Extended Data Fig. 5: The complete simulated time trajectories (a) for Fig. 2e and distance distributions during the simulation time (b). | Nature

Extended Data Fig. 5: The complete simulated time trajectories (a) for Fig. 2e and distance distributions during the simulation time (b).

From: DNA-based programmable gate arrays for general-purpose DNA computing

Extended Data Fig. 5: The complete simulated time trajectories (a) for Fig. 2e and distance distributions during the simulation time (b).

With 1-nt gap, the toehold domain bound reversibly to S3 (middles panel of Distance 1 trajectory, inset), which did not lead to further branch migration (high fluctuation for Distance 2 and 3). Therefore, the presence of only in1H cannot generate a fault result, permitting neglectable leakage similar to that of 0-nt gap. However, 2-nt gap allowed stable binding of in1H (left panel of Distance 1 trajectory, indicated by H-bond arrow), and the output strand was replaced via branch migration (left panels of Distance 2 and 3 trajectories, indicated by H-bond arrows). Insets in (b): Distributions of Distance 1 ranging from 0.5 nm to 2.5 nm.

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