Supplemental Material
An Improved DNA Force Field for ssDNA Interactions with
Gold Nanoparticles
Xiankai Jiang1, Jun Gao2, Tien Huynh3, Ping Huai1, Chunhai Fan1, Ruhong Zhou3*, and
Bo Song1*
1
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800204, Shanghai 201800, China
2
School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100,
PR China
3
IBM Thomas J. Watson Research Center, NY 10598, USA
2
Contact area per base (nm )
Preparing Initial Conformations
1.4
AAAAAAA
T = 300 K
TTTTTTT
1.2
1.0
0.8
0
50
100
Time (ns)
150
200
Fig. S1. Trajectories of the contact area per base (CApB) for the poly(A) (black
curve) and poly(T) (red curve) adsorbed on the gold surface for initial sampling
at a low temperature T = 300 K.
In order to prepare initial conformations for the desorption process, we carried out
two MD simulations of the poly(A) and poly(T) on the AuNP’s Au(111) surface in an
NVT ensemble at 300 K for 200 ns, respectively, after energy minimization, in which
the ssDNA segment was adsorbed on the gold surface with most of the bases lying flatly
on the surface (see Fig. 1b). A contact area per base (CApB) between the ssDNA and
Au surface was calculated to describe the adsorption strength between them, where the
contact area was defined as a half of the difference between the solvent accessible
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surface area (SASA) of the ssDNA-Au complex and the sum of the SASAs of the
ssDNA and the gold separately. The trajectories of CApB from the simulations are
shown Fig. S1. It is observed that the two systems (poly(A)@Au and poly(T)@Au)
reach equilibrium after 5 ns, respectively. For each case, we selected one conformation
per 15 ns in the time interval from 50 ns to 200 ns, and obtained ten samples as initial
conformations.
Trajectories from Molecular Dynamics Simulations under the Improve Force
2
CApB (nm )
Field
1.0
0.5
0.0
1.0
0.5
0.0
1.0
0.5
0.0
1.0
0.5
0.0
1.0
0.5
0.0
0
T = 350 K
50
100
150
0
Time (ns)
50
100
150
Time (ns)
200
Fig. S2. Trajectories of the contact area per base (CApB) for the poly(A) sequence
desorbing from the gold surface at a temperature T = 350 K.
2
2
CApB (nm )
1.0
0.5
0.0
1.0
0.5
0.0
1.0
0.5
0.0
1.0
0.5
0.0
1.0
0.5
0.0
0
T = 350 K
50
100
150
0
50
Time (ns)
100
150
Time (ns)
200
2
CApB (nm )
Fig. S3. Trajectories of the contact area per base (CApB) for the poly(T) sequence
desorbing from the gold surface at a temperature T = 350 K.
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
0
T = 350 K
50
100
150
Time (ns)
200
0
50
100
150
Time (ns)
200
Fig. S4. Trajectories of the contact area per base (CApB) for the poly(G) sequence
desorbing from the gold surface at a temperature T = 350 K.
3
2
CApB (nm )
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
1.2
0.8
0.4
0.0
0
T = 350 K
50
100
150
Time (ns)
200
0
50
100
150
Time (ns)
200
Fig. S5. Trajectories of the contact area per base (CApB) for the poly(C) sequence
desorbing from the gold surface at a temperature T = 350 K.
4