Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme

ACS Catalysis vol. 9  p. 10612-10617  DOI: 10.1021/acscatal.9b02035  Published: 2019-10-27 


Abir Ganguly [ ] , Benjamin P. Weissman, Joseph A. Piccirilli, Darrin M. York [ ]

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Abstract

<p>An unique catalytic strategy was recently reported for the <em>glm</em>S ribozyme [Bingaman et al., <cite>Nat. Chem. Biol.</cite> <span class="NLM_year">2017</span>, <em>13</em>, 439&minus;445] that involves promotion of productive hydrogen bonding of the O2&prime; nucleophile to facilitate its activation. We provide broad evidence of this strategy in the hammerhead, pistol, and VS ribozymes and 8-17 DNAzyme, enabled by a functionally important divalent metal ion that interacts with the scissile phosphate and disrupts nonproductive competitive hydrogen bonding with the O2&prime; nucleophile. This strategy, designated tertiary gamma (3&deg;&gamma;) catalysis, illustrates an additional role for divalent ions in ribozyme catalysis.</p>