1
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Putnam WC, Bashkin JK. Oligonucleotides containing abasic threoninol-terpyridine residues as potential artificial ribonucleases. J Inorg Biochem 2022; 232:111831. [DOI: 10.1016/j.jinorgbio.2022.111831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022]
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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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Kuzuya A, Machida K, Shi Y, Tanaka K, Komiyama M. Site-Selective RNA Activation by Acridine-Modified Oligodeoxynucleotides in Metal-Ion Catalyzed Hydrolysis: A Comprehensive Study. ACS OMEGA 2017; 2:5370-5377. [PMID: 31457805 PMCID: PMC6644747 DOI: 10.1021/acsomega.7b00966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/21/2017] [Indexed: 06/10/2023]
Abstract
Various types of acridine were conjugated to DNA and used for site-selective RNA scission together with another unmodified DNA and a Lu(III) ion. The target phosphodiester linkage in the substrate RNA was selectively and efficiently activated, and was hydrolyzed by the free Lu(III) ion. Among the investigated 14 conjugates, the conjugate bearing 9-amino-2-isopropoxy-6-nitroacridine was the best RNA-activator. Systematic evaluation of the RNA-activating ability of the acridines showed that (1) the acridines act as an acid catalyst within the RNA activation, (2) the amino-group at the 9-position of acridine is essential to modulate the acidity of acridine, (3) the electron-withdrawing group at the 3-position further enhances the acid catalysis, and (4) the substituent at the 2-position sterically modulates the orientation of acridine-intercalation favorably for the catalysis. Moreover, it is revealed that the opposite base of acridine does not inhibit direct interaction of acridine with the target phosphodiester linkage.
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Affiliation(s)
- Akinori Kuzuya
- Department
of Chemistry and Materials Engineering, Kansai University, 3-3-35
Yamate, Suita, Osaka 564-8680, Japan
| | - Kenzo Machida
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Yun Shi
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Keita Tanaka
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- International
Center for Materials Nanoarchitechtonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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5
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Hossain MM, Shyu SG. Biphasic copper-catalyzed C–H bond activation of arylalkanes to ketones with tert-butyl hydroperoxide in water at room temperature. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.05.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Williams A, Staroseletz Y, Zenkova MA, Jeannin L, Aojula H, Bichenkova EV. Peptidyl-oligonucleotide conjugates demonstrate efficient cleavage of RNA in a sequence-specific manner. Bioconjug Chem 2015; 26:1129-43. [PMID: 25955796 DOI: 10.1021/acs.bioconjchem.5b00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Described here is a new class of peptidyl-oligonucleotide conjugates (POCs) which show efficient cleavage of a target RNA in a sequence-specific manner. Through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to amphiphilic peptide sequences containing leucine, arginine, and glycine, zero-linker conjugates are created which exhibit targeted phosphodiester cleavage under physiological conditions. tRNA(Phe) from brewer's yeast was used as a model target sequence in order to probe different structural variants of POCs in terms of selective TΨC-arm directed cleavage. Almost quantitative (97-100%) sequence-specific tRNA cleavage is observed for several POCs over a 24 h period with a reaction half-life of less than 1 h. Nontargeted cleavage of tRNA(Phe) or HIV-1 RNA is absent. Structure-activity relationships reveal that removal of the peptide's central glycine residue significantly decreases tRNA cleavage activity; however, this can be entirely restored through replacement of the peptide's C-terminal carboxylic acid group with the carboxamide functionality. Truncation of the catalytic peptide also has a detrimental effect on POC activity. Based on the encouraging results presented, POCs could be further developed with the aim of creating useful tools for molecular biology or novel therapeutics targeting specific messenger, miRNA, and genomic viral RNA sequences.
