Fig. 3: Kinetic analysis of state transitions during dLbCas12a R-loop formation.

A Schematic of 4-state model: Dwells are assigned to R-loop states corresponding to different ranges of unwinding, and all transitions between states are scored to obtain effective transition rates as a function of imposed twist. B Clustering and kinetic analysis for dLbCas12a with FM Seq 1 gRNA. Left: dwells from Fig. 2 were clustered into 4 states; merged dwells (see Supplementary Fig. 6) are plotted and color coded by state. The weighted average of the change in equilibrium twist for each state is labeled below in units of bp. Middle: Twist-dependent observed rates k are plotted for all 12 possible transitions between states, shown as ln (k) where k is the rate expressed in s^-1. Not all transitions are represented for each condition, due to omitting rates for undersampled bins (see Methods). Right: Rates are used to calculate twist-dependent equilibrium constants K. Best-fit lines are shown for data sets with at least 3 plotted points after omitting undersampled bins. C–E Same as (B) for other experimental conditions. Legends corresponding to all plots are shown in (E). All error bars represent standard errors (see Methods). See Supplementary Table 2 for trace statistics. Source data are provided for this figure.