Table 1.
Averaged differences in free energy components (kcal mol−1) calculated for the binding of 2QN to the DTDT- and GCGC-containing decanucleotides according to the thermodynamic cycles depicted in Figure 4
| (A) | ΔG(4)cycle1 | ΔG(3)cycle1 |
| 2QN:DTDT→2QN:D[mC]GT | DTDT→D[mC]GT | |
| ΔGtot | 82.8 ± 0.3 | 81.6 ± 0.3 |
| ΔGele | 77.5 ± 0.2 | 76.9 ± 0.1 |
| ΔGvdW | 0.5 ± 0.0 | 0.5 ± 0.1 |
| ΔGpmf | 4.8 ± 0.1 | 4.5 ± 0.2 |
| (B) | ΔG(4)cycle2 | ΔG(3)cycle2 |
| 2QN:D[mC]GT→2QN:G[mC]G[mC] | D[mC]GT→G[mC]G[mC] | |
| ΔGtot | 79.3 ± 0.1 | 77.7 ± 0.1 |
| ΔGele | 74.8 ± 0.2 | 72.7 ± 0.1 |
| ΔGvdW | 0.1 ± 0.1 | 0.1 ± 0.1 |
| ΔGpmf | 4.7 ± 0.1 | 5.0 ± 0.1 |
| (C) | ΔG(4)cycle3 | ΔG(3)cycle3 |
| 2QN:G[mC]G[mC]→2QN:GCGC | G[mC]G[mC]→GCGC | |
| ΔGtot | 353.8 ± 0.1 | 354.8 ± 0.1 |
| ΔGele | 346.5 ± 0.1 | 346.0 ± 0.1 |
| ΔGvdW | 0.7 ± 0.1 | 2.1 ± 0.1 |
| ΔGpmf | 6.8 ± 0.1 | 7.0 ± 0.1 |