1
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Onizuka K, Yamano Y, Abdelhady AM, Nagatsugi F. Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids. Org Biomol Chem 2022; 20:4699-4708. [PMID: 35622064 DOI: 10.1039/d2ob00551d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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2
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Paderes MC, Diaz MJ, Pagtalunan CA, Bruzon DA, Tapang GA. Photo-Controlled [4+4] Cycloaddition of Anthryl-Polymer Systems: A Versatile Approach to Fabricate Functional Materials. Chem Asian J 2022; 17:e202200193. [PMID: 35452165 DOI: 10.1002/asia.202200193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/11/2022] [Indexed: 11/07/2022]
Abstract
The reversible photo-induced [4+4] cycloaddition reaction of anthracene enables multiple cycles of dimerization and scission, allowing phototunable linkage of molecular fragments for the synthesis of polymer scaffolds. New functional materials ranging from hydrogels to shape-memory polymers were designed from anthryl-polymer systems because of their diverse photochemical reactivity and responsiveness. Light as an external stimulus allows for the remote and precise spatiotemporal control of materials without the need for additional reagents. Depending on how the photoreactive anthracene moieties were introduced, the interaction of anthryl-polymer systems with light results in various processes such as polymerization, cyclization, and cross-linking. Structural modifications of anthracene derivatives could shift their absorption from the ultraviolet to the visible light region, widening their range of applications including biologically relevant studies. These applications are further diversified and enhanced by the reversibility of the dimerization reaction using light and heat as stimuli. In this review, current developments in the synthesis and photodimerization of anthracene-containing polymers and their emerging applications in the fabrication of new materials are discussed.
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Affiliation(s)
- Monissa C Paderes
- University of the Philippines Diliman, Institute of Chemistry, Regidor St., 1101, Quezon City, PHILIPPINES
| | - Mark Jeffrey Diaz
- University of the Philippines Diliman, Institute of Chemistry, 1101, Quezon City, PHILIPPINES
| | - Cris Angelo Pagtalunan
- University of the Philippines Diliman, Institute of Chemistry, 1101, Quezon City, PHILIPPINES
| | - Dwight Angelo Bruzon
- University of the Philippines Diliman, Materials Science and Engineering, 1101, Quezon City, PHILIPPINES
| | - Giovanni A Tapang
- University of the Philippines Diliman, National Institute of Physics, 1101, Quezon City, PHILIPPINES
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3
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Yamaoka K, Oikawa R, Abe N, Nakamoto K, Tomoike F, Hashiya F, Kimura Y, Abe H. Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells. Chembiochem 2021; 22:3273-3276. [PMID: 34519401 DOI: 10.1002/cbic.202100312] [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: 06/25/2021] [Revised: 09/11/2021] [Indexed: 11/10/2022]
Abstract
Chemical ligation reaction of DNA is useful for the construction of long functional DNA using oligonucleotide fragments that are prepared by solid phase chemical synthesis. However, the unnatural linkage structure formed by the ligation reaction generally impairs the biological function of the resulting ligated DNA. We achieved the complete chemical synthesis of 78 and 258 bp synthetic DNAs via multiple chemical ligation reactions with phosphorothioate and haloacyl-modified DNA fragments. The latter synthetic DNA, coding shRNA for luciferase genes with a designed truncated SV promoter sequence, successfully induced the expected gene silencing effect in HeLa cells.
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Affiliation(s)
- Kazuki Yamaoka
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ryota Oikawa
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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4
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Kitamura Y, Yoshimura K, Kuramoto R, Katsuda Y, Ihara T. Catalytic Amplification of Electrochemical Signal in Homogeneous Solution Using an Entropy-driven DNA Circuit. ANAL SCI 2021; 37:533-537. [PMID: 33162418 DOI: 10.2116/analsci.20scn04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The electrochemical signal from ferrocene on a DNA probe was successfully modulated in a homogeneous solution by the template-directed formation and dissociation of an inclusion complex with β-cyclodextrin on another probe. The electrochemical response was amplified by combining with a DNA circuit, in which the target DNA served as a catalyst. This system did not require any modification of a complementary DNA with the ferrocene-modified probe on the electrode surface to separate the bound/free probe for the detection of 200 nM target DNA.
