Table 2.
The sequence motifs associated with each defect
| Simulation | Disruption type | Sequence | Bend | Roll |
|---|---|---|---|---|
| 65A(−1) | Bubble | GCTATC | ||
| 65A(−1) | Bubble | AGGTG | ||
| 65B(−1) | Bubble | GTGCAAT | ||
| 65B(−1) | Bubble | GATAT | ||
| 65B(−1) | Wrinkle | T C_T T_A T | ||
| 65B(0) | Type II kink | CTA | 80° | −76° |
| 65C(0) | Type II kink | CAA | 85° | −81° |
| 65C(0) | Type I kink | GC | 95° | −92° |
| 65A(+1) | Bubble | CAATG | ||
| 65A(+1) | Type II kink | CAA | 67° | −64° |
| 65B(+1) | Bubble | TATC | ||
| 65B(+1) | Type II kink (Bubble) | GGTG | 108° | −102° |
| 104A(−1.5) | Bubble | CGAACAA | ||
| 104A(−1.5) | Bubble | TATC | ||
| 104A(−1.5) | Wrinkle | C A_G G | ||
| 104B(−0.5) | Wrinkle | T C_A_G G | ||
| 110A(−1) | Type II kink | TCG | 114° |
For defects involving broken base pairs, the identity of the intact base pair either side of the denatured region is also provided. For wrinkled sequences the under-wound steps have been indicated by underlining. Bending and roll angles are listed for the kink defects where appropriate.