1
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Kalhor S, Zarei M, Sepehrmansourie H, Zolfigol MA, Shi H, Wang J, Arjomandi J, Hasani M, Schirhagl R. Novel uric acid-based nano organocatalyst with phosphorous acid tags: Application for synthesis of new biologically-interest pyridines with indole moieties via a cooperative vinylogous anomeric based oxidation. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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2
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An efficient tRNA cleaver without additional co-reactants at physiological condition. Biochem Biophys Res Commun 2019; 510:8-12. [PMID: 30661788 DOI: 10.1016/j.bbrc.2018.12.041] [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: 11/20/2018] [Accepted: 12/05/2018] [Indexed: 11/23/2022]
Abstract
A square-planar Cu(II) complex, [Cu(Me-Im)(gly-gly)]∙H2O 1 (Me-Im = 1-methyl-imidazole, gly-gly = glycylglycinato), has been prepared and structurally characterized by single crystal X-ray. The complex 1 was tested for its ability to the transfer RNA by UV-vis spectroscopy, cyclic voltammetry (CV), capillary electrophoresis (CE). Comparative spectroscopic analysis shows a maximum fluorescence-quenching ratio of 0.41 of 1 upon binding to RNA, which gives a binding constant (Kb) of 1.24 × 105 M-1. Cyclic voltammograms of complex 1 attached on the mercaptoethanol (-SH) linked Au electrodes in phosphate buffer solution give a well-defined and quasi-reversible redox couple, indicate complex 1 can efficiently degrade the high-order structure of RNA in physiological conditions (pH 7.0 phosphate buffer solution at 37 °C) without additional co-reactants, yielding a digestion coefficient more than 90% within 113 h. This study targeting the genetic biomacromolecule degradation based on the strong binding of chemical nucleases paves an important way to the novel materials in the decontamination of microorganisms (e.g., bacteria and viruses) at mild condition.
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3
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Jian FF, Liu E, Li Z. Structural and functional study for tRNA cleavage by Glycine o-phenanthroline Cu II complex, [CuCl(phen)(gly)]∙4H 2O. Biochem Biophys Res Commun 2019; 509:354-358. [PMID: 30587337 DOI: 10.1016/j.bbrc.2018.12.138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 02/01/2023]
Abstract
The o-phenanthroline gly Cu(II) complex, [CuCl(phen)(gly)]∙4H2O 1, has been prepared and structurally characterized. The transfer RNA binding and degradation properties of complex 1 have been investigated by UV-vis spectroscopy, cyclic voltammetry (CV), capillary electrophoresis (CE) and atomic force microscopy (AFM) methods. The results showed that 1 can efficiently cleave tRNA in the physiological conditions (pH 7.0, and 37 °C), and has a digestion coefficient nearly up to 100% within 75 h. AFM image for 1/RNA exhibited arrayed tandem repetitions of tRNA segments. This study is targeting the destruction of the high-order structures of genetic biomacromolecules which paves an important way to novel materials for the decontamination of microorganisms (e.g., bacteria and viruses).
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Affiliation(s)
- Fang Fang Jian
- School of Chemical Engineering and Pharmaceutics, Henan University of Science and Technology, Luoyang, Henan, PR China.
| | - E Liu
- School of Chemical Engineering and Pharmaceutics, Henan University of Science and Technology, Luoyang, Henan, PR China.
| | - Zhuangyu Li
- School of Chemical Engineering and Pharmaceutics, Henan University of Science and Technology, Luoyang, Henan, PR China.
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4
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Synthesis and catalysis of hydrolysis of phosphate esters by Zn(II), Cu(II), and Ni(II) Schiff base complexes. INORG CHEM COMMUN 2018. [DOI: 10.1016/j.inoche.2018.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Tóth EN, May NV, Rockenbauer A, Peintler G, Gyurcsik B. Exploring the boundaries of direct detection and characterization of labile isomers - a case study of copper(ii)-dipeptide systems. Dalton Trans 2017; 46:8157-8166. [PMID: 28607997 DOI: 10.1039/c7dt00884h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The investigation of the linkage isomers of biologically essential and kinetically labile metal complexes in aqueous solutions poses a challenge, as these microspecies cannot be separately studied. Therefore, derivatives are commonly used to initially determine the stability or spectral characteristics of at least one of the isomers. Here we directly detect the isomers, describe the metal ion coordination sphere, speciation and thermodynamic parameters by a synergistic application of temperature dependent EPR and CD spectroscopic measurements in copper(ii)-dipeptide systems including His-Gly and His-Ala ligands. The ΔH = (-23 ± 4) kJ mol-1 value of the standard enthalpy change corresponding to the peptide-type to histamine-type isomerisation equilibrium of the [CuL]+ complex was corroborated by several techniques. The preferential coordination of the side-chains was observed at lower temperatures, whereas, metal-binding of the backbone atoms became favourable upon increasing temperature. This study exemplifies the necessity of using temperature dependent multiple methodologies for a reliable description of similar systems for upstream applications.