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Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University
| | - Keisuke Yoshimura
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University
| | - Ryo Kuramoto
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University
| | - Yousuke Katsuda
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University
| | - Toshihiro Ihara
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University
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5
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Minami H, Itamoto N, Watanabe W, Li Z, Nakamura K, Kobayashi N. Chiroptical property enhancement of chiral Eu(III) complex upon association with DNA-CTMA. Sci Rep 2020; 10:18917. [PMID: 33144619 PMCID: PMC7609531 DOI: 10.1038/s41598-020-75808-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
DNA-based materials have attracted much attention due to their unique photo-functional properties and potential applications in various fields such as luminescent and biological systems, nanodevices, etc. In this study, the photophysical properties of a chiral Eu(III) complex, namely (Eu(D-facam)3), within DNA films were extensively investigated. The enhancement of photoluminescence (more than 25-folds increase of luminescence quantum yield) and degree of circularly polarization in luminescence (glum = − 0.6) was observed upon interaction with DNA. Various photophysical analyses suggested that the emission enhancement was mainly due to an increase of the sensitization efficiency (high ηsens) from the ligands to Eu(III) and suppression of the vibrational deactivation upon immobilization onto the DNA molecule. From CD and VCD measurements, it was suggested that the coordination structure of Eu(D-facam)3 was affected by the interaction with DNA, suggesting that the structural change of Eu(D-facam)3 contributed to the improvement of its luminescent properties.
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Affiliation(s)
- Haruki Minami
- Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Natsumi Itamoto
- Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Wataru Watanabe
- Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Ziying Li
- Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Kazuki Nakamura
- Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Norihisa Kobayashi
- Graduate School of Science and Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
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6
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Kitamura Y, Nozaki A, Ozaki R, Katsuda Y, Ihara T. Catalytic Formation of Luminescent Complex Clusters Based on Autonomous Strand Exchange Reaction of DNA. ACS APPLIED BIO MATERIALS 2019; 2:2988-2993. [DOI: 10.1021/acsabm.9b00326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Akihiro Nozaki
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rie Ozaki
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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7
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Onizuka K, Ishida K, Mano E, Nagatsugi F. Alkyne-Alkyne Photo-cross-linking on the Flipping-out Field. Org Lett 2019; 21:2833-2837. [PMID: 30951316 DOI: 10.1021/acs.orglett.9b00817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base flip-inducing nucleic acids are expected to create a specific field for various chemical reactions. We now report a novel type of base-flip-inducing oligodeoxynucleotide and photo-cross-linking reaction. Two 3-arylethynyl-5-methyl-2-pyridone nucleosides, Ph and An, were synthesized, and their properties were investigated. The alkyne-alkyne photo-cross-linking rapidly proceeded by taking advantage of the base-flipping-out field where two alkynes overlap each other. This photo-cross-linking would be a new candidate to form cross-linked DNAs.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Kei Ishida
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
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8
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9
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Duprey JLHA, Bassani DM, Hyde EI, Jonusauskas G, Ludwig C, Rodger A, Spencer N, Vyle JS, Wilkie J, Zhao ZY, Tucker JHR. Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes. Org Biomol Chem 2018; 16:6576-6585. [DOI: 10.1039/c8ob01710g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.
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Affiliation(s)
| | - Dario M. Bassani
- Institut des Sciences Moléculaires, CNRS UMR 5255
- Université Bordeaux
- Talence 33405
- France
| | - Eva I. Hyde
- School of Biosciences
- The University of Birmingham
- Edgbaston
- UK
| | - Gediminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine
- UMR CNRS 5798
- Université Bordeaux
- Talence 33405
- France
| | - Christian Ludwig
- Henry Wellcome Building for Biomolecular NMR Spectroscopy
- Institute of Cancer & Genomic Sciences
- College of Medical & Dental Sciences
- University of Birmingham
- Edgbaston
| | - Alison Rodger
- Department of Molecular Sciences
- Faculty of Science and Engineering
- Macquarie University
- North Ryde
- Australia
| | - Neil Spencer
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
| | - Joseph S. Vyle
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
| | - John Wilkie
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
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10
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Kashida H, Asanuma H. Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012
| | - Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
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11
