1
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Wang D, Zhang Y, Wang P, Guo Y, Zhao Y, Cao S. Investigation of the Asymmetric Addition Reactions Induced by Pentacoordinated Hydrospirophosphorane Substrate. J Org Chem 2023; 88:1385-1402. [PMID: 36633837 DOI: 10.1021/acs.joc.2c02231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pentacoordinated bisaminoacyl hydrospirophosphoranes were first found to induce the asymmetric addition reactions as a novel chiral organic framework. Asymmetric addition reactions of bisaminoacyl hydrospirophosphoranes with aromatic aldehyde and in situ generated imine were investigated, and the corresponding α-hydroxyspirophosphonates and α-amino spirophosphonates were obtained. The addition reaction of hydrospirophosphoranes with ΔP configuration showed better stereoselectivity than that with ΛP configuration, not only for the addition reaction to aromatic aldehyde but also to in situ generated imine. Furthermore, the stereochemical mechanisms of asymmetric addition reactions induced by pentacoordinated hydrospirophosphorane were proposed by 31P NMR tracing experiment and X-ray diffraction analysis.
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Affiliation(s)
- Di Wang
- College of Chemistry, The Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Yang Zhang
- College of Chemistry, The Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Peipei Wang
- College of Chemistry, The Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Yanchun Guo
- College of Chemistry, The Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou 450052, P. R. China
| | - Yufen Zhao
- College of Chemistry, The Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou 450052, P. R. China.,Institute Drug Discovery Technology, Ningbo University, Ningbo 315211, P. R. China
| | - Shuxia Cao
- College of Chemistry, The Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou 450052, P. R. China
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2
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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3
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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4
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Dasgupta S, Karim S, Banerjee S, Saha M, Das Saha K, Das D. Designing of novel zinc(ii) Schiff base complexes having acyl hydrazone linkage: study of phosphatase and anti-cancer activities. Dalton Trans 2020; 49:1232-1240. [DOI: 10.1039/c9dt04636d] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The phosphatase and anti-cancer activities of three novel acyl hydrazone based zinc(ii) Schiff base complexes have been unveiled.
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Affiliation(s)
| | - Suhana Karim
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
| | - Saswati Banerjee
- Cancer Biology and Inflammatory Disorder Division
- CSIR – Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Moumita Saha
- Cancer Biology and Inflammatory Disorder Division
- CSIR – Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Krishna Das Saha
- Cancer Biology and Inflammatory Disorder Division
- CSIR – Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Debasis Das
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
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5
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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6
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Cui X, Sun C, Zhao P, Wang Y, Guo Y, Zhao Y, Cao S. The investigation of substituent effects on the fragmentation pathways of pentacoordinated phenoxyspirophosphoranes by ESI-MS n. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:314-322. [PMID: 29336509 DOI: 10.1002/jms.4064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/05/2018] [Accepted: 01/06/2018] [Indexed: 06/07/2023]
Abstract
The fragmentation pathways of pentacoordinated phenoxyspirophosphoranes were investigated in the positive mode by electrospray ionization multistage mass spectrometry. The results demonstrate that the sodium adducts of the title compounds undergo two competitive fragmentation pathways, and the fragmentation patterns are heavily dependent on the various substituent patterns at the phenolic group. An electron-withdrawing substituent at the ortho-position always results in the removal of a corresponding phenol analogue, while cleavage by spiroring opening becomes the predominant fragmentation pathway if an electron-donating substituent is at the phenolic group. The substituent effects on the competitive fragmentation pathways were further elucidated by theoretical calculations, single crystal structure analysis, and high-resolution mass spectrometry. The results contribute to the understanding of the gas-phase fragmentation reactions and the structure identification of spirophosphorane analogues by electrospray ionization multistage mass spectrometry.
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Affiliation(s)
- Xiaoyan Cui
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
| | - Can Sun
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
| | - Pei Zhao
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
| | - Yanyan Wang
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
| | - Yanchun Guo
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
| | - Yufen Zhao
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Shuxia Cao
- College of Chemistry and Molecular Engineering, Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Zhengzhou University, Zhengzhou, 450052, China
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7
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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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8
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Staroseletz Y, Nechaev S, Bichenkova E, Bryce RA, Watson C, Vlassov V, Zenkova M. Non-enzymatic recombination of RNA: Ligation in loops. Biochim Biophys Acta Gen Subj 2017; 1862:705-725. [PMID: 29097301 DOI: 10.1016/j.bbagen.2017.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND While the RNA world hypothesis is widely accepted, it is still far from complete: the existence of self-replicating ribozyme, consisting of potentially hundreds of nucleotides, is a core assumption for the majority of RNA world models. The appearance of such long RNA molecules under prebiotic conditions is not self-evident. Recombination seems to be a plausible way of creating RNA diversity, resulting in the appearance of functional RNAs, capable of self-replicating. METHODS We report here on the study of recombination process modelled with two 96 nts RNA fragments. Detection of recombination products was performed with RT-PCR followed by TA-cloning and Sanger sequencing. RESULTS A wide range of recombinant products was detected. We found that (i) the most efficient ligation was observed for RNA species forming bulges or internal loops, with ligation partners located within the loop; (ii) a strong preference was observed for formation of a few types of major products with a large variety of minor products; (iii) ligation could occur with participation of either 2',3'-cyclophosphate or 5'-ppp; (iv) the presence of key reaction components, i.e. 5'ppp-RNAs, enabled the formation of additional types of product; (v) molecular dynamics simulations of one of the most abundant products suggests that the ligation results in a preferable formation of 2'-5'- rather than 3'-5'-linkages. CONCLUSIONS The study demonstrates regularities of new RNA molecules formation with non-enzymatic recombination process. GENERAL SIGNIFICANCE Our findings provide new data supporting the RNA World hypothesis and show the way of new RNA sequences emergence under prebiotic conditions.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Sergey Nechaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Elena Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Catherine Watson
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
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9
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Polyancev FM, Metlushka KE, Sadkova DN, Khisametdinova ZR, Kataeva ON, Alfonsov VA, Latypov SK, Sinyashin OG. The isomeric structure of pentacoordinate chiral spirophosphoranes in solution by the combined use of NMR experiments and GIAO DFT calculations of NMR parameters. Dalton Trans 2017; 46:8146-8156. [PMID: 28607987 DOI: 10.1039/c7dt01605k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The interplay of NMR experiments and DFT calculations of NMR parameters is a reliable method for determining the relative configurations of pentacoordinate chiral spirophosphoranes bearing two six- or five-membered rings at the phosphorus atom in solution. The major product of the Betti based derivatives corresponds to the isomers with both substituents at chiral carbons being opposite to the P-H proton. The next populated product corresponds to the isomer with different chiralities at carbons. The least populated isomer is one with both substituents being at the same side of the heterocycle as the P-H bond.
