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Mikkola S, Eguaogie O, Nieminen A, Conlon PF, Jakeman DL, Moore K, Lane IC, Vyle JS. 5'-Chalcogen-Substituted Nucleoside Pyrophosphate and Phosphate Monoester Analogues: Preparation and Hydrolysis Studies. Int J Mol Sci 2022; 23:ijms232415582. [PMID: 36555224 PMCID: PMC9778984 DOI: 10.3390/ijms232415582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Novel sulfur and selenium substituted 5',5'-linked dinucleoside pyrophate analogues were prepared in a vibration ball mill from the corresponding persilylated monophosphate. The chemical hydrolysis of pyrophosphorochalcogenolate-linked dimers was studied over a wide pH-range. The effect of the chalcogeno-substitution on the reactivity of dinucleoside pyrophosphates was surprisingly modest, and the chemical stability is promising considering the potential therapeutic or diagnostic applications. The chemical stability of the precursor phosphorochalcogenolate monoesters was also investigated. Hydrolytic desilylation of these materials was effected in aqueous buffer at pH 3, 7 or 11 and resulted in phosphorus-chalcogen bond scission which was monitored using 31P NMR. The rate of dephosphorylation was dependent upon both the nature of the chalcogen and the pH. The integrity of the P-S bond in the corresponding phosphorothiolate was maintained at high pH but rapidly degraded at pH 3. In contrast, P-Se bond cleavage of the phosphoroselenolate monoester was rapid and the rate increased with alkalinity. The results obtained in kinetic experiments provide insight on the reactivity of the novel pyrophosphates studied as well as of other types of thiosubstituted biological phosphates. At the same time, these results also provide evidence for possible formation of unexpectedly reactive intermediates as the chalcogen-substituted analogues are metabolised.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
- Correspondence: (S.M.); (J.S.V.)
| | - Olga Eguaogie
- School of Chemistry and Chemical Engineering, Queen’s University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
| | - Anu Nieminen
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Patrick F. Conlon
- School of Chemistry and Chemical Engineering, Queen’s University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
- College of Pharmacy, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - David L. Jakeman
- College of Pharmacy, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Keith Moore
- School of Chemistry and Chemical Engineering, Queen’s University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
| | - Ian C. Lane
- School of Chemistry and Chemical Engineering, Queen’s University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
| | - Joseph S. Vyle
- School of Chemistry and Chemical Engineering, Queen’s University of Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
- Correspondence: (S.M.); (J.S.V.)
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2
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Gulumkar V, Äärelä A, Moisio O, Rahkila J, Tähtinen V, Leimu L, Korsoff N, Korhonen H, Poijärvi-Virta P, Mikkola S, Nesati V, Vuorimaa-Laukkanen E, Viitala T, Yliperttula M, Roivainen A, Virta P. Controlled Monofunctionalization of Molecular Spherical Nucleic Acids on a Buckminster Fullerene Core. Bioconjug Chem 2021; 32:1130-1138. [PMID: 33998229 PMCID: PMC8382215 DOI: 10.1021/acs.bioconjchem.1c00187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
An azide-functionalized
12-armed Buckminster fullerene has been
monosubstituted in organic media with a substoichiometric amount of
cyclooctyne-modified oligonucleotides. Exposing the intermediate products
then to the same reaction (i.e., strain-promoted alkyne–azide
cycloaddition, SPAAC) with an excess of slightly different oligonucleotide
constituents in an aqueous medium yields molecularly defined monofunctionalized
spherical nucleic acids (SNAs). This procedure offers a controlled
synthesis scheme in which one oligonucleotide arm can be functionalized
with labels or other conjugate groups (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic
acid, DOTA, and Alexa-488 demonstrated), whereas the rest of the 11
arms can be left unmodified or modified by other conjugate groups
in order to decorate the SNAs’ outer sphere. Extra attention
has been paid to the homogeneity and authenticity of the C60-azide scaffold used for the assembly of full-armed SNAs.
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Affiliation(s)
- Vijay Gulumkar
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Antti Äärelä
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Olli Moisio
- Turku PET Centre, University of Turku, FI-20520 Turku, Finland
| | - Jani Rahkila
- Instrument Centre, Faculty of Science and Engineering, Åbo Akademi University, FI-20500 Åbo, Finland
| | - Ville Tähtinen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Laura Leimu
- Department of Biologics, Orion Pharma, 20101 Turku, Finland
| | - Niko Korsoff
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Heidi Korhonen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | | | - Satu Mikkola
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Victor Nesati
- Department of Biologics, Orion Pharma, 20101 Turku, Finland
| | | | - Tapani Viitala
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, FI-00014, Helsinki, Finland
| | - Marjo Yliperttula
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, FI-00014, Helsinki, Finland
| | - Anne Roivainen
- Turku PET Centre, University of Turku, FI-20520 Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland.,Department of Biologics, Orion Pharma, 20101 Turku, Finland
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3
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Jaakkola J, Nieminen A, Kivelä H, Korhonen H, Tähtinen P, Mikkola S. Kinetic and NMR spectroscopic study of the chemical stability and reaction pathways of sugar nucleotides. Nucleosides Nucleotides Nucleic Acids 2020; 40:178-193. [PMID: 33331238 DOI: 10.1080/15257770.2020.1856870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The alkaline cleavage of two types of sugar nucleotides has been studied by 1H and 31P NMR in order to obtain information on the stability and decomposition pathways in aqueous solutions under alkaline conditions. The reaction of glucose 1-UDP is straightforward, and products are easy to identify. The results obtained with ribose 5-UDP and ribose 5-phosphate reveal, in contrast, a more complex reaction system than expected, and the identification of individual intermediate species was not possible. Even though definite proof for the mechanisms previously proposed could not be obtained, all the spectroscopic evidence is consistent with them. Results also emphasise the significant effect of conditions, pH, ionic strength, and temperature, on the reactivity under chemical conditions.
