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Seio K, Kanamori T, Masaki Y. Synthesis of Fluorescent Nucleic Acids bearing Nucleobases Modified with Heteroaryl Group and Fluorophores. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology
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Kanamori T, Takamura A, Tago N, Masaki Y, Ohkubo A, Sekine M, Seio K. Fluorescence enhancement of oligodeoxynucleotides modified with green fluorescent protein chromophore mimics upon triplex formation. Org Biomol Chem 2018; 15:1190-1197. [PMID: 28084483 DOI: 10.1039/c6ob01278g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Green fluorescent protein (GFP)-based molecular-rotor chromophores were attached to the 5-positions of deoxyuridines, and subsequently, incorporated into the middle positions of oligodeoxynucleotides. These oligonucleotides were designed to form triplex DNA in order to encapsulate the GFP chromophores, mimicking GFP structures. Upon triplex formation, the embedded GFP chromophores exhibited fluorescence enhancement, suggesting the potential application of these fluorescent probes for the detection of nucleic acids.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Takamura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Nobuhiro Tago
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
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Paragi G, Kupihár Z, Endre G, Fonseca Guerra C, Kovács L. The evaluation of 5-amino- and 5-hydroxyuracil derivatives as potential quadruplex-forming agents. Org Biomol Chem 2018; 15:2174-2184. [PMID: 28054065 DOI: 10.1039/c6ob02574a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-Substituted uracils (NH2 or OH groups in position 5) have been examined theoretically and experimentally as potential building blocks in quadruplex structures. Our high level Density Functional Theory (DFT) calculations showed that the tetramer formation and stacking energies for 5-substituted uracils are similar to the energies of purine-based xanthine (X) or guanine (G) structures. As tetrads of 5-substituted uracils cover almost exactly the same area as purine tetrads, mixed tetrads or quadruplex structures based on X or G and 5-substituted uracil motifs are possible. According to the calculations, 5-hydroxyuracil-based structures are the best candidates for experimental implementation which was corroborated by the existence of higher complexes in the mass spectra of 1-benzyl-5-hydroxyuracil. These pyrimidine-based molecules can be used as efficient building blocks in different applications including aptamers, bio-sensors or - taking into account the larger cavity in the central region of 5-hydroxyuracil structures - as an artificial ion channel.
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Affiliation(s)
- Gábor Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam (VU), De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and MTA-SZTE Supramolecular and Nanostructured Materials Research Group, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary
| | - Zoltán Kupihár
- Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary.
| | - Gábor Endre
- Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary.
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam (VU), De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Lajos Kovács
- Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary.
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Balintová J, Špaček J, Pohl R, Brázdová M, Havran L, Fojta M, Hocek M. Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA-protein interactions. Chem Sci 2014; 6:575-587. [PMID: 28970873 PMCID: PMC5618110 DOI: 10.1039/c4sc01906g] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/09/2014] [Indexed: 12/17/2022] Open
Abstract
A new azido-based DNA redox label which can be transformed into nitrophenyltriazole by a CuAAC click reaction was developed. It was used for the mapping of DNA–protein interactions with electrochemical detection.
New redox labelling of DNA by an azido group which can be chemically transformed to nitrophenyltriazole or silenced to phenyltriazole was developed and applied to the electrochemical detection of DNA–protein interactions. 5-(4-Azidophenyl)-2′-deoxycytidine and 7-(4-azidophenyl)-7-deaza-2′-deoxyadenosine nucleosides were prepared by aqueous-phase Suzuki cross-coupling and converted to nucleoside triphosphates (dNTPs) which served as substrates for incorporation into DNA by DNA polymerase. The azidophenyl-modified nucleotides and azidophenyl-modified DNA gave a strong signal in voltammetric studies, at –0.9 V, due to reduction of the azido function. The Cu-catalyzed click reaction of azidophenyl-modified nucleosides or azidophenyl-modified DNA with 4-nitrophenylacetylene gave nitrophenyl-substituted triazoles, exerting a reduction peak at –0.4 V under voltammetry, whereas the click reaction with phenylacetylene gave electrochemically silent phenyltriazoles. The transformation of the azidophenyl label to nitrophenyltriazole was used for electrochemical detection of DNA–protein interactions (p53 protein) since only those azidophenyl groups in the parts of the DNA not shielded by the bound p53 protein were transformed to nitrophenyltriazoles, whereas those covered by the protein were not.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jan Špaček
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Marie Brázdová
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Luděk Havran
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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Gourdain S, Petermann C, Harakat D, Clivio P. Highly efficient and facile synthesis of 5-azido-2'-deoxyuridine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 29:542-6. [PMID: 20589573 DOI: 10.1080/15257770.2010.487507] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Previously reported syntheses of the photoaffinity label 5-azido-2'-deoxyuridine are rather inefficient and involve the tedious preparation of a 5-nitro intermediate. To overcome these inconveniences, we have developed a new approach from the commercially available 5-bromo-2'-deoxyuridine nucleoside. Our synthetic route makes use of a benzylamination reduction sequence. Using this strategy, the 5-azido-2'-deoxyuridine photolabel is prepared in three steps and quantitative yields.
