Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 116

the confinement effect. Accordingly, electrophoretic translocation velocity of
DNA decreases with reducing pore diameter. Both of the parameters have an
exponential relation with the SSN diameter. At lower diameter, they showed linear
behavior before finally trying to stabilize at higher diameter values. This analysis
is very helpful in determining the optimal pore diameter for a better signal yield.
Ionic current showed a parabolic relation with increasing diameter as shown
in Fig. 5.5c .
They found that the translocation time is the same for different DNA
sequences at certain applied conditions, which is contrary to previous experi-
mental reports [ 30 , 31 ]. The discrepancy could be from the smaller lengths of
8 bases of single-stranded DNA (ss-DNA) considered.
5.3.2 Applied Voltage Dependant Interactions
The ionic current is linearly dependant on applied voltage. Iqbal and co-workers
found that ionic current showed a parabolic relation with the applied voltage as
shown in Fig. 5.6c . They explained that this might be due the presence of DNA
inside the SSN during simulations. The van der Waals forces also showed a
parabolic dependence on the voltage (Fig. 5.6a ). At higher applied voltages the
translocation velocity of DNA is very high due to its linear behavior and trans-
location time is observed to be less than 100 ns. Such a small value of translocation
time can be limiting factor on analyzing the DNA interactions. They suggested that
a coarse grain model would be required to simulate the behavior of DNA at lower
applied voltage.
5.3.3 Applied Voltage Dependant Effective Nanopore Diameter
The effective diameter of a functionalized nanopore depends on the applied voltage.
In a bare nanopore, the ions of the electrolyte form a double layer which reduces
the DNA translocation speed through the pore. But in the cases of ss-DNA attachment
or polymer deposition on the inner pore surface, the SSN shows different kinetics.
Liu et al. considered 8-base long ss-DNA coating on the inner walls of the nano-
pores [ 27 ]. The tethered DNA has a negative charge due to the phosphate backbone.
The separation between the two attached DNA strands can be assumed to be approxi-
mately equal to the radius of gyration. They showed that the tethered DNA began to
straighten in the direction of the oppositely-charged electrode due to negative charge
on its backbone. It increased the effective diameter of the nanopore.
Besides applied voltage, the effective pore diameter is also influenced by ion
condensation and ion flow. The state of the pore after ss-DNA attachment, as
well as the effect of applied voltage on the effective pore diameter, is shown in