Temporal Control of Aptamer Biosensors Using Covalent Self-Caging To Shift Equilibrium

Aptamer-based sensors provide a versatile and effective platform for the detection of chemical and biological targets. These sensors have been optimized to function in multiple formats, however, a remaining limitation is the inability to achieve temporal control over their sensing function. To overcome this challenge, we took inspiration from nature's ability to temporally control the activity of enzymes and protein receptors through covalent self-caging. We applied this strategy to structure-switching aptamer sensors through the installation of a cleavable linker between the two DNA fragments that comprise the sensor. Analogous to self-caged proteins, installation of this linker shifts the equilibrium of the aptamer sensor to disfavor target binding. However, activity can be restored in a time-resolved manner by cleavage of the linker. To demonstrate this principle, we chose a photocleavable linker and found that installation of the linker eliminates target binding, even at high target concentrations. However, upon irradiation with 365 nm light, sensor activity is restored with response kinetics that mirror those of the linker cleavage reaction. A key benefit of our approach is generality, which is demonstrated by grafting the photocleavable linker onto a different aptamer sensor and showing that an analogous level of temporal control can be achieved for sensing of the new target molecule. These results demonstrate that nature's self-caging approach can be effectively applied to non-natural receptors to provide precise temporal control over function. We envision that this will be of especially high utility for deploying aptamer sensors in biological environments.