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Affiliation(s)
- Fedor M Polyancev
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str. 8, Kazan, 420088, Russian Federation.
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10
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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11
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Characterization of tRNALeu binding interactions with Cu2+ and Pb2+ and their biological implications. J Inorg Biochem 2017; 171:90-99. [DOI: 10.1016/j.jinorgbio.2017.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/12/2017] [Accepted: 03/19/2017] [Indexed: 11/17/2022]
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12
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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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13
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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14
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Abstract
Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg2+) confirming their roles as independent molecular entities which help drive RNA-mediated processes.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
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15
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Wang ZY, Ren ZN, Liu FZ, Liu SY, Wang ZX, Zhu XL. Fabrication of stable and reversible DNA–RNA hammerhead ribozyme on a solid surface. RSC Adv 2014. [DOI: 10.1039/c4ra07170k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Huang PJJ, Lin J, Cao J, Vazin M, Liu J. Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation. Anal Chem 2014; 86:1816-21. [PMID: 24383540 DOI: 10.1021/ac403762s] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Po-Jung Jimmy Huang
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jenny Lin
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jing Cao
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Mahsa Vazin
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry,
Waterloo Institute for Nanotechnology , University of Waterloo 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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17
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Abstract
The glmS ribozyme is the first natural self-cleaving ribozyme known to require a cofactor. The d-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed to serve as a general acid, but its role in the catalytic mechanism has not been established conclusively. We surveyed GlcN6P-like molecules for their ability to support self-cleavage of the glmS ribozyme and found a strong correlation between the pH dependence of the cleavage reaction and the intrinsic acidity of the cofactors. For cofactors with low binding affinities, the contribution to rate enhancement was proportional to their intrinsic acidity. This linear free-energy relationship between cofactor efficiency and acid dissociation constants is consistent with a mechanism in which the cofactors participate directly in the reaction as general acid-base catalysts. A high value for the Brønsted coefficient (β ~ 0.7) indicates that a significant amount of proton transfer has already occurred in the transition state. The glmS ribozyme is the first self-cleaving RNA to use an exogenous acid-base catalyst.
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Affiliation(s)
- Júlia Viladoms
- Department of Chemical Physiology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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18
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Siluvai GS, Vargheese B, Murthy NN. Synthesis and characterization of trivalent tribridged dicobalt complexes incorporating alkoxide, aqua-hydroxide, acetate and phosphate ligating groups. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.02.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Valles SM, Strong CA, Buss EA, Oi DH. Non-enzymatic hydrolysis of RNA in workers of the ant Nylanderia pubens. JOURNAL OF INSECT SCIENCE (ONLINE) 2012; 12:146. [PMID: 23461820 PMCID: PMC3646609 DOI: 10.1673/031.012.14601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 02/01/2012] [Indexed: 06/01/2023]
Abstract
During preparation of total RNA from Nylanderia pubens (Forel) (Hymenoptera: Formicidae) workers for use in expression library construction, severe RNA degradation consistently occurred. This degradation was masked by spectrophotometric analysis but clearly evident by microfluidic-based assay. Although not specifically identified, the degrading entity was endogenous and localized to the abdomen (terminal abdominal segments) of adult ants. RNA degradation was not observed in preparations of larvae, non-melanized pupae, or eggs. Various RNase and protease inhibitors had no protective effect. However, the metal chelating agent ethylenediaminetetraacetic acid prevented RNA degradation and provides insight into the occurrence.
