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Abstract DNAzymes – synthetic enzymes made of DNA — have long attracted attention as RNA-targeting therapeutic agents. Yet, as of now, no DNAzyme-based drug has been approved, partially due to our lacking understanding of their molecular mode of action. In this work we report the solution structure of 8–17 DNAzyme bound to a Zn 2+ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb 2+ -bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb 2+ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions — Mg 2+ , Na + , and Pb 2+ – suggest that at DNAzyme concentrations used in NMR all these ions induce a similar tertiary fold. Based on these findings, we propose a model for 8–17 DNAzyme interactions with metal ions postulating the existence of only a single catalytically-active structure, yet populated to a different extent depending on the metal ion cofactor. Our results provide structural information on the 8-17 DNAzyme in presence of non-Pb 2+ cofactors, including the biologically relevant Mg 2+ ion.
Wieruszewska et al. (Fri,) studied this question.