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

MOLECULAR DYNAMICS SIMULATIONS FOR DNA
DEFORMATIONS AFFECTED BY NANOPILLARS
WITH APPLIED ELECTRIC VOLTAGES
Kaito Morita 1 , Kentaro Doi 1 , Sakon Rahong 2 , Takeshi Yanagida 2 , Tomoji Kawai 2
and Satoyuki Kawano 1
1. ABSTRACT
In this study, we develop a coarse-grained model of single-stranded DNA (ssDNA) to
simulate the deformation and stretching phenomenon near a nanopillar by the use of
molecular dynamics (MD) method. In this simulation, the behavior of counter cations,
such as Mg 2+ ions, are also taken into account to represent the aggregation of ssDNA.
As a result of our simulations, it is found that the cations move away from DNA and
adsorb to the nanopillar on which negative voltages are applied; then the ssDNA is
loosened near the surface of nanopillar due to the Coulomb interactions with cations.
2. INTRODUCTION
In recent, a tailor-made medicine has attracted much attention due to the progress of
DNA sequencing technologies, based on the fact that the genetic information is
determined by base sequences of DNA. It is well known that there is a difficulty to
obtain a separated ssDNA, which is needed in the sequencing process, in comparison
with a double-stranded one. One of effective techniques for the pre-process in order to
separate and linearize single-stranded DNA (ssDNA) is suggested by the use of
nanopillar devices. We focus on the detailed physicochemical and electrical effects of
the device on ssDNA which is initially aggregated in aqueous solution. In this study,
based on our previous research [1], a coarse-grained model of ssDNA is developed and
molecular dynamics (MD) simulations are performed to investigate the behavior near
the nanopillar structure.
3. COMPUTATIONAL METHODS
In the present system, it is simulated that a ssDNA and counter cations move interacting
with a metallic nanopillar under the background homogeneous electric field. A
bead-spring model is employed for modeling the ssDNA, in which three nucleotides are
presented by one bead and the nearest neighbors are connected by linear spring. Each
nucleotide has negative charges due to the phosphate group. The existence of cations
Mg 2+ is assumed to neutralize the negative charges of a ssDNA. The validity of the
ssDNA model is confirmed by calculating the diffusion coefficient, comparing with
1 Department of Mechanical Science and Bioengineering, Graduate School of
Engineering Science, Osaka University, Machikaneyama-cho 1-3, Toyonaka, Osaka
560-8531, Japan
2 The Institute of Science and Industrial Research (ISIR), Osaka University, Mihogaoka
8-1, Ibaraki, Osaka 567-0047, Japan