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Affiliation(s)
- Aled Williams
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Yaroslav Staroseletz
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Marina A Zenkova
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Laurent Jeannin
- §Peptisyntha S.A., 310 Rue de Ransbeek, 1120 Brussels, Belgium
| | - Harmesh Aojula
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Elena V Bichenkova
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
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7
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Niittymäki T, Burakova E, Laitinen E, Leisvuori A, Virta P, Lönnberg H. Zn2+Complexes of 3,5-Bis[(1,5,9-triazacyclododecan-3-yloxy)methyl]phenyl Conjugates of Oligonucleotides as Artificial RNases: The Effect of Oligonucleotide Conjugation on Uridine Selectivity of the Cleaving Agent. Helv Chim Acta 2013. [DOI: 10.1002/hlca.201200153] [Citation(s) in RCA: 3] [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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8
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Desbouis D, Troitsky IP, Belousoff MJ, Spiccia L, Graham B. Copper(II), zinc(II) and nickel(II) complexes as nuclease mimetics. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Tang SP, Chen S, Wu GF, Chen HY, Mao ZW, Ji LN. Ester catalytic hydrolysis by a tridentate N,N′,N″-copper bridged cyclodextrin dimer. INORG CHEM COMMUN 2011. [DOI: 10.1016/j.inoche.2010.10.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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11
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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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12
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Dijk EW, Feringa BL, Roelfes G. DNA in Metal Catalysis. TOP ORGANOMETAL CHEM 2008. [DOI: 10.1007/3418_2008_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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McCrory CCL, Ottenwaelder X, Stack TDP, Chidsey CED. Kinetic and Mechanistic Studies of the Electrocatalytic Reduction of O2 to H2O with Mononuclear Cu Complexes of Substituted 1,10-Phenanthrolines. J Phys Chem A 2007; 111:12641-50. [DOI: 10.1021/jp076106z] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - T. Daniel P. Stack
- Department of Chemistry, Stanford University, Stanford, California 94305
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14
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Ma Q, Xu Z, Schroeder BR, Sun W, Wei F, Hashimoto S, Konishi K, Leitheiser CJ, Hecht SM. Biochemical evaluation of a 108-member deglycobleomycin library: viability of a selection strategy for identifying bleomycin analogues with altered properties. J Am Chem Soc 2007; 129:12439-52. [PMID: 17887752 DOI: 10.1021/ja0722729] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bleomycins (BLMs) are clinically used glycopeptide antitumor antibiotics that have been shown to mediate the sequence-selective oxidative damage of both DNA and RNA. Previously, we described the solid-phase synthesis of a library of 108 unique analogues of deglycoBLM A6, a congener that cleaves DNA analogously to BLM itself. Each member of the library was assayed for its ability to effect single- and double-strand nicking of duplex DNA, sequence-selective DNA cleavage, and RNA cleavage in the presence and absence of a metal ion cofactor. All of the analogues tested were found to mediate concentration-dependent plasmid DNA relaxation to some extent, and a number exhibited double-strand cleavage with an efficiency comparable to or greater than deglycoBLM A6. Further, some analogues having altered linker and metal-binding domains mediated altered sequence-selective cleavage, and a few were found to cleave a tRNA3Lys transcript both in the presence and in the absence of a metal cofactor. The results provide insights into structural elements within BLM that control DNA and RNA cleavage. The present study also permits inferences to be drawn regarding the practicality of a selection strategy for the solid-phase construction and evaluation of large libraries of BLM analogues having altered properties.
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Affiliation(s)
- Qian Ma
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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15
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Ghatnekar J, Hägerlöf M, Oredsson S, Alm K, Elmroth SKC, Persson T. Construction of polyamine-modified uridine and adenosine derivatives--evaluation of DNA binding capacity and cytotoxicity in vitro. Bioorg Med Chem 2007; 15:7426-33. [PMID: 17869123 DOI: 10.1016/j.bmc.2007.07.030] [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: 04/30/2007] [Revised: 07/05/2007] [Accepted: 07/10/2007] [Indexed: 11/27/2022]
Abstract
We here report the synthesis of the two polyamine-based nucleoside derivatives 5-{[bis-(3-aminopropyl)amino]acetamido-1-propynyl}uridine and 2-{[bis-(3-aminopropyl)amino]-acetamido-1-propynyl}adenosine. The various polyamine derivatives have been used in thermal melting analysis using DNA from herring testes, and in cellular studies using four different cell lines. The compounds were all found to be non-toxic, thus holding good promise for future use as siRNA building blocks.
