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

COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS OF
SELF-ASSEMBLED DNA STRUCTURES ON HOPG SURFACES
Hiroshi Takeuchi 1 , Ryosuke Nii, Kentaro Doi and Satoyuki Kawano
1. ABSTRACT
In recent, DNA is expected to be applied for bio-nanotechnology by the use of
peculiar characteristics of base complementarity, self-replicability and self-assembly. In
this study, self-assembly of double-stranded DNAs (dsDNAs) is investigated by using
molecular dynamics (MD) method. In our computation, a coarse-grained bead-spring
model is utilized, in which the sticky-end or dissociated-end of DNA fragments is
presented by the Morse type potential. Modeling a certain experimental condition, we
can observe the adsorption of DNAs which form the monolayer of the network
structures on the highly oriented pyrolytic graphite (HOPG). As a result, it is indicated
that DNA fragments form bundled structures interacting with counter cations and that
they are connected with each other due to the hydrogen bonds of their ends.
2. INTRODUCTION
DNAs have attracted much attention to apply their characteristics for technological
applications. We have focused on the several interesting functions of DNA and have
reported that self-assembled network structures strongly depended on the condition of
substrates and the concentration of the solution [1]. However, the mechanism of
self-assembly should be understood in more detail in order to control and apply this
property concretely for bio-nanotechnologies. In particular, it is known to be difficult to
make DNAs adsorb on HOPG surfaces which have atomically-flat surfaces and electric
conductivity, since both of them have negative charges and repulsively interact with
each other. In this study, the adsorption and aggregation of double-stranded DNAs
(dsDNAs) on the solid surface are investigated by using molecular dynamics (MD)
simulations. Based on our previous research [2], a coarse-grained bead-spring model is
developed for the present problem to simulate the self-assembly structure formation.
3. DEVELOPMENT OF COARSE-GRAINED MODEL OF DNA
In our model, three nucleotide pairs are replaced by a coarse-grained bead and each
bead is connected by linear spring. A DNA fragment consists of 17 beads due to 50 bp
dsDNA employed in our experiment. A bead has -6e charges, since dsDNA has two
phosphate groups which correspond to two negative charges are in a nucleotide pair. In
1 Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science,
Osaka University, Machikaneyama-cho 1-3, Toyonaka, Osaka 560-8531, Japan