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Affiliation(s)
- Eszter N Tóth
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary. and PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Japan
| | - Nóra V May
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Magyar tudósok körútja 2, Hungary
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Magyar tudósok körútja 2, Hungary and Department of Physics, Budapest University of Technology and Economics and MTA-BME Lendület Spintronics Research Group (PROSPIN), P.O. Box 91, H-1521 Budapest, Hungary
| | - Gábor Peintler
- Department of Physical Chemistry and Material Sciences, University of Szeged, Aradi Vértanuk tere 1, H-6720 Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary.
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Nanjundan N, Narayanasamy R, Geib S, Velmurugan K, Nandhakumar R, Balakumaran MD, Kalaichelvan PT. Distorted tetrahedral bis-(N,S) bidentate Schiff base complexes of Ni(II), Cu(II) and Zn(II): Synthesis, characterization and biological studies. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.02.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Zhang X, Liu X, Phillips DL, Zhao C. Hydrolysis mechanisms of BNPP mediated by facial copper(ii) complexes bearing single alkyl guanidine pendants: cooperation between the metal centers and the guanidine pendants. Dalton Trans 2016; 45:1593-603. [DOI: 10.1039/c5dt03949e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inter-complex and intra-complex nucleophilic attacks by metal-bound hydroxide were investigated by considering the second coordination spheres.
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Affiliation(s)
- Xuepeng Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | - Xueping Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | | | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
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9
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Ning Y, Gao M, Zheng K, Zhang Z, Zhou J, Hao X, Cao R. Phosphate monoester hydrolysis at tricopper site: The advantage and disadvantage of closely assembled trimetallic active sites. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcata.2015.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Zhang X, Zhu Y, Gao H, Zhao C. Solvolysis Mechanisms of RNA Phosphodiester Analogues Promoted by Mononuclear Zinc(II) Complexes: Mechanisic Determination upon Solvent Medium and Ligand Effects. Inorg Chem 2014; 53:11903-12. [DOI: 10.1021/ic501084a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xuepeng Zhang
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yajie Zhu
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Hui Gao
- Key
Laboratory of Renewable Energy and Gas Hydrate, Guangzhou Institute
of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, P. R. China
| | - Cunyuan Zhao
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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11
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Messinger H, Bär A. Oral 4-week and 13-week toxicity studies of polyvinyl acetate vinyl laurate copolymer in rats. Regul Toxicol Pharmacol 2014; 70:1-6. [PMID: 24932800 DOI: 10.1016/j.yrtph.2014.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 11/27/2022]
Abstract
Polyvinyl acetate vinyl laurate copolymer (PVAcVL) is a useful component of gum base for chewing gum production. The safety of PVAcVL was examined in a 4-week and a 13-week oral toxicity study in rats. Finely powdered PVAcVL was administered with the diet at levels of 1.25%, 2.0% and 5% in the 4-week study and 1.25%, 2.5% and 5% in the 13-week study. There were no treatment related effects on mortality, bodyweight gains feed efficiency, ophthalmoscopic findings, hematological and clinical chemical parameters, neurobehavioral observations as well as gross and histopathological changes of standard organs and tissues. The highest dose tested in the 13-week study (3783 and 4396mg/kgbw/d for males and females, respectively) proved to be a NOAEL.
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Affiliation(s)
| | - Albert Bär
- Bioresco Ltd., Bundesstrasse 29, 4054 Basel, Switzerland.
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12
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13
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Lanthanide-mediated dephosphorylation used for peptide cleavage during solid phase peptide synthesis. Molecules 2013; 18:3894-905. [PMID: 23549296 PMCID: PMC3955260 DOI: 10.3390/molecules18043894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 02/27/2013] [Accepted: 03/27/2013] [Indexed: 12/01/2022] Open
Abstract
Lanthanide(III) ions can accelerate the hydrolysis of phosphomonoesters and phosphodiesters in neutral aqueous solution. In this paper, lanthanide-mediated dephosphorylation has been applied in aqueous media as an orthogonal cleavage condition that can be employed in conventional solid phase peptide synthesis (SPPS). A phosphorylated polymeric support for SPPS was developed using Boc chemistry. The cleavage of resin-bound phosphates was investigated with the addition of Eu(III), Yb(III), acid or base, a mixture of solvents or different temperatures. To demonstrate the utility of this approach for SPPS, a peptide sequence was synthesized on a phosphorylated polymeric support and quantitatively cleaved with lanthanide ions in neutral aqueous media. The protecting groups for side chains were retained during peptide cleavage using lanthanide ions. This new methodology provides a mild orthogonal cleavage condition of phosphoester as a linker during SPPS.
