Designing reversible photoswitching azobenzene modified nucleotide for controlling biological function

RNA plays vital roles in numerous normal and diseased cellular functions and processes. Reversible photoregulation of oligonucleotide’s structure and function is a powerful strategy for both regulating biological processes and developing novel RNA-based therapeutics. Here, we designed an azobenzene modified cytidine phosphoramidite and synthesized a series of RNA oligonucleotides containing this photoswitchable residue. We validated the reversible photoisomerization in both nucleoside and oligonucleotide contexts, and studied the overall impact of this cytidine modification through all-atom molecular dynamics (MD) simulations and UV melting experiments. We also showed that the modified oligonucleotide can switch reverse transcription (RT) process upon light irradiation in the presence of various RT enzymes. In addition, the optical control mechanism of HIV reverse transcriptase mediated RT process was elucidated by MD simulation. This new chemical biology toolset enables reversible optical control of RNA structures and functions for gene regulation and novel drug development.