Table 1.
RMS differences between the crystal structure of the DNA fragment within the TBP-TATA-box complex (1) and various model DNA conformations
| Sequence | Constrained segment | Stretched
|
Unwound
|
||||
|---|---|---|---|---|---|---|---|
| B | A | BAB | B | A | BAB | ||
| (AT)n | 4 | 1.2/2.6 | 1.7/2.9 | 1.5/2.2 | 1.7/2.9 | 1.5/2.9 | 1.5/1.7 |
| 50/40 | 25/38 | 23/27 | 44/38 | 32/40 | 26/28 | ||
| 5 | 1.5/2.3 | 1.8/2.9 | 1.7/2.5 | 2.0/2.8 | 1.9/3.5 | 1.8/2.2 | |
| 47/39 | 24/38 | 21/27 | 44/38 | 25/38 | 25/28 | ||
| 6 | 1.9/1.8 | 2.2/3.5 | 2.1/2.9 | 2.1/2.8 | 1.6/2.2 | 1.7/1.7 | |
| 46/39 | 25/38 | 23/27 | 42/39 | 27/39 | 26/28 | ||
| TATA-box | 4 | 1.1/2.8 | 1.5/2.7 | ||||
| 29/23 | 29/23 | ||||||
(In each line, the first value refers to the constrained segment of DNA and the second to the complete 12 base pair oligomer. For each model, the first line gives the Cartesian RMSD in Å and the second line gives the angular RMSD in degrees. B, A and BAB refer respectively to starting conformations in the B-form, the A-form and a mixed B-A-B hybrid).