Fig. 2: Formation and collapse rates of R-loop intermediates of different lengths.

a Sketch of the DNA construct containing a limited number of matching PAM-proximal bases such that only R-loop intermediates form (left). Example trajectory of the transitions between unbound state (\(U\)) and intermediate R-loop (\(I\)) for a target with 12 matching bases. b Formation and collapse of R-loop intermediates recorded at different torques \(\tau\) for a target with 12 matching bases. Shown are the recorded DNA length smoothed to 7.5 Hz (light blue) and a two-state approximation of the trajectory (dark blue). Solid lines in the histograms on the right represent Gaussian fits to the 2 different states, while horizontal dashed lines indicate the average DNA length of each state. Bars represent theoretically predicted occupancies using best fit parameters from (d) and (e). c Formation and collapse of R-loop intermediates of different lengths at a torque of −4.7 pN nm. d, e Measured mean formation (d) and collapse (e) rates of the R-loop intermediates as a function of torque for different lengths of the matching region (open circles). A global fit to the data is shown as solid lines. Rate errors are given as SEM; torque errors correspond to 0.25 pN nm. Precise sample sizes are given in the Supplementary Table 6. Source data are provided as a Source Data file. f Occupancies of the \(I\) state for two different negative torques (upper panel) and R-loop lengths (lower panel) together with the corresponding free energy landscapes.