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Affiliation(s)
- Juho Jaakkola
- Department of Chemistry, University of Turku, Turku, Finland
| | - Anu Nieminen
- Department of Chemistry, University of Turku, Turku, Finland
| | - Henri Kivelä
- Department of Chemistry, University of Turku, Turku, Finland
| | - Heidi Korhonen
- Department of Chemistry, University of Turku, Turku, Finland
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Turku, Finland
| | - Satu Mikkola
- Department of Chemistry, University of Turku, Turku, Finland
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4
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Abstract
Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, 20014 Turku, Finland
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5
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Conway LP, Mikkola S, O'Donoghue AC, Hodgson DRW. The synthesis, conformation and hydrolytic stability of an N,S-bridging thiophosphoramidate analogue of thymidylyl-3',5'-thymidine. Org Biomol Chem 2018; 14:7361-7. [PMID: 27417455 DOI: 10.1039/c6ob01270a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 3'-N,5'-S-bridging thiophosphoramidate analogue of thymidylyl-3',5'-thymidine was synthesised under aqueous conditions. (1)H NMR conformational measurements show that the 3'-N-substituted deoxyribose ring is biased towards the 'north', RNA-like conformation. Rate constants for hydrolysis of the analogue were measured at 90 °C in the pH range 1.3-10.9. The pH-log kobs profile displays a pH-independent region between approximately pH 7 and 10 (t1/2 ∼13 days). Under acidic conditions, kobs displays a first order dependence on [H3O(+)].
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Affiliation(s)
- Louis P Conway
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Satu Mikkola
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland
| | | | - David R W Hodgson
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.
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6
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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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7
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Dano M, Elmeranta M, Hodgson DRW, Jaakkola J, Korhonen H, Mikkola S. Metal ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester bonds in carbohydrates. J Biol Inorg Chem 2015; 20:1299-306. [DOI: 10.1007/s00775-015-1308-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022]
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8
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9
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Korhonen H, Koivusalo T, Toivola S, Mikkola S. There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts. Org Biomol Chem 2013; 11:8324-39. [DOI: 10.1039/c3ob41554f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Korhonen H, Williams NH, Mikkola S. βLG
values in mechanistic studies on the transesterification of RNA models and their application in a metal ion complex promoted transesterification. J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.2942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Heidi Korhonen
- Department of Chemistry; University of Turku; 20014 Turku Finland
| | - Nicholas H. Williams
- Centre for Chemical Biology, Department of Chemistry; University of Sheffield; S3 7HF UK
| | - Satu Mikkola
- Department of Chemistry; University of Turku; 20014 Turku Finland
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11
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Korhonen H, Mikkola S, Williams NH. The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex. Chemistry 2011; 18:659-70. [PMID: 22162262 DOI: 10.1002/chem.201100721] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Indexed: 11/11/2022]
Abstract
The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.
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Affiliation(s)
- Heidi Korhonen
- Department of Chemistry, 20014 University of Turku, Turku, Finland
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12
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Huhta E, Parjanen A, Mikkola S. A kinetic study on the chemical cleavage of nucleoside diphosphate sugars. Carbohydr Res 2010; 345:696-703. [PMID: 20138257 DOI: 10.1016/j.carres.2009.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 12/11/2009] [Accepted: 12/22/2009] [Indexed: 10/20/2022]
Abstract
Nucleoside diphosphate sugars serve in essential roles in metabolic processes. They have, therefore, been used in mechanistic studies on glycosylation reactions, and their analogues have been synthesised as enzyme and receptor inhibitors. Despite extensive biochemical research, little is known about their chemical reactions. In the present work the chemical cleavage of two different types of nucleoside diphosphate sugars has been studied. UDP-Glc is phosphorylated at the anomeric carbon, whereas in ADP-Rib C-1 is unsubstituted, allowing hence the equilibrium between cyclic hemiacetal and acyclic carbonyl forms. Due to the structural difference, these substrates react via different pathways under slightly alkaline conditions: while UDP-Glc reacts exclusively by a nucleophilic attack of a glucose hydroxyl group on the diphosphate moiety, ADP-Rib undergoes a complex reaction sequence that involves isomerisation processes of the acyclic ribose sugar and results in a release of ADP.
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Affiliation(s)
- Eija Huhta
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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13
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Maanpää L, Luzet V, Guillaume G, Taherpour S, Mäki E, Mikkola S. Bimetallic Cu2+ complexes of bis-terpyridine ligands as catalysts of the cleavage of mRNA 5′-cap models. The effect of linker length and base moiety. NEW J CHEM 2009. [DOI: 10.1039/b821724f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Maanpää L, Taherpour S, Zhang Z, Guillaume C, Szilagy I, Mäki E, Mikkola S. Cu2+TerPy complexes as catalysts of the cleavage of the 5'-cap structure of mRNA. Nucleosides Nucleotides Nucleic Acids 2008; 26:1423-6. [PMID: 18066797 DOI: 10.1080/15257770701539393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cu(2+)TerPy is a fairly good catalyst of the cleavage of dinucleoside triphosphates, but its efficiency is not sufficient for use in artificial RNA cleaving enzymes. The present work is aimed at improving the catalysis by Cu(2+)TerPy with additional catalysts. Electrophilic and general acid catalysis have been studied and bifunctional catalysts have been synthesized. The most efficient catalysis was achieved with a Cu(2+)TerPy-dimer.
