101
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Self-assembled synthesis, characterization and antimicrobial activity of zinc(II) salicylaldimine complexes. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.02.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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102
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Linear disulfide-containing low polymer as efficient DNA cleavage reagent. Bioorg Med Chem Lett 2009; 19:3458-60. [DOI: 10.1016/j.bmcl.2009.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/17/2009] [Accepted: 05/06/2009] [Indexed: 11/19/2022]
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103
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Kuzuya A, Shi Y, Tanaka K, Machida K, Komiyama M. Efficient Site-selective RNA Activation and Scission Achieved by Geometry Control of Acridine Intercalation in RNA/DNA Heteroduplex. CHEM LETT 2009. [DOI: 10.1246/cl.2009.432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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104
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Gamble C, Trotard M, Le Seyec J, Abreu-Guerniou V, Gernigon N, Berrée F, Carboni B, Felden B, Gillet R. Antiviral effect of ribonuclease conjugated oligodeoxynucleotides targeting the IRES RNA of the hepatitis C virus. Bioorg Med Chem Lett 2009; 19:3581-5. [PMID: 19450979 DOI: 10.1016/j.bmcl.2009.04.139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 04/27/2009] [Accepted: 04/27/2009] [Indexed: 02/05/2023]
Abstract
Hepatitis C virus (HCV) translation initiation is mediated by a highly structured and conserved RNA, termed the Internal Ribosome Entry Site (IRES), located at the 5'-end of its single stranded RNA genome. It is a key target for the development of new antiviral compounds. Here we made use of the recently developed HCV cell culture system to test the antiviral activity of artificial ribonucleases consisting of imidazole(s) linked to antisense oligodeoxynucleotides targeting the HCV IRES. Results from the cell culture model indicate that the naked antisense oligodeoxynucleotide displayed an efficient antiviral activity. Despite the increased activity observed with the addition of imidazole moieties when tested with the cell-free system, it appears that these improvements were not reproduced in the cellular model.
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Affiliation(s)
- Carly Gamble
- Université de Rennes 1, UPRES JE 2311, INSERM U835, Biochimie Pharmaceutique, 2, Avenue du Prof. Léon Bernard, 35043 Rennes, France
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105
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+). Nucleic Acids Res 2009; 37:1638-49. [PMID: 19153138 PMCID: PMC2655665 DOI: 10.1093/nar/gkn1070] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 12/04/2022] Open
Abstract
The selection of modified DNAzymes represents an important endeavor in expanding the chemical and catalytic properties of catalytic nucleic acids. Few examples of such exist and to date, there is no example where three different modified bases have been simultaneously incorporated for catalytic activity. Herein, dCTP, dATP and dUTP bearing, respectively, a cationic amine, an imidazole and a cationic guanidine, were enzymatically polymerized on a DNA template for the selection of a highly functionalized DNAzyme, called DNAzyme 9-86, that catalyzed (M(2+))-independent self-cleavage under physiological conditions at a single ribo(cytosine)phosphodiester linkage with a rate constant of (0.134 +/- 0.026) min(-1). A pH rate profile analysis revealed pK(a)'s of 7.4 and 8.1, consistent with both general acid and base catalysis. The presence of guanidinium cations permits cleavage at significantly higher temperatures than previously observed for DNAzymes with only amines and imidazoles. Qualitatively, DNAzyme 9-86 presents an unprecedented ensemble of synthetic functionalities while quantitatively it expresses one of the highest reported values for any self-cleaving nucleic acid when investigated under M(2+)-free conditions at 37 degrees C.
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Affiliation(s)
| | | | | | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T 1Z1, Canada
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106
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107
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Razkin J, Lindgren J, Nilsson H, Baltzer L. Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs. Chembiochem 2008; 9:1975-84. [PMID: 18600814 DOI: 10.1002/cbic.200800057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HJ1, a 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle, successfully catalyzes the cleavage of "early stage" DNA model substrates in an aqueous solution at pH 7.0, with a rate enhancement in the hydrolysis of heptyl 4-nitrophenyl phosphate of over three orders of magnitude over that of the imidazole-catalyzed reaction, k(2)(HJ1)/k(2)(Im) = 3135. The second-order rate constant, k(2)(HJ1) was determined to be 1.58x10(-4) M(-1) s(-1). The catalyst successfully assembles residues that in a single elementary reaction step are capable of general-acid and general-base catalysis as well as transition state stabilization and proximity effects. The reactivity achieved with the HJ1 polypeptide, rationally designed to catalyze the hydrolysis of phosphodiesters, is based on two histidine residues flanked by four arginines and two adjacent tyrosine residues, all located on the surface of a helix-loop-helix motif. The introduction of Tyr residues close to the catalytic site improves efficiency, in the cleavage of activated aryl alkyl phosphates as well as less activated dialkyl phosphates. HJ1 is also effective in the cleavage of an RNA-mimic substrate, uridine-3'-2,2,2-trichloroethyl phosphate (leaving group pK(a) = 12.3) with a second-order rate constant of 8.23x10(-4) M(-1) s(-1) in aqueous solution at pH 7.0, some 500 times faster than the reaction catalyzed by imidazole, k(2)(HJ1)/k(2)(Im) = 496.
