Table 1.
Helical, backbone and groove parameters calculated with Curves+ for (panel A) A-DNA and (panel B) B-DNA and (panel C) standard deviations of helical and groove parameters along the oligomers
| Panel A: A-DNA (using PDB file 1d13) | |||||||||
| BP-axis | Xdisp | Ydisp | Incl | Tip | |||||
| A | −3.95 | 0.00 | 16.8 | 0.0 | |||||
| Aold | −4.71 | 0.00 | 16.8 | 0.0 | |||||
| Intra-BP | Shear | Stretch | Stagger | Buckle | Propel | Opening | |||
| A | 0.00 | −0.01 | 0.04 | 0.0 | −15.3 | 4.2 | |||
| Aold | 0.00 | 0.03 | −0.17 | 0.0 | −15.3 | 4.0 | |||
| Inter-BP | Shift | Slide | Rise | Tilt | Roll | Twist | H-Rise | H-Twist | |
| A | 0.00 | −1.23 | 3.26 | 0.0 | 8.4 | 31.7 | 2.72 | 33.1 | |
| Aold | 0.00 | −1.65 | 3.37 | 0.0 | 8.4 | 31.7 | 2.69 | 33.1 | |
| Backbone | α | β | γ | δ | ϵ | ζ | χ | Pha | Amp |
| A | −31.5 | 157.8 | 9.2 | 97.3 | −157.1 | −81.3 | −152.6 | 16.7 | 41.3 |
| Grooves | Min-W | Min-D | Maj-W | Maj-D | |||||
| A | 9.7 | 1.4 | 2.8 | 9.6 | |||||
| Panel B: B-DNA (using PDB file 1bna) | |||||||||
| BP-axis | Xdisp | Ydisp | Incl | Tip | |||||
| B | 0.27 | 0.11 | −0.1 | −1.0 | |||||
| Bold | −0.48 | 0.11 | −0.1 | −1.0 | |||||
| Intra-BP | Shear | Stretch | Stagger | Buckle | Propel | Opening | |||
| B | −0.04 | −0.17 | 0.21 | 0.3 | −13.7 | 1.0 | |||
| Bold | −0.04 | −0.08 | 0.03 | 0.3 | −13.7 | 0.8 | |||
| Inter-BP | Shift | Slide | Rise | Tilt | Roll | Twist | H-Rise | H-Twist | |
| B | −0.02 | 0.14 | 3.36 | −0.2 | −0.3 | 35.8 | 3.35 | 36.0 | |
| Bold | −0.02 | −0.33 | 3.36 | −0.2 | −0.3 | 35.0 | 3.35 | 36.0 | |
| Backbone | α | β | γ | δ | ϵ | ζ | χ | Pha | Amp |
| B | −73.3 | 179.7 | 66.0 | 121.1 | 173.7 | −88.5 | −122.2 | 127.3 | 50.2 |
| Grooves | Min-W | Min-D | Maj-W | Maj-D | |||||
| B | 4.2 | 4.9 | 10.5 | 5.4 | |||||
| Panel C: Standard deviations of parameters along the A-DNA (1d13) and B-DNA (1bna) oligomers | |||||||||
| BP-axis | Xdisp | Ydisp | Incl | Tip | |||||
| A | 0.39 | 0.62 | 1.1 | 5.4 | |||||
| B | 0.56 | 0.23 | 4.7 | 3.1 | |||||
| Intra-BP | Shear | Stretch | Stagger | Buckle | Propel | Opening | |||
| A | 0.18 | 0.08 | 0.25 | 5.3 | 4.5 | 4.6 | |||
| B | 0.27 | 0.08 | 0.19 | 5.9 | 6.9 | 4.3 | |||
| Inter-BP | Shift | Slide | Rise | Tilt | Roll | Twist | H-Rise | H-Twist | |
| A | 0.70 | 0.29 | 0.09 | 3.4 | 0.6 | 4.9 | 0.14 | 4.9 | |
| B | 0.55 | 0.43 | 0.18 | 2.9 | 5.9 | 4.1 | 0.18 | 4.1 | |
| Grooves | Min-W | Min-D | Maj-W | Maj-D | |||||
| A | 0.17 | 0.20 | 0.0 | 0.0 | |||||
| B | 1.29 | 0.30 | 0.71 | 0.96 | |||||
Helical parameters are averages over the oligomers. Backbone parameters refer to G5 in the first strand of 1d13 and to A6 in the first strand of 1bna. Groove parameters refer to the level involving the same central base pairs. Aold and Bold refer to an analysis of 1d13 and 1bna respectively using the old Curves base reference frame. Translational parameters are in Å (shown with two decimal places) and rotational parameters are in degrees (shown with a single decimal place).