Table 1.
Kinetic and thermodynamic values (mean ± SD) measured and calculated respectively from magnetic tweezers assays
| Force (pN) | Event number | τloop (S) | τunloop (S) | τunloop/τloop | ΔGl,F (kBT) | Δl (nm) |
|---|---|---|---|---|---|---|
| A1 DNA heterodimer | ||||||
| 0.7 | 100 | 41.1 ± 2.9 | 4.7 ± 0.3 | 0.1 ± 0.01 | −2.3 ± 0.1 | 79.9 ± 2.5 |
| 0.8 | 152 | 24.6 ± 1.4 | 8.3 ± 0.5 | 0.3 ± 0.03 | −1.2 ± 0.1 | 78.9 ± 2.3 |
| 0.9 | 215 | 17.3 ± 1.3 | 16.7 ± 0.9 | 1.0 ± 0.1 | 0 ± 0.1 | 75.0 ± 1.8 |
| 1.0 | 196 | 10.2 ± 0.9 | 30.1 ± 1.8 | 3.0 ± 0.3 | 1.1 ± 0.1 | 57.9 ± 1.9 |
| 1.2 | 136 | 7.8 ± 0.7 | 67.5 ± 6.1 | 8.6 ± 1.1 | 2.2 ± 0.1 | 60.1 ± 2.9 |
| A2 DNA heterodimer | ||||||
| 0.7 | 165 | 38.0 ± 2.8 | 2.5 ± 0.1 | 0.1 ± 0.01 | −2.3 ± 0.1 | 72.4 ± 1.3 |
| 0.8 | 152 | 15.7 ± 0.5 | 5.4 ± 0.2 | 0.3 ± 0.02 | −1.2 ± 0.1 | 69.3 ± 1.5 |
| 0.9 | 103 | 7.0 ± 0.3 | 10.8 ± 0.3 | 1.5 ± 0.1 | 0.4 ± 0.1 | 66.6 ± 1.9 |
| 1.0 | 280 | 4.7 ± 0.2 | 15.4 ± 0.7 | 3.3 ± 0.2 | 1.2 ± 0.1 | 66.1 ± 1.8 |
| 1.2 | 100 | 2.4 ± 0.2 | 38.4 ± 3.2 | 16.0 ± 1.9 | 2.8 ± 0.1 | 56.2 ± 2.0 |
| A1 DNA wt | ||||||
| 0.7 | 183 | 41.5 ± 2.5 | 6.3 ± 0.6 | 0.2 ± 0.02 | −1.6 ± 0.1 | 81.5 ± 1.4 |
| 0.8 | 277 | 30.1 ± 2.0 | 13.7 ± 0.5 | 0.5 ± 0.04 | −0.7 ± 0.1 | 82.0 ± 1.4 |
| 0.9 | 208 | 18.9 ± 0.8 | 20.8 ± 1.9 | 1.1 ± 0.1 | 0.1 ± 0.1 | 57.4 ± 0.7 |
| 1.0 | 251 | 11.5 ± 0.5 | 23.7 ± 2.0 | 2.1 ± 0.2 | 0.7 ± 0.2 | 53.8 ± 1.2 |
| 1.1 | 135 | 7.1 ± 0.6 | 57.7 ± 16.2 | 8.1 ± 2.4 | 2.1 ± 0.3 | 51.0 ± 1.5 |
τloop and τunloop are the average lifetimes for the looped and unlooped configurations, respectively, calculated from the dwell time distributions in each case. From the data, it is possible to directly extract the free energy for the looping reaction at a given force, A Gl,F, using the following equation: Gl,F = kBT ln(τunloop/τloop). Δl is the average change in the DNA length associated with looping.