Table 1.
Selected helicoidal and backbone angle values
| Canonical A | A-DNA | A-DNAV2=0.3 | A-RNA | B (in water) | |
|---|---|---|---|---|---|
| Twist, ° | 32.7 | 32.6 | 31.0 | 30.9 | 30.9 |
| Rise, Å | 2.56 | 2.92 | 2.95 | 2.70 | 3.26 |
| Inclination, ° | 19.1 | 15.8 | 10.9 | 15.0 | 4.9 |
| x-disp., Å | −5.43 | −4.0 | −3.4 | −5.19 | −2.96 |
| RMS to A, Å | 0.00 | 1.66 | 1.68 | 2.09 | 3.85 |
| Pucker, ° | 13.1 | 80.1 | 72.7 | 22.6 | 122.8 |
| χ, ° | 205.8 | 222.6 | 220.7 | 201.7 | 234.2 |
| δ, ° | 84.3 | 102.8 | 96.7 | 79.3 | 116.6 |
Values of selected average helicoidal parameters, backbone angles, and sugar pucker values are presented for a canonical A-DNA model structure (canonical-A), the simulation of A-DNA in mixed ethanol/water solution (A-DNA, 2,000–3,000 ps), the simulation of B-DNA with the modified V2 term on the O–C–C–O torsions (from 1.0 to 0.3 kcal/mol), which underwent a B-DNA to A-DNA transition (A-DNAV2=0.3, 2,000–3,000 ps), A-RNA in pure water (A-RNA, 1,030–2,030 ps) (23), and B-DNA in pure water (B-DNA, 400–1,400 ps) (16). All of the helicoidal values were calculated using the Dials and Windows interface (27) to Curves (28) from average structures over 1 ns portions of the trajectories (except in the case of the canonical A-DNA structure). The average structures were created by RMS fitting all DNA atoms at 1 ps intervals from the trajectories and coordinate averaging. Helicoidal values reported are averages over all base pairs or base pair steps where appropriate. The sugar pucker, χ and δ angles are 1 ps averages over 1 ns portions of the dynamics, averaged over all nucleotides (except in the case of the canonical A model structure). It should be noted, as discussed in our previous work (23), that the means of the calculated values from each snapshot at 1 ps intervals over the same range are notably different in the rise, x-displacement (x-disp.), and base pair inclination from those reported in this table and are more B-like. The means of the values calculated from each individual snapshot at 1 ps intervals over the same range for the rise, x-displacement, and base pair inclination are 3.15 Å, −2.67 Å, and 6.3°, respectively, for the A-DNA trajectory and 3.48 Å, −1.27 Å, and −6.2°, respectively, for the B-DNA trajectory (16).