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Affiliation(s)
- Steven M. Valles
- USDA-ARS Center for Medical, Agricultural and Veterinary Entomology, 1600 SW 23 Drive, Gainesville, FL 32604
| | - Charles A. Strong
- USDA-ARS Center for Medical, Agricultural and Veterinary Entomology, 1600 SW 23 Drive, Gainesville, FL 32604
| | - Eileen A. Buss
- University of Florida, Department of Entomology and Nematology, Gainesville, FL 32611
| | - David H. Oi
- USDA-ARS Center for Medical, Agricultural and Veterinary Entomology, 1600 SW 23 Drive, Gainesville, FL 32604
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20
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Hu X, Gao X, Zhu J, Zeng Z, Zhang X, Lin Z, Xu P, Liu Y, Zhao Y. Fragmentation of pentacoordinate spirobicyclic aminoacyl-phosphoranes (P-AAs) by electrospray ionization tandem mass spectrometry concerning P-O and P-N bond cleavage. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3151-3160. [PMID: 21953971 DOI: 10.1002/rcm.5210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The fragmentation pathways of both protonated and sodiated pentacoordinate spirobicyclic aminoacylphosphoranes (P-AAs) have been studied by electrospray ionization multi-stage mass spectrometry (ESI-MS(n)) in positive mode. The possible pathways and their mechanisms are elucidated through the combination of ESI-MS/MS, isotope ((15)N and (2)H) labeling and high-resolution Fourier transform ion cyclotron resonance (FTICR)-MS/MS. The relative Gibbs free energies (ΔG) of the product ions and possible fragmentation pathways are estimated at the B3LYP/6-31 G(d) level of theory. The theoretical calculations show that both protonated and sodiated P-AAs would quickly fragment before Berry pseudorotation. For protonated P-AAs, they have different tendencies to P-O or P-N bond cleavage. For sodiated P-AAs, the P-N bond is easier to cleave and produces the tetracoordinated phosphorus ion H. These results to some extent may give a clue to the chemistry of the active sites of phosphoryl transfer enzymes and will enrich the gas-phase ESI-MS ion chemistry of pentacoordinate phosphoranes.
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Affiliation(s)
- Xiaomei Hu
- Department of Chemistry and The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, PR China
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21
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Lönnberg T. Understanding Catalysis of Phosphate‐Transfer Reactions by the Large Ribozymes. Chemistry 2011; 17:7140-53. [DOI: 10.1002/chem.201100009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20140 Turku (Finland), Fax: (+358) 2‐333‐6700
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22
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Cao S, Guo Y, Wu X, Zhao H, Zhao Y. Fragmentation studies of pentacoordinated bisaminoacylspirophosphoranes by negative electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:352-358. [PMID: 21438084 DOI: 10.1002/jms.1900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Fragmentation pathways of a series of pentacoordinated bisaminoacylspirophosphoranes were elucidated by electrospray ionization multistage mass spectrometry (ESI-MS(n)) in negative mode. The deprotonated ions of pentacoordinated bisaminoacylspirophosphoranes tend to eliminate a corresponding amino acid to form base peak. The hydrogen/deuterium exchange experiment, the high-resolution mass spectrometry, (13)C stable isotope labeling experiment and theoretical calculations were used to rationalize the proposed fragmentation pathways and to verify the differences between the fragmentation pathways. The results indicate that the negative molecular ions of pentacoordinated bisaminoacylspirophosphoranes dissociate through its open-chain tricoordinated tautomers. The relative Gibbs free energies (ΔG) of the product ions and proposed fragmentation pathways were estimated using the B3LYP/6-31 + + G(d, p) model. The results have some potential applications in the identification structures of similar spirophosphorane compounds by ESI-MS(n).
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Affiliation(s)
- Shuxia Cao
- Key Laboratory of Chemical Biology and Organic Chemistry of Henan Province, Department of Chemistry, Zhengzhou University, Zhengzhou 450052, China.
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23
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Benda L, Schneider B, Sychrovský V. Calculating the Response of NMR Shielding Tensor σ(31P) and 2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+ Cation. J Phys Chem A 2011; 115:2385-95. [DOI: 10.1021/jp1114114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic
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24
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Mazumdar D, Nagraj N, Kim HK, Meng X, Brown AK, Sun Q, Li W, Lu Y. Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions. J Am Chem Soc 2010; 131:5506-15. [PMID: 19326878 DOI: 10.1021/ja8082939] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K(+), Rb(+), or Cs(+) or in the presence of 80 mM, [Co(NH(3))(6)](3+). Only 4 M Li(+), NH(4)(+) and, to a lesser extent, Na(+) conferred detectable activity. The observed rate constants (k(obs) approximately 10(-3) min(-1) for Li(+) and NH(4)(+)) are approximately 1000-fold lower than that in the presence of 10 mM Mg(2+), and approximately 200,000-fold slower than that in the presence of 100 microM Pb(2+). Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within approximately 10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb(2+) sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K(d) approximately 0.35 M for Rb(+) and Cs(+)), while those that confer DNAzyme activity possess stronger affinity (K(d) approximately 0.22 M for Li(+), Na(+) and NH(4)(+)). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb(2+); higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn(2+) and Mg(2+); the K(d) values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb(2+). These results indicate that Pb(2+)-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.
