Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 281

net force on the DNA will be dependent on the displacement of the DNA relative to
the nanopore ( ). The net force on the DNA vs. the displacement of DNA is

summarized in Fig. 11.29b and the potential associated with the net force on the
DNA is summarized in Fig. 11.29c . The potential is a trapping potential with
effective trapping barrier

d

DE TR
is dependent on electrical breakdown field of the dielectric material. For a reasonable
estimation of trapping energy on a single-stranded DNA, assuming unscreened DNA
charges, the dielectric thickness 1.5 d (1.05 nm), the voltage V 0 ¼

DE TR ¼ q * E TR (1/2-

e

)d. The maximum attainable

1 V on the order of

the electrical breakdown voltage 1 V for 1 nm thick SiO 2 ), DE TR is 13.6 k B T

thermal energy k B T , k B is Boltzmann constant and T is room temperature 300 K.
To move the single-stranded DNA through the DNA transistor base by base, one
will need to adjust the gate voltages and voltage bias across the nanopore. Referring
to Fig. 11.29c , for the case

0 under the condition that a voltage bias is applied
across the nanopore to break the symmetry, the trapping potential of the DNA vs.
the displacement of the DNA is represented in Fig. 11.30a . The peak to peak
distance is the inter-charge-space or inter-base-space. The DNA center of mass is
initially trapped at the position indicated with the solid circle and labeled “0”. If one
reverses the polarity of the gate voltage, the minimum and maximum trapping
potential locations are swapped, as shown in Fig. 11.30b . Due to the broken
symmetry, the DNA will move to the new potential minimum point to the right
of the original potential minimum position, as shown by the solid circle labeled “1”.
As the polarity of the gate voltage is switched back and forth cyclically, the DNA
will be moved to the right at a rate of one base per cycle.

e ¼

Fig. 11.30 (a) A schematic of trapping potential vs. the displacement of the DNA in the DNA
transistor when a voltage bias is applied across the DNA transistor. (b) A schematic of trapping
potential vs. the displacement of the DNA in the DNA transistor when the polarity of the gate
voltage in (a) is reversed. The solid circle labeled “ 0 ” shows the initial position of DNA. Circles
“ 1, ”“ 2, ”“ 3, ”“ 4, ” and “ 5 ” show the sequential positions of the DNA when the polarity of the gate
voltage is switched back and forth