Table 3.
Population (%) of various α/γ substates of syn-χ guanines in the stem of antiparallel d(G4T4G4) G-DNA structure. Na+ net neutral simulations in TIP3P, 500 ns. X-ray data correspond to the 2GWQ structure. Gauche +, gauche - and trans states are denoted as (g+), (g-) and (t). Green color indicates native states, light green indicates rare states (discussed in the text).
| nucleotides | X-ray α/γ | α/γ | ||||
|---|---|---|---|---|---|---|
| g-/g+ | g+/g- | g+/t | g-/g- | |||
| ffbsc0 | G3 | g+/g- (g-/g-)1 | 91 | 8 | 0 | 1 |
| G9 | g+/t | 0 | 0 | 95 | 0 | |
| G11 | g+/g- (g-/g-)1 | 81 | 16 | 0 | 3 | |
| G15 | g+/g- | 93 | 6 | 0 | 1 | |
| G21 | g+/t | 11 | 0 | 68 | 0 | |
| G23 | g+/g- | 66 | 25 | 0 | 10 | |
|
| ||||||
| ff99bsc0χOL4 | G3 | g+/g- (g-/g-)1 | 35 | 48 | 0 | 17 |
| G9 | g+/t | 7 | 0 | 80 | 0 | |
| G11 | g+/g- (g-/g-)1 | 14 | 53 | 0 | 32 | |
| G15 | g+/g- | 32 | 51 | 0 | 17 | |
| G21 | g+/t | 4 | 0 | 82 | 0 | |
| G23 | g+/g- | 10 | 53 | 0 | 36 | |
|
| ||||||
| ff99bsc0 χOL4εζOL1 | G3 | g+/g- (g-/g-)1 | 27 | 69 | 0 | 4 |
| G9 | g+/t | 19 | 0 | 72 | 0 | |
| G11 | g+/g- (g-/g-)1 | 13 | 80 | 0 | 7 | |
| G15 | g+/g- | 25 | 70 | 0 | 4 | |
| G21 | g+/t | 31 | 0 | 61 | 0 | |
| G23 | g+/g- | 8 | 85 | 0 | 6 | |
|
| ||||||
| ff99bsc0εζOL1 | G3 | g+/g- (g-/g-)1 | 87 | 12 | 0 | 1 |
| G9 | g+/t | 7 | 0 | 85 | 0 | |
| G11 | g+/g- (g-/g-)1 | 60 | 38 | 0 | 1 | |
| G15 | g+/g- | 84 | 15 | 1 | 1 | |
| G21 | g+/t | 14 | 0 | 68 | 0 | |
| G23 | g+/g- | 73 | 25 | 0 | 2 | |
1
G3 and G11 nucleotides can be found also in g-/g+ state (see text)