Fluorescent nucleobase analogs constructed by aldol‐type condensation: Design, properties, and synthetic optimization for fluorogenic labeling of 5‐formyluracil

Abstract

AbstractFluorescent nucleosides play essential roles in designing functional nucleic acid systems for various biological applications. Therefore, expanding the scope of fluorescent nucleosides with unique properties has become an important challenge. Herein, we report novel fluorescent nucleosides constructed by aldol‐type condensation between 5‐formylpyrimidine and a fluorogenic dye. Two new fluorescent nucleobase analogs (4a and 4c), derived from 2‐dicyanomethylene‐3‐cyano‐4,5,5‐trimethyl‐2,5‐dihydrofuran and a quinolinium moiety, respectively, were determined through reaction screening, and their photophysical properties and formation kinetics were investigated. Among the two, 4a exhibits a unique fluorescence featuring a large Stokes shift (67–117 nm) and high environmental sensitivity, as evidenced by its viscosity‐induced fluorescence and aggregation‐induced emission behavior. The kinetic study revealed that 4a was readily synthesized even in aqueous solutions with pH 7 (kobs = 6.4 × 10−5/s). The overall results indicate that 4a is a promising molecule for use in fluorescent nucleic acid systems, particularly for selective fluorogenic labeling of 5‐formyluracil.