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Affiliation(s)
- Debapriya Mazumdar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Active centrum hypothesis: the origin of chiral homogeneity and the RNA-world. Biosystems 2010; 103:1-12. [PMID: 20851736 DOI: 10.1016/j.biosystems.2010.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 11/22/2022]
Abstract
I propose a hypothesis on the origin of chiral homogeneity of bio-molecules based on chiral catalysis. The first chiral active centre may have formed on the surface of complexes comprising metal ions, amino acids, other coenzymes and oligomers (short RNAs). The complexes must have been dominated by short RNAs capable of self-reproduction with ligation. Most of the first complexes may have catalysed the production of nucleotides. A basic assumption is that such complexes can be assembled from their components almost freely, in a huge variety of combinations. This assumption implies that "a few" components can constitute "a huge" number of active centre types. Moreover, an experiment is proposed to test the performance of such complexes in vitro. If the complexes were built up freely from their elements, then Darwinian evolution would operate on the assembly mechanism of complexes. For the production of complexes, first their parts had to appear by forming a proper three-dimensional structure. Three possible re-building mechanisms of the proper geometric structure of complexes are proposed. First, the integration of RNA parts of complexes was assisted presumably by a pre-intron. Second, the binding of RNA parts of a complex may give rise to a "polluted" RNA world. Third, the pairing of short RNA parts and their geometric conformation may have been supported by a pre-genetic code. Finally, an evolutionary step-by-step scenario of the origin of homochirality and a "polluted" RNA world is also introduced based on the proposed combinatorial complex chemistry. Homochirality is evolved by Darwinian selection whenever the efficiency of the reflexive autocatalysis of a dynamical combinatorial library increases with the homochirality of the active centres of reactions cascades and the homochirality of the elements of the dynamical combinatorial library. Moreover, the potential importance of phospholipid membrane is also discussed.
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26
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Ennifar E, Walter P, Dumas P. Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site. Nucleic Acids Res 2010; 38:5807-16. [PMID: 20460458 PMCID: PMC2943608 DOI: 10.1093/nar/gkq344] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion.
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Affiliation(s)
| | | | - Philippe Dumas
- *To whom correspondence should be addressed. Tel: +33 388 41 70 02; Fax: +33 388 60 22 18;
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27
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Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? Molecules 2010; 15:5389-407. [PMID: 20714304 PMCID: PMC6257768 DOI: 10.3390/molecules15085389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/29/2010] [Accepted: 08/04/2010] [Indexed: 11/17/2022] Open
Abstract
The hammerhead ribozyme was first considered as a metalloenzyme despite persistent inconsistencies between structural and functional data. In the last decade, metal ions were confirmed as catalysts in self-splicing ribozymes but displaced by nucleobases in self-cleaving ribozymes. However, a model of catalysis just relying on nucleobases as catalysts does not fully fit some recent data. Gathering and comparing data on metal ions in self-cleaving and self-splicing ribozymes, the roles of divalent metal ions and nucleobases are revisited. Hypothetical models based on cooperation between metal ions and nucleobases are proposed for the catalysis and evolution of this prototype in RNA catalysis.
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28
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López-Cortina S, Medina-Arreguin A, Hernández-Fernández E, Bernès S, Guerrero-Alvarez J, Ordoñez M, Fernández-Zertuche M. Stereochemistry of base-induced cleavage of methoxide ion on cis- and trans-1,4-diphenylphosphorinanium salts. A different behavior with a phenyl substituent. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Zon G. Automated synthesis of phosphorus–sulfur analogs of nucleic acids—25 years on: potential therapeutic agents and proven utility in biotechnology. NEW J CHEM 2010. [DOI: 10.1039/b9nj00577c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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30
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Wrzesinski J, Wichłacz A, Nijakowska D, Rebowska B, Nawrot B, Ciesiołka J. Phosphate residues of antigenomic HDV ribozyme important for catalysis that are revealed by phosphorothioate modification. NEW J CHEM 2010. [DOI: 10.1039/b9nj00727j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Hou JB, Tang G, Guo JN, Liu Y, Zhang H, Zhao YF. Stereochemistry of chiral pentacoordinate spirophosphoranes correlated with solid-state circular dichroism and 1H NMR spectroscopy. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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33
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34
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Pentikäinen U, Shaw KE, Senthilkumar K, Woods CJ, Mulholland AJ. Lennard−Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases. J Chem Theory Comput 2009; 5:396-410. [DOI: 10.1021/ct800135k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulla Pentikäinen
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Katherine E. Shaw
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Kittusamy Senthilkumar
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Christopher J. Woods
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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35
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Schlatterer JC, Greenbaum NL. Specificity of Mg2+ binding at the Group II intron branch site. Biophys Chem 2008; 136:96-100. [PMID: 18555583 DOI: 10.1016/j.bpc.2008.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 05/05/2008] [Accepted: 05/06/2008] [Indexed: 11/15/2022]
Abstract
Metal ions play a crucial role in the conformation and splicing activity of Group II introns. Results from 2-aminopurine fluorescence and solution NMR studies suggest that metal ion binding within the branch site region of native D6 of the Group II intron is specific for alkaline earth metal ions and involves inner sphere coordination. Although Mg(2+) and Ca(2+) still bind to a mutant stem loop sequence from which the internal loop had been deleted, ion binding to the mutant RNA results in decreased, rather than increased, exposure of the branch site residue to solvent. These data further support the role of the internal loop in defining branch site conformation of the Group II intron. The specific bound Mg(2+) may play a bivalent role: facilitates the extrahelical conformation of the branch site and has the potential to act as a Lewis acid during splicing.
