The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor.

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 Zn²⁺ ion solved through NMR spectroscopy. Surprisingly, it turned out to be very similar to the previously solved Pb²⁺-bound form (catalytic domain RMSD = 1.28 Å), despite a long-standing literature consensus that Pb²⁺ recruits a different DNAzyme fold than other metal ion cofactors. Our follow-up NMR investigations in the presence of other ions - Mg²⁺, Na⁺, and Pb²⁺ - 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-Pb²⁺ cofactors, including the biologically relevant Mg²⁺ ion.