Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane - Nanopores: Sensing and Fundamental Biological Interactions - page 170

Fig. 7.12 (a) Electric response of the C 3 AC 7 sequence ( solid line ) and its backbone ( dashed line )
computed on the upper electrode by the SPICE circuit model. (b) Electric response of the C 3 AC 7
sequence and its backbone computed on the upper electrode by the multi-scale approach [ 19 , 31 ]

On this figure we also display the calculated electrical response (dashed line) of
the molecule backbone. The molecule axis coincides with the axis of the pore
while the strand moves through the pore at a constant velocity of 2 m/s in a fixed
conformation.
The simulation starts at position x¼ 25 nm with the

same convention as above. At first sight, the trace in Fig. 7.12a is comprised of ten
dips including the first one characterized by a smaller magnitude and a shoulder.
Actually, the third dip is a superposition of the two dips corresponding to the third
and fourth bases of the C 3 AC 7 molecule: It is clearly seen in Fig. 7.13 that displays
the simulation of each fragment of the strand translocating independently through
the pore. Each base of the C 3 AC 7 molecule is associated with a sugar ring and a
phosphate group except the first one which does not include a phosphate group. As a
consequence, the first base signature exhibits a short positive shoulder that arises
from the missing, negatively charged, phosphate group that usually offset the
positive charge of the sugar ring and the base thereby resulting in a positively
charged fragment. The maximum of the recorded fluctuations reaches 212

25 nm and ends at x ¼

m

V for