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Affiliation(s)
- Leena Maanpää
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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16
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Linjalahti H, Feng G, Mareque-Rivas JC, Mikkola S, Williams NH. Cleavage and isomerization of UpU promoted by dinuclear metal ion complexes. J Am Chem Soc 2008; 130:4232-3. [PMID: 18324817 DOI: 10.1021/ja711347w] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalysis of phosphoryl transfer by metal ions has been intensively studied in both biological and artificial systems, but the status of the transient pentacoordinate phosphoryl species (as transition state or intermediate) is the subject of considerable debate. We report that dinuclear metal ion complexes that incorporate second sphere hydrogen bond donors not only promote the cleavage of RNA fragments just as efficiently as the activated analogue HPNPP but also provide the first examples of metal ion catalyzed phosphate diester isomerization close to neutral pH. This observation implies that the reaction catalyzed by these complexes involves the formation of a phosphorane intermediate that is sufficiently long-lived to pseudorotate.
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Affiliation(s)
- Heidi Linjalahti
- Department of Chemistry, FI-20014 University of Turku, Turku, Finland
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17
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Abstract
The transesterification of RNA oligonucleotides was studied over a wide pH range. The rate constants obtained indicate that, under neutral conditions, oligonucleotides with an adenosine moiety as the 5'-linked nucleoside can be up to 1000-fold more reactive than the reference oligonucleotide, a 13-mer oligo-U (1). Experiments with the modified oligonucleotide with N6,N6-dimethyladenosine (9) as the 5'-linked nucleoside moiety suggest that the exocyclic amino group is involved in the reaction, influencing the reactivity of the neighboring phosphodiester bond. In addition to such intramolecular interactions, weak intermolecular interactions most probably contribute to the reactivity.
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18
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Wang Q, Niittymaki T, Virta P, Ketomaki K, Mikkola S, Lonnberg H. Metal ion promoted cleavage of RNA phosphodiester bonds: from Zn(II) aqua ion to artificial ribonucleases. ACTA ACUST UNITED AC 2007:65-6. [DOI: 10.1093/nass/nrm033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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19
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Zhang Z, Mikkola S, Lonnberg H. Regio-selective synthesis of polyazacyclophanes incorporating a pendant group as potential cleaving agents of mRNA 5′-cap structure. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.08.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Szilágyi I, Mikkola S, Lönnberg H, Labádi I, Pálinkó I. Hydrolysis of dinucleoside phosphates - mRNA 5' cap analogues - promoted by a binuclear copper(II)-zinc(II) complex. J Inorg Biochem 2007; 101:1400-3. [PMID: 17640737 DOI: 10.1016/j.jinorgbio.2007.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 05/19/2007] [Accepted: 05/23/2007] [Indexed: 10/23/2022]
Abstract
The hydrolysis of a 5' cap analogue, diadenosinyl-5',5'-triphosphate (ApppA), and two dinucleoside monophosphates: adenylyl(3',5')adenosine (ApA) and uridylyl(3',5')uridine (UpU) promoted by an imidazolate-bridged heterobinuclear copper(II)-zinc(II) complex, Cu(II)-diethylenetriamino-micro-imidazolato-Zn(II)- tris(aminoethyl)amine trisperchlorate (denoted as Cu,Zn-complex in the followings) has been investigated. Kinetic measurements were performed in order to explore the effects of pH, the total concentration of the Cu,Zn-complex and temperature on the cleavage rate. The catalytic activity of the Cu,Zn-complex was quantified by pseudo-first-order rate constants obtained in the excess of the cleaving agent. The results show that the Cu,Zn-complex and its deprotonated forms have phosphoesterase activity and with ApppA the metal complex promoted cleavage takes place selectively within the triphosphate bridge.
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Affiliation(s)
- I Szilágyi
- Bioinorganic Chemistry Research Group of the Hungarian Academy of Sciences, University of Szeged, Dóm tér 7, Szeged H-6720, Hungary
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21
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Abstract
The ability of bimetallic homo- and heteronuclear complexes of two spiro-linked ligands, viz. a biazacrown (i.e., 2,6,10,14,18,22-hexaazaspiro[11.11]tricosane (1)) and an azacrown-crown ether (i.e., 14,17,20,23,26-pentaoxa-2,6,10-triaza-spiro[11.15]heptacosane (2)), to promote the cleavage of the phosphoester linkage of dinucleoside 3',5'-phosphates and the phosphoric anhydride bridge of dinucleoside 5',5'-triphosphates was studied. In both reactions, the bimetallic homonuclear Cu2+ and Zn2+ complexes were better catalysts than their monometallic counterparts. The acceleration was two- to five-fold with the phosphoester cleavage and 3- to 20-fold with the phosphoric anhydride cleavage. Interestingly, the most-efficient catalyst of the phosphoester cleavage was the heterodinuclear Ni2+,Zn2+ complex of 1, the catalytic activity of which was up to 5- and 100-fold that of the homodinuclear Zn2+ and Ni2+ complexes, respectively. Moreover, this cooperative acceleration was observed to depend on the identity of the 5'-linked nucleoside: 3',5'-UpU and 3',5'-ApU were cleaved much faster than 3',5'-UpA, and no cooperative acceleration was observed with 3',5'-ApA. The reaction was second-order in hydroxide ion concentration, suggesting that a double deprotonation took place on going from the initial to the transition state. Evidently, in addition to deprotonation of the attacking 2'-OH group, N(3)H of the 5'-linked uridine was displaced by one of the metal ions of the cleaving agent. With the phosphoric anhydride cleavage, no similar cooperativity of two different metal ions was observed, but the greatest rate-acceleration was achieved with the homodinuclear Cu2+ complexes.
