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Journal of Nucleic Acids
/
2010
/
Article
/
Tab 5
/
Research Article
Structural Properties of G,T-Parallel Duplexes
Table 5
Cross RMSd (in Å) between trajectories and the average structures obtained in the other trajectories. When parallel duplexes and triplexes are compared only, the Hoogsteen duplex embedded in the triplex is considered.
ps-Duplex
ps-Triplex (H)
Starting structure
Average structure
Starting structure
Average structure
ps-Duplex I
2
.
3
±
0
.
5
2
.
2
±
0
.
5
2
.
3
±
0
.
5
2
.
1
±
0
.
6
ps-Triplex I (H)
1
.
7
±
0
.
2
2
.
2
±
0
.
1
1
.
6
±
0
.
2
1
.
1
±
0
.
2
ps-Duplex II
3
.
4
±
0
.
7
2
.
8
±
0
.
7
3
.
3
±
0
.
7
3
.
5
±
0
.
8
ps-Triplex II (H)
2
.
0
±
0
.
2
4
.
1
±
0
.
3
2
.
0
±
0
.
2
1
.
3
±
0
.
3