Table 1.

Average Strand–Strand Interaction Energies (kilocalories per mole) Calculated over a 5–30 ns MD Simulation for the Five Central Bases^a

strandsb	A:T·T	A:T·5a	G:C·T	G:C·5a	C:GT	C:G·5a
I–II (Watson–Crick)	−81.20	−61.60	−76.56	−56.76	−97.67	−94.20
I–III (Hoogsteen)	−78.40	−55.88	−65.91	−53.69	−56.58	−67.87
II–III	3.83	4.16	0.97	4.81	1.25	3.18
Hoogsteen-Watson–Crick	−74.58	−51.72	−64.95	−48.89	−55.33	−64.69
Tm (°C)	59	29			39	50
bioactivity (%)	100	<1			~10	~45

^aAll energies are given in kilocalories per mole.

^bInteraction energies are interstrand base–base contributions calculated for the five central bases.