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Affiliation(s)
- Jesus Razkin
- Department of Applied Chemistry, Public University of Navarra, 31006 Pamplona, Navarra, Spain.
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108
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Macchion BN, Strömberg R, Nilsson L. Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes. J Biomol Struct Dyn 2008; 26:163-73. [PMID: 18597538 DOI: 10.1080/07391102.2008.10507232] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Molecular dynamics simulations of RNA molecules consisting of an antisense oligonucleotide forming a complex with a target strand thereby creating an internal bulge-loop with 3, 4, or 5 nucleotides have been performed with and without O2' methylation of the antisense strand. The methylation influences minor groove hydration, in particular near guanines but also around the methylated O2', and it also reduces the flexibility of both RNA strands. A G.U wobble pair adjacent to the bulge-loop is also found to increase the flexibility of the bulge nucleotides, compared to the situation with a standard Watson-Crick G-C base-pair in the same position.
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Affiliation(s)
- Boel Nyström Macchion
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden
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109
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Bonomi R, Selvestrel F, Lombardo V, Sissi C, Polizzi S, Mancin F, Tonellato U, Scrimin P. Phosphate Diester and DNA Hydrolysis by a Multivalent, Nanoparticle-Based Catalyst. J Am Chem Soc 2008; 130:15744-5. [DOI: 10.1021/ja801794t] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renato Bonomi
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Francesco Selvestrel
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Valentina Lombardo
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Claudia Sissi
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Stefano Polizzi
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Umberto Tonellato
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
| | - Paolo Scrimin
- Dipartimento di Scienze Chimiche and CNR-ITM, Università di Padova, Padova, Italy, Dipartimento di Scienze Farmaceutiche, Università di Padova, Padova, Italy, and Dipartimento di Chimica Fisica, Università di Venezia, Venice, Italy
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110
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Murtola M, Strömberg R. PNA based artificial nucleases displaying catalysis with turnover in the cleavage of a leukemia related RNA model. Org Biomol Chem 2008; 6:3837-42. [PMID: 18843415 DOI: 10.1039/b810106j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several peptide nucleic acid based artificial nucleases (PNAzymes) are designed to create a bulge in the target RNA, which is a short model of the leukemia related bcr/abl mRNA. The target RNA is cleaved by the PNAzymes with a half-life of down to 11 h (using a 1 : 1 ratio of PNA-conjugate to target) and only upon base-pairing with the substrate. The PNA based systems are also shown to act in a catalytic fashion with turnover of substrate and are thus the first reported peptide nucleic acid based artificial RNA-cleaving enzymes.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet Novum, 14157 Huddinge, Sweden
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111
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Murtola M, Ossipov D, Sandbrink J, Strömberg R. RNA cleavage by 2,9-diamino-1,10-phenanthroline PNA conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1479-83. [PMID: 18066810 DOI: 10.1080/15257770701542769] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report on the synthesis of 2,9-diamino-1,10-phenanthroline PNA conjugates as well as on their action in cleavage of a target RNA. Synthesis of the PNA conjugates are performed on solid support and the phenanthroline derivative is conjugated either to the amino-end or to a centrally positioned diaminopropionic acid in the PNA via a urea linker. Cleavage of the target RNA is achieved and compared to cleavage with the corresponding 2,9-dimethyl-1,10-phenanthroline and glycine conjugates.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, NOVUM, S-14157 Huddinge, Sweden
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112
