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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure–Activity Relationships in Nonenzymatic Template‐Directed RNA Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Harry R. M. Aitken
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Angew Chem Int Ed Engl 2021; 60:22925-22932. [PMID: 34428345 PMCID: PMC8490286 DOI: 10.1002/anie.202109714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 11/11/2022]
Abstract
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a 3 E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Harry R M Aitken
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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Radak BK, Lee TS, Harris ME, York DM. Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. RNA (NEW YORK, N.Y.) 2015; 21:1566-1577. [PMID: 26170378 PMCID: PMC4536318 DOI: 10.1261/rna.051466.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
The hepatitis delta virus ribozyme is an efficient catalyst of RNA 2'-O-transphosphorylation and has emerged as a key experimental system for identifying and characterizing fundamental features of RNA catalysis. Recent structural and biochemical data have led to a proposed mechanistic model whereby an active site Mg(2+) ion facilitates deprotonation of the O2' nucleophile, and a protonated cytosine residue (C75) acts as an acid to donate a proton to the O5' leaving group as noted in a previous study. This model assumes that the active site Mg(2+) ion forms an inner-sphere coordination with the O2' nucleophile and a nonbridging oxygen of the scissile phosphate. These contacts, however, are not fully resolved in the crystal structure, and biochemical data are not able to unambiguously exclude other mechanistic models. In order to explore the feasibility of this model, we exhaustively mapped the free energy surfaces with different active site ion occupancies via quantum mechanical/molecular mechanical (QM/MM) simulations. We further incorporate a three-dimensional reference interaction site model for the solvated ion atmosphere that allows these calculations to consider not only the rate associated with the chemical steps, but also the probability of observing the system in the presumed active state with the Mg(2+) ion bound. The QM/MM results predict that a pathway involving metal-assisted nucleophile activation is feasible based on the rate-controlling transition state barrier departing from the presumed metal-bound active state. However, QM/MM results for a similar pathway in the absence of Mg(2+) are not consistent with experimental data, suggesting that a structural model in which the crystallographically determined Mg(2+) is simply replaced with Na(+) is likely incorrect. It should be emphasized, however, that these results hinge upon the assumption of the validity of the presumed Mg(2+)-bound starting state, which has not yet been definitively verified experimentally, nor explored in depth computationally. Thus, further experimental and theoretical study is needed such that a consensus view of the catalytic mechanism emerges.
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Affiliation(s)
- Brian K Radak
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Tai-Sung Lee
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Darrin M York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
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