Table 1.
Watson-Crick H-bond distances d1 and d2 and distance d3 (O2/F2…C2) for T:A and F:A pairs in crystal structures of B-form DNA.
| B-form DNA duplex |
Base pair |
d1 [Å] |
d2 [Å] |
d3 [Å] |
Resol. [Å] |
PDB code |
Ref. |
|---|---|---|---|---|---|---|---|
| Native DDDa | A5:T20 T8:A17 |
2.98 2.96 |
2.77 2.82 |
3.54 3.62 |
1.1 | 436D | 12a |
| Native DDDa | A5:T20 T8:A17 |
3.01 3.11 |
2.83 2.77 |
3.55 3.46 |
1.4 | 355D | 12b |
| Native DDD : BhRNase Hb |
F8:A17 F8:A17 |
2.95 2.99 |
2.81 2.76 |
3.57 3.47 |
1.8 | 3D0P | 11 |
| F8-DDD : BhRNase Hb |
F8:A17 F8:A17 |
3.09 3.12 |
3.41 3.34 |
4.40 4.34 |
1.6 | 3I8D | this work |
a
The duplex [d(CGCGAATTCGCG)]2 (nucleotides in one strand are numbered 1–12 and 13–24 in the other) lies in a general position, and the A5:T20 and T8:A17 base pairs (bold font) exhibit different geometries.
b
The first base pair is from duplex 1 and the second from duplex 2. Both duplexes sit on a dyad and F8:A17 and A5:F20 are symmetry-equivalent.