Table 7.
Groove width (Å) of DNA duplex (CGCGAATTCGCG)2 and RNA duplex (CGCGAAUUCGCG)2 from GB-neck2 and explicit water MD simulations.
| Groove width (Å) | DNA (CGCGAATTCGCG)2 | RNA (CGCGAAUUCGCG)2 | ||||
|---|---|---|---|---|---|---|
| GB-neck2 | explicit water | Experiment (NMR/ X-ray)6a | GB-neck2 | explicit water | Experiment (X-ray) | |
| Major | 18.7±0.1 | 18.8±0.1 | 18.0 ± 3.0/18.0 ± 0.3 | 15.1±0.5 | 19.2±0.1 | 16.2+/−3.0 |
| Minor | 12.8±0.1 | 12.1±0.1 | 12.0 ± 1.0 /10.0 ± 0.2 | 15.9±0.1 | 15.1±0.1 | 17.4 +/− 1.4 |
Two runs were performed for each solvent model, starting from A and B-forms. Uncertainties in MD data were calculated from two simulations. RNA experimental values reflect average and standard deviation from a survey of 50 crystal structures. DNA experimental values are from a published survey of crystal structures.6a