Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 282

Further realistic molecular dynamics simulations [ 46 ] confirmed that single
DNA molecules can be driven through the nanopore in a ratchet-like fashion,
with a step size equal to the spacing between neighboring phosphate groups in
the ssDNA backbone during the simulation time scale of tens of nanoseconds.
Fig. 11.31a illustrates the DNA transistor system in the simulations. In order to
characterize the field of the electric force in the DNA transistor, a fragment of a
single stranded DNA (ssDNA) containing 20 adenine deoxynucleotides, poly
(dA 20 ), was simulated as being pulled by a spring while submerged in a NaCl
electrolyte solution confined in a 4 nm diameter nano-channel. The nanochannel
was assumed to be an opening through multiple layers of amorphous SiO 2 (regions
where the electric field indicated with the arrows is present) and metal (light grey).
As for the trapping electric field, we used the maximum value that SiO 2 can take
before dielectric breakdown ( E ¼

108 mV/ ˚ ). This field was applied in the dielec-
tric regions, as shown in the figure. The thickness of each dielectric region is 2.5 d ,
and the thickness of middle metal region is 2 d , where d is the spacing between
neighboring phosphate groups. After equilibration in the NVT (T ¼ 300 K)

Fig. 11.31 Simulation of DNA's motion in a DNA transistor when DNA is pulled by harmonic
spring. (a) Illustration of the simulation system. (b) Measured force exerted by the spring vs. DNA
position relative to the DNA transistor when E ¼ 0. (c) Measured force exerted by the spring vs.

DNA position relative to the DNA transistor when E ¼ 108 mv/ ˚ . Adapted from [ 46 ]