Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 121

would not bind to the outer membrane and this would help in pushing the sensing of
the nanopore to the next level.
Another important requirement is to improve the wetability of the nanopore by
functionalization with hydrophilic molecules. Hydrophobic nanopores, even at
hundreds of nanometers diameter, form a high potential barrier to the penetration
of ions and charged molecules. SiO 2 and Si 3 N 4 nanopores can be made hydrophilic
by treating these with UV ozone plasma for 1 min. Immersion of a SiO 2 nanopore
in piranha solution also makes the pore surface hydrophilic by the formation of
OH - functional groups.
Nanopore devices having membranes with more than one channel have also been
used for selective sensing of biological molecules, but single-nanopore-based solid
state devices are preferred because of real time stochastic sensing of individual
hybridization and binding events. If localized nanopore functionalization is per-
formed, a lesser number of probe molecules will be required for sensing. During
sensing, the time interval between adding the target molecules to the solution and its
binding with probe molecules depends on the concentration of target molecules.
Depending on the time interval, we can analyze the concentration of the target
molecules by first making our system intelligent by known concentrations. Ideally
SSN can detect if we have just one target molecule in the solution, but the probability
of binding events will be much less.
Single nucleotide polymorphism (SNP) occurs when one gene has two different
alleles. With the addition of restriction enzymes, solid state nanopores can be
used for identifying SNPs. Restriction enzymes are used for cleaving double strand
DNA with specific sequences. Enzyme-DNA complex was used to detect SNPs
in one report by Zhao et al. [ 54 ]. When DNA passed through silicon nitride
nanopore, some threshold voltage is required to apply shear force. They found a
different threshold voltage during the permeation of DNA and enzyme-DNA com-
plex. For enzyme-DNA complex, more threshold voltage is required to dissociate
the bond between enzyme and DNA which allows DNA to pass through the pore.
Restriction enzyme was reported to show different binding forces depending on the
sequence of DNA. Based on required threshold voltage differences, SNPs can be
detected. Their approach can be used for genotyping instead of analyzing
the complete DNA sequence.
5.4.2 Perfect Complementary and Mismatch
DNA Discrimination
One of the motives behind solid state nanopores was to have a device which can be
used to analyze DNA precisely without the loss of any useful information about
its structure and dynamics. Many reports have aimed at improving the sensitivity
and selectivity of nanopores. The inner walls of nanopores have been modified
with different chemistries. In one report, Kohli et al. used synthetic membranes