Table 1.
Main Minima for All the Free Energy Maps
| Local Minimum |
A1 |
A2 |
A3 |
B1 |
B2 |
B3 |
C1 |
C2 |
D1 |
|
|---|---|---|---|---|---|---|---|---|---|---|
| A-A Form |
Anti-Anti |
Anti-Syn |
Syn-Syn |
|||||||
| Main H-Bond | N1-H2, H61-N1 | N7-H61, H62-N1 | N3-H62 | N7-H61 | N7-H2, H62-N1 | H61-N1, N1-H61 | N7-H62, N6-H61 | N7-H61, H62-N1 | N1-H2, H61-N1 | |
| RNA-CAG | approximate location (Ω, χ14) | (75,195) | (−35, 190) | — | (50,45) | — | (−35, 60) | — | — | — |
| relative free energy (kcal/mol) | 0 | 3.5 ± 0.1 | — | 1.2 ± 0.2 | — | 5.4 ± 0.4 | — | — | — | |
| approximate location (χ5, χ14) | (−168, −168) | (−165, 55) for B, (58, −165) for B′ | (55,55) | — | ||||||
| relative free energy (kcal/mol) | 0 | 2.7 ± 0.2 | 10.3 ± 0.3 | — | ||||||
| DNA-CAG | approximate location (Ω, χ14) | (40, 250) | — | — | (61,40) | (23,43) | — | — | — | — |
| relative free energy (kcal/mol) | 0 | — | — | 0.2 ± 0.3 | 2.9 ± 0.3 | — | — | — | — | |
| approximate location (χ5, χ14) | (−110, −110) | — | — | (−100, 40) for B, (45,−100) for B′ | — | — | (45,45) | — | (−50, −50) | |
| relative free energy (kcal/mol) | 0 | — | — | 2.0 ± 1.0 | — | — | 2.2 ± 0.5 | — | 5.4 ± 0.6 | |
| RNA-GAC | approximate location (Ω, χ14) | (70, 195) | (−35, 190) | — | (78,50) | (50,40) | (−3, 52) | — | — | — |
| relative free energy (kcal/mol) | 0 | 5.9 ± 0.1 | — | 5.6 ± 0.1 | 5.5 ± 0.1 | 5.9 ± 0.1 | — | — | — | |
| approximate location (χ5, χ14) | (−163, −163) | — | — | (−165, 46) for B, (44, −162) for B′ | (44,78) | — | ||||
| relative free energy (kcal/mol) | 0 | — | — | 4.7 ± 0.2 | 9.8 ± 0.1 | — | ||||
| DNA-GAC | approximate location (Ω, χ14) | (40, 255) | — | — | (78,43) | (61,52) | — | — | — | — |
| relative free energy (kcal/mol) | 0 | — | — | 0.6 ± 0.4 | 0.2 ± 0.2 | — | — | — | — | |
| approximate location (χ5, χ14) | (−101, −101) | — | — | (−140,50) for B, (50, −140) for B′ | — | (50,50) | — | (−46, −46) | ||
| relative free energy (kcal/mol) | 0 | — | — | 0.9 ± 0.5 | — | 0.9 ± 0.2 | — | 2.4 ± 0.1 | ||
The mirror images of B(B1,B2,B3), B′(B1′,B2′,B3′), are not shown. The free energy values in the B columns are the average of B and B′. All the values and errors are calculated based on the last 20 ns of the ABMD simulations.