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Ketomäki K, Virta P. Synthesis of aminoglycoside conjugates of 2'-O-methyl oligoribonucleotides. Bioconjug Chem 2008; 19:766-77. [PMID: 18281927 DOI: 10.1021/bc7004279] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aminoglycoside conjugates of 2'- O-methyl oligoribonucleotides have been synthesized entirely on a solid phase using conventional phosphoramidate chemistry. For this purpose, appropriately protected neamine-derived phosphoramidites, viz., 2-cyanoethyl [6,3',4'-tri- O-levulinoyl- N (1), N (3), N (2) (') , N (6) (') -tetra(trifluoroacetyl)neamine-5- O-ethyl] N,N-diisopropylphosphoramidite, 1, and 2-cyanoethyl [6,3',4',2'',3''-penta- O-levulinoyl- N (1), N (3), N (2) (') , N (6) (') -tetra(trifluoroacetyl) ribostamycin-5''-yl] N, N-diisopropylphosphoramidite, 2, have been prepared and attached via phosphodiester linkage to an appropriate 2'- O-methyl oligoribonucleotide. Levulinoyl esters are used to cap the hydroxyl groups of the aminoglycoside moieties, since they may be selectively removed prior to ammonolysis. In this manner, the potential O-->N acyl migration is excluded. Applicability of the strategy has been demonstrated by the synthesis of eight different aminoglycoside conjugates, in which 1 and 2 are attached directly to the 5'-end ( 6 and 10) or, alternatively, to an inserted non-nucleosidic hydroxyalkyl armed branching unit ( 3, 4, or 5), which results in intrachain conjugates ( 7- 9, 11- 13). The potential of these conjugates to act as a sequence-selective artificial nuclease has been studied.
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Affiliation(s)
- Kaisa Ketomäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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113
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Orth ES, Brandão TAS, Milagre, Eberlin MN, Nome F. Intramolecular Acid−Base Catalysis of a Phosphate Diester: Modeling the Ribonuclease Mechanism. J Am Chem Soc 2008; 130:2436-7. [DOI: 10.1021/ja710693x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elisa S. Orth
- Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil. ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil
| | - Tiago A. S. Brandão
- Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil. ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil
| | - Milagre
- Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil. ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil
| | - Marcos N. Eberlin
- Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil. ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil
| | - Faruk Nome
- Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brazil. ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil
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114
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Bal-Demirci T. Synthesis, spectral characterization of the zinc(II) mixed-ligand complexes of N(4)-allyl thiosemicarbazones and N,N,N′,N′-tetramethylethylenediamine, and crystal structure of the novel [ZnL2(tmen)] compound. Polyhedron 2008. [DOI: 10.1016/j.poly.2007.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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115
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Kalek M, Benediktson P, Vester B, Wengel J. Identification of efficient and sequence specific bimolecular artificial ribonucleases by a combinatorial approach. Chem Commun (Camb) 2008:762-4. [DOI: 10.1039/b712532a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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116
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Efficient enhancement of DNA cleavage activity by introducing guanidinium groups into diiron(III) complex. Bioorg Med Chem Lett 2008; 18:109-13. [DOI: 10.1016/j.bmcl.2007.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 10/19/2007] [Accepted: 11/01/2007] [Indexed: 11/18/2022]
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117
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Guerniou V, Gillet R, Berrée F, Carboni B, Felden B. Targeted inhibition of the hepatitis C internal ribosomal entry site genomic RNA with oligonucleotide conjugates. Nucleic Acids Res 2007; 35:6778-87. [PMID: 17921501 PMCID: PMC2175329 DOI: 10.1093/nar/gkm770] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Hepatitis C is a major public health concern, with an estimated 170 million people infected worldwide and an urgent need for new drug development. An attractive therapeutic approach is to prevent the ‘cap-independent’ translation initiation of the viral proteins by interfering with both the structure and function of the hepatitis C viral internal ribosomal entry site (HCV IRES). Towards this goal, we report the design, synthesis and purification of novel bi-functional molecules containing DNA or RNA antisenses attached to functional groups performing RNA hydrolysis. These 5′ or 3′-coupled conjugates bind the HCV IRES with affinity and specificity and elicit targeted hydrolysis of the viral genomic RNA after short (1 h) incubation at low (500 nM) concentration at 37°C in vitro. Additional secondary cleavage sites are induced and their mapping within the RNA structure indicates that functional domains IIIb-e are excised from the IRES that, based on cryo-EM studies, becomes incapable of binding the small ribosomal subunit and initiation factor 3 (eIF3). All these molecules inhibit, in a dose-dependent manner, the ‘IRES-dependent’ translation in vitro. The 5′-coupled imidazole conjugate reduces viral protein synthesis by half at a 300 nM concentration (IC50), corresponding to a 4-fold increase of activity when compared to the naked oligonucleotide. These new conjugates are now being tested for activity on infected hepatic cell lines.
