Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 119

They proposed a new idea of protein biosensors for channel stochastic sensing.
They attached biotin at the entrance of the gold nanotube. This resulted in the
complete blockage of ionic current, rather than transient charge, upon the attach-
ment of the target molecule to the biochemical molecular-recognition agent [ 40 ].
They investigated biotin-streptavidin, protein-G to immunoglobulin, and antibody
to protein ricin interactions. In another report, the same group used thiol-modified
single strand DNA for attachment on the gold nanotube. They related the
rectification of the ionic current through artificial ion channels to mimic the
functionality of biological channels [ 15 ].
Saline chemistry was used by Nillson et al. for local functionalization of
SiO 2 nanopores with DNA probes [ 14 ]. The localized deposition for nanopore diame-
ter reduction was achieved with Tetraethylorthosilicate (TEOS) gas in an FIB
system. Alkanethiol linkers were used for selective derivatization of nanopore
entrance. The nanopores were then functionalized with acrylamide-terminated
ss-DNA probes. Each funcationalization step was performed by immersing each
chip in the appropriate solution. Contact angle measurement and X-ray photoelectron
spectroscopy were used for confirming the DNA attachment. They explained that
the ss-DNA attachment on the pore entrance had reduced the nanopore diameter,
which was confirmed by IV measurements. Iqbal et al. used a similar method
and implemented a bilayer scheme [ 1 ]. They used 3-aminopropyltrimethoxysilane,
forming a silane layer, and the nanopore channel was further functionalized with
a homo-bifunctional agent [ 41 ]. An amine-modified DNA probe was attached to
the pore surface. In order to make a hair pin loop out of the probe DNA, the probe
was engineered to have complementary sequences at both ends of the molecule.
The hair-pin loop orientation was required for analyzing single-mismatch base
pairs of DNA during translocation. When the target DNA passed through the functio-
nalized nanopore, it perturbed the ionic current due to blockade and DNA-nanopore
interactions.
The structure of a single translocation molecule or DNA segment can't be
determined until the current signal magnitude is high and translocation velocity
is low. At higher translocation velocity, it's very difficult to get useful information
about a single base pair of DNA. The typical translocation velocity in a 10 nm
nanopore at 120 mV is 27 nucleotides/ m s[ 42 ]. This is not desirable due to the
limitations of the electronic detection systems. DNA translocation speed can
be decreased by varying the electrolyte temperature, applied potential, and electro-
lyte viscosity [ 31 , 43 , 44 ], but these variations also decrease the signal-to-noise
ratio resulting from reduced ion mobility.
At this point the idea of sizing, quantifying and analyzing short DNA seems
unrealistic. Kim et al. explored the idea of reducing the translocation time by
functionalizing the pore with positively charged material [ 45 ]. First they reduced
the pore diameter by atomic layer deposition (ALD) from 100 nm to 30 nm in a
250 nm free standing membrane. They used alumina (Al 2 O 3 ) for the ALD process.
The alumina provided the conformal coating on all sides of the nanopore walls [ 16 ].
The membrane thickness was increased to 320 nm after Al 2 O 3 deposition. After
cleaning with piranha the chip was immersed at room temperature for 1 h in