Table 2.
Relative interaction energies (kcal mol-1) between A- and B-DNA configurations.
| Sequence | ΔE (B-A) | |||
|---|---|---|---|---|
|
| ||||
| QMa | C36 | Drude-2013 | Drude-New | |
| AA | -1.75 | -0.56 | 0.27 | -0.05 |
| AC | -1.21 | -0.48 | -1.70 | -1.42 |
| AG | -0.61 | -0.47 | -0.80 | -1.14 |
| AT | -0.71 | -0.70 | -0.62 | -1.22 |
|
| ||||
| CA | -0.43 | 0.01 | 0.62 | 0.14 |
| CC | 1.04 | 2.54 | 0.57 | -0.42 |
| CG | 0.91 | -0.37 | 0.16 | -0.19 |
| CT | -0.13 | 0.17 | -0.19 | -0.33 |
|
| ||||
| GA | -1.43 | -1.07 | 0.62 | 0.21 |
| GC | -0.01 | -1.96 | 0.78 | -0.16 |
| GG | -1.75 | 1.04 | -1.63 | -2.22 |
| GT | -1.54 | 0.79 | -0.41 | -1.21 |
|
| ||||
| TA | 1.24 | 0.59 | 0.88 | 0.66 |
| TC | 0.33 | 1.09 | 0.57 | 0.90 |
| TG | -1.46 | -0.20 | -1.51 | -1.98 |
| TT | -2.75 | -0.49 | -1.53 | -2.02 |
|
| ||||
| Avg. Diff. | 0.64 | 0.40 | -0.01 | |
| AUE | 1.12 | 0.69 | 0.70 | |
| RMSD | 1.39 | 0.94 | 0.86 | |
a
Calculated as the difference in B-DNA and A-DNA stacked monomer interaction energies listed in Table 1.