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14
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Dalle KE, Daumann LJ, Schenk G, McGeary RP, Hanton LR, Gahan LR. Ligand modifications modulate the mechanism of binuclear phosphatase biomimetics. Polyhedron 2013. [DOI: 10.1016/j.poly.2012.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Daumann LJ, Gahan LR, Comba P, Schenk G. Cadmium(II) Complexes: Mimics of Organophosphate Pesticide Degrading Enzymes and Metallo-β-lactamases. Inorg Chem 2012; 51:7669-81. [DOI: 10.1021/ic300687y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lena J. Daumann
- School of
Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lawrence. R. Gahan
- School of
Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Comba
- Anorganisch-Chemisches Institut, Universitat Heidelberg, Im Neuenheimer Feld 270, 69120
Heidelberg, Germany
| | - Gerhard Schenk
- School of
Chemistry and Molecular
Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Department
of Chemistry, National University of Ireland, Maynooth, County Kildare,
Ireland
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16
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Daumann LJ, Dalle KE, Schenk G, McGeary RP, Bernhardt PV, Ollis DL, Gahan LR. The role of Zn–OR and Zn–OH nucleophiles and the influence of para-substituents in the reactions of binuclear phosphatase mimetics. Dalton Trans 2012; 41:1695-708. [DOI: 10.1039/c1dt11187f] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Jiang W, He X, Wang Y, Xu B, Li J, Liu F. Reactivity of Schiff Base Manganese(III) Complexes with Different Pendants toward the Hydrolysis of p-Nitrophenyl Picolinate. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Grygorenko OO, Radchenko DS, Volochnyuk DM, Tolmachev AA, Komarov IV. Bicyclic Conformationally Restricted Diamines. Chem Rev 2011; 111:5506-68. [DOI: 10.1021/cr100352k] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Oleksandr O. Grygorenko
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
| | - Dmytro S. Radchenko
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
| | | | - Andrey A. Tolmachev
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
| | - Igor V. Komarov
- Kyiv National Taras Shevchenko University, Volodymyrska Street, 64, Kyiv 01601, Ukraine
- Enamine Ltd., Alexandra Matrosova Street, 23, Kyiv 01103, Ukraine
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A novel 1,2,4-triazole-based copper(II) complex: Synthesis, characterization, magnetic property and nuclease activity. J Inorg Biochem 2010; 104:171-9. [DOI: 10.1016/j.jinorgbio.2009.10.020] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 10/21/2009] [Accepted: 10/26/2009] [Indexed: 11/20/2022]
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21
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Yue Y, Li J, Zhang J, Zhang ZW, Lin HH, Chen SY, Yu XQ. Synthesis and DNA-Cleavage Activities of Dinuclear Copper(II) Complexes of Urea-Bridged Macrocyclic Polyamines. Chem Biodivers 2009; 6:2236-43. [DOI: 10.1002/cbdv.200800305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Abstract
The final cut. Two types of artificial tools (artificial restriction DNA cutter and zinc finger nuclease) that cut double-stranded DNA through hydrolysis of target phosphodiester linkages, have been recently developed. The chemical structures, preparation, properties, and typical applications of these two man-made tools are reviewed.Two types of artificial tools that cut double-stranded DNA through hydrolysis of target phosphodiester linkages have been recently developed. One is the chemistry-based artificial restriction DNA cutter (ARCUT) that is composed of a Ce(IV)-EDTA complex, which catalyses DNA hydrolysis, and a pair of pseudo-complementary peptide nucleic acid fragments for sequence recognition. Another type of DNA cutter, zinc finger nuclease (ZFN), is composed of the nuclease domain of naturally occurring FokI restriction endonuclease and a designed zinc finger DNA-binding domain. For both of these artificial tools, the scission site and specificity can be freely chosen according to our needs, so that even huge genomic DNA sequences can be selectively cut at the target site. In this article, the chemical structures, preparation, properties, and typical applications of these two man-made tools are described.
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Affiliation(s)
- Hitoshi Katada
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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23
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Gahan LR, Smith SJ, Neves A, Schenk G. Phosphate Ester Hydrolysis: Metal Complexes As Purple Acid Phosphatase and Phosphotriesterase Analogues. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900231] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lawrence R. Gahan
- School of Chemistry and Molecular BioSciences, The University of Queensland, 4072 Brisbane, Australia
| | - Sarah J. Smith
- School of Chemistry and Molecular BioSciences, The University of Queensland, 4072 Brisbane, Australia
| | - Ademir Neves
- Laboratorio de Bioinorgânica e Cristalografica, Departamento de Química, Universidade Federal de Santa Catarina, 88040‐900, Florianópolis, SC, Brazil
| | - Gerhard Schenk
- School of Chemistry and Molecular BioSciences, The University of Queensland, 4072 Brisbane, Australia
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Huang Y, Chen SY, Zhang J, Tan XY, Jiang N, Zhang JJ, Zhang Y, Lin HH, Yu XQ. Dinuclear Copper(II) Complexes of Macrocyclic Polyamines: Synthesis, Characterization, and DNA Cleavage. Chem Biodivers 2009; 6:475-86. [DOI: 10.1002/cbdv.200800005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Chen KL, Lin HC, Huang CS, Shen YH, Huang JJ, Wong FF. Amphiphatic Piperazine, Pyrazine, and Pyridine Derivaties as the Thermal Latency for Epoxy-Phenolic Resins. Polym J 2009. [DOI: 10.1295/polymj.pj2009058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Komiyama M, Aiba Y, Yamamoto Y, Sumaoka J. Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity. Nat Protoc 2008; 3:655-62. [PMID: 18388948 DOI: 10.1038/nprot.2008.7] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The artificial restriction DNA cutter (ARCUT) method to cut double-stranded DNA at designated sites has been developed. The strategy at the base of this approach, which does not rely on restriction enzymes, is comprised of two stages: (i) two strands of pseudo-complementary peptide nucleic acid (pcPNA) anneal with DNA to form 'hot spots' for scission, and (ii) the Ce(IV)/EDTA complex acts as catalytic molecular scissors. The scission fragments, obtained by hydrolyzing target phosphodiester linkages, can be connected with foreign DNA using DNA ligase. The location of the scission site and the site-specificity are almost freely tunable, and there is no limitation to the size of DNA substrate. This protocol, which does not include the synthesis of pcPNA strands, takes approximately 10 d to complete. The synthesis and purification of the pcPNA, which are covered by a related protocol by the same authors, takes an additional 7 d, but pcPNA can also be ordered from custom synthesis companies if necessary.
