Atomic Force Microscopy and Anodic Voltammetry Characterization of a 49-Mer Diels-Alderase Ribozyme

Abstract

Atomic force microscopy and differential pulse voltammetry were used to characterize the interaction of small highly structured ribozymes with two carbon electrode surfaces. The ribozymes spontaneously self-assemble in two-dimensional networks that cover the entire HOPG surface uniformly. The full-length ribozyme was adsorbed to a lesser extent than a truncated RNA sequence, presumably due to the formation of a more compact overall structure. All four nucleobases composing the ribozyme could be detected by anodic voltammetry on glassy carbon electrodes, and no signals corresponding to free nucleobases were found, indicating the integrity of the ribozyme molecules. Mg2+ cations significantly reduced the adsorption of ribozymes to the surfaces, in agreement with the stabilization of this ribozyme's compact, stable, and tightly folded tertiary structure by Mg2+ ions that could prevent the hydrophobic bases from interacting with the HOPG surface. Treatment with Pb2+ ions, on the other hand, resulted in an increased adsorption of the RNA due to well-known hydrolytic cleavage. The observed dependence of anodic peak currents on different folding states of RNA may provide an attractive method to electrochemically monitor structural changes associated with RNA folding, binding, and catalysis.