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Bibal B, Mongin C, Bassani DM. Template effects and supramolecular control of photoreactions in solution. Chem Soc Rev 2014; 43:4179-98. [DOI: 10.1039/c3cs60366k] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Dutta S, Fülöp A, Mokhir A. Fluorogenic, Catalytic, Photochemical Reaction for Amplified Detection of Nucleic Acids. Bioconjug Chem 2013; 24:1533-42. [DOI: 10.1021/bc400152n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Subrata Dutta
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
| | - Annabelle Fülöp
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
| | - Andriy Mokhir
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
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Oligonucleotide-templated reactions for sensing nucleic acids. Molecules 2012; 17:2446-63. [PMID: 22374329 PMCID: PMC6268776 DOI: 10.3390/molecules17032446] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points.
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Dutta S, Flottmann B, Heilemann M, Mokhir A. Hybridization and reaction-based fluorogenic nucleic acid probes. Chem Commun (Camb) 2012; 48:9664-6. [DOI: 10.1039/c2cc33827k] [Citation(s) in RCA: 18] [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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Nakamura S, Ogasawara S, Matuda S, Saito I, Fujimoto K. Template directed reversible photochemical ligation of oligodeoxynucleotides. Molecules 2011; 17:163-78. [PMID: 22202805 PMCID: PMC6268978 DOI: 10.3390/molecules17010163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 12/12/2022] Open
Abstract
We demonstrated that 5-vinyldeoxyuridine ((V)U) and 5-carboxyvinyldeoxyuridine ((CV)U) can be used to photoligate a longer oligonucleotide (ODN) from smaller ODNs on a template. By performing irradiation at 366 nm, these artificial nucleotides make photoligated ODNs with high efficiency without any side reactions. Moreover, by performing irradiation at 312 nm, these photoligated ODNs were reversed to the original ODN. (V)U needs to be irradiated 366 nm for 6 h, but (CV)U needs to be irradiated at 366 nm for 15 min. Finally, we made a self-assembled structure with an ODN containing (CV)U and observed the photoligated ODN by photoirradiation.
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Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | - Shinzi Ogasawara
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | - Shigeo Matuda
- Department of Synthetic Chemistry and Biological Chemistry, Factly of Enginnering, Kyoto University, Kyoto 606-8501, Japan
| | - Isao Saito
- Department of Synthetic Chemistry and Biological Chemistry, Factly of Enginnering, Kyoto University, Kyoto 606-8501, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
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Arian D, Kovbasyuk L, Mokhir A. Control of the photocatalytic activity of bimetallic complexes of pyropheophorbide-a by nucleic acids. Inorg Chem 2011; 50:12010-7. [PMID: 22047611 DOI: 10.1021/ic201408h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photocatalytic activity of a photosensitizer (PS) in an oligodeoxyribonucleotide duplex 5'-PS~ODN1/ODN2~Q-3' is inhibited because of close proximity of a quencher Q. The ODN2 in this duplex is selected to be longer than the ODN1. Therefore, in the presence of a nucleic acid (analyte), which is fully complementary to the ODN2 strand, the duplex is decomposed with formation of an analyte/ODN2~Q duplex and a catalytically active, single stranded PS~ODN1. In this way the catalytic activity of the PS can be controlled by the specific nucleic acids. We applied this reaction earlier for the amplified detection of ribonucleic acids in live cells (Arian, D.; Cló, E.; Gothelf, K.; Mokhir, A. Chem.-Eur. J.2010, 16(1), 288). As a photosensitizer (PS) we used In(3+)(pyropheophorbide-a)chloride and as a quencher (Q)--Black-Hole-Quencher-3 (BHQ-3). The In(3+) complex is a highly active photocatalyst in aqueous solution. However, it can coordinate additional ligands containing thiols (e.g., proteins, peptides, and aminoacids), that modulate properties of the complex itself and of the corresponding bio- molecules. These possible interactions can lead to undesired side effects of nucleic acid controlled photocatalysts (PS~ODN1/ODN2∼Q) in live cells. In this work we explored the possibility to substitute the In(3+) complex for those ones of divalent metal ions, Zn(2+) and Pd(2+), which exhibit lower or no tendency to coordinate the fifth ligand. We found that one of the compounds tested (Pd(pyropheophorbide-a) is as potent and as stable photosensitizer as its In(3+) analogue, but does not coordinate additional ligands that makes it more suitable for cellular applications. When the Pd complex was introduced in the duplex PS~ODN1/ODN2~Q as a PS, its photocatalytic activity could be controlled by nucleic acids as efficiently as that of the corresponding In(3+) complex.