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Affiliation(s)
- Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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Taran O, Medrano F, Yatsimirsky AK. Rapid hydrolysis of model phosphate diesters by alkaline-earth cations in aqueous DMSO: speciation and kinetics. Dalton Trans 2008:6609-18. [DOI: 10.1039/b807030j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Buchholz RR, Etienne ME, Dorgelo A, Mirams RE, Smith SJ, Chow SY, Hanton LR, Jameson GB, Schenk G, Gahan LR. A structural and catalytic model for zinc phosphoesterases. Dalton Trans 2008:6045-54. [DOI: 10.1039/b806391e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Zhao YC, Zhang J, Huang Y, Wang GQ, Yu XQ. DNA cleavage promoted by 2,9-dimethyl-4,7-diazadecane-2,9-dithiol (DDD) derivatives. Bioorg Med Chem Lett 2007; 17:2745-8. [PMID: 17369043 DOI: 10.1016/j.bmcl.2007.02.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 02/03/2007] [Accepted: 02/27/2007] [Indexed: 11/29/2022]
Abstract
Three piperidine derivatives of 2,9-dimethyl-4,7-diazadecane-2,9-dithiol (DDD), NEPDDD, NEMPDDD, and NEMMPDDD, were synthesized and used as catalysts in DNA cleavage. Under physiological conditions, a series of experiments have been done. The effects of DNA cleavage with three ligands were studied under different concentrations, cleavage time, and pH values. The results strongly suggested that the plasmid DNA (pUC 19) can be cleaved efficiently by these ligands. For the cleavage reaction catalyzed by NEMPDDD, Form I DNA could convert to Form II completely, and the DNA-cleavage mechanism involved an oxidative pathway.
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Affiliation(s)
- Yuan-Cong Zhao
- Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, PR China
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30
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Yamamoto Y, Mori M, Aiba Y, Tomita T, Chen W, Zhou JM, Uehara A, Ren Y, Kitamura Y, Komiyama M. Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA. Nucleic Acids Res 2007; 35:e53. [PMID: 17376805 PMCID: PMC1874645 DOI: 10.1093/nar/gkm052] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A monophosphate group was attached to the terminus of pseudo-complementary peptide nucleic acid (pcPNA), and two of thus modified pcPNAs were combined with Ce(IV)/EDTA for site-selective hydrolysis of double-stranded DNA. The site-selective DNA scission was notably accelerated by this chemical modification of pcPNAs. These second-generation artificial restriction DNA cutters (ARCUTs) differentiated the target sequence so strictly that no scission occurred even when only one DNA base-pair was altered to another. By using two of the activated ARCUTs simultaneously, DNA substrate was selectively cut at two predetermined sites, and the desired fragment was clipped and cloned. The DNA scission by ARCUT was also successful even when the target site was methylated by methyltransferase and protected from the corresponding restriction enzyme. Furthermore, potentiality of ARCUT for manipulation of huge DNA has been substantiated by site-selective scission of genomic DNA of Escherichia coli (composed of 4,600,000 bp) at the target site. All these results indicate promising applications of ARCUTs for versatile purposes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Makoto Komiyama
- *To whom correspondence should be addressed. +81 3 5452 5200+81 3 5452 5209
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31
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An Y, Lin YY, Wang H, Sun HZ, Tong ML, Ji LN, Mao ZW. Cleavage of double-strand DNA by zinc complexes of dicationic 2,2′-dipyridyl derivatives. Dalton Trans 2007:1250-4. [PMID: 17353958 DOI: 10.1039/b616754c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two highly charged zinc complexes, [Zn(L1)3](ClO4)8.4H2O (1) and [Zn(L2)2Br](ClO4)5.H2O (2) (L1 = 5,5'-di(1-(triethylammonio)methyl)-2,2'-dipyridyl and L2= 5,5'-di(1-(tributylammonio)methyl)-2,2'-dipyridyl) were synthesized and structurally characterized by crystallography. The zinc atom in 1 shows a distorted octahedral sphere. Variable-pH NMR studies on 1 demonstrated that the saturated six-coordinated [Zn(L1)3]8+ species can partially change into five-coordinated [Zn(L1)2(H2O)]6+ species in aqueous solution. The zinc atom in 2 shows a distorted trigonal-bipyramidal sphere. The average distance of the coordinated Br atom to the cationic N atom in 2 is ca 5.9 A, which is comparable to that of adjacent phosphodiesters in the DNA (ca. 6 A). Both complexes exhibited high nuclease activities towards cleavage of supercoiled plasmid DNA with the activity being the maximum under physiological pH. The effective DNA cleavage may be attributed to the strong electrostatic interaction of the metal moiety and two positive pendants with phosphodiester groups of nucleic acid.