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Affiliation(s)
- Valérie Guerniou
- Biochimie Pharmaceutique, Inserm U835, Upres JE 2311, Université de Rennes 1, France
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118
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Niittymäki T, Virta P, Ketomäki K, Lönnberg H. Di(azacrown) conjugates of 2'-O-methyl oligoribonucleotides as sequence-selective artificial ribonucleases. Bioconjug Chem 2007; 18:1583-92. [PMID: 17711318 DOI: 10.1021/bc070071o] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functionalized 2'-O-methyl oligoribonucleotides bearing two 3-(3-hydroxypropyl)-1,5,9-triazacyclododecane ligands attached via a phosphodiester linkage to a single non-nucleosidic building block have been prepared on a solid-support by conventional phosphoramidite chemistry. The branching units employed for the purpose include 2,2-bis(3-hydroxypropylaminocarbonyl)propane-1,3-diol, 2-hydroxyethyl 3'-O-(2-hydroxyethyl)-beta-D-ribofuranoside, and 2-hydroxyethyl 2'-O-(2-hydroxyethyl)-beta-D-ribofuranoside. Each of these has been introduced as a phosphoramidite reagent either into the penultimate 3'-terminal site or in the middle of the oligonucleotide chain. The dinuclear Zn2+ complexes of these conjugates have been shown to exhibit enhanced catalytic activity over their monofunctionalized counterpart, the 3'-terminal conjugate derived from 2-hydroxyethyl 3'-O-(2-hydroxyethyl)-beta-D-ribofuranoside being the most efficient cleaving agent. This conjugate cleaves an oligoribonucleotide target at a single phosphodiester bond and shows turnover and 1000-fold cleaving activity compared to the free monomeric Zn2+ chelate of 1,5,9-triazacyclododecane.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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119
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Kalek M, Madsen AS, Wengel J. Effective modulation of DNA duplex stability by reversible transition metal complex formation in the minor groove. J Am Chem Soc 2007; 129:9392-400. [PMID: 17616191 DOI: 10.1021/ja071076z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we describe the reversible changing of DNA duplex thermal stability by exploiting transition metal complexation phenomena. A terpyridine ligand was conjugated to the N2'-atoms of 2'-amino-2'-deoxyuridine and its locked counterpart 2'-amino-LNA, and these metal-complexing monomers were incorporated into oligodeoxyribonucleotides. Upon addition of varying amounts of transition metal ions, the thermal stability of DNA duplexes containing these terpyridine-functionalized units in different constitutions was affected to different degrees (DeltaTm values = -15.5 to +49.0 degrees C, relative to the unmodified duplex). The most pronounced effects were observed when two complexing monomers were positioned in opposite strands. Addition of 1 equiv of Ni2+ to such a system induced extraordinary duplex stabilization. Molecular modeling studies suggest, as an explanation for this phenomenon, formation of nickel-mediated interstrand linkages in the minor groove. Addition of an excess of metal ions resulted in largely decreased Tm values. Alternating addition of metal ions and EDTA demonstrated reversibility of metal ion-induced changes in hybridization strength, proving that the described approach provides an efficient method for duplex stability modulation.
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Affiliation(s)
- Marcin Kalek
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense M, Denmark
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120
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Rossiter CS, Mathews RA, Morrow JR. Cleavage of an RNA analog by Zn(II) macrocyclic catalysts appended with a methyl or an acridine group. J Inorg Biochem 2007; 101:925-34. [PMID: 17462740 DOI: 10.1016/j.jinorgbio.2007.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 02/18/2007] [Accepted: 03/11/2007] [Indexed: 11/25/2022]
Abstract
Two macrocycles (1 and 2) are prepared that incorporate pendent groups in macrocycle 3 (3=1-oxa-4,7,10-triazacyclododecane) with the goal of studying the effect of these pendent groups on metal ion complexation, solution chemistry and catalysis. Zn(1) contains a macrocyclic ligand with a pendent acridine group and Zn(2) has an appended methyl group. Water ligand pK(a) values for Zn(1) (6.7) and Zn(2) (7.3) are lower than that of Zn(3) (7.7). Zn(II) complexes of 1 and 2 are studied as catalysts for the cleavage of 2-hydroxypropyl 4-nitrophenylphosphate (HpPNP), an RNA analog. Zn(2) has a lower catalytic activity over the pH range 7-10 for cleavage of HpPNP compared to the parent macrocyclic complex, Zn(3). In contrast, Zn(1) has a threefold larger rate constant at pH 7.0 compared to Zn(2), attributed to the presence of a catalytic species which has a protonated acridine amino group. The binding constant of 1.5mM at pH 8.0 for formation of the Zn(2)-uridine adduct is similar to that for Zn(3), suggesting that N-alkylation of the macrocyclic ligand does not interfere with binding of the Zn(II) complex to uridine groups. Binding of cytidine to Zn(2) was not detectable under similar conditions up to 25mM nucleoside. Binding experiments under similar conditions could not be carried out for adenosine or guanosine due to their low solubility.
