An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

Philip C. Bevilacqua, Michael E. Harris, Joseph A. Piccirilli, Colin Gaines, Abir Ganguly, Ken Kostenbader, Şölen Ekesan, Darrin M. York

Research output: Contribution to journalReview articlepeer-review

45 Scopus citations


A predictive understanding of the mechanisms of RNA cleavage is important for the design of emerging technology built from biological and synthetic molecules that have promise for new biochemical and medicinal applications. Over the past 15 years, RNA cleavage reactions involving 2′-O-transphosphorylation have been discussed using a simplified framework introduced by Breaker that consists of four fundamental catalytic strategies (designated α, β, γ, and δ) that contribute to rate enhancement. As more detailed mechanistic data emerge, there is need for the framework to evolve and keep pace. We develop an ontology for discussion of strategies of enzymes that catalyze RNA cleavage via 2′-O-transphosphorylation that stratifies Breaker's framework into primary (1°), secondary (2°), and tertiary (3°) contributions to enable more precise interpretation of mechanism in the context of structure and bonding. Further, we point out instances where atomic-level changes give rise to changes in more than one catalytic contribution, a phenomenon we refer to as "functional blurring". We hope that this ontology will help clarify our conversations and pave the path forward toward a consensus view of these fundamental and fascinating mechanisms. The insight gained will deepen our understanding of RNA cleavage reactions catalyzed by natural protein and RNA enzymes, as well as aid in the design of new engineered DNA and synthetic enzymes.

Original languageEnglish (US)
Pages (from-to)1068-1076
Number of pages9
JournalACS chemical biology
Issue number6
StatePublished - Jun 21 2019

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Medicine


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