Figure 5.

Temporally controlled ligand release from a DNA device. (a) Scheme of coupling delayed strand displacement to a DNA-based device that binds a 9 nt ligand DNA sequence by forming a triplex structure. The output strand of the delayed SDR binds the loop domain of the triplex structure and induces the ligand release. Tunable delays of SDR and thus of the downstream ligand release can be obtained in the presence of the blocker strand and its degrading enzyme UDG. (b) Time-course experiments using different concentrations of the uracil-blocker at a fixed concentration of UDG (1.0 U/mL). (c) Half-life values of ligand release obtained at different uracil-blocker concentrations. (d) Time-course experiments using different concentrations of UDG at a fixed concentration of the uracil-blocker (150 nM). (e) Half-life values of ligand release obtained at different UDG concentrations. In (b–e), experimental values (dots) are shown together with fits (b,d) and prediction (c,e) from a parameterized kinetic model (solid lines) described in Section 2g of Supporting Information. Experiments were performed in Tris HCl 10 mM, MgCl₂ 3 mM, pH 6 at T = 25 °C. [Target duplex] = 50 nM, [uracil-blocker] = 150 nM, [ligand] = 50 nM, [input strand] = 50 nM, [ligand-binding device] = 50 nM.