Ribozyme‐Catalyzed Late‐Stage Functionalization and Fluorogenic Labeling of RNA

Abstract

AbstractSite‐specific introduction of bioorthogonal handles into RNAs is in high demand for decorating RNAs with fluorophores, affinity labels or other modifications. Aldehydes represent attractive functional groups for post‐synthetic bioconjugation reactions. Here, we report a ribozyme‐based method for the synthesis of aldehyde‐functionalized RNA by directly converting a purine nucleobase. Using the methyltransferase ribozyme MTR1 as an alkyltransferase, the reaction is initiated by site‐specific N1 benzylation of purine, followed by nucleophilic ring opening and spontaneous hydrolysis under mild conditions to yield a 5‐amino‐4‐formylimidazole residue in good yields. The modified nucleotide is accessible to aldehyde‐reactive probes, as demonstrated by the conjugation of biotin or fluorescent dyes to short synthetic RNAs and tRNA transcripts. Upon fluorogenic condensation with a 2,3,3‐trimethylindole, a novel hemicyanine chromophore was generated directly on the RNA. This work expands the MTR1 ribozyme's area of application from a methyltransferase to a tool for site‐specific late‐stage functionalization of RNA.