Table 3.
Rotational diffusion tensor for the Dickerson DNA dodecamer, d(CGCGAATTCGCG)2, determined by ROTDIF from ribose CH 13C relaxation data. First model of 1NAJ was used for all computations.
| Method | Nucleotides | Dx * | Dy | Dz | α* | β | γ | τc * | ζ | η |
|---|---|---|---|---|---|---|---|---|---|---|
| Published (Boisbouvier et al, 2003) | coreb | 3.64 - |
3.64 - |
7.64 - |
- - |
- - |
- - |
3.35 ±0.03 | 2.1 ±0.04 | - - |
| ROTDIF 3 | corea | 4.30 ±0.10 | 4.30 ±0.10 | 6.93 ±0.15 | 94 ±1 | 85 ±2 | - - |
3.22 ±0.01 | 1.61 ±0.07 | - - |
| ROTDIF 3 | coreb | 3.77 ±0.09 | 3.77 ±0.09 | 7.66 ±0.16 | 95 ±1 | 97 ±1 | - - |
3.29 ±0.01 | 2.03 ±0.09 | - - |
| ROTDIF 3c | coreb | 3.65 ±0.10 | 3.82 ±0.09 | 7.73 ±0.17 | 95 ±1 | 97 ±1 | 92 ±8 | 3.29 ±0.01 | 2.07 ±0.10 | 0.06 ±0.01 |
| ELMd | - | 3.35 | 4.49 | 6.94 | 97 | 93 | 98 | 3.38 | 1.77 | 0.57 |
a
Single-stranded, where the relaxation data were assigned only to strand A.
b
Double-stranded, where due to the palindromic nature of the DNA, the same relaxation data were assigned to strands A and B.
c
Anisotropic rotational diffusion model was used.
d
Results from our built in ab initio diffusion tensor predictor ELM.
*
The units are 107s−1 for Dx, Dy, Dz, ns for τc, and degrees for α, β, and γ angles.