Fig. 3: Investigating kinetics of DODA transformation via single-molecule fluorescence imaging and real-time PCR.

a Design of DODA for fluorescence experiments. An ATTO647N and a quencher were labeled on the DNA strands on the left side of DNA origami arrays. Before transformation, fluorescence was quenched due to the close proximity with the quencher. After transformation, the fluorescence was enhanced due to the increased distance between ATTO647N and quencher. b Histograms showing percentages of transformed DODAs with two triggers at different time points via single-molecule fluorescence measurement repeated three times. c Representative fluorescence traces for single structure transformation of three DODAs. The black line represented the background signals. d Top: accumulative fluorescence signals from single-molecule fluorescence measurement showing the overall transformation kinetics of three DODAs with two triggers. The experiments were performed three times at 37 °C. Below: Apparent transformation rate constant k obtained from the kinetics data 0.126 ± 0.040 min⁻¹, 0.080 ± 0.006 min⁻¹, and 0.018 ± 0.005 min⁻¹ for G-, N-, R-DODAs, respectively. Error bars represent the mean values ± standard deviation of the three experiments. e to i Transformation kinetic study on ensemble samples with different numbers of triggers by using real-time PCR. Top: ensemble fluorescence for the transformation of three DODAs with different number of triggers. The experiments were performed for three times at 30 °C. Below: The apparent rate constant k for three DODAs with different number of trigger input during the transformation. The k for G-, N-, R-DODAs with five triggers are 0.124 ± 0.011/min, 0.117 ± 0.010/min, and 0.078 ± 0.006/min, respectively. The k for G-, N-, R-DODAs with four triggers are 0.088 ± 0.014/min, 0.077 ± 0.022/min, and 0.064 ± 0.011/min, respectively. The k for G-, N-, R-DODAs with three triggers are 0.071 ± 0.007/min, 0.052 ± 0.002/min and 0.035 ± 0.003/min, respectively. The k for G-, N-, R-DODAs with two triggers are 0.028 ± 0.001/min, 0.024 ± 0.001/min, and 0.006 ± 0.001/min, respectively. Error bars represent the mean values ± standard deviation of the three experiments. G, N, and R represent G-, N-, and R-DODAs, respectively. Source data is provided as a Source Data file.