Table 6. Mean Structural Parameters for Watson–Crick Duplex [U(UA)6A]2a.
| this work | ff10 | X-ray | |
|---|---|---|---|
| local base-pair parameters | |||
| shear [Å] | 0.02 (0.9) | 0.0 (0.5) | –0.1 (0.4) |
| stretch [Å] | –0.05 (0.5) | 0.01 (0.3) | –0.2 (0.1) |
| stagger [Å] | 0.08 (0.5) | –0.04 (0.6) | –0.01 (0.2) |
| buckle [deg] | 0.03 (13) | 0.5 (15) | 1.0 (5) |
| propeller [deg] | –12.2 (12) | –14.1 (14) | –18.8 (2) |
| opening [deg] | –0.3 (12) | 1.9 (9) | 0.1 (3) |
| local base-pair step parameters | |||
| shift [Å] | 0.0 (0.8) | –0.01 (0.7) | 0.03 (0.4) |
| slide [Å] | –1.4 (0.7) | –1.2 (0.6) | –1.3 (0.1) |
| rise [Å] | 3.1 (0.8) | 3.1 (0.9) | 3.3 (0.2) |
| tilt [deg] | 0.0 (6) | 0.07 (6) | –0.2 (3) |
| roll [deg] | 8.5 (8) | 12.2 (9) | 10.7 (5) |
| twist [deg] | 29.1 (10) | 27.7 (8) | 31.1 (5) |
| local base-pair helical parameters | |||
| X-displacement [Å] | –3.7 (3) | –3.8 (2) | –4.1 (1) |
| Y-displacement [Å] | 0.01 (2) | 0.03 (2) | –0.1 (0.7) |
| helical rise [Å] | 2.6 (1) | 2.3 (1) | 2.7 (0.3) |
| inclination [deg] | 14.5 (14) | 21.1 (15) | 19.5 (10) |
| tip [deg] | –0.03 (11) | –0.1 (10) | 0.02 (6) |
| helical twist [deg] | 31.4 (12) | 31.6 (10) | 33.3 (4) |
a
Closing base-pairs have been left out of analysis to avoid the noise from end fraying. Data presented is the average over all other nucleotides and over all four trajectories. The second column represents results using the revised force field from this work, and the third column represents the simulations with the conventional Amber force field. The last column contains the values from the starting X-ray structure (PDB 1RNA). The values in parentheses are standard deviations.