Figure 3.

(a) For either shearing or unzipping (shown here for main duplex length 30 bp), the transition barrier ΔG^‡ and ΔG_tot can be defined by the free energy of the transition state (1 bond) and the minimum free energy of the unbound states, respectively, relative to the initial 10-bond state. Cut-outs on the right correspond to insets in graphs (b), depicting the derivation of these free energies graphically. (b) The transition barrier (top) remains largely constant for shearing and shows a minimum of around 30 bp for unzipping; the total free-energy change (bottom) mostly decreases with increasing main duplex length. These can be fitted to eqs 1 and 2 of Section 2.4, where allowing the main duplex to kink at a critical torque of 29 pN nm (solid lines) improves fitting of the transition barrier but degrades fitting of the total free-energy difference of unzipping, relative to a model in which the main duplex does not kink (dashed lines).