1
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Fang Z, Pazienza LT, Zhang J, Tam CP, Szostak JW. Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension. J Am Chem Soc 2024; 146:10632-10639. [PMID: 38579124 PMCID: PMC11027144 DOI: 10.1021/jacs.4c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/22/2024] [Accepted: 03/22/2024] [Indexed: 04/07/2024]
Abstract
Nonenzymatic template-directed RNA copying requires catalysis by divalent metal ions. The primer extension reaction involves the attack of the primer 3'-hydroxyl on the adjacent phosphate of a 5'-5'-imidazolium-bridged dinucleotide substrate. However, the nature of the interaction of the catalytic metal ion with the reaction center remains unclear. To explore the coordination of the catalytic metal ion with the imidazolium-bridged dinucleotide substrate, we examined catalysis by oxophilic and thiophilic metal ions with both diastereomers of phosphorothioate-modified substrates. We show that Mg2+ and Cd2+ exhibit opposite preferences for the two phosphorothioate substrate diastereomers, indicating a stereospecific interaction of the divalent cation with one of the nonbridging phosphorus substituents. High-resolution X-ray crystal structures of the products of primer extension with phosphorothioate substrates reveal the absolute stereochemistry of this interaction and indicate that catalysis by Mg2+ involves inner-sphere coordination with the nonbridging phosphate oxygen in the pro-SP position, while thiophilic cadmium ions interact with sulfur in the same position, as in one of the two phosphorothioate substrates. These results collectively suggest that during nonenzymatic RNA primer extension with a 5'-5'-imidazolium-bridged dinucleotide substrate the interaction of the catalytic Mg2+ ion with the pro-SP oxygen of the reactive phosphate plays a crucial role in the metal-catalyzed SN2(P) reaction.
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Affiliation(s)
- Ziyuan Fang
- Department
of Chemistry, Howard Hughes Medical Institute,
The University of Chicago, Chicago, Illinois 60637, United States
| | - Lydia T. Pazienza
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Howard Hughes Medical Institute,
Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jian Zhang
- Department
of Chemistry, Howard Hughes Medical Institute,
The University of Chicago, Chicago, Illinois 60637, United States
| | - Chun Pong Tam
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Howard Hughes Medical Institute,
Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Department
of Chemistry, Howard Hughes Medical Institute,
The University of Chicago, Chicago, Illinois 60637, United States
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2
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Zhang Y, Zhang J, Wan H, Wu Z, Xu H, Zhang Z, Wang Y, Wang J. New Insights into the Dependence of CPEB3 Ribozyme Cleavage on Mn 2+ and Mg 2. J Phys Chem Lett 2024; 15:2708-2714. [PMID: 38427973 DOI: 10.1021/acs.jpclett.3c03221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
CPEB3 ribozyme is a self-cleaving RNA that occurs naturally in mammals and requires divalent metal ions for efficient activity. Ribozymes exhibit preferences for specific metal ions, but the exact differences in the catalytic mechanisms of various metal ions on the CPEB3 ribozyme remain unclear. Our findings reveal that Mn2+ functions as a more effective cofactor for CPEB3 ribozyme catalysis compared to Mg2+, as confirmed by its stronger binding affinity to CPEB3 by EPR. Cleavage assays of CPEB3 mutants and molecular docking analyses further showed that excessive Mn2+ ions can bind to a second binding site near the catalytic site, hindering CPEB3 catalytic efficiency and contributing to the Mn2+ bell-shaped curve. These results implicate a pivotal role for the local nucleobase-Mn2+ interactions in facilitating RNA folding and modulating the directed attack of nucleophilic reagents. Our study provides new insights and experimental evidence for exploring the divalent cation dependent cleavage mechanism of the CPEB3 ribozyme.
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Affiliation(s)
- Yaoyao Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jing Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hengjia Wan
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ziwei Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huangtao Xu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Zhe Zhang
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yujuan Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- International Magnetobiology Frontier Research Center (iMFRC), Science Island, Hefei 230031, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
- International Magnetobiology Frontier Research Center (iMFRC), Science Island, Hefei 230031, China
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3
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Weissman B, Ekesan Ş, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA. Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. J Am Chem Soc 2023; 145:2830-2839. [PMID: 36706353 PMCID: PMC10112047 DOI: 10.1021/jacs.2c10079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.
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Affiliation(s)
- Benjamin Weissman
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hsuan-Chun Lin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shahbaz Gardezi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Nan-Sheng Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
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4
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Hunsicker-Wang LM, Vogt MJ, Hoogstraten CG, Cosper NJ, Davenport AM, Hendon CH, Scott RA, Britt RD, DeRose VJ. Spectroscopic characterization of Mn2+ and Cd2+ coordination to phosphorothioates in the conserved A9 metal site of the hammerhead ribozyme. J Inorg Biochem 2022; 230:111754. [DOI: 10.1016/j.jinorgbio.2022.111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
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5
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Saran R, Huang Z, Liu J. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Zhang Z, Vögele J, Mráziková K, Kruse H, Cang X, Wöhnert J, Krepl M, Šponer J. Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. J Phys Chem B 2021; 125:825-840. [PMID: 33467852 DOI: 10.1021/acs.jpcb.0c10192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single nonbridging oxygen of the phosphate is replaced with a sulfur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as a tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present molecular dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn: an H-bond, an anion-π interaction, and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulfur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases the dispersion component of the anion-π stacking. The sulfur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to the unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulfur parameters and provide suggestions for improving the force-field performance.
