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. 2018 Nov;24(11):1542–1554. doi: 10.1261/rna.067579.118

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© 2018 White et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 1. — Sequence and three-dimensional structure of the lead-dependent ribozyme. (A) Leadzyme secondary structure, indicating the adenosine residue (Ade-25) with a shifted pK_a of 6.5 as positively charged (Legault and Pardi 1997), the noncanonical dynamic A-G base-pairing interaction (Ade-8_°Gua-24), and the self-cleavage site (arrow). (B) Overall structure of the leadzyme as observed in solution (Hoogstraten et al. 1998). Residues flanking the cleavage site are colored red (Cyt-6) and yellow (Gua-7). (C) Expanded view of Cyt-6 and Gua-7 (colored as in B), illustrating the lack of in-line alignment for the reactive groups (dotted line connecting nucleophilic O2′, reaction center phosphorus, and leaving group O5′). (D) Schematic reaction scheme for the leadzyme, illustrating the requirement for dynamic sampling of a rare (“invisible”) conformational state ES* for self-cleavage. Structure panels were prepared with PyMol (Delano 2002).