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Affiliation(s)
- Yan An
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
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Mitra A, DePue LJ, Struss JE, Patel BP, Parkin S, Atwood DA. Mononuclear Schiff Base Boron Halides: Synthesis, Characterization, and Dealkylation of Trimethyl Phosphate. Inorg Chem 2006; 45:9213-24. [PMID: 17083219 DOI: 10.1021/ic0607890] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of mononuclear boron halides of the type LBX(2) [LH = N-phenyl-3,5-di-tert-butylsalicylaldimine, X = Cl (2), Br (3)] and LBX [LH2 = N-(2-hydroxyphenyl)-3,5-di-tert-butylsalicylaldimine, X = Cl (7), Br (8); LH2 = N-(2-hydroxyethyl)-3,5-di-tert-butylsalicylaldimine, X = Cl (9), Br (10); and LH2 = N-(3-hydroxypropyl)-3,5-di-tert-butylsalicylaldimine, X = Cl (11), Br (12)] were synthesized from their borate precursors LB(OMe)2 (1) (LH = N-phenyl-3,5-di-tert-butylsalicylaldimine) and LB(OMe) [LH2 = N-(2-hydroxyphenyl)-3,5-di-tert-butylsalicylaldimine (4), N-(2-hydroxyethyl)-3,5-di-tert-butylsalicylaldimine (5), N-(3-hydroxypropyl)-3,5-di-tert-butylsalicylaldimine (6)]. The boron halide compounds were air and moisture sensitive, and upon hydrolysis, compound 7 resulted in the oxo-bridged compound 13 that contained two seven-membered boron heterocycles. The boron halide compounds dealkylated trimethyl phosphate in stoichiometric reactions to produce methyl halide and unidentified phosphate materials. Compounds 8 and 12 were found to be the most effective dealkylating agents. On reaction with tert-butyl diphenyl phosphinate, compound 8 produced a unique boron phosphinate compound LB(O)OPPh2 (14) containing a terminal phosphinate group. Compounds 1-14 were characterized by 1H, 13C, 11B, 31P NMR, IR, MS, EA, and MP. Compounds 5, 6, and 11-14 also were characterized by single-crystal X-ray diffraction.
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Affiliation(s)
- Amitabha Mitra
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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Meyer F. Clues to Dimetallohydrolase Mechanisms from Studies on Pyrazolate‐Based Bioinspired Dizinc Complexes – Experimental Evidence for a Functional Zn–O
2
H
3
–Zn Motif. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600590] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Franc Meyer
- Institut für Anorganische Chemie, Georg‐August‐Universität Göttingen Tammannstrasse 4, 37077 Göttingen, Germany, Fax: +49‐551‐393063
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Berreau LM. Bioinorganic Chemistry of Group 12 Complexes Supported by Tetradentate Tripodal Ligands Having Internal Hydrogen‐Bond Donors. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200500886] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lisa M. Berreau
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, 84322‐0300, USA, Fax: + 1‐435‐797‐3390
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Mitra A, Depue LJ, Parkin S, Atwood DA. Five-Coordinate Aluminum Bromides: Synthesis, Structure, Cation Formation, and Cleavage of Phosphate Ester Bonds. J Am Chem Soc 2006; 128:1147-53. [PMID: 16433530 DOI: 10.1021/ja054684s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alkane elimination reaction between Salen((t)Bu)H(2) ligands and diethylaluminum bromide was used to prepare three Salen aluminum bromide compounds salen((t)Bu)AlBr (1) (salen = N,N'-ethylenebis(3,5-di-tert-butylsalicylideneimine)), salpen((t)Bu)AlBr (2) (salpen = N,N'-propylenebis(3,5-di-tert-butylsalicylideneimine)), and salophen((t)Bu)AlBr (3) (salophen = N,N'-o-phenylenenebis(3,5-di-tert-butylsalicylideneimine)). The compounds contain five-coordinate aluminum either in a distorted square pyramidal or a trigonal bipyramidal environment. The bromide group in these compounds could be displaced by triphenylphosphine oxide or triphenyl phosphate to produce the six-coordinate cationic aluminum compounds [salen((t)Bu)Al(Ph(3)PO)(2)]Br (4), [salpen((t)Bu)Al(Ph(3)PO)(2)]Br (5), [salophen((t)Bu)Al(Ph(3)PO)(2)]Br (6), and [salophen((t)Bu)Al[(PhO)(3)PO)](2)]Br (7). All the compounds were characterized by (1)H, (13)C, (27)Al, and (31)P NMR, IR, mass spectrometry, and melting point. Furthermore, compounds 1-3 and 5-7 were structurally characterized by single-crystal X-ray diffraction. Compounds 1-3 dealkylated a series of organophosphates in stoichiometric reactions by breaking the ester C-O bond. Also, they were catalytic in the dealkylation reaction between trimethyl phosphate and added boron tribromide.