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Affiliation(s)
- Johannes Ghatnekar
- Organic Chemistry, Chemical Center, Lund Univesity, PO Box 124, SE-22100 Lund, Sweden
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16
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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17
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Mironova NL, Pyshnyi DV, Stadler DV, Prokudin IV, Boutorine YI, Ivanova EM, Zenkova MA, Gross HJ, Vlassov VV. G-specific RNA-cleaving conjugates of short peptides and oligodeoxyribonucleotides. J Biomol Struct Dyn 2006; 23:591-602. [PMID: 16615805 DOI: 10.1080/07391102.2006.10507084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Artificial ribonucleases, conjugates of short oligodeoxyribonucleotides and peptides built of arginine, leucine, proline, and serine, were synthesized and assessed in terms of ribonuclease activity and specificity of RNA cleavage. A specific group of the conjugates was identified that display T1-ribonuclease-like activity and cleave RNA predominantly at G-X sequences. Circular dichroism study of the structures of the most active conjugates, free peptide (LR)4G, and oligonucleotides revealed that conjugation of oligonucleotide to the peptide results in a specific peptide folding that possibly provides ribonuclease activity to the conjugate.
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Affiliation(s)
- Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Russian Federation, Novosibirsk, 630090
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18
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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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19
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Putnam WC, Bashkin JK. Synthesis and evaluation of RNA transesterification efficiency using stereospecific serinol-terpyridine conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1309-23. [PMID: 16252668 DOI: 10.1080/15257770500230426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Six novel artificial ribonucleases were synthesized employing a stereochemically pure abasic serinol backbone residue for attachment of the RNA transesterification agent copper(II) terpyridine. These stereochemically pure abasic residues were synthesized as phosphoramidite building blocks from the parent L-serine and D-serine starting building blocks and incorporated into oligonucleotides via solid-phase DNA synthesis. These artificial ribonucleases were constructed to determine if the stereochemistry of the alpha carbon of an abasic serinol residue has influence over RNA transesterification through selective placement of a pendant transesterification agent in either the major or minor groove. The novel artificial ribonucleases and previously synthesized artificial ribonucleases were challenged with a 28-mer and 159-mer RNA substrate. It was determined that the stereochemistry of the carbon atom derived from the alpha-carbon of serine did not influence the extent of cleavage in these studies using copper(II) terpyridine conjugated artificial ribonucleases.
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Affiliation(s)
- William C Putnam
- Department of Chemistry, Washington University, St. Louis, Missouri, USA.
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20
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Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
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21
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Schiller A, Scopelliti R, Benmelouka M, Severin K. Highly Cross-linked Polymers Containing N,N‘,N‘ ‘-Chelate Ligands for the Cu(II)-Mediated Hydrolysis of Phosphoesters. Inorg Chem 2005; 44:6482-92. [PMID: 16124831 DOI: 10.1021/ic0504588] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three immobilized Cu(II) complexes were generated by the following: (a) homopolymerization of the N,N',N' '-chelate ligand tris[2-(1-vinylimidazolyl)]phosphine (1) and subsequent metalation with CuCl2; (b) copolymerization of 1 with ethyleneglycol dimethacrylate (EGDMA) und subsequent metalation with CuCl2; or (c) molecular imprinting with the organometallic Mo-complex [Mo(eta3-C4H7)(CO)2(1)](TsO) (5) and EGDMA and subsequent replacement of Mo(II) by Cu(II). All three polymeric Cu complexes were found to efficiently promote the hydrolysis of activated phosphoesters with the relative activity being dependent on the nature of the polymer and the substrate.