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Affiliation(s)
- Zhengyue Zhang
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Faculty of Science, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic
| | - Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Klaudia Mráziková
- Faculty of Science, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Xiaohui Cang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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7
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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8
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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9
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Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R. Crucial Roles of Two Hydrated Mg
2+
Ions in Reaction Catalysis of the Pistol Ribozyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Marianna Teplova
- Structural Biology ProgramMemorial Sloan-Kettering Cancer Center New York New York 10065 USA
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
| | - Michaela Egger
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
| | - Aiming Ren
- Life Sciences InstituteZhejiang University Hangzhou Zhejiang 310058 China
| | - Dinshaw J. Patel
- Structural Biology ProgramMemorial Sloan-Kettering Cancer Center New York New York 10065 USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80–82 6020 Innsbruck Austria
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10
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Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R. Crucial Roles of Two Hydrated Mg 2+ Ions in Reaction Catalysis of the Pistol Ribozyme. Angew Chem Int Ed Engl 2020; 59:2837-2843. [PMID: 31804735 PMCID: PMC7027511 DOI: 10.1002/anie.201912522] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 12/19/2022]
Abstract
Pistol ribozymes constitute a new class of small self‐cleaving RNAs. Crystal structures have been solved, providing three‐dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre‐catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg2+ ion remains innersphere‐coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg2+ ion that approaches the scissile phosphate from its binding site in the pre‐cleavage state to reach out for water‐mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg2+ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme‐catalyzed backbone cleavage.
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Affiliation(s)
- Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Michaela Egger
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80-82, 6020, Innsbruck, Austria
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11
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Cepeda-Plaza M, Peracchi A. Insights into DNA catalysis from structural and functional studies of the 8-17 DNAzyme. Org Biomol Chem 2020; 18:1697-1709. [DOI: 10.1039/c9ob02453k] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The review examines functional knowledge gathered over two decades of research on the 8-17 DNAzyme, focusing on three aspects: the structural requirements for catalysis, the role of metal ions and the participation of general acid-base catalysis.
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Affiliation(s)
| | - Alessio Peracchi
- Department of Chemistry
- Life Sciences and Environmental Sustainability
- University of Parma
- Parma
- Italy
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12
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Ma L, Kartik S, Liu B, Liu J. From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation. Nucleic Acids Res 2019; 47:8154-8162. [PMID: 31276580 PMCID: PMC6736077 DOI: 10.1093/nar/gkz578] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Recently, a few Na+-specific RNA-cleaving DNAzymes were reported, where nucleobases are likely to play critical roles in catalysis. The NaA43 and NaH1 DNAzymes share the same 16-nt Na+-binding motif, but differ in one or two nucleotides in a small catalytic loop. Nevertheless, they display an opposite pH-dependency, implicating distinct catalytic mechanisms. In this work, rational mutation studies locate a catalytic adenine residue, A22, in NaH1, while previous studies found a guanine (G23) to be important for the catalysis of NaA43. Mutation with pKa-perturbed analogs, such as 2-aminopurine (∼3.8), 2,6-diaminopurine (∼5.6) and hypoxanthine (∼8.7) affected the overall reaction rate. Therefore, we propose that the N1 position of G23 (pKa ∼6.6) in NaA43 functions as a general base, while that of A22 (pKa ∼6.3) in NaH1 as a general acid. Further experiments with base analogs and a phosphorothioate-modified substrate suggest that the exocyclic amine in A22 and both of the non-bridging oxygens at the scissile phosphate are important for catalysis for NaH1. This is an interesting example where single point mutations can change the mechanism of cleavage from general base to general acid, and it can also explain this Na+-dependent DNAzyme scaffold being sensitive to a broad range of metal ions and molecules.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Sanjana Kartik
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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13
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Maurel MC, Leclerc F, Hervé G. Ribozyme Chemistry: To Be or Not To Be under High Pressure. Chem Rev 2019; 120:4898-4918. [DOI: 10.1021/acs.chemrev.9b00457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle, EPHE, F-75005 Paris, France
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France
| | - Guy Hervé
- Laboratoire BIOSIPE, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Campus Pierre et Marie Curie, F-75005 Paris, France
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14
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Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC. Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study. Nucleic Acids Res 2019; 47:29-42. [PMID: 30462314 PMCID: PMC6326823 DOI: 10.1093/nar/gky1118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 10/24/2018] [Indexed: 01/02/2023] Open
Abstract
Design of RNA sequences that adopt functional folds establishes principles of RNA folding and applications in biotechnology. Inverse folding for RNAs, which allows computational design of sequences that adopt specific structures, can be utilized for unveiling RNA functions and developing genetic tools in synthetic biology. Although many algorithms for inverse RNA folding have been developed, the pseudoknot, which plays a key role in folding of ribozymes and riboswitches, is not addressed in most algorithms. For the few algorithms that attempt to predict pseudoknot-containing ribozymes, self-cleavage activity has not been tested. Herein, we design double-pseudoknot HDV ribozymes using an inverse RNA folding algorithm and test their kinetic mechanisms experimentally. More than 90% of the positively designed ribozymes possess self-cleaving activity, whereas more than 70% of negative control ribozymes, which are predicted to fold to the necessary structure but with low fidelity, do not possess it. Kinetic and mutation analyses reveal that these RNAs cleave site-specifically and with the same mechanism as the WT ribozyme. Most ribozymes react just 50- to 80-fold slower than the WT ribozyme, and this rate can be improved to near WT by modification of a junction. Thus, fast-cleaving functional ribozymes with multiple pseudoknots can be designed computationally.
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Affiliation(s)
- Ryota Yamagami
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mohammad Kayedkhordeh
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, NY 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, NY 14642, USA.,Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, New York, NY 14642, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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15
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Obenchain DA, Spada L, Alessandrini S, Rampino S, Herbers S, Tasinato N, Mendolicchio M, Kraus P, Gauss J, Puzzarini C, Grabow JU, Barone V. Unveiling the Sulfur-Sulfur Bridge: Accurate Structural and Energetic Characterization of a Homochalcogen Intermolecular Bond. Angew Chem Int Ed Engl 2018; 57:15822-15826. [PMID: 30303600 DOI: 10.1002/anie.201810637] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Indexed: 11/11/2022]
Abstract
By combining rotational spectroscopy in supersonic expansion with the capability of state-of-the-art quantum-chemical computations in accurately determining structural and energetic properties, the genuine nature of a sulfur-sulfur chalcogen bond between dimethyl sulfide and sulfur dioxide has been unveiled in a gas-jet environment free from collision, solvent and matrix perturbations. A SAPT analysis pointed out that electrostatic S⋅⋅⋅S interactions play the dominant role in determining the stability of the complex, largely overcoming dispersion and C-H⋅⋅⋅O hydrogen-bond contributions. Indeed, in agreement with the analysis of the quadrupole-coupling constants and of the methyl internal rotation barrier, the NBO and NOCV/CD approaches show a marked charge transfer between the sulfur atoms. Based on the assignment of the rotational spectra for 7 isotopologues, an accurate semi-experimental equilibrium structure for the heavy-atom backbone of the molecular complex has been determined, which is characterized by a S⋅⋅⋅S distance (2.947(3) Å) well below the sum of van der Waals radii.
