Structural Properties of G,T-Parallel Duplexes

Table 3

Average root mean square deviation (RMSd in Å) between trajectories of the different duplexes and triplexes and the starting and average structures. The prefixes ps and aps refer to parallel and antiparallel topologies. Standard deviations in the averages are noticed in all cases.

	Sequence	Starting structure	Average structure
aps-Duplex	5^-AGAGGAGGAAG-3^	2.5±0.4	1.7±0.3
	3^-TCTCCTCCTTC-5^
ps-Duplex I	5^-AGAGGAGGAAG-3^	2.3±0.5	2.2±0.5
	5^-TC^+TC^+C^+TC^+C^+TTC^+-3^
ps-Duplex II	5^-AGAGGAGGAAG-3^	3.4±0.7	2.8±0.7
	5^-TGTGGTGGTTG-3^
ps-Triplex I	5^-AGAGGAGGAAG-3^	1.8±0.3	1.2±0.2
	3^-TCTCCTCCTTC-5^
	5^-TC^+TC^+C^+TC^+C^+TTC^+-3^
ps-Triplex II	5^-AGAGGAGGAAG-3^	1.9±0.2	1.3±0.3
	3^-TCTCCTCCTTC-5^
	5^-TGTGGTGGTTG-3^