Table 1. Helicoidal Parameters for the GC-Rich Dodecamer Compared to Experimental Resultsa.
| canonicalb |
MD simulationsc |
|||||
|---|---|---|---|---|---|---|
| X-rayd | A-DNA | B-DNA | ε = 20 | ε = 40 | ε = 80 | |
| propeller (deg) | –12.49 (2.0) | –9.00 (7.1) | –11.72 (5.8) | 2.16 (15.5) | –2.85 (12.0) | –7.26 (14.1) |
| slide (Å) | –1.71 (0.4) | –1.67 (0.4) | 0.17 (0.7) | –1.48 (0.8) | –1.23 (0.9) | –0.52 (1.4) |
| twist (deg) | 29.59 (3.5) | 30.24 (4.0) | 34.81 (5.7) | 27.50 (10.0) | 29.70 (7.3) | 36.27 (17.7) |
| X-displacement (Å) | –5.01 (1.1) | –4.54 (1.3) | –0.13 (1.1) | –2.68 (3.6) | –2.80 (2.9) | –1.19 (2.5) |
| helical rise (Å) | 2.66 (0.6) | 2.77 (0.5) | 3.25 (0.2) | 3.42 (1.0) | 3.36 (0.8) | 3.36 (0.8) |
| inclination (deg) | 20.71 (11.4) | 16.00 (10.7) | 4.01 (6.7) | 0.45 (20.7) | 3.73 (15.1) | 5.43 (16.4) |
a
All values are averaged over nonterminal base pairs with standard deviations given in parentheses.
b
Averages over the A-form structures 3V9D, 3QK4, 2B1B, 1ZEX, 1ZEY, 1ZF1,1ZF6, 1ZF8, 1ZF9, 1ZFA and the B-form structures 2M2C, 4AGZ, 4AH0, 4AH1, 3U05, 3U08, 1VTJ, 3U2N, 3OIE, 3BSE.
c
Averages over snapshots at 300 K from replica exchange MD simulations.
d
PDB ID code: 399D.