Fig. 2: Experimental verification of the engine’s switching behavior and dwell time analysis.
A Representative 2D particle tracking data under different conditions: left (blue dots)—engine remains in the unfolded state in the absence of RNA/RNase H; middle (red dots)—engine folds upon addition of RNA linker; right (light blue dots)—engine unfolds again after addition of RNase H, which cleaves the RNA at the DNA/RNA duplex region. B Time series of particle relative position (Supplementary Fig. 5), showing autonomous switching behavior in the presence of both RNA (500 nM) and RNase H (80 nM). Raw trajectory (gray dots) and smoothed curve (black line) indicate transitions between folded and unfolded states. The top binary trace represents the idealized conformational state of the engine, assigned as either folded or unfolded based on threshold analysis of the particle’s position. Each upward or downward step corresponds to a transition between the two states. Arrows indicate dwell times in folded (closed, τC, red) and unfolded (open, τO, blue) states. C Cumulative distribution of dwell times fitted with a double-exponential model to extract τO and τC. (N is the particle number and n is switching event number). The τO and τC are expressed as mean +/− standard error based on 1000 bootstrap resamples. Data were collected at 37 °C with a frame rate of 20 frame per second (FPS). Source data are provided as a Source Data file.
