Figure 6.

A kinetic three-state model with microscopic rates and α_off. (a) Scheme of the kinetic model representing the different accessible states: unbound ligand (green), fully bis-intercalated (blue) and mono-intercalated intermediate (red). The binding of the first intercalating moiety is bimolecular (with a rate α_on proportional to ligand concentration), whereas the transition from the mono-intercalated intermediate to a fully bis-intercalated state is unimolecular (with rate ). On the other hand, the removal of any of the two intercalative moieties is driven by a single off-rate α_off. (b) Microscopic rates , α_on and α_off that best describe the experiments. The values of (blue points) and α_off (red points) are determined from the macroscopic rates measured in wash-off experiments (Figure 5b). A fit to Equation (7) (red and blue lines) is used to extrapolate the high force values and their associated uncertainty range (shaded area). The rates α_on are determined from intercalation experiments with naked DNA (panel (e) and Supplementary Section S5). (c) Ratio of amplitudes of the fast and slow macroscopic off-rates measured in the wash-off experiments (black) compared with the model prediction (red). (d) Fractional elongation of the force-jump experiments from Figure 3a (solid lines) and comparison to the kinetics predicted by the model (dashed lines). (e) Fractional elongation of intercalation experiments (100-nM Thiocoraline) starting from a naked DNA molecule at 5 and 15 pN (solid lines) and comparison to the kinetics predicted by the model (dashed lines).