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.
Subject(s)
DNA, Catalytic , Lead , Magnesium , Zinc , DNA, Catalytic/chemistry , DNA, Catalytic/metabolism , Magnesium/metabolism , Magnesium/chemistry , Zinc/metabolism , Zinc/chemistry , Lead/chemistry , Lead/metabolism , Nucleic Acid Conformation , Catalytic Domain , Models, Molecular , Sodium/metabolism , Sodium/chemistry , Metals/metabolism , Metals/chemistry , Magnetic Resonance Spectroscopy , IonsABSTRACT
We report the synthesis and characterization of a coordination architecture with a Fe(ii) center obtained by subcomponent self-assembly in water. The complex is based on very rare hemi-iminal ligands spontaneously generated from commercially available materials. The complex can be further transformed into another species by oxidation reaction of both the metal center and organic ligand.