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Affiliation(s)
- Amitabha Mitra
- Department of Chemistry, University of Kentucky, Lexington, 40506-0055, USA
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Schiller A, Scopelliti R, Severin K. Enhanced hydrolytic activity of Cu(ii) and Zn(ii) complexes in highly cross-linked polymers. Dalton Trans 2006:3858-67. [PMID: 16896445 DOI: 10.1039/b605676h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chelate ligand tris[(1-vinylimidazol-2-yl)methyl]amine (5) was synthesized in five steps from commercially available starting materials. Upon reaction with ZnCl2 or CuCl2 in the presence of NH4PF6, the complexes [Zn5Cl]PF6 (6) and [Cu5Cl]PF6 (7) were obtained. The structure of both complexes was determined by single-crystal X-ray crystallography. Immobilization of 6 and 7 was achieved by co-polymerization with ethylene glycol dimethacrylate. The supported complexes P6-Zn and P7-Cu were found to be efficient catalysts for the hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) at 50 degrees C. At pH 9.5, the heterogeneous catalyst P7-Cu was 56 times more active than the homogeneous catalyst 7. Partitioning effects, which increase the local concentration of BNPP in the polymer, are shown to contribute to the enhanced activity of the immobilized catalyst.
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Affiliation(s)
- Alexander Schiller
- Institut des Sciences et Ingénieries Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Kinetic and mechanistic studies of the reactivity of Zn–OHn (n=1 or 2) species in small molecule analogs of zinc-containing metalloenzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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38
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Fanning AM, Plush SE, Gunnlaugsson T. Tuning the properties of cyclen based lanthanide complexes for phosphodiester hydrolysis; the role of basic cofactors. Chem Commun (Camb) 2006:3791-3. [PMID: 16969459 DOI: 10.1039/b609923h] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of several cyclen based lanthanide [Eu(III) and La(III)] complexes is described; these metallo ribonuclease mimics are based on the use of alkyl amines as pendent arms, which give rise to fast hydrolysis within the physiological pH range of HPNP (an RNA model compound) that is highly dependent on the length of the alkyl spacer.
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Affiliation(s)
- Ann-Marie Fanning
- School of Chemistry, Centre for Synthesis and Chemical Biology, Trinity College Dublin, Dublin 2, Ireland
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Zhong H, Yuanjie S, Rong‐rong Z, Xiang‐guang M, Xian‐cheng Z. Metallomicellar Catalytic Hydrolysis of NPP by CuIINiIIHeterodinuclear Complexes Containing Diamine Groups in Brij35 Micellar Solution. J DISPER SCI TECHNOL 2005. [DOI: 10.1081/dis-200062984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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40
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Bauer-Siebenlist B, Meyer F, Farkas E, Vidovic D, Dechert S. Effect of Zn⋅⋅⋅Zn Separation on the Hydrolytic Activity of Model Dizinc Phosphodiesterases. Chemistry 2005; 11:4349-60. [PMID: 15880544 DOI: 10.1002/chem.200400932] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
From the study of highly preorganized model systems, experimental support has been obtained for a possible functional role of the Zn-(H)O...HO(H)-Zn motif in oligozinc hydrolases. The mechanistic relevance of such an array, which may be described as a hydrated form of a pseudo-terminal Zn-bound hydroxide, has recently been supported by DFT calculations on various metallohydrolase active sites. In the present targeted approach, the Zn...Zn distance in two related dizinc complexes has been controlled through the use of multifunctional pyrazolate-based ligand scaffolds, giving either a tightly bridged Zn-O(H)-Zn or a more loosely bridged Zn-(H)O...HO(H)-Zn species in the solid state. Zn-bound water has been found to exhibit comparable acidity irrespective of whether the resulting hydroxide is supported by strong hydrogen-bonding in the O(2)H(3) moiety or is in a bridging position between two zinc ions, indicating that water does not necessarily have to adopt a bridging position in order for its pK(a) to be sufficiently lowered so as to provide a Zn-bound hydroxide at physiological pH. Comparative reactivity studies on the cleavage of bis(4-nitrophenyl)phosphate (BNPP) mediated by the two dizinc complexes have revealed that the system with the larger Zn...Zn separation is hydrolytically more potent, both in the hydrolysis and the transesterification of BNPP. The extent of active site inhibition by the reaction products has also been found to be governed by the Zn...Zn distance, since phosphate diester coordination in a bridging mode within the clamp of two zinc ions is only favored for Zn...Zn distances well above 4 A. Different binding affinities are rationalized in terms of the structural characteristics of the product-inhibited complexes for the two different ligand scaffolds, with dimethyl phosphate found as a bridging ligand within the bimetallic pocket.
