Structure-Encoded Oxidation Enables Nucleotide-Resolved RNA Editing, Conjugation, and Structural Probing

RNA oxidation is pervasive in stress and disease biology and has also been harnessed in chemical biology through proximity labeling, ligand-directed photochemistry, and oxidative RNA targeting. In most settings, the regioselectivity is specified by spatial proximity or a specialized RNA-binding ligand, and the resulting modification is typically distributed across a local region rather than at a designated nucleotide. Here we show that, with selected oxidants, RNA secondary structure can itself serve as a programmable handle to control RNA oxidation site-selectively. We define practical structure-reactivity rules that determine which guanosine is oxidized and which lesions predominate, based on loop geometry and oxidant identity. Guided by these rules, we develop LOCAL (Localized Oxidation Constrained at Loops), a DNA-programmed, postsynthetic method that directs guanosine oxidation to predetermined sites in transcribed RNAs with nucleotide-resolved selectivity. LOCAL enables oxidative base editing to modulate RNA interactions and stability, provides a plug-and-play tool for site-specific bioconjugation via nucleophile trapping of oxidized guanosines, and serves as a blue-light-gated, guanosine-focused structural readout of RNA single-strandedness and ligand-induced structural changes. Together, these results position RNA oxidation as a nucleotide-resolved, structure-encoded reaction manifold that complements existing ligand-encoded oxidative targeting chemistry, and 2´-OH- and enzyme-based RNA chemistries.