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Affiliation(s)
- Jörg C Schlatterer
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, United States
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36
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Fedoruk-Wyszomirska A, Wyszko E, Giel-Pietraszuk M, Barciszewska MZ, Barciszewski J. High hydrostatic pressure approach proves RNA catalytic activity without magnesium. Int J Biol Macromol 2007; 41:30-5. [PMID: 17222901 DOI: 10.1016/j.ijbiomac.2006.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 12/08/2006] [Indexed: 10/23/2022]
Abstract
High hydrostatic pressure (HHP) technique was used to evaluate a mechanism of RNA hydrolysis with RNA. We showed that hammerhead ribozyme specifically cleaves RNA substrate at HHP in the absence of Mg(2+). A deoxyribozyme "10-23" was active in the same conditions. These results pointed out that the hydrolytic activity of nucleic acid depends on proper tertiary structure of a complex with a substrate. They prove that magnesium ion is not directly involved in catalysis process. On that basis we show the mechanism of RNA hydrolysis catalyzed with nucleic acids at HHP.
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37
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Kim HK, Liu J, Li J, Nagraj N, Li M, Pavot CMB, Lu Y. Metal-Dependent Global Folding and Activity of the 8-17 DNAzyme Studied by Fluorescence Resonance Energy Transfer. J Am Chem Soc 2007; 129:6896-902. [PMID: 17488081 DOI: 10.1021/ja0712625] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 8-17 DNAzyme is a DNA metalloenzyme catalyzing RNA transesterification in the presence of divalent metal ions, with activity following the order Pb2+ >> Zn2+ >>Mg2+. Since the DNAzyme has been used as a metal ion sensor, its metal-induced global folding was studied by fluorescence resonance energy transfer (FRET) by labeling the three stems of the DNAzyme with the Cy3/Cy5 FRET pair two stems at a time in order to gain deeper insight into the role of different metal ions in its structure and function. FRET results indicated that, in the presence of Zn2+ and Mg2+, the DNAzyme folds into a compact structure, stem III approaching a configuration defined by stems I and II without changing the angle between stems I and II. Correlations between metal-induced folding and activity were also studied. For Zn2+ and Mg2+, the metal ion with higher affinity for the DNAzyme in global folding (Kd(Zn) = 52.6 microM and Kd(Mg) = 1.36 mM) also displays higher affinity in activity (Kd(Zn) = 1.15 mM and Kd(Mg) = 53 mM) under the same conditions. Global folding was saturated at much lower concentrations of Zn2+ and Mg2+ than the cleavage activities, indicating the global folding of the DNAzyme occurs before the cleavage activity for those metal ions. Surprisingly, no Pb2+-dependent global folding was observed. These results suggest that for Pb2+ global folding of the DNAzyme may not be a necessary step in its function, which may contribute to the DNAzyme having the highest activity in the presence of Pb2+.
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Affiliation(s)
- Hee-Kyung Kim
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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38
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Liu H, Robinet JJ, Ananvoranich S, Gauld JW. Density Functional Theory Investigation on the Mechanism of the Hepatitis Delta Virus Ribozyme. J Phys Chem B 2006; 111:439-45. [PMID: 17214496 DOI: 10.1021/jp064292n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory methods have been used to investigate the hepatitis delta virus (HDV) ribozyme and its catalyzed phosphodiester cleavage. In particular, the effects of the environment's polarity and/or specific hydrogen-bond interactions on the proton affinity of the active site cytosine's N3 ring center have been considered. In addition, the basicities of possible hydrated Mg2+ ion species were also examined. The mechanism previously proposed for the HDV ribozyme in which the active site cytosine (C75) is protonated and thus acts as an acid while the Mg2+ species acts as the complementary base was then investigated. The possible role of tautomerization of C75 is also discussed.
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Affiliation(s)
- Haining Liu
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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39
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Andersen TE, Kirpekar F, Haselmann KF. RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: mechanisms of general applicability to nucleic acids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1353-1368. [PMID: 16875834 DOI: 10.1016/j.jasms.2006.05.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 05/26/2006] [Accepted: 05/26/2006] [Indexed: 05/11/2023]
Abstract
To reveal the gas-phase chemistry of RNA and DNA fragmentation during MALDI mass spectrometry in positive ion mode, we performed hydrogen/deuterium exchange on a series of RNA and DNA tetranucleotides and studied their fragmentation patterns on a high-resolution MALDI TOF-TOF instrument. We were specifically interested in elucidating the remarkably different fragmentation behavior of RNA and DNA, i.e., the characteristic and abundant production of c- and y-ions from RNA versus a dominating generation of (a-B)- and w-ions from DNA analytes. The analysis yielded important information on all significant backbone cleavages as well as nucleobase losses. Based on this, we suggest common fragmentation mechanisms for RNA and DNA as well as an important RNA-specific reaction requiring a 2'-hydroxyl group, leading to c- and y-ions. The data is viewed and discussed in the context of previously published data to obtain a coherent picture of the fragmentation of singly protonated nucleic acids.
