Table 2.
Calculated and experimental rate constants in Hz for an applied torque Γc, corresponding to a free energy cost of 5.8 kcal/mol/supercoil at a tension of 0.2 pN
| Rate constants | Experimental value | First rotation | Second rotation |
|---|---|---|---|
| Topo/DNA (+) | ∼75 | 6.4 | 34.8 |
| Topo/DNA/TPT (+) | ∼3.6 | 0.012 | 1.4 |
| Topo/DNA (−) | ∼61 | 4.7 | 147 (61) |
| Topo/DNA/TPT (−) | ∼12 | 268 | 192 |
Rates for the relaxation of the second supercoil (from a semiopen state) show good agreement for positive supercoil relaxation, whereas negative supercoils show less agreement but also appear less strongly affected by the presence of TPT, in accord with experiments. For Topo/DNA(−), changing plectoneme stiffness to 21 nm yields the value in parentheses, in accord with experiment. Rates for the first relaxation show a poor agreement with experiments, furthering our hypothesis that rotations from a semiopen state predominate.