Table 1.
Label conformer distributions in molecular dynamics simulations of DNA duplexes of sequence d(CTACTGpSC7Y8TTAG).d(CTAAAGCAGTAG) (Y = T or U) labeled with a 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a) or a 1-oxyl-2,2,5,5-tetramethylpyrroline (R5) radical at pSdC7.
| Label | Chirality | dY8 | n a | t1 (%) b,c | t2 (%) b,c | t3 (%) b,d | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| g+ | t | g- | g+ | t | g- | +100° | -100° | ||||
| R5a | Rp | dT8 | 8 | 46.6±24.3 | 11.6±13.5 | 41.8±27.7 | 0.5±0.7 | 98.9±2.3 | 0.6±1.8 | 64.4±39.6 | 35.6±39.6 |
| R5a | Rp | dU8 | 6 | 17.7±9.7 | 23.9±16.3 | 58.4±25.4 | 2.9±4.4 | 93.6±6.0 | 3.5±4.1 | 57.5±33.7 | 42.5±33.7 |
| R5 | Rp | dT8 | 3 | 18.5±4.9 | 23.8±9.5 | 57.6±13.0 | 8.8±6.5 | 72.7±5.7 | 18.5±1.0 | 52.8±7.9 | 47.2±7.9 |
| R5 | Rp | dU8 | 3 | 14.2±8.8 | 16.8±9.7 | 68.9±4.8 | 13.3±6.9 | 67.0±17.1 | 19.7±21.6 | 51.3±10.1 | 48.7±10.1 |
| R5a | Sp | dT8 | 8 | 48.6±9.7 | 48.7±9.3 | 2.6±1.4 | 5.8±4.7 | 88.7±8.2 | 5.5±7.0 | 69.1±35.8 | 31.1±35.9 |
| R5a | Sp | dU8 | 6 | 37.0±14.2 | 59.0±14.9 | 3.9±2.1 | 4.9±7.9 | 91.0±7.2 | 4.2±4.6 | 60.1±35.5 | 39.9±35.5 |
| R5 | Sp | dT8 | 3 | 52.7±19.5 | 45.3±18.2 | 2.0±1.7 | 21.2±9.3 | 59.7±3.7 | 19.1±12.6 | 46.3±20.6 | 53.7±20.6 |
| R5 | Sp | dU8 | 3 | 38.8±18.2 | 58.8±17.3 | 2.4±1.3 | 8.9±4.7 | 58.0±5.6 | 33.1±8.9 | 54.0±6.9 | 46.0±6.9 |
a
Number of simulations of 10 ns each.
b
Torsion angles are defined in Figure 1A. Average and standard deviations are calculated from the corresponding individual 10-ns simulations.
c
g+: 0-120°; t: 120-240°; g-: 240-360°
d
Torsion angle t3 adopts values centered on +100° and -100°. Each distribution was determined based on conformations with t3 > 0° and t3 < 0°, respectively, for a torsional angle range from +180° to -180°.