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Affiliation(s)
- Daniel A Obenchain
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Lorenzo Spada
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | | | - Sergio Rampino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Sven Herbers
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | | | - Peter Kraus
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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16
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Unveiling the Sulfur-Sulfur Bridge: Accurate Structural and Energetic Characterization of a Homochalcogen Intermolecular Bond. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Jimmy Huang PJ, Moon WJ, Liu J. Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA. Biochemistry 2018; 58:422-429. [PMID: 30272443 DOI: 10.1021/acs.biochem.8b00900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I2) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the Rp and Sp stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I2 also required Na+, consistent with the property of Ce13d and confirming the similar role of I2 as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I2 detection. With EDTA for masking metal ions, I2 was selectively detected down to 4.7 nM. Oxidation of I- with Fe3+ produced I2 in situ, allowing detection of Fe3+ down to 78 nM. By harnessing nonelectrostatic interactions, such as the I2/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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18
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Lu J, Koo SC, Weissman BP, Harris ME, Li NS, Piccirilli JA. Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State. Biochemistry 2018; 57:3465-3472. [PMID: 29733591 DOI: 10.1021/acs.biochem.8b00031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p Ka, consistent with the expected electron-withdrawing effect. In HDV ribozyme reactions, we observed that the RNA substrates undergo transphosphorylation relatively efficiently, suggesting that the conformational constraints imposed by a ribofuranose ring are not strictly required for ribozyme catalysis. In contrast to the nonenzymatic reactions, however, substrate fluorination modestly increases the ribozyme reaction rate, consistent with a mechanism in which (1) the 2'-hydroxyl nucleophile exists predominantly in its neutral, protonated form in the ground state and (2) the 2'-hydroxyl bears some negative charge in the rate-determining step, consistent with a transition state in which the extent of 2'-OH deprotonation exceeds the extent of P-O bond formation.
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Affiliation(s)
- Jun Lu
- Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Selene C Koo
- Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Benjamin P Weissman
- Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Michael E Harris
- Department of Chemistry , University of Florida , 214 Leigh Hall , Gainesville , Florida 32611 , United States
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
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19
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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20
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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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21
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Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel DJ, Micura R, Ren A. Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme. Nat Commun 2017; 8:1180. [PMID: 29081514 PMCID: PMC5660989 DOI: 10.1038/s41467-017-01276-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/01/2017] [Indexed: 11/13/2022] Open
Abstract
Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62–A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme. Twister-sister is a self-cleaving ribozyme. Here, the authors report the 2.0 Å crystal structure of the four-way junctional twister-sister ribozyme in the pre-catalytic state and discuss mechanistic implications based on their mutagenesis experiments and comparisons with other ribozyme structures.
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Affiliation(s)
- Luqian Zheng
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry, Leopold Franzens University, A6020, Innsbruck, Austria
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ye Zhang
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jinbiao Ma
- Department of Biochemistry, State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Collaborative Innovation Centre of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold Franzens University, A6020, Innsbruck, Austria.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China. .,Collaborative Innovation Centre of Genetics and Development, Fudan University, 200438, Shanghai, China.
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22
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Zhou W, Saran R, Ding J, Liu J. Two Completely Different Mechanisms for Highly Specific Na + Recognition by DNAzymes. Chembiochem 2017; 18:1828-1835. [PMID: 28658518 DOI: 10.1002/cbic.201700184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Indexed: 02/06/2023]
Abstract
Our view of the interaction between Na+ and nucleic acids was changed by a few recently discovered Na+ -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na+ binding. Mutation studies indicate that they have different sequence requirements. Phosphorothioate (PS) substitution at the scissile phosphate drops the activity of EtNa 140-fold, and it cannot be rescued by thiophilic Cd2+ or Mn2+ , whereas the activity of PS-modified Ce13d can be rescued. Na+ -dependent activity assays indicate that two Na+ ions bind cooperatively in EtNa, and each Na+ likely interacts with a nonbridging oxygen atom in the scissile phosphate, whereas Ce13d binds only one Na+ ion in a well-defined Na+ aptamer, and this Na+ ion does not directly interact with the scissile phosphate. Both DNAzymes display a normal pH-rate profile, with a single deprotonation reaction required for catalysis. For EtNa, Na+ fails to protect the conserved nucleotides from dimethyl sulfate attack, and no specific Na+ binding is detected by 2-aminopurine fluorescence, both of which are different from those observed for Ce13d. This work suggests that EtNa binds Na+ mainly through its scissile phosphate without significant involvement of the nucleotides in the enzyme strand, whereas Ce13d has a well-defined aptamer for Na+ binding. Therefore, DNA has at least two distinct ways to achieve highly selective Na+ binding.
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Affiliation(s)
- Wenhu Zhou
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Runjhun Saran
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Jinsong Ding
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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23
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Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence. Biochimie 2017; 145:145-150. [PMID: 28711684 DOI: 10.1016/j.biochi.2017.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/04/2017] [Indexed: 12/28/2022]
Abstract
The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag+ ions for activity. The Ag10c contains a well-defined Ag+ binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag+. The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand, one at a time. Ag+-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding. The measured Kd at the A9 position was 18 μM Ag+ with a Hill coefficient of 2.17, similar to those obtained from the previous cleavage activity based assays. However, labeling a 2AP at the A2 position inhibited the activity and folding. Compared to other metal ions, Ag+ has a unique sigmoidal folding profile indicative of multiple silver binding cooperatively. This suggests that Ag+ can induce a local folding in the enzyme loop and this folding is important for activity. This study provides important biophysical insights into this new DNAzyme, suggesting the possibility of designing folding-based biosensors for Ag+.
