ABSTRACT
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. Herein, we present experimental evidence of a cooperative role of the monovalent cation Na+ in catalysis that is in line with these theoretical suggestions. Our findings show a clear influence of the concentration of Na+ on the activity of the 8-17 DNAzyme when Pb2+ is used as the cofactor. Interestingly, this effect is not noticed with Mg2+, indicating a particular contribution of the monovalent ion to catalysis that would operate preferentially with Pb2+. We have also found that Na+ affects the pKa of the general base and the general acid, indicating its influence on general acid-base catalysis, already identified as part of the mechanism of the 8-17 DNAzyme. Finally, our results emphasize the need to consider Na+ carefully in the design and analysis of functional studies of catalytic DNAs and its possible specific role in their mechanisms.