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Affiliation(s)
- Qi Wang
- Department of Chemistry, University of Turku, FIN-20014 Turku
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22
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Zhang Z, Mikkola S, Lönnberg H. Polyazacyclophanes incorporating two pyridine units and a heteroaromatic pendant group as potential cleaving agents of mRNA 5'-cap structure. Chem Biodivers 2007; 2:1116-26. [PMID: 17193195 DOI: 10.1002/cbdv.200590081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Four hexaazacyclophanes, 16a-d, incorporating two pyridine units and a (pyridin-2-yl)methyl or (quinolin-2-yl)methyl pendant group at one of the ring N-atoms have been prepared. The key step of the synthesis is an intermolecular cyclization of N,N-bis{[6-(tosyloxymethyl)pyridin-2-yl]methyl}-2-nitrobenzenesulfonamide (7) with either tert-butyl bis{2-[(2-nitrophenylsulfonyl)amino]ethyl}carbamate (2a) or tert-butyl bis{3-[(2-nitrophenylsulfonyl)amino]propyl}carbamate (2b) in the presence of anhydrous Cs(2)CO(3). Removal of the acid-labile tert-butoxycarbonyl protection then allows attachment of the pendant group by reductive alkylation to the exposed secondary amino group, and deprotection of the remaining aliphatic ring N-atoms completes the synthesis. The ability of the cyclophanes and their dinuclear Cu(2+) and Zn(2+) complexes to cleave the mRNA cap structure, m(7)G(5')pppG(5') (1), has been studied.
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Affiliation(s)
- Zhibo Zhang
- Department of Chemistry, Turku University, FIN-20014 Turku
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23
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Zhang Z, Lönnberg H, Mikkola S. Metal ion complexes of macrocyclic polyamines enhance both the phosphate hydrolysis and imidazole ring opening of RNA 5'-cap structure. Chem Biodivers 2007; 2:92-103. [PMID: 17191922 DOI: 10.1002/cbdv.200490169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The cleavage of P1-(7-methylguanosyl-5') P3-(guanosyl-5') triphosphate, a RNA 5'-cap model, by 2-hydroxyethyl- (6a-6c) and 2-aminoethyl- (7a-7c) substituted macrocycles in the presence and absence of Zn2+ and Cu2+ ions has been studied at pH 7.2 and 60 degrees. In the presence of the metal ions, hydrolysis of the phosphate group is enhanced. The mono- and dinuclear Zn2+ complexes promote solely the phosphate hydrolysis, whereas the corresponding Cu2+ complexes accelerate both the phosphate hydrolysis and the imidazole ring opening of the 7-methylguanine base. In the absence of the metal ions, the macrocycles mainly promote breakdown of the 7-methylguanine base, most probably by enhancing the nucleophilic attack of hydroxide ion on the C(8)-atom by shielding the repulsive negative charge on the phosphate moiety. The 2-hydroxyethyl and 2-aminoethyl side arms exhibit a two- to three-fold rate acceleration. Opening of the imidazole ring eventually results in cleavage of the triphosphate bridge.
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Affiliation(s)
- Zhibo Zhang
- University of Turku, Department of Chemistry, FIN-20014 Turku
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Virtanen N, Nevalainen V, Lehtinen T, Mikkola S. Transesterification of an RNA model in buffer solutions in H2O and D2O. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jancsó A, Paksi Z, Mikkola S, Rockenbauer A, Gajda T. Iron(III)- and copper(II) complexes of an asymmetric, pentadentate salen-like ligand bearing a pendant carboxylate group. J Inorg Biochem 2005; 99:1480-9. [PMID: 15927258 DOI: 10.1016/j.jinorgbio.2005.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 04/07/2005] [Accepted: 04/07/2005] [Indexed: 10/25/2022]
Abstract
The equilibrium and solution structural properties of the iron(III) and copper(II) complexes of an asymmetric salen-like ligand (N,N'-bis(2-hydroxybenzyl)-2,3-diamino-propionic acid, H(3)bhbdpa) bearing a pendant carboxylate group were characterized in aqueous solution by potentiometric, pH-dependent electron paramagnetic resonance (EPR) and UV-Vis (UV-Visible) measurements. In the equimolar systems the pentadentate ligand forms very stable, differently protonated mononuclear complexes with both metal ions. In the presence of iron(III) {NH, PhO(-), COO(-)}, {2NH, 2PhO(-), COO(-)} and {2NH, 2PhO(-), COO(-), OH(-)} coordinated complexes are dominant. The EPR titrations reflected the presence of microscopic complex formation pathways, leading to the formation of binding isomers in case of Cu(H(2)bhbdpa)(+), Cu(Hbhbdpa) and Cu(bhbdpa)(-). The {2NH, 2PhO(-)+COO(-)/H(2)O} coordinated Cu(bhbdpa) is the only species between pH 6-11. At twofold excess of metal ion dinuclear complexes were detected with both iron(III) and copper(II). In presence of iron(III) a mu-carboxylato-mu-hydroxo-bridged dinuclear complex (Fe(2)(bhbdpa)(OH)(3)) is formed from Fe(H(2)bhbdpa)(2+) through overlapping proton release processes, providing one of the rare examples for the stabilization of an endogenous carboxylate bridged diiron core in aqueous solution. The complex Cu(2)(bhbdpa)(+) detected in the presence of copper(II) is a paramagnetic (S=1) species with relatively weakly coupled metal ions.