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24
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Saran R, Kleinke K, Zhou W, Yu T, Liu J. A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity. Biochemistry 2017; 56:1955-1962. [PMID: 28345892 DOI: 10.1021/acs.biochem.6b01131] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag+-specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag+. Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag+ binding is unrelated to C-Ag+-C interaction. Its activity is enhanced by increasing Na+ concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li+ > Na+ > K+. Ag10c binds one Na+ ion and two Ag+ ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na+ interacts with the pro-Rp oxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag+ ions. Therefore, Ag+ exerts its function allosterically, while the scissile phosphate interacts with Na+, Li+, Na+, or Mg2+. This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag+ aptamer.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Kimberly Kleinke
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Wenhu Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Tianmeng Yu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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25
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Bingaman JL, Messina KJ, Bevilacqua PC. Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics. Methods 2017; 120:125-134. [PMID: 28315484 DOI: 10.1016/j.ymeth.2017.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/28/2017] [Accepted: 03/10/2017] [Indexed: 11/24/2022] Open
Abstract
Reaction kinetics on the millisecond timescale pervade the protein and RNA fields. To study such reactions, investigators often perturb the system with abiological solution conditions or substrates in order to slow the rate to timescales accessible by hand mixing; however, such perturbations can change the rate-limiting step and obscure key folding and chemical steps that are found under biological conditions. Mechanical methods for collecting data on the millisecond timescale, which allow these perturbations to be avoided, have been developed over the last few decades. These methods are relatively simple and can be conducted on affordable and commercially available instruments. Here, we focus on using the rapid quench-flow technique to study the fast reaction kinetics of RNA enzymes, or ribozymes, which often react on the millisecond timescale under biological conditions. Rapid quench of ribozymes is completely parallel to the familiar hand-mixing approach, including the use of radiolabeled RNAs and fractionation of reactions on polyacrylamide gels. We provide tips on addressing and preventing common problems that can arise with the rapid-quench technique. Guidance is also offered on ensuring the ribozyme is properly folded and fast-reacting. We hope that this article will facilitate the broader use of rapid-quench instrumentation to study fast-reacting ribozymes under biological reaction conditions.
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Affiliation(s)
- Jamie L Bingaman
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Kyle J Messina
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States.
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26
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Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes. Sci Rep 2016; 6:28179. [PMID: 27302490 PMCID: PMC4908430 DOI: 10.1038/srep28179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/31/2016] [Indexed: 11/09/2022] Open
Abstract
Self-cleaving ribozymes fold into intricate structures, which orient active site groups into catalytically competent conformations. Most ribozyme families have distinct catalytic cores stabilized by tertiary interactions between domains peripheral to those cores. We show that large hepatitis delta virus (HDV)-like ribozymes are activated by peripheral domains that bring two helical segments, P1 and P2, into proximity – a “pinch” that results in rate acceleration by almost three orders of magnitude. Kinetic analysis of ribozymes with systematically altered length and stability of the peripheral domain revealed that about one third of its free energy of formation is used to lower an activation energy barrier, likely related to a rate-limiting conformational change leading to the pre-catalytic state. These findings provide a quantitative view of enzyme regulation by peripheral domains and may shed light on the energetics of allosteric regulation.
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27
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Skilandat M, Rowinska-Zyrek M, Sigel RKO. Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme. RNA (NEW YORK, N.Y.) 2016; 22:750-763. [PMID: 26966151 PMCID: PMC4836649 DOI: 10.1261/rna.053843.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
Most of today's knowledge of the CPEB3 ribozyme, one of the few small self-cleaving ribozymes known to occur in humans, is based on comparative studies with the hepatitis delta virus (HDV) ribozyme, which is highly similar in cleavage mechanism and probably also in structure. Here we present detailed NMR studies of the CPEB3 ribozyme in order to verify the formation of the predicted nested double pseudoknot in solution. In particular, the influence of Mg(2+), the ribozyme's crucial cofactor, on the CPEB3 structure is investigated. NMR titrations, Tb(3+)-induced cleavage, as well as stoichiometry determination by hydroxyquinoline sulfonic acid fluorescence and equilibrium dialysis, are used to evaluate the number, location, and binding mode of Mg(2+)ions. Up to eight Mg(2+)ions interact site-specifically with the ribozyme, four of which are bound with high affinity. The global fold of the CPEB3 ribozyme, encompassing 80%-90% of the predicted base pairs, is formed in the presence of monovalent ions alone. Low millimolar concentrations of Mg(2+)promote a more compact fold and lead to the formation of additional structures in the core of the ribozyme, which contains the inner small pseudoknot and the active site. Several Mg(2+)binding sites, which are important for the functional fold, appear to be located in corresponding locations in the HDV and CPEB3 ribozyme, demonstrating the particular relevance of Mg(2+)for the nested double pseudoknot structure.
