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1.8.2 Kinetics of Binding and Unbinding Events and DNA‐PAINT
ОглавлениеFluorescence microscopy was successfully applied to study the kinetics of dynamic DNA binding and dissociation [82]. For kinetic analysis, a long rectangular DNA origami structure was used to incorporate a green label dye (ATTO532) at a corner and a docking strand was positioned in the middle of the rectangle (Figure 1.10c) [83]. The addition of a red dye (ATTO655)‐modified imager strand led to the formation of a duplex with the complementary docking strand. The formation of the duplex structure was monitored and the kinetics of the binding and unbinding events were determined. The association rate was calculated to be 2.3 × 106 M/s (for 600 mM NaCl), which is comparable with the results of bulk measurements. In contrast, the dissociation rate was independent of the concentration, but strongly dependent on the length of the duplex formed by the imager and docking strands. The dissociation rate was estimated at 1.6 and 0.2 s–1 for 9 and 10 base pairs, respectively. The distance between multiple fluorescence dyes on DNA origami was precisely measured using DNA‐PAINT (Figure 1.10d). Images and distance distribution histograms revealed that the fitted distances for adjacent dyes and the outer dyes were 111 ± 27 and 212 ± 44 nm, respectively, which is in good agreement with the initial design but slightly lower than the expected distance. These results indicate that, in addition to static analyses, dynamic processes in the subsecond range can be investigated on DNA origami in real time and are comparable with the results of ensemble measurements.