Fig. 2: Nanopore and fluorometer-based comparison of catalytic DSD circuit kinetics.

a Diagram of a seesaw catalytic DSD circuit. Single-stranded input displaces the 3’ labeled biotin-streptavidin single-stranded output from the gate complex, forming an intermediate with the bottom strand. The displaced output strand is now free to capture in a nanopore. Single-stranded fuel displaces input from the intermediate, recycling the input. b Displaced output ssDNA can be read out using two detection strategies: (i) Spectrofluorometer-based detection. Output strand displaces the quencher-labeled strand from a fluorophore-labeled reporter gate complex, triggering fluorescence. Blunt end stacking can occur in this reporter strategy, in which a double-stranded gate complex displaces the quencher strand, resulting in undesired leaky fluorescence. (ii) Nanopore-based detection. A single-stranded output strand is displaced by an input strand and can then be captured in a nanopore, resulting in a detectable drop in ionic current that is diagnostic of the strand’s barcode sequence. c DSD reaction kinetics plot determined by nanopore (pink) and, for comparison, a spectrofluorometer (green), showing the normalized concentration of output strand after addition of input.