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Affiliation(s)
- Bernhard Bauer-Siebenlist
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, 37077 Göttingen, Germany
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41
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Delehanty JB, Stuart TC, Knight DA, Goldman ER, Thach DC, Bongard JE, Chang EL. RNA hydrolysis and inhibition of translation by a Co(III)-cyclen complex. RNA (NEW YORK, N.Y.) 2005; 11:831-836. [PMID: 15840822 PMCID: PMC1370767 DOI: 10.1261/rna.7156805] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 01/18/2005] [Indexed: 05/24/2023]
Abstract
Metal ion-chelator catalysts based on main-group, lanthanide, or transition metal complexes have been developed as nonenzymatic alternatives for the hydrolysis of the phosphodiester bonds in DNA and RNA. Cobalt (III), with its high-charge density, is known for its ability to hydrolyze phosphodiesters with rate constants as high as 2 x 10(-4) s(-1). We have developed a kinetically inert Co(III)-cyclen-based complex, Co(III)-cycmmb that is very potent in inhibiting the translation of RNA into protein. Contact time as short as 10 min is sufficient to achieve the complete inhibition of the translation of a concentrated luciferase RNA solution into the enzyme in a cell-free translation system. The inhibition appears to proceed through two pathways. The first pathway involves the kinetic or substitutional inertness of Co(III) for the RNA template at short contact times. This interaction is mediated through the kinetic inertness of Co(III) for the phosphate groups of the nucleotides, as well as coordination of Co(III) to the nitrogenous bases. The second pathway occurs at longer contact times and is mediated by the hydrolysis of the phosphodiester backbone. This report represents the first demonstrated use of a metal-chelate complex to achieve the inhibition of the translation of RNA into protein. This Co(III) system can be useful in its present nonsequence-specific form as a novel viral decontamination agent. When functionalized to recognize specific nucleic acid sequences, such a system could potentially be used in gene-silencing applications as an alternative to standard antisense or RNAi technologies.
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Affiliation(s)
- James B Delehanty
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
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42
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Cyclen based lanthanide ion ribonuclease mimics: the effect of pyridine cofactors upon phosphodiester HPNP hydrolysis. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.150] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Chandrasekhar V, Athimoolam A, Krishnan V, Azhakar R, Madhavaiah C, Verma S. A Copper-Metalated, Hybrid Inorganic-Organic Polymer as an Oxidative Nuclease. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200400727] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Carlsson H, Haukka M, Nordlander E. Structural and Functional Models of the Active Site of Zinc Phosphotriesterase. Inorg Chem 2004; 43:5681-7. [PMID: 15332820 DOI: 10.1021/ic0354522] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In an attempt to prepare structural and functional models for the active site of the hydrolytic enzyme zinc phosphotriesterase, five new zinc complexes of the ligands 2,6-bis[N-(N-(carboxylmethyl)-N-((1-methylimidazol)methyl)amine)methyl]-4-methylphenolate (BCIMP) and the corresponding asymmetric ligand 2-(N-isopropyl-N-((1-methylimidazolyl)methyl)aminomethyl)-6-(N-carboxylmethyl-N-((1-methylimidazolyl)methyl)aminomethyl)-4-methylphenol (ICIMP) have been synthesized, viz. Na[Zn(2)(BCIMP)Ac(2)] (1), [Zn(2)(BCIMP)(Ph(2)Ac)] (2), [Zn(2)(ICIMP)Ac(2)] (3), [Zn(4)(ICIMP)(2)(Me(3)Ac)(2)][ClO(4)](2) (4), and [Zn(4)(ICIMP)(2)(Ph(2)Ac)(2)][ClO(4)](2) (5). The X-ray structure of complex 5 has been determined and reveals that the complex is a dimer of dimers in the solid state, which in solution dissociates to potent structural models. Studies using NMR show that only one carboxylate coligand bridges the dizinc units in the case of diphenyl acetate and pivalate, while the steric bulk of acetate is sufficiently small to permit the coordination of two acetates/dizinc unit. Functional studies involving the hydrolysis/transesterification of 2-hydroxypropyl p-nitrophenyl phosphate (HPNP) show that the complex with ICIMP (compound 5) has a significantly higher rate of catalysis than the BCIMP complex (compound 2). This is attributed to the vacant/labile coordination site that is available in the ICIMP complex but not the BCIMP complex.
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Affiliation(s)
- Håkan Carlsson
- Inorganic Chemistry, Kemicentrum, Lund University, Box 124, SE-221 00 Lund, Sweden
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45
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Boseggia E, Gatos M, Lucatello L, Mancin F, Moro S, Palumbo M, Sissi C, Tecilla P, Tonellato U, Zagotto G. Toward efficient Zn(II)-based artificial nucleases. J Am Chem Soc 2004; 126:4543-9. [PMID: 15070372 DOI: 10.1021/ja039465q] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of cis-cis-triaminocyclohexane Zn(II) complex-anthraquinone intercalator conjugates, designed in such a way to allow their easy synthesis and modification, have been investigated as hydrolytic cleaving agents for plasmid DNA. The ligand structure comprises a triaminocyclohexane platform linked by means of alkyl spacers of different length (from C(4) to C(8)) to the anthraquinone group which may intercalate the DNA. At a concentration of 5 microM, the complex of the derivative with a C(8) alkyl spacer induces the hydrolytic stand scission of supercoiled DNA with a rate of 4.6 x 10(-6) s(-1) at pH 7 and 37 degrees C. The conjugation of the metal complex with the anthraquinone group leads to a 15-fold increase of the cleavage efficiency when compared with the anthraquinone lacking Zn-triaminocyclohexane complex. The straightforward synthetic procedure employed, allowing a systematic change of the spacer length, made possible to gain more insight on the role of the intercalating group in determining the reactivity of the systems. Comparison of the reactivity of the different complexes shows a remarkable increase of the DNA cleaving efficiency with the length of the spacer. In the case of too-short spacers, the advantages due to the increased DNA affinity are canceled due to the incorrect positioning of the reactive group, thus leading to cleavage inhibition.