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Affiliation(s)
- Miriam Skilandat
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Roland K O Sigel
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
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28
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Huang PJJ, Vazin M, Liu J. In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage. Biochemistry 2016; 55:2518-25. [PMID: 27054549 DOI: 10.1021/acs.biochem.6b00132] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trivalent lanthanide ions (Ln(3+)) were recently employed to select RNA-cleaving DNAzymes, and three new DNAzymes have been reported so far. In this work, dysprosium (Dy(3+)) was used with a library containing 50 random nucleotides. After six rounds of in vitro selection, a new DNAzyme named Dy10a was obtained and characterized. Dy10a has a bulged hairpin structure cleaving a RNA/DNA chimeric substrate. Dy10a is highly active in the presence of the five Ln(3+) ions in the middle of the lanthanide series (Sm(3+), Eu(3+), Gd(3+), Tb(3+), and Dy(3+)), while its activity descends on the two sides. The cleavage rate reaches 0.6 min(-1) at pH 6 with just 200 nM Sm(3+), which is the fastest among all known Ln(3+)-dependent enzymes. Dy10a binds two Ln(3+) ions cooperatively. When a phosphorothioate (PS) modification is introduced at the cleavage junction, the activity decreases by >2500-fold for both the Rp and Sp diastereomers, and thiophilic Cd(2+) cannot rescue the activity. The pH-rate profile has a slope of 0.37 between pH 4.2 and 5.2, and the slope was even lower at higher pH. On the basis of these data, a model of metal binding is proposed. Finally, a catalytic beacon sensor that can detect Ho(3+) down to 1.7 nM is constructed.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
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29
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Huang PJJ, Liu J. An Ultrasensitive Light-up Cu(2+) Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate. Anal Chem 2016; 88:3341-7. [PMID: 26857405 DOI: 10.1021/acs.analchem.5b04904] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cu(2+) is a very important metal ion in biology, environmental science, and industry. Developing biosensors for Cu(2+) is a key topic in analytical chemistry. DNAzyme-based sensors are highly attractive for their excellent sensitivity, stability, and programmability. In the past decade, a few Cu(2+) biosensors were reported using DNAzymes with DNA cleavage or DNA ligation activity. However, they require unstable ascorbate or imidazole activation. So far, no RNA-cleaving DNAzymes specific for Cu(2+) are known. In this work, a phosphorothioate (PS) RNA-containing library was used for in vitro selection, and a few new Cu(2+)-specific RNA-cleaving DNAzymes were isolated. Among them, a DNAzyme named PSCu10 was studied further. It has only eight nucleotides in the enzyme loop with a cleavage rate of 0.1 min(-1) in the presence of 1 μM Cu(2+) at pH 6.0 (its optimal pH). Between the two diastereomers of the PS RNA chiral center, the R(p) isomer is 37 times more active than the S(p) one. Among the other divalent metal ions, only Hg(2+) can cleave the substrate due to its extremely high thiophilicity. A catalytic beacon sensor was designed with a detection limit of 1.6 nM Cu(2+) and extremely high selectivity. PSCu10 is specific for Cu(2+), and it has no cleavage in the presence of ascorbate, which reduces Cu(2+) to Cu(+).
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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30
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Lee TS, Radak BK, Harris ME, York DM. A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 2016; 6:1853-1869. [PMID: 27774349 DOI: 10.1021/acscatal.5b02158] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path. Building upon recent crystallographic data, our results provide a dynamic model of the HDVr reaction mechanism involving a conformational switch between multiple non-canonical G25:U20 base pair conformations in the active site. These local nucleobase dynamics play an important role in catalysis by modulating the metal binding environments of two Mg2+ ions that support catalysis at different steps of the reaction pathway. The first ion plays a structural role by inducing a base pair flip necessary to obtain the catalytic fold in which C75 moves towards to the scissile phosphate in the active site. Ejection of this ion then permits a second ion to bind elsewhere in the active site and facilitate nucleophile activation. The simulations collectively describe a mechanistic scenario that is consistent with currently available experimental data from crystallography, phosphorothioate substitutions, and chemical probing studies. Avenues for further experimental verification are suggested.
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Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Brian K. Radak
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
- Argonne National Laboratory, Argonne, Illinois 60439, United State
| | - Michael E. Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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31
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Panteva MT, Giambaşu GM, York DM. Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids. J Phys Chem B 2015; 119:15460-70. [PMID: 26583536 DOI: 10.1021/acs.jpcb.5b10423] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Divalent metal ions are of fundamental importance to the function and folding of nucleic acids. Divalent metal ion-nucleic acid interactions are complex in nature and include both territorial and site specific binding. Commonly employed nonbonded divalent ion models, however, are often parametrized against bulk ion properties and are subsequently utilized in biomolecular simulations without considering any data related to interactions at specific nucleic acid sites. Previously, we assessed the ability of 17 different nonbonded Mg(2+) ion models to reproduce different properties of Mg(2+) in aqueous solution including radial distribution functions, solvation free energies, water exchange rates, and translational diffusion coefficients. In the present work, we depart from the recently developed 12-6-4 potential models for divalent metal ions developed by Li and Merz and tune the pairwise parameters for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) binding dimethyl phosphate, adenosine, and guanosine in order to reproduce experimental site specific binding free energies derived from potentiometric pH titration data. We further apply these parameters to investigate a metal ion migration previously proposed to occur during the catalytic reaction of the hammerhead ribozyme. The new parameters are shown to be accurate and balanced for nucleic acid binding in comparison with available experimental data and provide an important tool for molecular dynamics and free energy simulations of nucleic acids where these ions may exhibit different binding modes.
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Affiliation(s)
- Maria T Panteva
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States
| | - George M Giambaşu
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute and Department of Chemistry & Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States
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32
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Li S, Lünse CE, Harris KA, Breaker RR. Biochemical analysis of hatchet self-cleaving ribozymes. RNA (NEW YORK, N.Y.) 2015; 21:1845-1851. [PMID: 26385510 PMCID: PMC4604424 DOI: 10.1261/rna.052522.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/22/2015] [Indexed: 06/01/2023]
Abstract
Hatchet RNAs are members of a novel self-cleaving ribozyme class that was recently discovered by using a bioinformatics search strategy. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides interspersed among bulges linking four base-paired substructures. A representative hatchet ribozyme from a metagenomic source requires divalent ions such as Mg(2+) to promote RNA strand scission with a maximum rate constant of ∼4 min(-1). As with all other small self-cleaving ribozymes discovered to date, hatchet ribozymes employ a general mechanism for catalysis involving the nucleophilic attack of a ribose 2'-oxygen atom on an adjacent phosphorus center. Kinetic characteristics of the reaction demonstrate that members of this ribozyme class have an essential requirement for divalent metal ions and that they might have a complex active site that employs multiple catalytic strategies to accelerate RNA cleavage by internal phosphoester transfer.
