Solid-State Nanopore Sensors for Nucleic Acid Analysis - Nanopores: Sensing and Fundamental Biological Interactions - page 22

counterions in the pore during DNA transport [ 12 , 81 ]. Current enhancements were
observed at concentrations below 0.4 M, a phenomenon that seems localized to only
large SiO 2 nanopores. Distinct current blockades were observed in 100 mM
salt solution during the transport of

l -DNA through 2.2 nm SiN nanopores [ 23 ].

In biological a-hemolysin , Benner et al. demonstrated that current blockades were

still observed at low salt concentrations (300 mM KCl) during the entry of dsDNA
into the lumen of the pore [ 2 ]. Current blockades were also observed during the
transport of dsDNA through Al 2 O 3 nanopores in 100 mM KCl salt [ 90 ].
Polymer velocity in the nanopore is also a key topic of interest. Translocation
velocities of up to ~30 bases/ s have been reported at relatively low bias voltages in

Si 3 N 4 nanopores [ 26 ]. Chen et al. observed similar translocation velocities in large
Al 2 O 3 coated Si 3 N 4 nanopores estimated at ~27 bases/

m

s[ 14 , 15 ]. Such high
translocation velocities limit the utility of conventional nanopore technologies in
high end DNA sensing and analysis applications including single nucleotide detec-
tion. Fologea et al. demonstrated that by increasing electrolyte viscosity using
glycerol and by decreasing temperature and bias voltage, an order of magnitude
reduction in translocation velocity could be achieved [ 26 ]. Remarkably, even
with these improvements, the translocation velocities through a solid-state nanopore
are still more than an order of magnitude faster than that observed in biological
a-hemolysin [ 14 , 15 ]. Lubensky accredited the slow translocation rates in

m

a-hemolysin
to strong polymer interactions with the pore walls [ 56 ]. High translocation velocities
were also observed in large ~10 nm SiO 2 nanopores [ 85 ]. Despite these high
velocities, Storm et al. showed that it is indeed possible to size long dsDNA using
solid-state nanopores, in a rapid and label free manner [ 85 ]. In contrast to bulk
gel-electrophoresis methods, length separation using solid-state nanopores allows
each molecule to be screened and interrogated individually.
The kinetics of DNA transport through solid-state nanopores is also of interest
from a polymer physics stand point. Translocation kinetics suggests that the
majority of events in larger nanopores are fast translocation events, where the
dwell time, t D , is significantly less than the characteristic relaxation time or Zimm
time [ 85 ]. The Zimm time, t Z , is an upper bound on the time taken by a polymer to
reach an entropically and sterically favored state. For events where t D < t Z , the
molecule was said to exhibit a frozen polymer configuration during transport,
hindered by only the hydrodynamic drag on the part of the molecule outside the
pore [ 85 ]. The effects of specific polymer-pore interactions were not accounted for
in these studies. Wanunu et al. discussed the importance of surface interactions on
dsDNA transport through Si 3 N 4 nanopores [ 94 ]. Studies performed using small
2.7-5 nm pores revealed an order of magnitude increase in dwell times as pore
diameter was decreased from 5 to 2.7 nm. In addition, strong temperature depen-
dence was observed confirming that surface interactions play an important role in
polymer transport. Surface interactions were also seen to play an important
role in the transport of dsDNA through small ~5 nm Al 2 O 3 nanopores [ 89 ].
These interactions were characterized by a monoexponential decay in dwell
time histograms with time constants consistent with timescales observed in Si 3 N 4
systems [ 89 ].