Table 2.
Distances from the 5-methyl carbon atom of dT8 to Rp-R5a and Rp-R5 labels in key conformers found in simulations of the labeled DNA duplex d(CTACTGpSC7T8TTAG).d(CTAAAGCAGTAG).a
| Conformer b (t1,t2,t3) | DNA c | R5a | R5a d | R5a d | R5a d | R5 | R5 d | R5 d |
|---|---|---|---|---|---|---|---|---|
| Occupancy (%) | Pyrroline ring center (Å) | Closest ring methyl (Å) | Ring 4-Br (Å) | Occupancy (%) | Pyrroline ring center (Å) | Closest ring methyl (Å) | ||
| g+,t,+100 | BI | 0.0 e | --- | --- | --- | 0.0 e | --- | --- |
| g+,t,-100 | BI | 0.0 e | --- | --- | --- | 0.0 e | --- | --- |
| g+,t,+100 | BII | 32.9 | 4.9 ± 0.5 | 4.1 ± 0.5 | 4.9 ± 0.9 | 8.8 | 5.4 ± 0.7 | 4.0 ± 0.5 |
| g+,t,-100 | BII | 13.6 | 5.1 ± 0.7 | 4.3 ± 0.6 | 5.0 ± 1.2 | 9.2 | 5.3 ± 0.7 | 4.2 ± 0.6 |
| g-,t,+100 | BI | 27.9 | 6.6 ± 0.8 | 5.8 ± 0.9 | 4.2 ± 0.5 | 9.6 f | 6.9 ± 1.6 | 6.1 ± 1.9 |
| g-,t,-100 | BI | 8.3 | 6.3 ± 0.8 | 4.1 ± 0.8 | 8.9 ± 0.7 | 16.1 | 6.4 ± 0.9 | 4.2 ± 1.0 |
| g-,t,+100 | BII | 1.7 | 7.0 ± 0.8 | 6.4 ± 1.0 | 4.4 ± 0.8 | 6.6 f | 8.4 ± 1.3 | 8.1 ± 1.5 |
| g-,t,-100 | BII | 3.1 f | 8.1 ± 1.4 | 6.0 ± 1.6 | 9.6 ± 1.1 | 5.0 f | 7.7 ± 1.5 | 5.7 ± 1.7 |
| g-,g-,+100 | BI | 0.0 e | --- | --- | --- | 2.8 f | 8.9 ± 1.4 | 7.5 ± 1.6 |
| g-,g-,-100 | BI | 0.2 | 9.3 ± 1.0 | 9.4 ± 1.2 | 7.8 ± 0.9 | 2.9 f | 8.3 ± 1.3 | 8.1 ± 1.5 |
| g-,g-,+100 | BII | 0.0 e | --- | --- | --- | 10.0 | 9.7 ± 0.7 | 9.1 ± 0.8 |
| g-,g-,-100 | BII | 0.4 | 9.4 ± 0.8 | 9.0 ± 0.9 | 8.8 ± 0.8 | 2.5 | 9.4 ± 0.9 | 9.4 ± 1.0 |
a
Analyses carried out on 400,000 Rp-R5a-dT8 structures (eight 10-ns simulations) and 150,000 Rp-R5-dT8 structures (three 10-ns simulations). Data for all conformers are shown in Tables S4 (R5a) and S5 (R5).
b
g+: 0-120°; t: 120-240°; g-: 240-360°
c
Backbone conformation at the dG6-pSdC7 dinucleotide (see Table S6)
d
Average ± standard deviation of distance (Å) determined for the corresponding ensemble of conformers.