The role of Na in catalysis by the 8-17 DNAzyme.

The 8-17 DNAzyme is the most studied deoxyribozyme in terms of its molecular mechanism; hence it has become a model system to understand the basis behind DNA catalysis. New functional studies and the recent attainment of high-resolution X-ray structures, in addition to theoretical calculations have offered a great opportunity to gain a broader comprehension of its mechanism; however many aspects are unclear yet, especially regarding the precise role of metal ions in catalysis. Recently, molecular dynamics simulations have suggested for the first time a specific and dynamical participation of Na in the mechanism through the reaction pathway, besides the roles proposed for divalent metal cofactors.

Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme.

The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for its function, is the most studied catalytic DNA in terms of its mechanism. By the end of 2017, a report of the crystal structure of the enzyme-substrate complex in the presence of Pb probed some of the previous findings and opened new questions, especially around the participation of the metal ion in the catalytic mechanism and the promiscuity exhibited by the enzyme in terms of the metal cofactor required for catalysis. In this article we explore the role of the divalent metal ion in the mechanism of the 8-17 DNAzyme as a general acid, by measuring the influence of pH over the activity of a slower variant of the enzyme in the presence of Pb.