Table 7. Mean Values of Backbone and Glycosidic Torsions, as Well as Sugar Puckers, from the Simulations of Watson–Crick Duplex [U(UA)6A]2a.
| this work | ff10 | X-ray | A-RNA PDB average | |
|---|---|---|---|---|
| α [deg] | 263 (66)b | 277 (33) | 287 (36)c | 295 (8) |
| β [deg] | 167 (32) | 174 (11) | 171 (14) | 174 (8) |
| γ [deg] | 86 (54)d | 64 (16) | 65 (31)e | 54 (6) |
| δ [deg] | 83 (15) | 81 (13) | 80 (5) | 81 (3) |
| ε [deg] | 217 (18) | 203 (16) | 213 (17) | 212 (10) |
| ζ [deg] | 268 (54) | 284 (40) | 280 (12) | 289 (7) |
| χ [deg] | 200 (20) | 208 (17) | 201 (9) | NA |
| pucker (% C3′-endo) | 95.7 | 97.1 | 100 | NA |
Closing base-pairs have been left out to avoid noise from fraying of ends. The numbers are values in degrees averaged over all internal nucleotides and over all trajectories, except for pucker where % of C3′-endo conformation is indicated. The second column are the results using the parameters derived in this work, and the third column are the results from the conventional Amber current force field. The fourth column contains average values taken from the starting X-ray structure (PDB ID 1RNA). The fifth column contains averages from analysis of many structures with the A-RNA conformation taken from work of Richardson et al.5 The values in parentheses are standard deviations. The notes indicate angles were the average is affected by the presence of secondary peak. See Figure S6 for more details.
20% of population is in a trans conformation with a peak at 150°, 76.4% is in a gauche– population with a peak at 295°, and the remaining 3.6% is in gauche+ confirmation.
The X-ray structure has 2 out of 24 nucleotides in trans position, that is, 8%; the rest is gauche–.
21.5% of population is in a trans conformation with a peak at 180°; the remaining 78.5% is in a gauche+ population with a peak at 58°.
The X-ray structure has 2 out of 24 nucleotides in trans position, that is, 8%; the rest is gauche+.