Table 1.
Structural parameters of GCC33, G5mCC, and G5hmCC Holliday junctions. Parameters that describe the helical structure42 around the modified C7 cytosine of the crossover GCC trinucleotide core are listed. The standard values for these parameters in B-DNA are shown in parentheses33. The overall conformation of the junction are reflected in the parameters Jroll and Jtwist (schematics for these two are shown at the bottom, adapted from Watson et. al.43).
| DNA Core: | GCC | G5mCC | G5hmCC |
|---|---|---|---|
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| |||
| Rotational Parameters | |||
|
| |||
| Helical Twist (34.7) | 37.3° | 34.5° | 34.4° |
| Propeller Twist (−12.0) | −20.1° | −17.6° | −14.2° |
| Tilt (−0.62) | −0.7° | 4.9° | 5.0° |
| Roll (1.74) | −2.7° | 0.9° | 3.6° |
| Buckle (−0.23) | 4.8° | −0.8° | 5.3° |
| Opening | 1.6° | 1.6° | 0.2° |
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| Translational Parameters | |||
|
| |||
| Rise (3.30) | 3.52 Å | 3.49 Å | 3.41 Å |
| Slide (0.66) | 0.84 Å | 0.38 Å | 0.51 Å |
| Shear | 0.14 Å | −0.10 Å | −0.03 Å |
| Stretch | 0.08 Å | −0.08 Å | −0.07 Å |
| Stagger | 0.24 Å | 0.23 Å | 0.42 Å |
| Shift | −0.43 Å | 0.75 Å | 0.82 Å |
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| Junction Parameters | |||
|
| |||
| Jroll | 135.31° | 143.04° | 150.46° |
| Jtwist | 39.95° | 40.81° | 41.10° |
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