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Affiliation(s)
- Thomas E Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| | - Kim F Haselmann
- Department of Chemistry, University of Southern Denmark, Odense, Denmark
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40
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Roychowdhury-Saha M, Burke DH. Extraordinary rates of transition metal ion-mediated ribozyme catalysis. RNA (NEW YORK, N.Y.) 2006; 12:1846-52. [PMID: 16912216 PMCID: PMC1581984 DOI: 10.1261/rna.128906] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In pre-steady-state, fast-quench kinetic analysis, the tertiary-stabilized hammerhead ribozyme "RzB" cleaves its substrate RNA with maximal measured k (obs) values of approximately 3000 min(-1) in 1 mM Mn(2+) and approximately 780 min(-1) in 1 mM Mg(2+) at 37 degrees C (pH 7.4). Apparent pKa for the catalytic general base is approximately 7.8-8.5, independent of the corresponding metal hydrate pKa, suggesting potential involvement of a nucleobase as general base as suggested previously from nucleobase substitution studies. The pH-rate profile is bell-shaped for Cd(2+), for which the general catalytic acid has a pKa of 7.3 +/- 0.1. Simulations of the pH-rate relation suggest a pKa for the general catalytic acid to be approximately 9.5 in Mn(2+) and >9.5 in Mg(2+). The acid pKa's follow the trend in the pKa of the hydrated metal ions but are displaced by approximately 1-2 pH units in the presence of Cd(2+) and Mn(2+). One possible explanation for this trend is direct metal ion coordination with a nucleobase, which then acts as general acid.
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41
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Feldman AR, Leung EKY, Bennet AJ, Sen D. The RNA-Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme. Chembiochem 2005; 7:98-105. [PMID: 16345112 DOI: 10.1002/cbic.200500264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Much interest has focused on the mechanisms of the five naturally occurring self-cleaving ribozymes, which, in spite of catalyzing the same reaction, adopt divergent strategies. These ribozymes, with the exception of the recently described glmS ribozyme, do not absolutely require divalent metal ions for their catalytic chemistries in vitro. A mechanistic investigation of an in vitro-selected, RNA-cleaving DNA enzyme, the bipartite, which catalyzes the same chemistry as the five natural self-cleaving ribozymes, found a mechanism of significant complexity. The DNAzyme showed a bell-shaped pH profile. A dissection of metal usage indicated the involvement of two catalytically relevant magnesium ions for optimal activity. The DNAzyme was able to utilize manganese(II) as well as magnesium; however, with manganese it appeared to function complexed to either one or two of those cations. Titration with hexaamminecobalt(III) chloride inhibited the activity of the bipartite; this suggests that it is a metalloenzyme that utilizes metal hydroxide as a general base for activation of its nucleophile. Overall, the bipartite DNAzyme appeared to be kinetically distinct not only from the self-cleaving ribozymes but also from other in vitro-selected, RNA-cleaving deoxyribozymes, such as the 8-17, 10-23, and 614.
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Affiliation(s)
- Anat R Feldman
- Department of Molecular Biology and Biochemistry 1 and Department of Chemistry 2 Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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42
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Kikovska E, Mikkelsen NE, Kirsebom LA. The naturally trans-acting ribozyme RNase P RNA has leadzyme properties. Nucleic Acids Res 2005; 33:6920-30. [PMID: 16332695 PMCID: PMC1310964 DOI: 10.1093/nar/gki993] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Divalent metal ions promote hydrolysis of RNA backbones generating 5′OH and 2′;3′P as cleavage products. In these reactions, the neighboring 2′OH act as the nucleophile. RNA catalyzed reactions also require divalent metal ions and a number of different metal ions function in RNA mediated cleavage of RNA. In one case, the LZV leadzyme, it was shown that this catalytic RNA requires lead for catalysis. So far, none of the naturally isolated ribozymes have been demonstrated to use lead to activate the nucleophile. Here we provide evidence that RNase P RNA, a naturally trans-acting ribozyme, has leadzyme properties. But, in contrast to LZV RNA, RNase P RNA mediated cleavage promoted by Pb2+ results in 5′ phosphate and 3′OH as cleavage products. Based on our findings, we infer that Pb2+ activates H2O to act as the nucleophile and we identified residues both in the substrate and RNase P RNA that most likely influenced the positioning of Pb2+ at the cleavage site. Our data suggest that Pb2+ can promote cleavage of RNA by activating either an inner sphere H2O or a neighboring 2′OH to act as nucleophile.
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Affiliation(s)
| | - Nils-Egil Mikkelsen
- Department of Molecular Biology, Swedish Agricultural UniversityBox 590, Biomedical Centre, SE-751 23 Uppsala, Sweden
| | - Leif A. Kirsebom
- To whom correspondence should be addressed. Tel: +46 18 471 4068; Fax: +46 18 53 03 96;
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43
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Lönnberg T, Korhonen J. Hydrolysis of 2',3'-O-methyleneadenosin-5'-yl bis-5'-O-methyluridin-3'-yl phosphate: the 2'-hydroxy group stabilizes the phosphorane intermediate, not the departing 3'-oxyanion, by hydrogen bonding. J Am Chem Soc 2005; 127:7752-8. [PMID: 15913365 DOI: 10.1021/ja050325l] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolytic reactions of 2',3'-O-methyleneadenosin-5'-yl bis-5'-O-methyluridin-3'-yl phosphate (1a) have been followed by RP HPLC over a wide pH range to elucidate the role of the 2'-OH group as an intermolecular hydrogen bond donor facilitating the cleavage of 1a. At pH < 2, where the decomposition of 1 is first-order in hydronium-ion concentration, the P-O5' and P-O3' bonds are cleaved equally rapidly. Over a relatively wide range from pH 2 to 4, the hydrolysis is pH-independent and the P-O5' bond is cleaved 1.6 times as rapidly as the P-O3' bond. At pH 6, the reaction becomes first-order in hydroxide-ion concentration and cleavage of the P-O3' bond starts to predominate, accounting for 89% of the overall hydrolysis in 10 mmol L(-)(1) aqueous sodium hydroxide. Under alkaline conditions, the 2'-OH group facilitates the cleavage of 1 by a factor of 27 compared to the 2'-OMe counterpart, the influence on the P-O3' and P-O5' bond cleavage being equal. Accordingly, the 2'-hydroxy group stabilizes the phosphorane intermediate, not the departing 3'-oxyanion, by hydrogen bonding.
