Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions

Nucleic acid enzymes require specific metal ions to be catalytically active. The functions of the metal ions having structural and catalytic roles are affected by competing cations. Large-sized tetraalkylammonium ions have a propensity to preferentially bind to single strands of RNA and DNA. Here, the large cations are used in the reactions of lead-dependent ribozyme and 17E deoxyribozyme that require divalent metal ions to cleave a nucleic acid substrate. Kinetic analysis shows that tetraalkylammonium ions influence the rate of substrate cleavage, and the effects are different depending on the nucleic acid enzymes and metal ions used. Importantly, the large cations used here increase the dependence of cleavage rates on metal ion concentration and enhance the ability of the enzyme to monitor changes in metal ion concentrations. The same effect is also observed for the metal ion concentration dependence of the thermal stability of RNA and DNA structures, indicating that the large cations affect the binding of structural metal ions. The use of large tetraalkylammonium ions provides new ways to study the importance of metal ions to nucleic acid enzymes, and also to modulate the functionality of nucleic acid enzymes.