Molecular dynamics studies of the 3D structure and planar ligand binding of a Quadruplex dimer

Ming-Hui Li, Quan Luo, Xiang-Gui Xue and Ze-Sheng Li

Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China

Correspondence to: Ze-Sheng Li; e-mail:

Supplementary Information

Fig. S1 RMSD values of the atoms of plane of ligand for DT1 (black) and DT2 (red) model versus simulation time with the final minimized structures as a reference point.

Fig. S2 RMSD values (Å) (y-axis) of the atoms of planes of ligands for DTT1, DTT2 and DTT3 model versus simulation time (ps) (x-axis) with the final minimized structures as a reference point. Top ligand: black; below ligand: red.

Fig. S3 The projection of the MD trajectories for all systems onto the first and the second principal components.

Table S1. Standard angles of all bases for monomer and dimer.

monomer
base / alpha / beta / gamma / delta / epsilon / zeta / chi / P / Puckering
1 G
2 G
3 G
4 T
5 G
6 G
7 G
8 T
9 G
10 G
11 G
12 T
13 G
14 G
15 G
16 T / ---
-69.7
-65.5
63.5
68.8
-75.5
-61.8
64.2
69.0
-75.7
-65.5
71.6
69.1
-75.3
-77.1
-68.1 / ---
173.8
174.6
170.4
173.9
171.7
170.8
169.9
170.5
175.0
170.0
170.6
165.5
175.5
-179.7
168.2 / 61.5
59.1
58.9
46.0
56.6
53.8
60.6
43.4
57.0
53.1
60.1
50.9
53.8
57.7
55.9
56.7 / 112.4
109.4
130.9
145.1
136.4
103.2
139.0
148.3
139.9
111.8
127.3
143.6
122.5
114.9
140.3
105.7 / -175.4
-177.8
-77.3
-97.2
-164.3
-179.1
-79.1
-80.6
-166.3
-173.8
-81.2
-97.0
-165.5
-168.1
-175.8
--- / -88.5
-92.5
79.2
98.1
-85.9
-93.7
78.3
85.1
-87.5
-94.6
74.2
79.4
-88.4
-101.2
-88.1
--- / -129.4
-132.2
-126.4
-122.0
-136.1
-134.4
-124.0
-123.7
-133.1
-131.8
-131.2
-127.3
-141.8
-130.7
-111.4
-130.5 / 114.9
114.5
139.5
160.1
164.1
105.9
148.3
166.1
167.9
116.9
133.9
158.5
137.3
117.4
161.1
103.1 / C1'-exo
C1'-exo
C1'-exo
C2'-endo
C2'-endo
O4'-endo
C2'-endo
C2'-endo
C2'-endo
C1'-exo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C2'-endo
O4'-endo
dimer
base / alpha / beta / gamma / delta / epsilon / zeta / chi / P / Puckering
1 G
2 G
3 G
4 T
5 G
6 G
7 G
8 T
9 G
10 G
11 G
12 T
13 G
14 G
15 G
16 T
17 G
18 G
19 G
20 T
21 G
22 G
23 G
24 T
25 G
26 G
27 G
28 T
29 G
30 G
31 G
32 T / ---
-70.3
-72.1
69.3
74.3
-72.4
-70.7
70.6
74.0
-74.3
-68.1
65.3
70.9
-72.5
-79.1
-66.3
---
-70.4
-69.7
72.8
71.7
-69.5
-70.9
72.7
72.4
-70.5
-71.1
69.6
70.6
-71.7
-77.9
-66.8 / ---
-173.0
171.7
175.4
-160.5
178.3
170.5
175.3
-173.9
179.4
171.9
173.4
-175.9
-176.7
177.3
169.9
---
-177.3
168.6
172.2
-178.2
-175.3
172.7
176.3
-176.4
-172.9
169.1
174.4
175.3
-175.7
178.8
168.9 / 63.1
52.2
54.6
52.5
59.0
52.6
55.7
51.6
59.5
53.5
57.0
48.0
55.8
53.0
53.6
58.4
61.6
53.5
58.0
49.9
59.0
53.4
56.7
52.5
60.1
49.1
57.5
48.4
58.8
51.9
51.6
57.4 / 125.1
128.7
126.6
135.4
124.7
118.5
120.2
140.0
120.0
114.9
130.7
139.6
117.3
120.9
133.6
105.6
123.7
118.6
117.2
142.1
120.6
123.0
116.3
138.4
127.1
125.2
121.6
140.9
118.7
121.8
133.5
103.9 / -175.7
-170.0
-79.1
-159.8
-167.9
-170.1
-80.2
-148.7
-168.0
-172.4
-80.6
-127.6
-168.6
-167.7
179.9
---
-172.4
-170.3
-82.1
-136.9
-172.9
-170.5
-79.0
-156.3
-171.3
-169.6
-81.6
-126.1
-169.5
-169.3
-178.5
--- / -95.7
-90.8
78.0
143.4
-90.9
-89.5
77.7
125.1
-88.6
-90.4
78.9
115.8
-90.9
-90.3
-87.3
---
-92.1
-85.8
75.6
110.0
-92.6
-89.4
78.4
128.5
-92.2
-91.7
75.7
108.6
-89.1
-90.9
-87.6
--- / -136.9
-122.4
-118.0
-124.1
-141.1
-127.9
-125.1
-132.8
-146.0
-132.4
-121.5
-121.5
-147.0
-128.8
-107.3
-130.1
-142.6
-131.5
-125.4
-110.1
-143.4
-130.5
-125.6
-125.1
-143.1
-124.2
-122.7
-132.0
-149.5
-129.0
-108.0
-129.7 / 133.8
146.4
131.3
152.8
133.7
127.9
124.0
155.6
127.8
119.9
137.1
150.9
122.6
130.1
148.8
104.6
133.1
127.9
121.0
155.6
127.5
133.0
119.3
153.0
136.2
138.2
125.1
154.1
125.8
130.9
147.4
101.2 / C1'-exo
C2'-endo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C2'-endo
O4'-endo
C1'-exo
C1'-exo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C1'-exo
C2'-endo
C1'-exo
C1'-exo
C2'-endo
O4'-endo

DT1 (black) and DT2 (red)

Fig. S1

DTT1 DTT2

DTT3

Fig. S2

Monomer D

DT1 DT2

DTT1 DTT2

DTT3

Fig. S3

1