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Affiliation(s)
- Elisa Boseggia
- Dipartimento di Scienze Chimiche e Istituto CNR Tecnologia delle Membrane-Sezione di Padova, Università di Padova, via Marzolo 1, I-35131 Padua, Italy
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46
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Bauer-Siebenlist B, Meyer F, Farkas E, Vidovic D, Cuesta-Seijo JA, Herbst-Irmer R, Pritzkow H. Correlation of Structure and Function in Oligonuclear Zinc(II) Model Phosphatases. Inorg Chem 2004; 43:4189-202. [PMID: 15236530 DOI: 10.1021/ic035491d] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of pyrazolate-based dizinc(II) complexes has been synthesized and investigated as functional models for phosphoesterases, focusing on correlations between hydrolytic activity and molecular parameters of the bimetallic core. The Zn...Zn distance, the (bridging or nonbridging) position of the Zn-bound hydroxide nucleophile, and individual metal ion coordination numbers are controlled by the topology of the compartmental ligand scaffold. Species distributions of the various dizinc complexes in solution have been determined potentiometrically, and structures in the solid state have been elucidated by X-ray crystallography. The hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) promoted by the dinuclear phosphoesterase model complexes has been investigated in DMSO/buffered water (1:1) at 50 degrees C as a function of complex concentration, substrate concentration, and pH. Coordination of the phosphodiester has been followed by ESI mass spectrometry, and bidentate binding could be verified crystallographically in two cases. Drastic differences in hydrolytic activity are observed and can be attributed to molecular properties. A significant decrease of the pK(a) of zinc-bound water is observed if the resulting hydroxide is involved in a strongly hydrogen-bonded intramolecular O(2)H(3) bridge, which can be even more pronounced than for a bridging hydroxide. Irrespective of the pK(a) of the Zn-bound water, a hydroxide in a bridging position evidently is a relatively poor nucleophile, while a nonbridging hydroxide position is more favorable for hydrolytic activity. Additionally, the metal array has to provide a sufficient number of coordination sites for activating both the substrate and the nucleophile, where phosphate diesters such as BNPP preferentially bind in a bidentate fashion, requiring a third site for water binding. Product inhibition of the active site by the liberated (p-nitrophenyl)phosphate is observed, and the product-inhibited complex could be characterized crystallographically. In that complex, the phosphate monoester is found to cap a rectangular array of four zinc ions composed of two bimetallic entities.
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Affiliation(s)
- Bernhard Bauer-Siebenlist
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
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47
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Pavone M, Barone V, Ciofini I, Adamo C. First-principle molecular dynamics of the Berry pseudorotation: Insights on 19F NMR in SF4. J Chem Phys 2004; 120:9167-74. [PMID: 15267853 DOI: 10.1063/1.1707012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
First-principles [density-functional theory (DFT)] molecular-dynamic simulations of the Berry pseudorotation mechanism in SF4 were performed using the atom-centered density-matrix propagation method. The reaction was monitored by following the chemical shieldings of the fluorine atoms, computed on snapshots along the trajectories. In particular we compared the results obtained using a standard functional based on the generalized gradient approximation with those issuing from its hybrid Hartree-Fock-DFT counterpart using a number of basis sets. Our results show that both the basis set and the functional choice rule the quality of the molecular properties monitored as well as the trajectory over the potential-energy surface.
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Affiliation(s)
- Michele Pavone
- Laboratorio di Struttura e Dinamica Molecolare, Dipartimento di Chimica, Complesso Universitario Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy
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48
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Reddy P, Nethaji M, Chakravarty A. Hydrolytic Cleavage of DNA by Ternary Amino Acid Schiff Base Copper(II) Complexes Having Planar Heterocyclic Ligands. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300514] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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49
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Zhu L, dos Santos O, Koo CW, Rybstein M, Pape L, Canary JW. Geometry-dependent phosphodiester hydrolysis catalyzed by binuclear copper complexes. Inorg Chem 2004; 42:7912-20. [PMID: 14632508 DOI: 10.1021/ic0340985] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two isomeric binuclear ligands PBTPA and MBTPA and their copper(II) complexes were prepared and examined for hydrolysis of a model phosphodiester substrate: bis(p-nitrophenyl)phosphate. A bell-shaped pH vs rate profile, which is in agreement with one mechanism proposed for bimetallonucleases/phosphatases, was observed for the binuclear complex of copper(II) and PBTPA. At pH 8.4, a maximum rate of 1.14 x 10(-6) s(-1)--more than 10(4)-fold over uncatalyzed reactions--was achieved. However, the analogous complex of MBTPA did not show significant rate enhancement. The binuclear complex of copper(II) and PBTPA also showed 10-fold acceleration over mononuclear complex of copper(II) and tris(2-pyridylmethyl)amine (TPA) catalyzed reaction. A phage phiX174 DNA assay showed that the complex of copper(II) and PBTPA promoted supercoiled phage phiX174 DNA relaxation under both aerobic and anaerobic conditions, in contrast to the hydrolytic inactivity of the mononuclear complex of copper(II) and TPA.
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Affiliation(s)
- Lei Zhu
- Department of Chemistry, New York University, New York, New York 10003, USA
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50
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Affiliation(s)
- Gerard Parkin
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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