Extended Data Fig. 9: Mean-squared-displacement (MSD) of R-loop length fluctuations over time in comparison to simulations.
From: The energy landscape for R-loop formation by the CRISPR–Cas Cascade complex
Mean squared displacement of the bare nanorotor (black) as well as of the R-loop length fluctuations as a function of time \(\left\langle {\left(\varphi \left(t\right)-\varphi \left(0\right)\right)}^{2}\right\rangle\) for starting positions φ(0) of 15, 21 and 26 bp corresponding to the 5-bp segments 3, 4 and 5, respectively. Shown are MSDs from the measurement on a molecule with a T6 target (solid lines) and Brownian dynamics simulation using the best-fit parameters: b=20 and kstep=7000, for its R-loop dynamics (dashed lines). The measured mean escape times (dotted vertical lines) from the wells 3, 4 and 5 were 31, 8.9 and 74 ms respectively. The good agreement between measurement and simulation for the MSD plots provides strong support for the obtained energy landscape and the stepping rate kstep. In particular, the agreement for short times in between the nanorotor response time (grey vertical line) and the corresponding escape times from the wells strongly supports that the intrawell R-loop dynamics is governed by a random walk-like process of 1 bp step size.