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Affiliation(s)
- Attila Jancsó
- Department of Chemistry, University of Turku, Finland
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Jancsó A, Mikkola S, Lönnberg H, Hegetschweiler K, Gajda T. Hydrolysis of a mRNA 5′-cap model substrate, 5′,5′-ApppA by di- and trinuclear zinc(II) complexes of a polyamino-polyol ligand. J Inorg Biochem 2005; 99:1283-93. [DOI: 10.1016/j.jinorgbio.2005.02.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Revised: 02/11/2005] [Accepted: 02/17/2005] [Indexed: 11/16/2022]
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lönnberg T, Kiiski J, Mikkola S. Hydrolytic stability of 2′,3′-O-methyleneadenos-5′-yl 2′,5′-di-O-methylurid-3′-yl 5′-O-methylurid-3′(2′)-yl phosphate: implications to feasibility of existence of phosphate-branched RNA under physiological conditions. Org Biomol Chem 2005; 3:1089-96. [PMID: 15750653 DOI: 10.1039/b500054h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl 2',5'-di-O-methylurid-3'-yl 5'-O-methylurid-3'(2')-yl phosphate (1a,b) have been followed by RP-HPLC over a wide pH range to evaluate the feasibility of occurrence of phosphate-branched RNA under physiological conditions. At pH <2, where the decomposition of is first order in [H3O+], the P-O5' bond is cleaved 1.5 times as rapidly as the P-O3' bond. Under these conditions, the reaction probably proceeds by an attack of the 2'-OH on the phosphotriester monocation. Over a relatively wide range from pH 2 to 5, the hydrolysis is pH-independent, referring to rapid initial deprotonation of the attacking 2'-OH followed by general acid catalyzed departure of the leaving nucleoside. The P-O5' bond is cleaved 3 times as rapidly as the P-O3' bond. At pH 6, the reaction becomes first order in [HO-], consistent with an attack of the 2'-oxyanion on neutral phosphate. The product distribution is gradually inversed: in 10 mmol L(-1) aqueous sodium hydroxide, cleavage of the P-O3' bond is favored over P-O5' by a factor of 7.3. The results of the present study suggest that the half-life for the cleavage of under physiological conditions is only 100 s. Even at pH 2, where is most stable, the half-life for its cleavage is less than one hour and the isomerization between and is even more rapid than cleavage. The mechanisms of the partial reactions are discussed.
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Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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Jancsó A, Mikkola S, Lönnberg H, Hegetschweiler K, Gajda T. Phosphodiester cleavage of ribonucleoside monophosphates and polyribonucleotides by homo- and heterodinuclear metal complexes of a cyclohexane-based polyamino-polyol ligand. Chemistry 2004; 9:5404-15. [PMID: 14613151 DOI: 10.1002/chem.200305149] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability of the dinuclear complexes of tdci [1,3,5-trideoxy-1,3,5-tris(dimethylamino)-cis-inositol] to promote the cleavage of the phosphodiester bonds of nucleoside 2',3'-cyclic monophosphates, dinucleoside monophosphates and polyribonucleotides has been studied. The homodinuclear copper(II) and zinc(II) complexes efficiently promote the hydrolysis of cyclic nucleotides. The second-order rate constant (k(2) approximately 0.44 M(-1) s(-1)) estimated for the cleavage of 2',3'-cAMP induced by dinuclear copper(II) complexes is about 107 times greater than that for the hydroxide-ion-catalysed reaction. The complex selectively cleaves the 2'O-P bond of 2',3'-cUMP and forms the 3'-product in 91 % yield. An equimolar mixture of copper(II), zinc(II) and tdci proved to be more efficient than either of the binary systems: a 7-20-fold rate enhancement was observed for the cleavage of 2',3'-cNMP substrates. The half-life for the hydrolysis of 2',3'-cAMP decreased from 300 days to five minutes at 25 degrees C when the concentration of each of the three components was 2.5 mM. In contrast to the copper(II) or zinc(II) complexes of tdci, the heterodinuclear species promoted the hydrolysis of several dinucleoside monophosphates. For two ApA isomers, cleavage of the 3',5'-bond was about 6.5 times faster than cleavage of the 2',5'-bond. On the basis of the kinetic data, a trifunctional mechanism is suggested for the heterodinuclear-complex-promoted cleavage of the phosphodiester bond. Double Lewis acid activation occurs when the metal ions bind to the phosphate oxygen atoms. In particular, a metal-bound hydroxide ion serves as a general base or a nucleophilic catalyst, and, presumably, a zinc(II)-bound aqua ligand behaves as a general acid and facilitates the departure of the leaving alkoxide group. The effect of the complexes on the hydrolysis of poly(U), poly(A) and type III native RNA was also investigated, and, for the first time, kinetic data on the cleavage of the phosphodiester bonds of polyribonucleotides by a dinuclear complex was obtained.
