Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 160

7.4.1 Translocation of a Single-Stranded DNA
in a Helical Conformation
The translocation of a 20 nucleotide long poly(dC) 20 single-stranded DNAmolecule
in a helical conformation [ 2 ] through the nanopore was simulated first [ 19 ], followed
by computations of the voltage signal induced on the Si electrodes. As described
above, we extract the DNA charge distribution from molecular dynamic simulation
by taking into account every atom's contribution of the DNA strand (the DNA data
used here and below were obtained from Dr. Aleksei Aksimentiev) and map the
charge distribution into the Poisson Solver. For this purpose, every atom's charge on
the DNA strand is distributed over a sphere of 3 ˚ in diameter, but solution charge
was excluded from this volume as it was also excluded in the two previous cases.
(Two DNA snapshots were used: one in the helical conformation 20 nucleotide long
poly(dC) 20 (this subsection), and one in the stretch conformation 11 nucleotide
long poly(dC) 11 with mutated base #4 (next subsection)).
Figure 7.3 shows the potential contours in the middle of the pore for four
different DNA positions as it proceeds along the pore axis. The DNA translocates
parallel to the axis on the nanopore and is slightly off the nanopore center, a
situation which is likely to happen in a real experimental set-up. Figure 7.3 shows
the merging of equipotential caused by the DNA molecule with the solid state
nanopore which induces a potential variation in the Si layers.
Figure 7.4a depicts the increased concentration of positive ions around the DNA,
which is dominantly negatively charged, while Fig. 7.4b shows the repulsion of
negative ions from the molecule. We note that K + ions are mainly localized around
the negatively charged backbone of the molecule. There is a mix of K + and Cl - ions
in the surrounding DNA bases solution. Of interest is also the change in ion concen-
trations caused by the DNA when compared to the concentrations in the empty pore.
Fig. 7.3 Potential contours taken in the middle of the nanopore for the single-stranded DNA
translocating through the nanopore