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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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2
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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202207590. [PMID: 38505292 PMCID: PMC10946891 DOI: 10.1002/ange.202207590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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3
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Egger M, Bereiter R, Mair S, Micura R. Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes. Angew Chem Int Ed Engl 2022; 61:e202207590. [PMID: 35982640 PMCID: PMC9826390 DOI: 10.1002/anie.202207590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 01/11/2023]
Abstract
Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.
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Affiliation(s)
- Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Stefan Mair
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnrain 80–826020InnsbruckAustria
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Bereiter R, Renard E, Breuker K, Kreutz C, Ennifar E, Micura R. 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis. J Am Chem Soc 2022; 144:10344-10352. [PMID: 35666572 PMCID: PMC9204769 DOI: 10.1021/jacs.2c01877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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Atomic mutagenesis
is the key to advance our understanding of RNA
recognition and RNA catalysis. To this end, deazanucleosides are utilized
to evaluate the participation of specific atoms in these processes.
One of the remaining challenges is access to RNA-containing 1-deazaguanosine
(c1G). Here, we present the synthesis of this nucleoside
and its phosphoramidite, allowing first time access to c1G-modified RNA. Thermodynamic analyses revealed the base pairing
parameters for c1G-modified RNA. Furthermore, by NMR spectroscopy,
a c1G-triggered switch of Watson-Crick into Hoogsteen pairing
in HIV-2 TAR RNA was identified. Additionally, using X-ray structure
analysis, a guanine–phosphate backbone interaction affecting
RNA fold stability was characterized, and finally, the critical impact
of an active-site guanine in twister ribozyme on the phosphodiester
cleavage was revealed. Taken together, our study lays the synthetic
basis for c1G-modified RNA and demonstrates the power of
the completed deazanucleoside toolbox for RNA atomic mutagenesis needed
to achieve in-depth understanding of RNA recognition and catalysis.
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Affiliation(s)
- Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 2 Allée Conrad Roentgen, Strasbourg 67084, France
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 2 Allée Conrad Roentgen, Strasbourg 67084, France
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
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Yan J, Zhu ZL, Lee CS, Liu SH, Chou PT, Chi Y. Probing Electron Excitation Characters of Carboline-Based Bis-Tridentate Ir(III) Complexes. Molecules 2021; 26:molecules26196048. [PMID: 34641591 PMCID: PMC8512491 DOI: 10.3390/molecules26196048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
In this work, we report a series of bis-tridentate Ir(III) metal complexes, comprising a dianionic pyrazole-pyridine-phenyl tridentate chelate and a monoanionic chelate bearing a peripheral carbene and carboline coordination fragment that is linked to the central phenyl group. All these Ir(III) complexes were synthesized with an efficient one-pot and two-step method, and their emission hue was fine-tuned by variation of the substituent at the central coordination entity (i.e., pyridinyl and phenyl group) of each of the tridentate chelates. Their photophysical and electrochemical properties, thermal stabilities and electroluminescence performances are examined and discussed comprehensively. The doped devices based on [Ir(cbF)(phyz1)] (Cb1) and [Ir(cbB)(phyz1)] (Cb4) give a maximum external quantum efficiency (current efficiency) of 16.6% (55.2 cd/A) and 13.9% (43.8 cd/A), respectively. The relatively high electroluminescence efficiencies indicate that bis-tridentate Ir(III) complexes are promising candidates for OLED applications.
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Affiliation(s)
- Jie Yan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong SAR, China;
| | - Ze-Lin Zhu
- Center of Super-Diamond and Advanced Films (COSDAF) and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China;
| | - Chun-Sing Lee
- Center of Super-Diamond and Advanced Films (COSDAF) and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China;
- Correspondence: (C.-S.L.); (P.-T.C.); (Y.C.)
| | - Shih-Hung Liu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan;
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan;
- Correspondence: (C.-S.L.); (P.-T.C.); (Y.C.)
| | - Yun Chi
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong SAR, China;
- Center of Super-Diamond and Advanced Films (COSDAF) and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China;
- Correspondence: (C.-S.L.); (P.-T.C.); (Y.C.)
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Bereiter R, Himmelstoß M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R. Impact of 3-deazapurine nucleobases on RNA properties. Nucleic Acids Res 2021; 49:4281-4293. [PMID: 33856457 PMCID: PMC8096147 DOI: 10.1093/nar/gkab256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic mutagenesis studies of functional RNAs. They were the key for our current mechanistic understanding of ribosomal peptide bond formation and of phosphodiester cleavage in recently discovered small ribozymes, such as twister and pistol RNAs. Here, we present a comprehensive study on the impact of c3A and the thus far underinvestigated 3-deazaguanosine (c3G) on RNA properties. We found that these nucleosides can decrease thermodynamic stability of base pairing to a significant extent. The effects are much more pronounced for 3-deazapurine nucleosides compared to their constitutional isomers of 7-deazapurine nucleosides (c7G, c7A). We furthermore investigated base pair opening dynamics by solution NMR spectroscopy and revealed significantly enhanced imino proton exchange rates. Additionally, we solved the X-ray structure of a c3A-modified RNA and visualized the hydration pattern of the minor groove. Importantly, the characteristic water molecule that is hydrogen-bonded to the purine N3 atom and always observed in a natural double helix is lacking in the 3-deazapurine-modified counterpart. Both, the findings by NMR and X-ray crystallographic methods hence provide a rationale for the reduced pairing strength. Taken together, our comparative study is a first major step towards a comprehensive understanding of this important class of nucleoside modifications.
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Affiliation(s)
- Raphael Bereiter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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Prima DO, Madiyeva M, Burykina JV, Minyaev ME, Boiko DA, Ananikov VP. Evidence for “cocktail”-type catalysis in Buchwald–Hartwig reaction. A mechanistic study. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01601f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The mechanism of the C–N cross-coupling reaction, catalyzed by Pd/NHC, was evaluated at the molecular and nanoscale levels. The first evidence for the involvement of a “cocktail”-type system in the Buchwald–Hartwig reaction is provided.
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Affiliation(s)
- Darya O. Prima
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
| | - Malena Madiyeva
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Julia V. Burykina
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
| | - Mikhail E. Minyaev
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
| | - Daniil A. Boiko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Valentine P. Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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