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Affiliation(s)
- Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Christina E Lünse
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Kimberly A Harris
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA
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33
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Košutić M, Neuner S, Ren A, Flür S, Wunderlich C, Mairhofer E, Vušurović N, Seikowski J, Breuker K, Höbartner C, Patel DJ, Kreutz C, Micura R. A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class. Angew Chem Int Ed Engl 2015; 54:15128-15133. [PMID: 26473980 DOI: 10.1002/anie.201506601] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/02/2015] [Indexed: 12/16/2022]
Abstract
Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a (13) C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg(2+) ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn(2+) or Cd(2+) accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X-ray structure of a 2'-OCH3 -U5 modified twister ribozyme.
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Affiliation(s)
- Marija Košutić
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Sandro Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Aiming Ren
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, NY, New York 10065 (USA)
| | - Sara Flür
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Nikola Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Jan Seikowski
- Max Planck Institute of Biophysical Chemistry and Institute of Organic and Biomolecular Chemistry, Georg August University of Göttingen, 37077 Göttingen (Germany)
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Claudia Höbartner
- Max Planck Institute of Biophysical Chemistry and Institute of Organic and Biomolecular Chemistry, Georg August University of Göttingen, 37077 Göttingen (Germany)
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, NY, New York 10065 (USA)
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Leopold-Franzens University, Innrain 80-82, 6020 Innsbruck (Austria)
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34
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Košutić M, Neuner S, Ren A, Flür S, Wunderlich C, Mairhofer E, Vušurović N, Seikowski J, Breuker K, Höbartner C, Patel DJ, Kreutz C, Micura R. A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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35
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Huang PJJ, Vazin M, Liu J. Desulfurization Activated Phosphorothioate DNAzyme for the Detection of Thallium. Anal Chem 2015; 87:10443-9. [PMID: 26393365 DOI: 10.1021/acs.analchem.5b02568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Thallium (Tl) is a highly toxic heavy metal situated between mercury and lead in the periodic table. While its neighbors have been thoroughly studied for DNA-based sensing, little is known about thallium detection. In this work, in vitro selection of RNA-cleaving DNAzymes is carried out using Tl(3+) as the target metal cofactor. Both normal DNA and phosphorothioate (PS)-modified DNA are tested for this purpose. While no Tl(3+)-dependent DNAzymes are obtained, a DNA oligonucleotide containing a single PS-modified RNA nucleotide is found to cleave by ∼7% by Tl(3+) at the RNA position. The remaining 93% are desulfurized. By hybridization of this PS-modified oligonucleotide with the Tm7 DNAzyme, the cleavage yield increases to ∼40% in the presence of Tl(3+) and Er(3+). Tm7 is an Er(3+)-dependent RNA-cleaving DNAzyme. It cleaves only the normal substrate but is completely inactive using the PS-modified substrate. Tl(3+) desulfurizes the PS substrate to the normal substrate to be cleaved by Tm7 and Er(3+). This system is engineered into a catalytic beacon for Tl(3+) with a detection limit of 1.5 nM, which is below its maximal contamination limit defined by the U.S. Environmental Protection Agency (10 nM).
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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36
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Vazin M, Huang PJJ, Matuszek Ż, Liu J. Biochemical Characterization of a Lanthanide-Dependent DNAzyme with Normal and Phosphorothioate-Modified Substrates. Biochemistry 2015; 54:6132-8. [DOI: 10.1021/acs.biochem.5b00691] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mahsa Vazin
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Po-Jung Jimmy Huang
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Żaneta Matuszek
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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37
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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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38
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Carvalho ATP, O'Donoghue AC, Hodgson DRW, Kamerlin SCL. Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge. Org Biomol Chem 2015; 13:5391-8. [PMID: 25797408 PMCID: PMC4425225 DOI: 10.1039/c5ob00309a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/12/2015] [Indexed: 01/19/2023]
Abstract
Recent experimental work (J. Org. Chem., 2012, 77, 5829) demonstrated pronounced differences in measured thio-effects for the hydrolysis of (thio)phosphodichloridates by water and hydroxide nucleophiles. In the present work, we have performed detailed quantum chemical calculations of these reactions, with the aim of rationalizing the molecular bases for this discrimination. The calculations highlight the interplay between nucleophile charge and transition state solvation in SN2(P) mechanisms as the basis of these differences, rather than a change in mechanism.
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Affiliation(s)
- Alexandra T. P. Carvalho
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , SE-751 24 , Uppsala , Sweden .
| | - AnnMarie C. O'Donoghue
- Biophysical Sciences Institute , Durham University , South Road , Durham DH1 3LE , UK
- Department of Chemistry , Durham University , South Road , Durham DH1 3LE , UK
| | - David R. W. Hodgson
- Biophysical Sciences Institute , Durham University , South Road , Durham DH1 3LE , UK
- Department of Chemistry , Durham University , South Road , Durham DH1 3LE , UK
| | - Shina C. L. Kamerlin
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , SE-751 24 , Uppsala , Sweden .
