Table 2. Helical parameters for structures from the crystallographic screen of the sequence motif d(CCnnnN6N7N8GG).
| Rotational parameters,°
|
Translational parameters, Å
|
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Structures | Helical twist | Propeller twist | Tilt | Roll | Buckle | Rise | Slide | X displacement | Zp |
| B-DNA | |||||||||
| <Base pairs> | 34.7 (15.5) | −12.0 (8.1) | −0.62 (10.9) | 1.74 (7.98) | −0.23 (8.57) | 3.30 (0.4) | 0.66 (1.02) | 0.53 (1.56) | −0.67 (0.59) |
| <Structures> | 35.6 (1.2) | −11.6 (2.8) | −0.05 (0.52) | 2.18 (1.51) | −0.31 (2.62) | 3.31 (0.06) | 0.71 (0.40) | 0.49 (0.48) | −0.68 (0.24) |
| GCA | 38.2* | −12.9 | −0.43 | −0.12* | −4.94* | 3.39 | 1.32* | 1.43* | −0.9 |
| Junctions | |||||||||
| <Base pairs> | 37.5 (4.3) | −11.2 (8.1) | −0.14 (4.69) | 1.90 (4.47) | −1.16 (6.09) | 3.40 (0.23) | 1.63 (1.11) | 2.11 (1.89) | −0.97 (1.07) |
| <Structures> | 37.5 (0.33) | −11.2 (3.0) | −0.14 (0.65) | 1.90 (0.52) | −1.16 (2.93) | 3.40 (0.03) | 1.63 (0.11) | 2.11 (0.13) | −0.97 (0.14) |
| A-DNA | |||||||||
| <Base pairs> | 30.4 (4.2) | −7.82 (8.47) | 0.62 (3.91) | 6.88 (5.69) | −0.57 (7.78) | 3.30 (0.24) | −1.74 (0.31) | −4.47 (1.25) | 2.27 (0.39) |
| <Structures> | 30.4 (0.8) | −7.82 (3.57) | 0.62 (0.67) | 6.88 (1.71) | −0.57 (2.42) | 3.30 (0.06) | −1.74 (0.15) | −4.47 (0.25) | 2.27 (0.15) |
| Amphimorphic junction structures | |||||||||
| ATC (B-DNA) | 36.8 | −17.3 | −0.06 | −0.08 | 7.35 | 3.34 | −0.07 | −0.16 | −0.26 |
| ATC (Junction-LS) | 37.8 | −13.0 | 0.47 | 1.53 | 0.91 | 3.34 | 1.63 | 1.99 | −1.08 |
| ATC (Junction-HS) | 37.2 | −16.5 | 0.20 | 2.28 | 0.37 | 3.38 | 1.77 | 2.11 | −1.15 |
| CCC (Junction) | 38.0 | −14.2 | −1.28 | 2.15 | −7.19 | 3.37 | 1.60 | 2.60 | −0.97 |
| CCC (A-DNA) | 30.5 | −8.09 | −0.29 | 7.1 | 0.83 | 3.24 | −1.76 | 13.66 | 2.38 |
The rotational and translational parameters that characterize the helical conformations of nucleic acid structures [as defined (31) and calculated by the program 3dna (32)] are compared for the mean values of all base pairs [<Base pairs> (standard deviations)] and as means averaged across the structures [<Structure> (standard deviation of mean)] for structures in the screen that are B-DNA, four-stranded junctions, and A-DNA.
*
Values that fall at least 1 SD outside the mean of the average structural class.