Figure 3.

(a) Experiment for monitoring chemical changes by two-color PAINT. R origami tiles were imaged in the presence of 10 nM each of α-Cy3 and β-Cy5. Incubation with 1 μM 8-17 deoxyribozyme (DNAzyme) and 1 mM Zn²⁺ results in the cleavage of S. The cleavage product can bind probe α, but not probe β, resulting in a change in the PAINT readout. (b) Two-color reconstructions of three individual R origami tiles after 0, 2, or 10 min total incubation with 8-17 DNAzyme and Zn²⁺ (α-Cy3, green; β-Cy5, red, scale bars 50 nm). (c) Mean ratio of β binding events to α binding events for 21 R origami after 0, 2, or 10 min total incubation with 1 μM 8-17 DNAzyme and 1 mM ZnSO₄ (black circles, error bars 1 s.d.). The time courses for 21 individual origami tiles are also shown (gray lines). An ensemble time course for the cleavage of substrate on R origami under identical conditions, normalized to the initial value of <N_β/N_α>, is shown for comparison (red squares, Figure S3).