Systematic investigation of bioorthogonal cellular DNA metabolic labeling in a photo-controlled manner

Abstract Bioorthogonal cleavage and ligation reactions together form one more integrated system about the repertoire of bioorthogonal chemistry, capacitating an array of thrilling new biological applications. The bond-cleavage type and position of biomolecular remain a great challenge, which determines the metabolic pathway of the targets in living systems. Herein we designed two linkages of methylene and carbonyl group attached the N-3 position of the 5-ethynyl-2′-deoxyuridine (EdU) base or the oxygen atom at deoxyribose 3′ position to a photocaging group, which would be cleaved by irradiation with 365 nm ultraviolet light. EdU derivatives linked by methylene at the N-3 position had better photodecage efficiency and stability in the absence of light. This paper provides a strategy for studying the nucleoside metabolic pathways in cells, which can easily and conveniently evaluate the effect of the position and type of the linkages. The developed strategy affords a reference for controlling spatial and temporal metabolism of small-molecule drugs, allowing direct manipulation of intact cells under physiological conditions.