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Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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44
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Boero M, Tateno M, Terakura K, Oshiyama A. Double-Metal-Ion/Single-Metal-Ion Mechanisms of the Cleavage Reaction of Ribozymes: First-Principles Molecular Dynamics Simulations of a Fully Hydrated Model System. J Chem Theory Comput 2005; 1:925-34. [DOI: 10.1021/ct050066q] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mauro Boero
- Institute of Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8501, Japan, Division of Frontier Research, Creative Research Initiative “Sousei”, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan, and Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono,
| | - Masaru Tateno
- Institute of Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8501, Japan, Division of Frontier Research, Creative Research Initiative “Sousei”, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan, and Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono,
| | - Kiyoyuki Terakura
- Institute of Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8501, Japan, Division of Frontier Research, Creative Research Initiative “Sousei”, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan, and Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono,
| | - Atsushi Oshiyama
- Institute of Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan, Center for Biological Resources and Informatics, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8501, Japan, Division of Frontier Research, Creative Research Initiative “Sousei”, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo 001-0021, Japan, and Research Institute for Computational Sciences, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono,
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45
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Virtanen N, Polari L, Välilä M, Mikkola S. Kinetic solvent deuterium isotope effect in transesterification of RNA models. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.883] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Chen J, Wang X, Zhu Y, Lin J, Yang X, Li Y, Lu Y, Guo Z. An Asymmetric Dizinc Phosphodiesterase Model with Phenolate and Carboxylate Bridges. Inorg Chem 2005; 44:3422-30. [PMID: 15877422 DOI: 10.1021/ic048654m] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A phosphodiesterase model with two zinc centers has been synthesized and characterized. The compound, [Zn(2)(L(-)(2H))(AcO)(H(2)O)](PF(6)).2H(2)O (Zn(2)L'), was formed using an "end-off" type compartmental ligand, 2,6-bis{[(2-pyridylmethyl)(2-hydroxyethyl)amino]methyl}-4-methylphenol (L), and zinc acetate dihydrate. The X-ray crystallographic analysis shows that Zn(2)L' contains a mu-acetato-mu-cresolato-dizinc(II) core comprised of a quasi-trigonal bipyramidal Zn and a distorted octahedral Zn, and the distance between them is 3.421 Angstroms which is close to the dizinc distance in related natural metalloenzymes. Phosphodiesterase activity of Zn(2)L' was investigated using bis(4-nitrophenyl) phosphate (BNPP) as the substrate. The pH dependence of the BNPP cleavage in aqueous buffer media shows a sigmoid-shaped pH-k(obs) profile with an inflection point around pH 7.13 which is close to the first pK(a) value of 7.20 for Zn(2)L' obtained from the potentiometric titration. The catalytic rate constant (k(cat)) is 4.60 x 10(-6) s(-1) at pH 7.20 and 50 degrees C which is ca. 10(5)-fold higher than that of the uncatalyzed reaction. The deprotonated alcoholic group appended on Zn(2)L' is responsible for the cleavage reaction. The possible mechanism for the BNPP cleavage promoted by Zn(2)L' is proposed on the basis of kinetic and spectral analysis. The dizinc complex formed in situ in anhydrous DMSO exhibits a similar ability to cleave BNPP. This study provides a less common example for the phosphodiesterase model in which the metal-bound alkoxide is the nucleophile.
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Affiliation(s)
- Jingwen Chen
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, Nanjing University, People's Republic of China
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47
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Ora M, Linjalahti H, Lönnberg H. Phosphodiester cleavage of guanylyl-(3',3')-(2'-amino-2'-deoxyuridine): rate acceleration by the 2'-amino function. J Am Chem Soc 2005; 127:1826-32. [PMID: 15701018 DOI: 10.1021/ja045060+] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrolytic reactions of the structural analogue of guanylyl-(3',3')-uridine, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine), having one of the 2'-hydroxyl groups replaced with an amino function, have been followed by RP HPLC in the pH range 0-13 at 90 degrees C. The results are compared to those obtained earlier with guanylyl-(3',3')-uridine, guanylyl-(3',3')-(2',5'-di-O-methyluridine), and uridylyl-(3',5')-uridine. Under basic conditions (pH > 8), the hydroxide ion-catalyzed cleavage of the P-O3' bond (first-order in [OH(-)]) yields a mixture of 2'-amino-2'-deoxyuridine and guanosine 2',3'-cyclic phosphate which is hydrolyzed to guanosine 2'- and 3'-phosphates. Under these conditions, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is 10 times less reactive than guanylyl-(3',3')-uridine. Under acidic and neutral conditions (pH 3-8), where the pH-rate profile for the cleavage consists of two pH-independent regions (from pH 3 to pH 4 and from 6 to 8), guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is considerably reactive. For example, in the latter pH range, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is more than 2 orders of magnitude more labile than guanylyl-(3',3')-(2',5'-di-O-methyluridine), while in the former pH range the reactivity difference is 1 order of magnitude. Under very acidic conditions (pH < 3), the isomerization giving guanylyl-(2',3')-(2'-amino-2'-deoxyuridine) and depurination yielding guanine (both first-order in [H(+)]) compete with the cleavage. The Zn(2+)-promoted cleavage ([Zn(2+)] = 5 mmol L(-)(1)) is 15 times faster than the uncatalyzed reaction at pH 5.6. The mechanisms of the reactions of guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) are discussed, particularly focusing on the possible stabilization of phosphorane intermediate and/or transition state via an intramolecular hydrogen bonding by the 2'-amino group.
