Molecular crowding effect on metal ion binding properties of the hammerhead ribozyme

Abstract

Although metal ion is essential for the DNA and RNA folding, there are a limited number of reports describing the influence of molecular environments on the metal ion binding. Here, we investigated the binding properties of Mg(2+) and Na(+) toward the hammerhead ribozyme in the presence of PEG [poly(ethylene glycol)] as a cosolute that changes the solvent property of the reaction. PEG8000 (PEG with the average molecular weight of 8000) increased the reaction rate at lower Mg(2+) concentrations but not at higher concentrations. We also found that PEG8000 unchanged the number of Mg(2+) bound while the binding cooperativity of Na(+) in the reaction without divalent metal ion was altered. The change of Na(+) condensation by cosolute has also been reported for diffusely bound Na(+) to Watson-Crick base pairs. It is thus supposed that diffusely bound Na(+) stabilizes the ribozyme active form in the absence of divalent metal ion. This study provides insights into the RNA-metal ion interaction and the hammerhead ribozyme activity under the molecular crowding condition occurred in a cell and on biosensor devices.