RNA Hairpin Synthesis by RNase-Catalyzed Dynamic Covalent Chemistry

Dynamic covalent chemistry (DCC) provides a powerful framework for assembling complex molecular architectures under thermodynamic control. Here, we extend RNA DCC by harnessing the ability of RNase T₁-traditionally used as a degradative enzyme-to catalyze reversible phosphodiester exchange. Although enzyme-mediated RNA ligation has been reported previously, such reactions typically required high substrate concentrations and yielded heterogeneous mixtures without structural control. By coupling catalysis to RNA folding, selective formation of well-defined hairpin products governed by thermodynamic stability was achieved. PAGE, LC-MS, and NMR analyses confirm high-fidelity ligation at low temperatures with yields up to 61%, directed by loop stability and stem complementarity. Four distinct RNA oligomers assemble into two hairpins in one pot without cross-ligation, demonstrating RNA DCC as a programmable strategy for equilibrium RNA assembly. This work outlines an RNase-catalyzed framework for structure-guided RNA recombination, showcasing an underexplored pathway for the ligation of folded RNA polymers.