Extended Data Fig. 9: Adding a third component.
From: Functional advantages of building nanosystems using multiple molecular components
(a) A trimeric assembly can also be created by introducing a new component, called the controller, that can interact with both the native DNAzyme and the substrate. (b) This controller strand can modulate the level of activity and the deactivation time via the formation of an inactive trimer. (c) In the presence of a 10 nM controller and DNAzyme, increasing the concentration of substrate increases the formation of the active dimer and the catalytic rate without substantially affecting the trimeric deactivation rate kTri. (d) At 100 nM substrate, increasing the concentration of controller and DNAzyme increases the rate of trimer formation and thus the rate of DNAzyme deactivation. Kinetic traces (left panel) are fitted using a single exponential (native) or a double exponential (with controller) to extract rate constants of dimeric and trimeric formation (that is, deactivation of the DNAzyme) (Eq. 6). The derivatives (middle panel) are plotted to better show the variation in initial rates and deactivation times. Fluorescence data were converted to the concentration of product using a calibration curve (data not shown) and normalized by the concentration of DNAzyme. All experiments have been done in PBS buffer (50 mM Na2HPO4, 400 mM NaCl, pH = 7.00) at 25 °C.