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Affiliation(s)
- Clifford S Rossiter
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, NY 14260, United States
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121
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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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122
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Synthesis of oligo-2′-O-methylribonucleotides containing α-amino acid residues in 2′-position. Russ Chem Bull 2007. [DOI: 10.1007/s11172-007-0120-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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123
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Cacciapaglia R, Casnati A, Mandolini L, Reinhoudt DN, Salvio R, Sartori A, Ungaro R. Di- and trinuclear arrangements of zinc(II)-1,5,9-triazacyclododecane units on the calix[4]arene scaffold: Efficiency and substrate selectivity in the catalysis of ester cleavage. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.07.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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124
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Mancin F, Tecilla P. Zinc(ii) complexes as hydrolytic catalysts of phosphate diester cleavage: from model substrates to nucleic acids. NEW J CHEM 2007. [DOI: 10.1039/b703556j] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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125
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Bianké G, Chaurin V, Egorov M, Lebreton J, Constable EC, Housecroft CE, Häner R. Copper Complex-Assisted DNA Hybridization. Bioconjug Chem 2006; 17:1441-6. [PMID: 17105222 DOI: 10.1021/bc0601830] [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: 11/29/2022]
Abstract
2,2'-Bipyridine (bpy) or 1,10-phenanthroline (phen) metal-binding domains were covalently attached to oligonucleotides, and the influence of metal ions on the hybridization of the conjugates was investigated. Metal-binding domains were attached to oligonucleotides at 3'- and 5'-terminal positions, thus placing them in juxtaposed positions after hybridization to a common target strand. While the ligands alone had a positive effect (increased Tm) on hybrid stability, the duplex was further stabilized by the addition of copper(I) and/or copper(II) through the formation of a metal complex in which the two short sequences are linked through {Cu(bpy)2}, {Cu(phen)}, or {Cu(bpy)(phen)} domains. The increase in Tm, due to formation of the {Cu(bpy)2}, {Cu(phen)2}, {Cu(bpy)(phen)} motifs is reversed upon addition of EDTA, consistent with the stripping of copper from the ligands. The effect of metal complex formation on the duplex strength was shown to be highest if the two metal-coordinating ligand strands are placed as close to each other as possible.
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Affiliation(s)
- Gapian Bianké
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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126
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Kovalev N, Burakova E, Silnikov V, Zenkova M, Vlassov V. Artificial ribonucleases: from combinatorial libraries to efficient catalysts of RNA cleavage. Bioorg Chem 2006; 34:274-86. [PMID: 16889817 DOI: 10.1016/j.bioorg.2006.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/21/2006] [Accepted: 06/21/2006] [Indexed: 11/23/2022]
Abstract
Combinatorial libraries of small organic compounds capable of cleaving RNA were synthesized. The compounds contain benzene ring substituted with two residues of bis quaternary salt of diazabicyclo[2.2.2]octane (DABCO) bearing hydrophobic fragments of different length and structure, attached to DABCO at the bridge position. These compounds, lacking traditional functionalities involved in transesterification reaction, exhibit pronounced RNA cleavage activity. To identify the most active artificial ribonucleases, sublibraries and truncated libraries, containing compounds lacking one of substituents were synthesized. Analysis of ribonuclease activity of truncated libraries resulted in identification of the most active compounds, which are characterized by the presence of at least one long oligomethylene substituent.
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Affiliation(s)
- N Kovalev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
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127
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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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128
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Editorial. Org Biomol Chem 2006. [DOI: 10.1039/b516549k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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