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

addition, Mg 2+ is also a particle which has two positive charges. Furthermore, the
HOPG surface is represented by a monolayer consisted of fixed carbon atoms, which
interacts with DNA fragments and Mg 2+ ions via the Lennard-Jones potential. Several
types of potential function are also adopted for interactions between particles. Assuming
the sticky-end or dissociated-end of DNA fragment, we define hydrogen bond at the end
of DNA fragment by the Morse-type potential. Using these potential functions to
develop the force fields, Langevin-dynamics computations are carried out for the
coarse-grained DNA fragments and Mg 2+ ions in aqueous solution.
4. RESULTS AND DISCUSSION
In this study, DNA fragments and Mg 2+ are randomly located near the surface at the
initial condition in order to focus on the mechanism of self-assembly formation, where
400 DNA fragments and 20400 Mg 2+ ions are contained maintaining electroneutrality.
The temperature is conserved at 300 K. Figure 1 shows an initial condition and the
snapshot at t = 50 ns. In this figure, Mg 2+ ions are hidden to visualize DNA structures
clearly. As shown in Fig. 1(b), at t = 50 ns, DNA fragments get concentrated to settle at
the bundled states and form network structures connecting with each other. The
self-assembled structure is observed by monolayer. These characteristics are confirmed
to be in reasonable agreement with the experimental result, although the image is
omitted here. It is indicated that the hydrogen bonds connecting via the ends of DNA
fragments and the charge screening effect due to the counter cations play important
roles in forming the self-assembled structure. In addition, the complicated patterns are
also caused by collisions from solvent molecules excited by thermal fluctuation.
(a) (b)
Fig. 1 Snapshots during MD simulations at (a) t = 0 ns and (b) t = 50 ns.
5. REFERENCES
1. Kawano, S., Fractal Dimension Analysis in Self-Assembled Poly(dA)·Poly(dT)
DNA Network on Mica Surface, JSME International Journal Series B, 2005, Vol.48
191-195.
2. 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.