Table 3. Average helical parameters measured using X3DNA for the quasi-continuous helical arms in the four-way junction and comparison with the B-DNA fibre model (Chandrasekaran & Arnott, 1989 ▶).
Minor-groove and major-groove widths were measured as the ‘refined’ phosphate–phosphate distances based on the method proposed by El Hassan & Calladine (1998 ▶) and incorporated in the program X3DNA (Lu & Olson, 2003 ▶).
| d(CGGGTACCCG)4 | B-DNA fibre model | |
|---|---|---|
| Helical rise (Å) | 3.46 | 3.38 |
| Helical twist (°) | 37.8 | 36.0 |
| Roll (°) | 1.6 | 0.0 |
| Tilt (°) | −0.9 | 0.0 |
| Inclination (°) | 1.9 | 2.8 |
| Propeller twist (°) | −15.7 | −15.1 |
| X-displacement (Å) | 2.35 | 0.00 |
| Slide (Å) | 1.62 | 0.00 |
| Major-groove width (Å) | 10.26 | 11.60 |
| Minor-groove width (Å) | 7.03 | 6.00 |