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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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22
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Nakano SI, Uotani Y, Uenishi K, Fujii M, Sugimoto N. Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside. J Am Chem Soc 2004; 127:518-9. [PMID: 15643864 DOI: 10.1021/ja045445s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
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23
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Shi Y, Niikura F, Kuzuya A, Komiyama M. Noncovalent Combination of Oligoamine and Oligonucleotide as Totally Organic Site-selective RNA Cutter. CHEM LETT 2004. [DOI: 10.1246/cl.2004.1012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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24
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Aström H, Strömberg R. Synthesis of new OBAN's and further studies on positioning of the catalytic group. Org Biomol Chem 2004; 2:1901-7. [PMID: 15227543 DOI: 10.1039/b403652b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two new zinc ion dependent oligonucleotide based artificial nucleases (OBAN's) have been synthesized. These consist of 2'-O-methyl modified RNA oligomers conjugated to 5-amino-2,9-dimethylphenanthroline (neocuproine)via a urea linker. OBAN 4 carries the catalytic group on a linker extending from the C-4 of an internal cytosine moiety. OBAN 5 has two neocuproine units attached, each to linkers extending from the C-5 position of uridine moieties, one placed internally and the other at the at the 5'-end of the oligonucleotide. The key step in the synthesis of the OBAN systems is conjugation of the catalytic group to the respective amino linkers of the modified oligonucleotides. This is achieved by first converting the 5-amino-2,9-dimethylphenanthroline to the phenylcarbamate. The reaction of this neocuproine phenylcarbamate with the oligonucleotide carrying one or two primary aliphatic amines in aqueous buffer (at pH 8.5) leads to nearly quantitative formation of the urea-linked conjugates. Both OBAN systems were found to cleave RNA in the bulged out regions formed from the non-complementary part of the target sequences, in the presence of Zn(II) ions. Differences in efficiency between these and previously reported systems are discussed.
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Affiliation(s)
- Hans Aström
- Division of Organic and Bioorganic Chemistry, MBB, Scheele Laboratory, Karolinska Institutet, S-17177, Stockholm, Sweden
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25
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Kuzuya A, Mizoguchi R, Sasayama T, Zhou JM, Komiyama M. Selective activation of two sites in RNA by acridine-bearing oligonucleotides for clipping of designated RNA fragments. J Am Chem Soc 2004; 126:1430-6. [PMID: 14759201 DOI: 10.1021/ja0389568] [Citation(s) in RCA: 21] [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
Artificial enzymes for selective scission of RNA at two designated sites, which are valuable for advanced RNA science, have been prepared by combining lanthanide(III) ion with an oligonucleotide bearing two acridine groups. When these modified oligonucleotides form heteroduplexes with substrate RNA, the two phosphodiester linkages in front of the acridines are selectively activated and preferentially hydrolyzed by lanthanide ion. This two-site RNA scission does not require any specific RNA sequence at the scission sites, and the length of clipped RNA fragment is easily and precisely controllable by changing the distance between two acridine groups in the modified oligonucleotide. The two-site scission is also successful even when the substrate RNA has higher-order structures. By using these two-site RNA cutters, RNA fragments of predetermined length were obtained from long RNA substrates and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Single nucleotide polymorphisms in homozygous and heterozygous samples were accurately and easily detected in terms of the difference in mass number. Multiplex analyses of in vitro transcripts from human genome were also successful.
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Affiliation(s)
- Akinori Kuzuya
- 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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DNA and RNA Cleavage Mediated by Phenanthroline-Cuprous Oligonucleotides: From Properties to Applications. ARTIFICIAL NUCLEASES 2004. [DOI: 10.1007/978-3-642-18510-6_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Gunnlaugsson T, Nieuwenhuyzen M, Nolan C. Synthesis, X-ray crystallographic, spectroscopic investigation and cleavage studies of HPNP by simple bispyridyl iron, copper, cobalt, nickel and zinc complexes as artificial nucleases. Polyhedron 2003. [DOI: 10.1016/s0277-5387(03)00471-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Yamamoto Y, Tsuboi W, Komiyama M. Oligoamine-acridine conjugates for promotion of gap-selective DNA hydrolysis by Ce(IV)/EDTA complex. Nucleic Acids Res 2003; 31:4497-502. [PMID: 12888510 PMCID: PMC169895 DOI: 10.1093/nar/gkg634] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Oligoamines (spermidine, dipropylenetriamine and propylenediamine) were covalently attached to acridine via a hexamethylene linker. These oligoamine-acridine conjugates were efficiently bound to gap sites in substrate DNA, and promoted the DNA hydrolysis by a homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (EDTA) complex at these sites. In contrast, the hydrolysis of the double-stranded portion in the DNA was little affected by these conjugates, although they were strongly bound thereto by the intercalation of their acridine moieties. As a result, the gap site was selectively and efficiently hydrolyzed by combining the Ce(IV)/EDTA complex with the oligoamine--acridine conjugate. Either the oligoamine or the acridine was only poorly active for the purpose, substantiating the essential role of cooperation between them. The promotion of gap-selective DNA hydrolysis by the conjugates has been ascribed to electrostatic stabilization of a negatively charged transition state by their positive charges.