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Affiliation(s)
- Mikko Ora
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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48
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Osborne EM, Schaak JE, Derose VJ. Characterization of a native hammerhead ribozyme derived from schistosomes. RNA (NEW YORK, N.Y.) 2005; 11:187-196. [PMID: 15659358 PMCID: PMC1370707 DOI: 10.1261/rna.7950605] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Accepted: 11/06/2004] [Indexed: 05/24/2023]
Abstract
A recent re-examination of the role of the helices surrounding the conserved core of the hammerhead ribozyme has identified putative loop-loop interactions between stems I and II in native hammerhead sequences. These extended hammerhead sequences are more active at low concentrations of divalent cations than are minimal hammerheads. The loop-loop interactions are proposed to stabilize a more active conformation of the conserved core. Here, a kinetic and thermodynamic characterization of an extended hammerhead sequence derived from Schistosoma mansoni is performed. Biphasic kinetics are observed, suggesting the presence of at least two conformers, one cleaving with a fast rate and the other with a slow rate. Replacing loop II with a poly(U) sequence designed to eliminate the interaction between the two loops results in greatly diminished activity, suggesting that the loop-loop interactions do aid in forming a more active conformation. Previous studies with minimal hammerheads have shown deleterious effects of Rp-phosphorothioate substitutions at the cleavage site and 5' to A9, both of which could be rescued with Cd2+. Here, phosphorothioate modifications at the cleavage site and 5' to A9 were made in the schistosome-derived sequence. In Mg2+, both phosphorothioate substitutions decreased the overall fraction cleaved without significantly affecting the observed rate of cleavage. The addition of Cd2+ rescued cleavage in both cases, suggesting that these are still putative metal binding sites in this native sequence.
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Affiliation(s)
- Edith M Osborne
- Department of Biochemistry, Texas A&M University, College Station, TX 77843, USA
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49
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Bantounas I, Glover CPJ, Kelly S, Iseki S, Phylactou LA, Uney JB. Assessing adenoviral hammerhead ribozyme and small hairpin RNA cassettes in neurons: Inhibition of endogenous caspase-3 activity and protection from apoptotic cell death. J Neurosci Res 2005; 79:661-9. [PMID: 15657876 DOI: 10.1002/jnr.20389] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Antisense technology, including ribozyme and small interfering RNA, is being developed to mediate the down-regulation of specific intracellular genes. It was observed in this study that both antiluciferase ribozymes and short hairpin RNAs (shRNAs) could significantly reduce the activity of exogenously expressed luciferase in primary hippocampal neurons in a viral titer-dependent manner. shRNAs were more effective gene-silencing agents than ribozymes, although they exhibited some nonspecific gene-silencing effects at high viral titers. We also attempted to increase ribozyme efficacy by using a woodchuck hepatitis posttranscriptional regulatory element (WPRE) in the ribozyme expression cassette. The results showed that adenoviral vectors encoding specific ribozymes could silence the cellular expression of luciferase and endogenous procaspase-3 significantly. Furthermore, the antiprocaspase-3 ribozyme was shown to inhibit staurosporine-mediated cell death. The addition of a WPRE did not, however, increase or decrease ribozyme activity. As far as we are aware, this is the first example of adenovirally mediated delivery of hammerhead ribozymes being used to manipulate gene expression in primary neurons. The results therefore suggest that hammerhead ribozymes may be useful tools for studying neuronal gene function and have potential as therapeutic agents to treat CNS diseases.
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Affiliation(s)
- Ioannis Bantounas
- The Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
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50
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Sano M, Kato Y, Taira K. Functional gene-discovery systems based on libraries of hammerhead and hairpin ribozymes and short hairpin RNAs. MOLECULAR BIOSYSTEMS 2005; 1:27-35. [PMID: 16880960 DOI: 10.1039/b503235k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abundant information about the nucleotide sequence of the human genome has become readily available and it is now necessary to develop methods for the identification of genes that are involved in important cellular, developmental and disease-related processes. Identification methods based on the activities of hammerhead and hairpin ribozymes and of short hairpin RNAs (shRNAs), whose target specificities are coupled with loss-of-function phenotypes, have received increasing attention as possible tools for the rapid identification of key genes involved in such processes. We describe here recent advances that have been made with libraries of ribozymes and shRNAs and compare the advantages of the different types of library. The use of such libraries has already revealed new details of several important physiological phenomena.
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Affiliation(s)
- Masayuki Sano
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City, Japan
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