Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 161

Fig. 7.4 (a) Cl - ion and (b) K + ion distribution in the surrounding salt solution in the presence of
the DNA
Figure 7.5 shows the electrode voltage signal obtained from the rigid translocation
of the DNAmolecule through the nanopore. One notices the magnitude of the signal
on the order of 10 mV, which is much larger than that in the case of the linear chain
due to the more densely packed charge on the DNA chain. Also, owing to the rigid
translocation, the signal at the lower electrode is shifted by 2 nm relative to the upper
electrode signal. From the non-zero voltage trace one can conclude that
the translocated DNA is about 75 ˚ long. In addition, the recorded signal reflects
the DNA strand structure and conformation with distinguishable features that are
about 4 ˚ apart (compared to 3.4 ˚ separation between the bases on a DNA strand).
This implies that it is possible to identify individual bases as they pass by the
electrodes. However, the off-center translocation of modeled DNA helix does not
allow one to identify all of the bases in the strand, but only those that come close to
the electrodes. Indeed, as the translocating DNA consists of 20 identical cytosine
bases, the variation in the recorded signal between 10 and 15 mV can be looked at as
the variation due to positional noise of a single cytosine base in the pore, which we
estimate to be ~2-3 mV.
Narrower nanopores would constrict the translocating molecules to smaller
volume and, thereby, reduce the distance between nucleotides and Si-electrodes,
resulting in larger and higher resolution signals. Also, it is well known that in
electrolytic solutions, each DNA base is characterized by a specific dipole moment,
which is electrically identifiable. Here again, the constriction of the DNA to very
narrow pore could be used to reduce the stochastic orientation of dipole moment
resulting from molecular dynamics, thus considerably lowering the conformational
noise of the bio-molecule.