- Biophysical Sciences Institute , Durham University , South Road , Durham DH1 3LE , UK
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39
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Huang PJJ, Liu J. Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing. Nucleic Acids Res 2015; 43:6125-33. [PMID: 25990730 PMCID: PMC4499143 DOI: 10.1093/nar/gkv519] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/07/2015] [Indexed: 11/30/2022] Open
Abstract
In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd2+ due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA, a single phosphorothioate modification might boost its affinity for thiophilic metals without complicating the selection process or using bases that are not commercially available. In this work, the first such in vitro selection for Cd2+ is reported. After using a blocking DNA and negative selections to rationally direct the library outcome, a highly specific DNAzyme with only 12 nucleotides in the catalytic loop is isolated. This DNAzyme has a cleavage rate of 0.12 min−1 with 10 μM Cd2+ at pH 6.0. The Rp form of the substrate is cleaved ∼100-fold faster than the Sp form. The DNAzyme is most active with Cd2+ and its selectivity against Zn2+ is over 100 000-fold. Its application in detecting Cd2+ is also demonstrated. The idea of introducing single modifications in the fixed region expands the scope of DNA/metal interactions with minimal perturbation of DNA structure and property.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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40
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Thaplyal P, Ganguly A, Hammes-Schiffer S, Bevilacqua PC. Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density. Biochemistry 2015; 54:2160-75. [PMID: 25799319 PMCID: PMC4824481 DOI: 10.1021/acs.biochem.5b00190] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The
hepatitis delta virus (HDV) ribozyme self-cleaves in the presence
of a wide range of monovalent and divalent ions. Prior theoretical
studies provided evidence that self-cleavage proceeds via a concerted
or stepwise pathway, with the outcome dictated by the valency of the
metal ion. In the present study, we measure stereospecific thio effects
at the nonbridging oxygens of the scissile phosphate under a wide
range of experimental conditions, including varying concentrations
of diverse monovalent and divalent ions, and combine these with quantum
mechanical/molecular mechanical (QM/MM) free energy simulations on
the stereospecific thio substrates. The RP substrate gives large normal thio effects in the presence of all
monovalent ions. The SP substrate also
gives normal or no thio effects, but only for smaller monovalent and
divalent cations, such as Li+, Mg2+, Ca2+, and Sr2+; in contrast, sizable inverse thio
effects are found for larger monovalent and divalent cations, including
Na+, K+, NH4+, and Ba2+. Proton inventories are found to be unity in the presence
of the larger monovalent and divalent ions, but two in the presence
of Mg2+. Additionally, rate–pH profiles are inverted
for the low charge density ions, and only imidazole plus ammonium
ions rescue an inactive C75Δ variant in the absence of Mg2+. Results from the thio effect experiments, rate–pH
profiles, proton inventories, and ammonium/imidazole rescue experiments,
combined with QM/MM free energy simulations, support a change in the
mechanism of HDV ribozyme self-cleavage from concerted and metal ion-stabilized
to stepwise and proton transfer-stabilized as the charge density of
the metal ion decreases.
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Affiliation(s)
- Pallavi Thaplyal
- †Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Abir Ganguly
- ‡Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- ‡Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Philip C Bevilacqua
- †Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Abstract
Lanthanides represent a group of very important but challenging analytes for biosensor development. These 15 elements are very similar in their chemical properties. So far, limited success has been realized using the rational ligand design approach. My laboratory has successfully accomplished the task of carrying out combinatorial selection to isolate lanthanide-dependent RNA-cleaving DNAzymes. We report two new DNAzymes, each discovered in a different selection condition and both are highly specific to lanthanides. When both DNAzymes are used together, it is possible to identify the last few heavy lanthanides. Upon introducing a phosphorothioate modification, one of the abovementioned DNAzymes becomes highly active with many toxic heavy metals. With the selection of more DNAzymes with different activity patterns cross the lanthanide series, a sensor array might be produced for identifying each ion. This article is a minireview of the current developments on this topic and some of the historical aspects. It reflects the main content of the Fred Beamish Award presentation delivered at the 2014 Canadian Society for Chemistry Conference in Vancouver. Future directions in this area are also discussed.
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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Mlýnský V, Walter NG, Šponer J, Otyepka M, Banáš P. The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys Chem Chem Phys 2015; 17:670-9. [PMID: 25412464 PMCID: PMC4256098 DOI: 10.1039/c4cp03857f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H(+) in the active site, which acts as the general acid, and a partially hydrated Mg(2+) ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with a distinct position and coordination of the catalytically important active site Mg(2+) ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal mol(-1), indicating that the specific position of the Mg(2+) ion in the active site is predicted to strongly affect the kinetics of self-cleavage. The deprotonation of the U-1(2'-OH) nucleophile and the nucleophilic attack of the resulting U-1(2'-O(-)) on the scissile phosphodiester are found to be separate steps, as deprotonation precedes the nucleophilic attack. This sequential mechanism of the HDV ribozyme differs from the concerted nucleophilic activation and attack suggested for the hairpin ribozyme. We estimate the pKa of the U-1(2'-OH) group to range from 8.8 to 11.2, suggesting that it is lowered by several units from that of a free ribose, comparable to and most likely smaller than the pKa of the solvated active site Mg(2+) ion. Our results thus support the notion that the structure of the HDV ribozyme, and particularly the positioning of the active site Mg(2+) ion, facilitate deprotonation and activation of the 2'-OH nucleophile.
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Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic.
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Huang PJJ, Vazin M, Matuszek Ż, Liu J. A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect. Nucleic Acids Res 2014; 43:461-9. [PMID: 25488814 PMCID: PMC4288186 DOI: 10.1093/nar/gku1296] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In vitro selection of RNA-cleaving DNAzymes was performed using three heavy lanthanide ions (Ln3+): Ho3+, Er3+ and Tm3+. The resulting sequences were aligned together and about half of the library contained a new family of DNAzyme. These DNAzymes have a simple loop structure, and they are active only with the seven heavy Ln3+. Among the tested non-lanthanide ions, only Y3+ induced cleavage and even Pb2+ failed to cleave, suggesting a very high specificity. A representative DNAzyme, Tm7, has a sigmoidal metal binding curve with a Hill coefficient of 3, indicating that three metal ions are involved in the catalytic step. Its pH-rate profile has a slope of 1, suggesting a single deprotonation step is involved in the rate-limiting step. Tm7 has a cleavage rate of 1.6 min−1 at pH 7.8 with 10 μM Er3+. Phosphorothioate substitution at the cleavage junction completely inhibits the activity, which cannot be rescued by Cd2+ alone, or by a mixture of Er3+ and Cd2+, suggesting that two interacting metal ions are involved in direct bonding to both non-bridging oxygen atoms. A new model involving three lanthanide ions is proposed based on this study. A biosensor is engineered using Tm7 to detect Dy3+ down to 14 nM.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Żaneta Matuszek
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada N2L 3G1
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Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res 2014; 42:12833-46. [PMID: 25326328 PMCID: PMC4227795 DOI: 10.1093/nar/gku992] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
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Affiliation(s)
- Gary J Kapral
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Swati Jain
- Department of Biochemistry, Duke University, Durham, NC 27710, USA Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Jonas Noeske
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. J Chem Theory Comput 2014; 10:1608-22. [PMID: 26580373 DOI: 10.1021/ct401015e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the hairpin ribozyme by evaluating potential and free energy surfaces of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38 (A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as a general acid which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Møller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d-PhoT and SCC-DFTBPR methods provided acceptable activation barriers with respect to the SCS-MP2 data but predicted significantly different reaction pathways. DFT functionals (BLYP and MPW1K) yielded the same reaction pathway as the SCS-MP2 method. The activation barriers were slightly underestimated by the GGA BLYP functional, although with accuracy comparable to the semiempirical methods. The SCS-MP2 method and hybrid MPW1K functional gave activation barriers that were closest to those derived from experimentally measured rate constants.
