A nitrone-based in vivo click SHAPE reagent for mapping RNA secondary structure

We report the synthesis and testing of a new reagent for selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). We report the synthesis and testing of a nitrone acyl imidazole that is capable of labelling RNA (DMImO-AI) for applications including in vivo click SHAPE (icSHAPE). The new reagent has a reasonable lifetime for in vivo applications and can undergo strain-promoted alkyne-nitrone cycloaddition reactions that more rapidly conjugates labelled RNA than 2-(azidomethyl)nicotinic acid imidazolide (NAI-N 3 ). We show that DMImO-AI is a useful reagent for SHAPE mapping experiments of RNA from A549 cells with a faster reacting nitrone moiety for bioorthogonal conjugation.