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Affiliation(s)
- Attila Jancsó
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
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Zhang Z, Lönnberg H, Mikkola S. Macrocyclic amines as catalysts of the hydrolysis of the triphosphate bridge of the mRNA 5'-cap structure. Org Biomol Chem 2004; 1:3404-9. [PMID: 14584804 DOI: 10.1039/b306268f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactions of a 5'-cap model compound P1-(7-methylguanosine) P3-guanosine 5',5'-triphosphate, m7GpppG, were studied in the presence of three different macrocyclic amines (2-4) under neutral conditions. The only products observed in the absence of the macrocycles resulted from the base-catalysed imidazole ring-opening and the acid-catalysed cleavage of the N7-methylguanosine base, whereas in the presence of these catalysts hydrolysis of the triphosphate bridge predominated. The latter reaction yielded guanosine 5'-monophosphate, guanosine 5'-diphosphate, 7-methylguanosine 5'-monophosphate and 7-methylguanosine 5'-diphosphate as the initial products, indicating that both of the phosphoric anhydride bonds were cleaved. The overall catalytic activity of all three macrocycles was comparable. The hydrolysis to guanosine 5'-diphosphate and 7-methylguanosine 5'-monophosphate was slightly more favoured than the cleavage to yield guanosine 5'-monophosphate and 7-methylguanosine diphosphate. All the macrocycles also enhanced the subsequent hydrolysis of the nucleoside diphosphates, 2 being more efficient than 3 and 4.
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Affiliation(s)
- Zhibo Zhang
- University of Turku, Department of Chemistry, FIN-20014 Turku, Finland
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Niittymäki T, Kaukinen U, Virta P, Mikkola S, Lönnberg H. Preparation of azacrown-functionalized 2'-O-methyl oligoribonucleotides, potential artificial RNases. Bioconjug Chem 2004; 15:174-84. [PMID: 14733598 DOI: 10.1021/bc034166b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An improved synthesis for 3-(3-aminopropyl)- and 3-(3-mercaptopropyl)-1,5,9-triazacyclododecane has been developed and alternative methods for their conjugation to oligonucleotides have been described. Accordingly, the 3-aminopropyl azacrown and its N-(3-aminopropanoyl)-3-aminopropyl analogue have been tethered to the 3'-terminus of a 2'-O-methyloligoribonucleotide by aminolytic cleavage of the thioester linker utilized for the chain assembly. Studies on a monomeric model compound verify that the reaction proceeds solely by the attack of the primary amino group. 5'-Conjugation has been achieved by introducing a 2-benzylthio-2-oxoethyl group to the 5'-terminus as a phosphoramidite reagent and cleaving the thioester bond with the 3-aminopropyl azacrown. For intrachain conjugation, a phosphoramidite reagent derived from 1-deoxy-1-(2-benzylthio-2-oxoethyl)-beta-d-erythro-pentofuranose has been inserted in a desired position within the chain and subjected to on-support aminolysis with the 3-aminopropyl azacrown or its N-(3-aminopropanoyl)-3-aminopropyl and N-(6-aminohexanoyl)-3-aminopropyl analogues. The 3-mercaptopropyl-derivatized azacrown has been tetherd by a disulfide bond to a 3'-(3-mercaptoalkyl)phosphate-tailed oligonucleotide. The 3'- and intrachain-tethered conjugates have been shown to cleave as their Zn(II) chelate complementary oligoribonucleotide sequences.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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Abstract
The hydrolysis of diadenosine 5',5'-triphosphate to AMP and ADP has been studied over a wide pH-range. Under acidic conditions the reaction shows a first-order dependence on the hydronium ion concentration. Below pH 3 the rate-increase begins to level off. From pH 6 to 9 the hydrolysis is slow and pH-independent. Base-catalysed hydrolysis is observed in NaOH-solutions. Under alkaline conditions an intramolecular nucleophilic attack on the phosphate producing 3',5'-cAMP is also observed, but it is slower than the intermolecular reaction. Depurination of the adenosine moieties competes with the hydrolysis both under acidic and alkaline conditions, but the mechanisms are different. The temperature-dependence of the hydrolysis of Ap(3)A and the depurination of adenosine moieties were studied under acidic conditions, and the activation parameters of the reactions were calculated. The results of the work reflect the fact that the negatively charged polyphosphate group is very resistant towards nucleophilic attack. An efficient catalysis is only observed under acidic conditions, where the phosphate group becomes protonated. General acids or bases did not catalyse the hydrolysis. Furthermore, hydroxide ion catalysed cleavage is only observed at high base concentrations and other negatively charged nucleophiles did not attack the phosphate groups of diadenosine polyphosphates.