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Affiliation(s)
- Stephanie Gourdain
- Universite de Reims Champagne Ardenne, Institut de Chimie Moleculaire de Reims, Reims cedex, France
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Mittapalli GK, Osornio YM, Guerrero MA, Reddy KR, Krishnamurthy R, Eschenmoser A. Mapping the landscape of potentially primordial informational oligomers: oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Angew Chem Int Ed Engl 2007; 46:2478-84. [PMID: 17111453 DOI: 10.1002/anie.200603209] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gopi Kumar Mittapalli
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Mittapalli G, Osornio Y, Guerrero M, Reddy K, Krishnamurthy R, Eschenmoser A. Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligodipeptides Tagged with 2,4-Disubstituted 5-Aminopyrimidines as Recognition Elements. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603209] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Van Hecke K, Uytterhoeven K, Mikhailov SN, Herdewijn P, Van Meervelt L. Incorporation of a disaccharide nucleoside into the backbone of double-stranded DNA: crystallization and preliminary X-ray diffraction. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:953-5. [PMID: 16511205 PMCID: PMC1991303 DOI: 10.1107/s1744309105030381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 09/22/2005] [Indexed: 11/11/2022]
Abstract
Incorporation of a disaccharide nucleoside into double-stranded DNA can be considered as a chemical (non-enzymatic) alternative for site-specific cleavage of DNA. Crystals of the sequence d(CGCGAATT*CGCG), where * is an incorporated ribose, were obtained by hanging-drop vapour diffusion and diffracted to 2.6 A. The crystals belong to the orthorhombic space group P222(1), with unit-cell parameters a = 41.52, b = 57.63, c = 81.39 A, indicating a new crystal packing motif for an oligonucleotide dodecamer sequence.
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Affiliation(s)
- Kristof Van Hecke
- Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, B-3001 Leuven (Heverlee), Belgium
| | - Koen Uytterhoeven
- Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, B-3001 Leuven (Heverlee), Belgium
| | - Sergey N. Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, Russia
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute, Katholieke Universiteit Leuven, Minderbroederstraat 10, B-3000 Leuven, Belgium
| | - Luc Van Meervelt
- Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, B-3001 Leuven (Heverlee), Belgium
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Nauwelaerts K, Vastmans K, Froeyen M, Kempeneers V, Rozenski J, Rosemeyer H, Van Aerschot A, Busson R, Lacey JC, Efimtseva E, Mikhailov S, Lescrinier E, Herdewijn P. Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside. Nucleic Acids Res 2004; 31:6758-69. [PMID: 14627809 PMCID: PMC290278 DOI: 10.1093/nar/gkg911] [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] [Indexed: 11/14/2022] Open
Abstract
A ribose residue inserted between the 3'-OH of one nucleotide and the 5'-phosphate group of the next nucleotide, functions as a site-specific cleavage site within DNA. This extra ribose does not interrupt helix formation and it protects duplex DNA against cleavage by restriction enzymes. Cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-specific cleavage and recovering of intact DNA occurs without loss of genetic information.
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Affiliation(s)
- Koen Nauwelaerts
- Rega Institute for Medical Research, Laboratory for Medicinal Chemistry, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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