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Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics , Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
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Riccitelli NJ, Delwart E, Lupták A. Identification of minimal HDV-like ribozymes with unique divalent metal ion dependence in the human microbiome. Biochemistry 2014; 53:1616-26. [PMID: 24555915 DOI: 10.1021/bi401717w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
HDV-like self-cleaving ribozymes have been found in a wide variety of organisms, implicated in diverse biological processes, and their activity typically shows a strong divalent metal dependence, but little metal specificity. Recent studies suggested that very short variants of these ribozymes exist in nature, but their distribution and biochemical properties have not been established. To map out the distribution of small HDV-like ribozymes, the drz-Spur-3 sequence was minimized to yield a core construct for structure-based bioinformatic searches. These searches revealed several microbial ribozymes, particularly in the human microbiome. Kinetic profile of the smallest ribozyme revealed two distinct metal binding sites, only one of which promotes fast catalysis. Furthermore, this ribozyme showed markedly reduced activity in Ca(2+), even in the presence of physiological Mg(2+) concentrations. Our study substantially expands the number of microbial HDV-like ribozymes and provides an example of cleavage regulation by divalent metals.
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Affiliation(s)
- Nathan J Riccitelli
- Department of Chemistry, ∥Department of Pharmaceutical Sciences, and ⊥Department of Molecular Biology and Biochemistry, University of California-Irvine , Irvine, California 92697, United States
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Ganguly A, Thaplyal P, Rosta E, Bevilacqua PC, Hammes-Schiffer S. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme. J Am Chem Soc 2014; 136:1483-96. [PMID: 24383543 PMCID: PMC3954522 DOI: 10.1021/ja4104217] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage
reaction using a combination of nucleobase and metal ion catalysis.
Both divalent and monovalent ions can catalyze this reaction, although
the rate is slower with monovalent ions alone. Herein, we use quantum
mechanical/molecular mechanical (QM/MM) free energy simulations to
investigate the mechanism of this ribozyme and to elucidate the roles
of the catalytic metal ion. With Mg2+ at the catalytic
site, the self-cleavage mechanism is observed to be concerted with
a phosphorane-like transition state and a free energy barrier of ∼13
kcal/mol, consistent with free energy barrier values extrapolated
from experimental studies. With Na+ at the catalytic site,
the mechanism is observed to be sequential, passing through a phosphorane
intermediate, with free energy barriers of 2–4 kcal/mol for
both steps; moreover, proton transfer from the exocyclic amine of
protonated C75 to the nonbridging oxygen of the scissile phosphate
occurs to stabilize the phosphorane intermediate in the sequential
mechanism. To explain the slower rate observed experimentally with
monovalent ions, we hypothesize that the activation of the O2′
nucleophile by deprotonation and orientation is less favorable with
Na+ ions than with Mg2+ ions. To explore this
hypothesis, we experimentally measure the pKa of O2′ by kinetic and NMR methods and find it to be
lower in the presence of divalent ions rather than only monovalent
ions. The combined theoretical and experimental results indicate that
the catalytic Mg2+ ion may play three key roles: assisting
in the activation of the O2′ nucleophile, acidifying the general
acid C75, and stabilizing the nonbridging oxygen to prevent proton
transfer to it.
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Affiliation(s)
- Abir Ganguly
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Bonneau E, Legault P. NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. Biochemistry 2014; 53:579-90. [PMID: 24364590 PMCID: PMC3906864 DOI: 10.1021/bi401484a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa's of two key nucleobases that contribute to the general acid-base mechanism. Recently, we determined the NMR structure of the A730 loop of the VS ribozyme active site (SLVI) that contributes the general acid (A756) in the enzymatic mechanism of the cleavage reaction. Our studies showed that magnesium (Mg(2+)) ions are essential to stabilize the formation of the S-turn motif within the A730 loop that exposes the A756 nucleobase for catalysis. In this article, we extend these NMR investigations by precisely mapping the Mg(2+)-ion binding sites using manganese-induced paramagnetic relaxation enhancement and cadmium-induced chemical-shift perturbation of phosphorothioate RNAs. These experiments identify five Mg(2+)-ion binding sites within SLVI. Four Mg(2+) ions in SLVI are associated with known RNA structural motifs, including the G-U wobble pair and the GNRA tetraloop, and our studies reveal novel insights about Mg(2+) ion binding to these RNA motifs. Interestingly, one Mg(2+) ion is specifically associated with the S-turn motif, confirming its structural role in the folding of the A730 loop. This Mg(2+) ion is likely important for formation of the active site and may play an indirect role in catalysis.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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Ranaghan KE, Hung JE, Bartlett GJ, Mooibroek TJ, Harvey JN, Woolfson DN, van der Donk WA, Mulholland AJ. A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase. Chem Sci 2014. [DOI: 10.1039/c3sc53009d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Novel role for methionine in enzyme catalysis.
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Affiliation(s)
- Kara E. Ranaghan
- Centre for Computational Chemistry
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Chemistry
| | - John E. Hung
- Department of Chemistry and The Howard Hughes Medical Institute
- University of Illinois at Urbana-Champaign
- Urbana, USA
| | | | | | - Jeremy N. Harvey
- Centre for Computational Chemistry
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Chemistry
| | - Derek N. Woolfson
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Biochemistry
- Medical Sciences
| | - Wilfred A. van der Donk
- Department of Chemistry and The Howard Hughes Medical Institute
- University of Illinois at Urbana-Champaign
- Urbana, USA
| | - Adrian J. Mulholland
- Centre for Computational Chemistry
- School of Chemistry
- University of Bristol
- Bristol, UK
- School of Chemistry
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