TABLE 1.
Comparison of conformational and helical parameters and minor groove distance of d(CGATTAATCG)2 DNA duplexes and MD simulated structures obtained with different force fields
| Average simulated structure* | |||||||
|---|---|---|---|---|---|---|---|
| Canonical A-DNA | Canonical B-DNA | Crystal structure | CHARMM22 | CHARMM27 | BMS | AMBER | |
| α (°) | 276 | 313.2 | 303.9(13.5) | 289.3(14.4) | 304.1(16.3) | 298.1(7.0) | 297.5(11.4) |
| β (°) | 208 | 214 | 179.1 (2.8) | 167.3(27.3) | 159.4(25.4) | 171.2(24.0) | 160.3(28.5) |
| γ (°) | 45.5 | 36.4 | 47.8(10.3) | 57.7(4.9) | 54.7(12.4) | 52.2(5.7) | 52.8(6.5) |
| δ (°) | 84.3 | 156.4 | 127.1(15.9) | 94.1(16.6) | 128.2(14.0) | 133.7(19.3) | 126.8(18.6) |
| ɛ (°) | 179.5 | 155 | 184.2(25.6) | 205.1(10.3) | 191.9(6.7) | 201.0(25.6) | 211.0(29.8) |
| ζ (°) | 311 | 264.8 | 260.1(28.9) | 282.9(7.5) | 244.7(17.8) | 242.1(40.8) | 237.3(46.7) |
| χ (°) | 206 | 262 | 245.4(16.2) | 203.4(14.9) | 247.8(15.4) | 249.1(17.8) | 246.6(18.3) |
| Pucker (°) | 13.3 | 191.8 | 139.4(38.1) | 45.8(47.7) | 136.4(39.1) | 138.1(39.1) | 137.6(25.1) |
| Amplitude (°) | 40.2 | 37.5 | 36.5(7.5) | 37.5(9.6) | 39.1(5.5) | 39.6(7.9) | 40.1(7.1) |
| Base step parameters: | |||||||
| Tilt (°) | 0 | 0 | 0.1(1.9) | −1.4(2.5) | −1.5(4.4) | 0.1(2.5) | −0.2(4.2) |
| Slide (Å) | −1.53 | −0.16 | −0.10(0.38) | −1.59(0.43) | −0.18(0.23) | 0.09(0.55) | −0.08(0.59) |
| Roll (°) | 10.7(2.2) | −3.6 | 0.0(5.1) | 6.4(7.5) | 3.9(8.8) | 1.3(4.4) | 1.7(5.8) |
| Shift (Å) | 0 | 0 | 0.03(0.27) | 0.16(0.56) | −0.17(0.69) | 0.07(0.75) | 0.03(0.78) |
| Twist (°) | 32.7 | 36 | 36.9(3.7) | 28.5(5.1) | 35.1(2.2) | 36.1(3.6) | 33.9(3.9) |
| Rise (Å) | 2.56 | 3.37 | 3.20(0.21) | 3.39(0.39) | 3.4(0.29) | 3.20(0.20) | 3.39(0.17) |
| Basepair parameters: | |||||||
| Tip (°) | 0 | 0 | −0.8(3.4) | 2.3(7.8) | 0.9(6.1) | 0.2(4.1) | 0.1(5.1) |
| Prop. twist (°) | 11.7 | 4.3 | −14.2(3.1) | −10.6(6.8) | −6.2(11.9) | −7.2(5.0) | −6.4(7.4) |
| Buckle (°) | 0 | 0 | −2.5(6.3) | −3.2(14.6) | 3.7(8.4) | −0.7(7.4) | 1.1(4.3) |
| Inclination (°) | 19.9 | −5.7 | 0.3(1.2) | 16.9(3.4) | 7.3(2.7) | 3.5(2.2) | 5.2(1.7) |
| X-disp. (Å) | −4.49 | 0.23 | −0.27(0.42) | −4.92(0.66) | −1.29(0.42) | −0.49(0.93) | −0.87(0.58) |
| Y-disp (Å) | 0 | 0 | 0.22(0.60) | −0.51(0.49) | 0.14(0.65) | 0.53(0.65) | −0.36(0.47) |
| Minor groove distances (Å)†: | |||||||
| PA4…PB10 | 16.95 | 13.17 | 10.48 | 15.33 | 14.57 | 14.47 | 12.91 |
| PA5…PB9 | 16.95 | 13.17 | 11.49 | 15.25 | 14.81 | 14.46 | 11.87 |
| PA6…PB8 | 16.95 | 13.17 | 13.15 | 14.87 | 13.31 | 15.01 | 13.05 |
| PA7…PB7 | 16.95 | 13.17 | 13.68 | 15.09 | 13.41 | 13.07 | 13.19 |
| PA8…PB6 | 16.95 | 13.17 | 12.68 | 15.31 | 12.71 | 11.72 | 13.24 |
| PA9…PB5 | 16.95 | 13.17 | 11.85 | 15.86 | 13.86 | 12.69 | 13.48 |
| PA10…PB4 | 16.95 | 13.17 | 11.09 | 14.65 | 15.82 | 15.12 | 13.62 |
Averages of conformational and helical parameters exclude the end basepairs of DNA. Values in parentheses correspond to standard deviations.
*
The values for the torsions, base step and basepair parameters are averaged over the simulation time.
†
The minor groove distances are calculated between the phosphorus atoms Pi on one strand and Pi+3 on the opposing strand.