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Lönnberg T, Mikkola S. Hydrolysis of 2‘,3‘-O-methyleneadenos-5‘-yl Bis(2‘,5‘-di-O-methylurid-3‘-yl) Phosphate, a Sugar O-Alkylated Trinucleoside 3‘,3‘,5‘-Monophosphate: Implications for the Mechanism of Large Ribozymes. J Org Chem 2004; 69:802-10. [PMID: 14750807 DOI: 10.1021/jo035094k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl bis(2',5'-di-O-methylurid-3'-yl) phosphate (1), a sugar O-alkylated trinucleoside 3',3',5'-monophosphate, have been followed by RP HPLC over a wide pH range. Under neutral and mildly acidic conditions, the only reaction observed was a pH-independent cleavage of the O-C5' bond of the 5'-linked nucleoside. Under more alkaline conditions nucleophilic attack by hydroxide ion starts to compete. The reaction is first order in [OH(-)] and becomes predominant at pH 10. Each of the 3'-linked nucleosides is displaced 2.9 times as readily as the 5'-linked one. To determine the beta(lg) value for the hydroxide ion catalyzed hydrolysis of 1, two diesters (2a,b) having 2',3'-O-methyleneadenosine (7) and 2',5'-di-O-methyluridine (4) as leaving groups were hydrolyzed under alkaline conditions. Since the beta(lg) value for this reaction is known, DeltapK(a) between 4 and 7 could be calculated. The beta(lg) for the hydrolysis of 1 was estimated to be -0.5 with use of this information. The mechanisms of the partial reactions and the role of leaving group properties in ribozyme reactions of large ribozymes are discussed.
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Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
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Ruohola AM, Koissi N, Andersson S, Lepistö I, Neuvonen K, Mikkola S, Lönnberg H. Reactions of 9-substituted guanines with bromomalondialdehyde in aqueous solution predominantly yield glyoxal-derived adducts. Org Biomol Chem 2004; 2:1943-50. [PMID: 15227548 DOI: 10.1039/b405117c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of 9-ethylguanine, 2'-deoxyguanosine and guanosine with bromomalondialdehyde in aqueous buffers over a wide pH-range were studied. The main products were isolated and characterized by (1)H and (13)C NMR and mass spectroscopy. The final products formed under acidic and basic conditions were different, but they shared the common feature of being derived from glyoxal. Among the 1 : 1 adducts, 1,N(2)-(trans-1,2-dihydroxyethano)guanine adduct (6) predominated at pH < 6 and N(2)-carboxymethylguanine adduct (10a,b) at pH > 7. In addition to these, an N(2)-(4,5-dihydroxy-1,3-dioxolan-2-yl)methylene adduct (11a,b) and an N(2)-carboxymethyl-1,N(2)-(trans-1,2-dihydroxyethano)guanine adduct (12) were obtained at pH 10. The results of kinetic experiments suggest that bromomalondialdehyde is significantly decomposed to formic acid and glycolaldehyde under the conditions required to obtain guanine adducts. Glycolaldehyde is oxidized to glyoxal, which then modifies the guanine base more readily than bromomalondialdehyde. Besides the glyoxal-derived adducts, 1,N(2)-ethenoguanine (5a-c) and N(2),3-ethenoguanine adducts (4a-c) were formed as minor products, and a transient accumulation of two unstable intermediates, tentatively identified as 1,N(2)-(1,2,2,3-tetrahydroxypropano)(8) and 1,N(2)-(2-formyl-1,2,3-trihydroxypropano)(9) adducts, was observed.
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Affiliation(s)
- Anne-Mari Ruohola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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Wang Q, Mikkola S, Lönnberg H. The cleavage of the triphosphate bridge of a model for the 5'-cap mRNA promoted by dinuclear bicyclic complexes with metal ions. Nucleosides Nucleotides Nucleic Acids 2003; 22:1391-3. [PMID: 14565426 DOI: 10.1081/ncn-120022993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Dinuclear bicyclic complexes, which have two active centers, can significantly promote the hydrolysis of the triphosphate bridge in ApppA, a 5'-cap model compound.
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Affiliation(s)
- Qi Wang
- Department of Chemistry, University of Turku, Turku, Finland.
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Zhang Z, Mikkola S, Lönnberg H. Preparation of hexaaza and heptaaza macrocycles functionalized with a single aminoalkyl pendant arm. Org Biomol Chem 2003; 1:854-8. [PMID: 12929370 DOI: 10.1039/b210663a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A practical and reproducible route for the preparation of 1,4,7,10,13,16,19-heptaazacyclohenicosane (1), 1,4,7,10,13,16-hexaazacyclooctadecane (2), and 1,4,7,10,13,17-hexaazacycloicosane (3) bearing a single N-(2-aminoethyl) pendant arm has been developed. Richman-Atkins cyclization in the presence of caesium carbonate was applied to construct the macrocycle from 3-benzoyl-N1,N5-ditosyl-3-azapentane-1.5-diamine and the appropriate fully N-tosylated N alpha, N omega-bis(2-mesyloxyethyl) tri- or tetra-amine. The benzoyl group was selectively removed with potassium tert-butoxide, and the exposed nitrogen atom was reacted with N-tosylaziridine. The tosyl protections were removed with hydrogen bromide in acetic acid, and the product was converted to a free base with the aid of a strong anion exchange resin (OH- form).
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Affiliation(s)
- Zhibo Zhang
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
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Mikkola S, Mikhailov SN, Efimtseva E, Neuvonen K, Oivanen M, Beigelman L, Lönnberg H. A comparative study on the cleavage of stereoisomeric uridylyl(3',5')uridines [D,D-, D,L- and L,D-UpU] by acid, base and metal ion catalysts. ORIGINS LIFE EVOL B 2002; 32:303-10. [PMID: 12458735 DOI: 10.1023/a:1020515212130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Stereoisomeric uridylyl(3',5')uridines D,L-UpU and L,D-UpU were synthesised. Their cleavage was followed in the presence of acid, base and metal ion catalysts to study whether the stereochemistry affects the inherent reactivity of the internucleosidic phosphodiester bond, and whether the low molecular weight catalysts can distinguish between the substrates. The rate constants obtained were compared to those of D,D-UpU. The comparison shows that the stability of the phosphodiester bond does not depend on the stereochemistry of the sugar rings. In contrast slight reactivity differences are observed in the presence of metal ion catalysts, which suggests that selective cleavage of stereoisomeric substrates even by small molecular weight chemical catalysts may be possible.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, Finland.