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Affiliation(s)
- Yoji Yamamoto
- 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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Shi Y, Kuzuya A, Komiyama M. Stereochemically Pure Acridine-modified DNA for Site-selective Activation and Scission of RNA. CHEM LETT 2003. [DOI: 10.1246/cl.2003.464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Synthesis, structural and biological evaluation of GlyAla based lanthanide macrocyclic conjugates as supramolecular ribonuclease mimics. Polyhedron 2003. [DOI: 10.1016/s0277-5387(02)01402-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Whitney A, Gavory G, Balasubramanian S. Site-specific cleavage of human telomerase RNA using PNA-neocuproine.Zn(II) derivatives. Chem Commun (Camb) 2003:36-7. [PMID: 12610953 DOI: 10.1039/b210135a] [Citation(s) in RCA: 24] [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
Here we report the synthesis of a novel PNA based neocuproine.Zn RNA cleaving agent; we demonstrate that such agents sequence specifically cleave a synthetic RNA target and in particular the RNA component of human telomerase.
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Affiliation(s)
- Andrew Whitney
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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Kitamura Y, Komiyama M. Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex. Nucleic Acids Res 2002; 30:e102. [PMID: 12364619 PMCID: PMC140562 DOI: 10.1093/nar/gnf101] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A new strategy for site-selective DNA hydrolysis, which takes advantage of the difference in reactivity between the phosphodiester linkages at the target site and the others, is presented. As the molecular scissors, homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (EDTA) complex is used without being bound to any sequence-recognizing moiety. When a gap structure is formed at the target site by using two short oligonucleotides and the composite is treated with the Ce(IV)/EDTA complex at pH 7.0 and 37 degrees C, the gap site in the substrate DNA is preferentially hydrolyzed over the double-stranded portion of the DNA. Site-selective DNA scission is also achieved by forming a bulge structure at the target site with the use of the appropriate oligonucleotide. These site-selective scissions are based on the following two factors: (i) the phosphodiester linkages in a single-stranded DNA are far more susceptible to the hydrolysis by the Ce(IV) complex than are the linkages in double-stranded DNA, and (ii) the phosphodiester linkages in the bulge sites are still more reactive than those in single-stranded DNA. In both cases, the addition of spermine significantly accelerates the scission.
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Affiliation(s)
- Yoshihito Kitamura
- 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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Kuzuya A, Mizoguchi R, Morisawa F, Machida K, Komiyama M. Metal ion-induced site-selective RNA hydrolysis by use of acridine-bearing oligonucleotide as cofactor. J Am Chem Soc 2002; 124:6887-94. [PMID: 12059210 DOI: 10.1021/ja025653p] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New types of noncovalent ribozyme-mimics for site-selective RNA scission are prepared by combining metal ions with oligonucleotides bearing an acridine. Lanthanide(III) ions and various divalent metal ions (Zn(II), Mn(II), Cu(II), Ni(II), Co(II), Mg(II), and Ca(II)) are employed without being bound to any sequence-recognizing moiety. The modified oligonucleotide forms a heteroduplex with the substrate RNA, and selectively activates the phosphodiester linkages in front of the acridine. As a result, these linkages are preferentially hydrolyzed over the others, even though the metal ions are not fixed anywhere. The scission is efficient under physiological conditions, irrespective of the sequence at the target site. Site-selective RNA scission is also successful with the combination of an oligonucleotide bearing an acridine at its terminus, another unmodified oligonucleotide, and the metal ion. In a proposed mechanism, the acridine pushes the unpaired ribonucleotide out of the heteroduplex and changes the conformation of RNA at the target site for the sequence-selective activation.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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