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Doi T, Kashida H, Asanuma H. Efficiency of [2 + 2] photodimerization of various stilbene derivatives within the DNA duplex scaffold. Org Biomol Chem 2016; 13:4430-7. [PMID: 25689316 DOI: 10.1039/c4ob02520b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A DNA duplex was used as a scaffold to evaluate the intrinsic reactivity of [2 + 2] photodimerization between stilbene derivatives; the duplex pre-organizes the substrates avoiding the need for an association step. Unmodified stilbenes were first introduced at base-pairing positions on complementary DNA strands. The duplex was then irradiated with 340 nm UV light. HPLC analyses revealed that [2 + 2] photodimerization proceeded rapidly without side reactions. Thus, it was confirmed that the DNA duplex could be used as an ideal scaffold for [2 + 2] photodimerization of stilbenes. Next, we examined homo-photodimerization abilities of various stilbene derivatives. Homo-photodimerization of p-cyanostilbene, p-methylstilbazolium, and p-stilbazole occurred efficiently, whereas homo-photodimerization of p-dimethylaminostilbene and p-nitrostilbene did not proceed at all, probably because the reaction was quenched by dimethylamino and nitro groups. Time-dependent density functional theory calculations revealed that excitation energy was correlated with quantum yield. We further investigated hetero-photodimerization. These reactions were made possible by the use of two complementary oligodeoxyribonucleotides tethering different stilbene derivatives. Reactivities in hetero-photodimerization were highly dependent on the combination of derivatives. A high correlation was observed between the quantum yields and energy gaps of HOMO and LUMO between reactive derivatives. Unexpectedly, nitrostilbene, which was non-reactive in homo-photodimerization, cross-reacted with p-methylstilbazolium and p-stilbazole, both of which had close HOMO or LUMO with nitrostilbene. Evaluation of the intrinsic reactivity of homo- and hetero-photodimerization of stilbene derivatives was made possible by the use of DNA as a scaffold.
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Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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12
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Matsumoto H, Nishimura Y, Arai T. Control of the intermolecular photodimerization of anthracene derivatives by hydrogen bonding of urea groups in dilute solution. Photochem Photobiol Sci 2016; 15:1071-9. [DOI: 10.1039/c6pp00125d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The control of the photodimerization reaction of anthracene–urea compounds was achieved by (1) aggregate conformation depending on the substitution site and (2) inhibition of aggregation by the addition of TBAAc.
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Affiliation(s)
- Hisato Matsumoto
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Yoshinobu Nishimura
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Tatsuo Arai
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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13
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Ihara T, Ohura H, Shirahama C, Furuzono T, Shimada H, Matsuura H, Kitamura Y. Metal ion-directed dynamic splicing of DNA through global conformational change by intramolecular complexation. Nat Commun 2015; 6:6640. [DOI: 10.1038/ncomms7640] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
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14
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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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15
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Kate AN, Kumbhar AA, Sapre AV, Peerannawar SR, Gejji SP. Interaction of a hydrated electron with anthracenethiosemicarbazone: a pulse radiolysis study. J Phys Chem A 2013; 117:5447-53. [PMID: 23734879 DOI: 10.1021/jp402202s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thiosemicarbazide derivative of anthracene, ATSC, has been synthesized and characterized by elemental analysis, IR, UV-visible, (1)H NMR, fluorescence, and mass spectroscopy experiments. The interaction of hydrated electron (e(-)aq) with ATSC proceeds via radical anion formation followed by intramolecular transfer that cleaves the thiosemicarbazide side chain on the anthracene moiety. HPLC and ESI-MS experiments suggested that the anthrylmethyl radical combines with different ATSC fragments during the reaction. ATSC, its one-electron reduction products, and dimers were analyzed combining experiments with density functional theory.
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Affiliation(s)
- Anup N Kate
- Department of Chemistry and §National Centre for Free Radical Research, Department of Chemistry, University of Pune , Pune-411007, India
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16
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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds. Chemistry 2013; 19:10526-35. [PMID: 23821253 DOI: 10.1002/chem.201300985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/10/2023]
Abstract
We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
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Affiliation(s)
- Akika Futamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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17
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Kashida H, Doi T, Sakakibara T, Hayashi T, Asanuma H. p-Stilbazole Moieties As Artificial Base Pairs for Photo-Cross-Linking of DNA Duplex. J Am Chem Soc 2013; 135:7960-6. [DOI: 10.1021/ja401835j] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiromu Kashida
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tetsuya Doi
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takumi Sakakibara
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takamitsu Hayashi
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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18
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Manchester J, Bassani DM, Duprey JLHA, Giordano L, Vyle JS, Zhao ZY, Tucker JHR. Photocontrolled binding and binding-controlled photochromism within anthracene-modified DNA. J Am Chem Soc 2012; 134:10791-4. [PMID: 22694485 PMCID: PMC3614019 DOI: 10.1021/ja304205m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modified DNA strands undergo a reversible light-induced reaction involving the intramolecular photodimerization of two appended anthracene tags. The photodimers exhibit markedly different binding behavior toward a complementary strand that depends on the number of bases between the modified positions. By preforming the duplex, photochromism can be suppressed, illustrating dual-mode gated behavior.
