Table 4. Orientation-Dependent Dynamics of poly-(dX)40 from 1 μs of Simulation in 1 M of KCl and Vmp = 120 mVa.
| en- trance |
velocity (Å/μs) | zRMSDa (Å) | zRMSDc (Å) | zRMSDr (Å) | |
|---|---|---|---|---|---|
| poly d(A)40 | 3′ | 1.6 | 5.1 ± 1.5 | 2.8 ± 1.5 | 4.1 ± 0.9 |
| 5′ | 2.7 | 7.0 ± 1.9 | 2.7 ± 1.6 | 6.3 ± 1.8 | |
| poly d(C)40 | 3′ | 1.1 | 3.7 ± 0.8 | 1.6 ± 1.4 | 3.4 ± 0.8 |
| 5′ | 1.7 | 5.3 ± 1.1 | 1.8 ± 1.3 | 5.0 ± 1.2 |
a
zRMSDa = absolute root mean square displacement of all phosphates. zRMSDc = root mean square displacement of geometric center of phosphates. zRMSDr = root mean square displacement of all phosphates relative to the geometric center. The standard errors were estimated from 20 separate simulations.