Table 2.
Sugar conformations, groove widths and selected helix parameters for the LNA quadruplexesa
| Nucleotide | TGLGLT | TL4T | ||||
|---|---|---|---|---|---|---|
| number | Pseudorotation angle (°) | Sugar pucker | Puckering amplitude (°) | Pseudorotation angle (°) | Sugar pucker | Puckering amplitude (°) |
| 1 | 143 | S-type | 39 | 148 | S-type | 40 |
| 2 | 156 | S-type | 43 | 20 | N-type | 58 |
| 3 | 23 | N-type | 62 | 28 | N-type | 59 |
| 4 | 25 | N-type | 23 | 15 | N-type | 58 |
| 5 | 23 | N-type | 59 | 5 | N-type | 56 |
| 6 | 64 | 28 | 148, −123b | 21 | ||
| Nucleotide step | Rise (Å) | Twist (°) | Groove width (Å) | Rise (Å) | Twist (°) | Groove width (Å) |
|---|---|---|---|---|---|---|
| 2–3 | 3.7 | 21 | 7.0 | 3.5 | 22 | 8.4 |
| 3–4 | 3.2 | 31 | 7.0 | 3.5 | 23 | 6.4 |
| 4–5 | 3.0 | 22 | 6.4 | 3.2 | 28 | 6.4 |
| Mean | 3.3 | 25 | 6.8 | 3.4 | 24 | 7.1 |
aThe groove width is measured as the shortest inter-strand phosphorus distances minus 5.8 Å, which is the combined Van der Waals radii of two phosphate groups.
bTwo different conformations are observed.