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Affiliation(s)
- Dumitru Arian
- Institute of Inorganic Chemistry, Ruprecht-Karls-University of Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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Fülöp A, Peng X, Greenberg MM, Mokhir A. A nucleic acid-directed, red light-induced chemical reaction. Chem Commun (Camb) 2010; 46:5659-61. [PMID: 20574574 DOI: 10.1039/c0cc00744g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first nucleic acid-directed catalytic photochemical reaction that is induced by nontoxic red light was developed. This reaction is fast, high yielding, sequence specific, and enables one to functionalize an oligonucleotide.
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Affiliation(s)
- Annabelle Fülöp
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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Yoshimura Y, Ohtake T, Okada H, Ami T, Tsukaguchi T, Fujimoto K. SNP genotyping by DNA photoligation: application to SNP detection of genes from food crops. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2009; 10:034603. [PMID: 27877298 PMCID: PMC5090425 DOI: 10.1088/1468-6996/10/3/034603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 07/14/2009] [Accepted: 04/01/2009] [Indexed: 06/06/2023]
Abstract
We describe a simple and inexpensive single-nucleotide polymorphism (SNP) typing method, using DNA photoligation with 5-carboxyvinyl-2'-deoxyuridine and two fluorophores. This SNP-typing method facilitates qualitative determination of genes from indica and japonica rice, and showed a high degree of single nucleotide specificity up to 10 000. This method can be used in the SNP typing of actual genomic DNA samples from food crops.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Tomoko Ohtake
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Hajime Okada
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takehiro Ami
- Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Tadashi Tsukaguchi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Innovation Plaza Ishikawa, Japan Science and Technology Agency, 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
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Ami T, Fujimoto K. Click chemistry as an efficient method for preparing a sensitive DNA probe for photochemical ligation. Chembiochem 2009; 9:2071-4. [PMID: 18666308 DOI: 10.1002/cbic.200800316] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Takehiro Ami
- School of Materials Science, Japan Advanced Institute of Science and Technology, Asahidai, Nomi, Ishikawa 923-1292, Japan
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Mukae M, Ihara T, Tabara M, Jyo A. Anthracene–DNA conjugates as building blocks of designed DNA structures constructed by photochemical reactions. Org Biomol Chem 2009; 7:1349-54. [DOI: 10.1039/b821869b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ami T, Ozaki G, Yoshimura Y, Fujimoto K. DNA Photoligation in Two-color Detection of DNA Point Mutation. CHEM LETT 2008. [DOI: 10.1246/cl.2008.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ami T, Ito K, Yoshimura Y, Fujimoto K. Sequence specific interstrand photocrosslinking for effective SNP typing. Org Biomol Chem 2008; 5:2583-6. [PMID: 18019532 DOI: 10.1039/b708264a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a simple and inexpensive SNP typing method by using sequence specific interstrand photocrosslinking via p-carbamoylvinyl phenol nucleosides. Interstrand photocrosslinking showed a high degree of single nucleotide specificity as high as 10(3)-fold and more, and can be used in the diagnostic detection of DNA sequences.
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Affiliation(s)
- Takehiro Ami
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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Ogasawara S, Yoshimura Y, Hayashi M, Saito I, Fujimoto K. Highly Efficient Method for Constructing a Single-Stranded Comb-Like Oligonucleotide via Reversible Photocrosslinking. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Affiliation(s)
- Shinzi Ogasawara
- School of Materials Science, Japan Advanced Institute of Science and Technology, Asahidai, Nomi, Ishikawa 923-1292, Japan
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Fujimoto K, Matsuda S, Yoshimura Y, Ami T, Saito I. Reversible photopadlocking on double-stranded DNA. Chem Commun (Camb) 2007:2968-70. [PMID: 17622447 DOI: 10.1039/b707524c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a highly efficient method for reversible photocircularization of oligonucleotide (ODN) on a double-stranded DNA template: 5-carboxyvinyl-2'-deoxyuridine-containing ODN was reversibly circularized around the target sequence of the double-stranded plasmid DNA resulting in formation of a catenated plasmid.
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Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, 923-1292, Japan.
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Yoshimura Y, Noguchi Y, Fujimoto K. Highly sequence specific RNA terminal labeling by DNA photoligation. Org Biomol Chem 2006; 5:139-42. [PMID: 17164918 DOI: 10.1039/b615715g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report the nonenzymatic terminal labeling of oligoribonucleotide (ORN) by using template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine ((CV)U) with high selectivity.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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