) for the
protonizable chemical sites across the pore. The resulting electrostatic interactions/
binding between the non-homogeneous, net positively charged nanopore surface
and anionic DNA is one factor contributing to the slow translocation velocities
observed in experiments involving Al 2 O 3 nanopores. This strong electrostatic
binding was not reported in SiO 2 and Si 3 N 4 , likely as these systems exhibit a net

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