ARUP; ISBN: 978-0-9562121-5-3 - CMBBE 2012 - Cardiff University

experimental results. Langevin-dynamics simulations are carried out for this model. A
cylindrical-shaped nanopillar which has metallic surface is assumed to be covered with
a dielectric layer due to the polar solution. The boundary conditions of metal-insulator
and insulator-insulator interfaces are considered. External electric voltages can be
applied on the metallic region of the nanopillar.
4. RESULTS AND DISSCUSSION
Figure 1 shows snapshots during the MD simulation. Structures of DNA at t=0.0, 1.0,
2.0 and 3.0 s are presented. The DNA moves against the external electric field, and the
counter cations appear to be attracted by the nanopillar on which the negative voltage of
-0.5 V is applied. They separate from DNA and adsorb on the surface of nanopillar. In
this study, the aggregation of ssDNA is mainly induced by the interaction with the
cations, since the negative charges on DNA, which enhance repulsive interactions
between nucleotides, are effectively screened. At t=1.0 s, the ssDNA appears to be
trapped by the nanopillar. From t=2.0 to 3.0 s, the aggregation of DNA is loosened
due to the electrophoretic flow accelerated by the background homogeneous electric
field and interactions with the surface of nanopillar. Radius of gyration Rg is obtained
from the results of MD samplings in order to evaluate the shape of DNA. It is found that
Rg tends to increase faster according to the applied voltage on the nanopillar. The
counter cations are attracted by the strong force fields around the nanopillar and
separate from DNA. Consequently, repulsive interactions between base molecules are
induced and cause to loosen the aggregation.
ssDNA Nanopillar
(a) (b)
z
y
x
Fig.1 Numerical results of simulation of top view between ssDNA and Mg 2+ ions near
the nanopillar at (a) t=0.0 s, (b) 1.0 s, (c) 2.0 s and (d) 3.0 s.
5. REFERENCES
E
(c) (d)
1. Doi, K., Haga, T., Shintaku, H. and Kawano, S., Development of Coarse-Graining
DNA Models for Single-Nucleotide Resolution Analysis, Phil. Trans. R. Soc. A,
2010, Vol. 368, 2615-2628.