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