Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 164

Fig. 7.7 (a) Calculated voltage trace from C 3 AC 7 strand ( dotted line ) and the backbone signal
of the same strand ( solid line ). (b) The difference between the whole DNA signal and the backbone
signal
shown in Fig. 7.7a we conclude, on one hand, that the maximum recorded voltage
caused by the DNA translocation is around 35 mV. This signal is appreciable and is
due to the DNA confinement in the constriction where screening by the solution is
minimized. In addition, due to the narrowness of the pore the DNA translocates in
close proximity to the electrodes. On the other hand, the maximum voltage induced
by the DNA's backbone is about 30 mV, resulting in a maximum signal from a base
of approximately 8 mV (Fig. 7.7b ). We point out that these numbers are obtained in
the absence of the conformational disorder. Also, measured from the non-zero
voltage trace, the DNA length is ~70 ˚ , which is in agreement with the actual
stretched DNA length. There are several distinct fluctuations on the voltage trace,
which, as we show later, correspond to the 11 segments of the backbone with a
DNA base in every segment.
In order to better understand the observed variations in the voltage trace
we separate the C 3 AC 7 DNA into 11 fragments, each containing a sugar ring,
a phosphate group and a base (with the exception of the first fragment which
does not contain the phosphate group). Each fragment was driven through the
pore separately and the corresponding voltage signal was calculated at the electrode.
The composite plot of traces of the 11 fragments and the trace of the whole
C 3 AC 7 sequence is shown in Fig. 7.8 . We observe that 10 of 11 fragments of
the DNA produce similar traces in the form of a negative dip. The remaining one