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Affiliation(s)
- Jack Manchester
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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19
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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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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IHARA T, KITAMURA Y. DNA Recognition and Analysis Through Cooperative Metal-ion Complex Formation of Split Probes. BUNSEKI KAGAKU 2012. [DOI: 10.2116/bunsekikagaku.61.193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Toshihiro IHARA
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Yusuke KITAMURA
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
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Pasternak K, Pasternak A, Gupta P, Veedu RN, Wengel J. Photoligation of self-assembled DNA constructs containing anthracene-functionalized 2'-amino-LNA monomers. Bioorg Med Chem 2011; 19:7407-15. [PMID: 22079866 DOI: 10.1016/j.bmc.2011.10.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/13/2011] [Accepted: 10/17/2011] [Indexed: 11/20/2022]
Abstract
Efficient synthesis of a novel anthracene-functionalized 2'-amino-LNA phosphoramidite derivative is described together with its incorporation into oligodeoxynucleotides. Two DNA strands with the novel 2'-N-anthracenylmethyl-2'-amino-LNA monomers can be effectively cross-linked by photoligation at 366 nm in various types of DNA constructs. Successful application of three differently functionalized 2'-amino-LNA monomers in self-assembled higher ordered structures for simultaneous cross-linking and monitoring of assembly formation is furthermore demonstrated.
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Affiliation(s)
- Karol Pasternak
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Ihara T, Kitamura Y, Tsujimura Y, Jyo A. DNA analysis based on the local structural disruption to the duplexes carrying a luminous lanthanide complex. ANAL SCI 2011; 27:585-90. [PMID: 21666354 DOI: 10.2116/analsci.27.585] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The two DNA conjugates (split probes) carrying a metal chelator form an integrated luminous lanthanide (Ln(3+): Tb(3+) or Eu(3+)) complex on the complementary template DNA (target). The luminous property of this Ln(3+) complex has been used for DNA assay. The intensity of the luminescence was affected by the local structural disruption caused by one-base mispairing around the complex. Among the mispairings systematically introduced around the Ln(3+) center, vicinal mispairings to the center decreased the emission intensity more. This would be a novel nucleobase-discriminating principle, in which the split probes bind the target tightly, yet still retain sequence selectivity.
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Affiliation(s)
- Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.
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Arslan P, Jyo A, Ihara T. Reversible circularization of an anthracene-modified DNA conjugate through bimolecular triplex formation and its analytical application. Org Biomol Chem 2010; 8:4843-8. [PMID: 20734012 DOI: 10.1039/c0ob00282h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We prepared an oligodeoxyribonucleotide conjugate (5-3ant(2)18) carrying two anthracenes, each of which was tethered to both ends of the conjugate through hexamethylene linker chains. The conjugate has a mirror repeat of two heptamer sequences, such that it forms a bimolecular triplex with the single stranded target, forming a two-fold U-shaped conformation. The conformation of the conjugate in its triplex structure could be frozen instantaneously by circularization through photodimerization of the anthracenes. Compared with the duplex formation of linear probes with relevant sequences, bimolecular triplex formation of 5-3ant(2)18 shows a unique feature in its target recognition; it binds the target tightly, yet still retains high sequence selectivity. Circularization of 5-3ant(2)18 by UV photoirradiation was verified as the probe reaction for a DNA assay. The probe reaction could be performed in a few seconds over a wide range of temperatures, at least between 0 and 25 °C. In addition, the reaction could be regarded as a reversible method for the preparation of circular DNA that shows higher affinity for the target.
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Affiliation(s)
- Pelin Arslan
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
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Bandy TJ, Brewer A, Burns JR, Marth G, Nguyen T, Stulz E. DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology. Chem Soc Rev 2010; 40:138-48. [PMID: 20694258 DOI: 10.1039/b820255a] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.
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Affiliation(s)
- Thomas J Bandy
- University of Southampton, School of Chemistry, Highfield, Southampton SO17 1BJ, UK
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