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Probing General Acid Catalysis in the Hammerhead Ribozyme

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journal contribution
posted on 28.01.2009, 00:00 by Jason M. Thomas, David M. Perrin
Recent crystallographic and computational studies have provided fresh insights into the catalytic mechanism of the RNA-cleaving hammerhead ribozyme. Based on these findings, specific ribozyme functional groups have been hypothesized to act directly as the general acid and base catalysts, although the catalytic role of divalent metal cations (M2+) remains uncertain. We now report a functional characterization of the general acid catalysis mechanism and the role of an M2+ cofactor therein, for the S. mansoni hammerhead (an “extended” hammerhead ribozyme). We have compared hammerhead cleavage of substrates with natural (ribo-phosphodiester) versus bridging-5′-phosphorothioate scissile linkages, in the contexts of active site mutations and M2+ substitution. Cleavage of the natural substrate is inhibited by modification of the G8 2′-OH ribozyme residue and depends strongly upon the presence and identity of an M2+ cofactor; in contrast, cleavage of the bridging-phosphorothioate substrate is conspicuously insensitive to any of these factors. These results imply that (1) both an M2+ cofactor and the G8 2′-OH play crucial roles in hammerhead general acid catalysis and (2) the M2+ cofactor does not contribute to general acid catalysis via Lewis acid stabilization of the leaving group. General acid pKa perturbation was also demonstrated for both M2+ substitution and G8 2′-OH modification, which suggests transition state M2+ coordination of the G8 2′-OH, to lower its pKa and improve its ability to transfer a proton to the leaving group. We also report a simple method for synthesizing radiolabeled bridging-5′-phosphorothioate substrates.