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Mikkola S, Kosonen (L, Lonnberg H. Cleavage and Isomerization of RNA Phosphodiester Bonds: Nucleoside Phosphotriesters and Chimeric Ribo / 2-O-Methylribo Oligonucleotides as Tools for Mechanistic Studies. CURR ORG CHEM 2002. [DOI: 10.2174/1385272024604934] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Valakoski S, Heiskanen S, Andersson S, Lähde M, Mikkola S. Metal ion-promoted cleavage of mRNA 5′-cap models: hydrolysis of the triphosphate bridge and reactions of the N7-methylguanine base. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b108222a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kaukinen U, Lyytikäinen S, Mikkola S, Lönnberg H. The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence. Nucleic Acids Res 2002; 30:468-74. [PMID: 11788709 PMCID: PMC99829 DOI: 10.1093/nar/30.2.468] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The cleavage of short chimeric oligonucleotides containing only one reactive ribonucleoside unit, all other nucleosides being 2'-O-methylated, has been studied at pH 8.5 and 35 degrees C. Among the 20 different sequences that did not exhibit any tendency to form a defined secondary structure, the scissile 5'-UpA-3' and 5'-CpA-3' phosphodiester bonds experienced >100- and up to 35-fold reactivity differences, respectively. Compared with dinucleoside monophosphates, both rate accelerations and retardations of more than one order of magnitude were observed. Even a change of a single base several nucleosides away from the scissile bond markedly affected the reaction rate. Duplex formation at the 3'- and/or 5'-side of the scissile bond was also studied and observed to be strongly rate retarding. The origin of the high sensitivity of phosphodiester bonds to the molecular environment is discussed.
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Affiliation(s)
- Ulla Kaukinen
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland
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Gajda T, Jancsó A, Mikkola S, Lönnberg H, Sirges H. Crystal structure, solution properties and hydrolytic activity of an alkoxo-bridged dinuclear copper(ii) complex, as a ribonuclease model. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b108948j] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
This review discusses the effects the secondary structure of an RNA molecule has on the inherent reactivity of its phosphodiester bonds, and on the catalytic activity of metal ion-based cleaving agents. The basic principles of the intramolecular transesterification of RNA phosphodiester bonds, particularly cleavage, are first briefly described. Studies of the structural effects on the cleavage, in the absence and in the presence of metal ion catalysts, are then reviewed, and the sources of the reactivity differences observed in different structures are discussed.
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Affiliation(s)
- S Mikkola
- Department of Chemistry, University of Turku, Finland
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Wang Q, Mikkola S, Lönnberg H. Synthesis of 2,6,10,14,18,22-hexaazaspiro[11.11]tricosane, the first example of a spiro aza crown derived from 2,2-bis(aminomethyl)propane-1,3-diamine. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00238-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kaukinen U, Bielecki L, Mikkola S, Adamiak RW, Lönnberg H. The cleavage of phosphodiester bonds within small RNA bulges in the presence and absence of metal ion catalysts †. ACTA ACUST UNITED AC 2001. [DOI: 10.1039/b102519h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mikkola S, Oivanen M, Neuvonen K, Piitari S, Ketomäki K, Lönnberg H. Cleavage of the phosphodiester bond of uridylyl-(3',5')-8-carboxymethylaminoadenosine by hydronium, hydroxide and zinc(II) ions: a model study aimed at elucidating the potential of a carboxylate function as an intramolecular catalyst. Nucleosides Nucleotides Nucleic Acids 2000; 19:1675-92. [PMID: 11200265 DOI: 10.1080/15257770008045452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Uridylyl-(3',5')-8-carboxymethylaminoadenosine has been synthesised, and its transesterification to uridine 2',3'-cyclic phosphate in the presence and absence of Zn2+ ion has been studied. The results show that a carboxylate function in the vicinity of the phosphodiester bond accelerates the metal ion promoted cleavage but not the metal ion independent reaction. Under acidic conditions, the predominant reaction is the cleavage of the side chain, giving the 8-amino derivative.
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Affiliation(s)
- S Mikkola
- Department of Chemistry, University of Turku, Finland.
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Mikkola S, Koissi N, Ketomäki K, Rauvala S, Neuvonen K, Lönnberg H. Reactions of Adenosine with Bromo- and Chloromalonaldehydes in Aqueous Solution: Kinetics and Mechanism. European J Org Chem 2000. [DOI: 10.1002/1099-0690(200006)2000:12<2315::aid-ejoc2315>3.0.co;2-g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zagorowska I, Mikkola S, Lönnberg H. Hydrolysis of Phosphodiester Bonds within RNA Hairpin Loops in Buffer Solutions: the Effect of Secondary Structure on the Inherent Reactivity of RNA Phosphodiester Bonds. Helv Chim Acta 1999. [DOI: 10.1002/(sici)1522-2675(19991215)82:12<2105::aid-hlca2105>3.0.co;2-n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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