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Neitz H, Bessi I, Kachler V, Michel M, Höbartner C. Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA. Angew Chem Int Ed Engl 2023; 62:e202214456. [PMID: 36344446 PMCID: PMC10107946 DOI: 10.1002/anie.202214456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Irene Bessi
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Valentin Kachler
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Manuela Michel
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Claudia Höbartner
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
- Center for Nanosystems Chemistry (CNC)University of WürzburgTheodor-Boveri-Weg97074WürzburgGermany
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2
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Nakamura M, Yoshioka H, Takada T. Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition. ChemistrySelect 2022. [DOI: 10.1002/slct.202200696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Hibiki Yoshioka
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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3
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Kashida H, Asanuma H. Pseudo Base Pairs that Exhibit High Duplex Stability and Orthogonality through Covalent and Non-covalent Interactions. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.1013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
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4
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Ito S, Sekine R, Munakata M, Yamashita M, Tachikawa T. Mechanochromic Luminescence (MCL) of Purely Organic Two-Component Dyes: Wide-Range MCL over 300 nm and Two-Step MCL by Charge-Transfer Complexation. Chemistry 2021; 27:13982-13990. [PMID: 34405922 DOI: 10.1002/chem.202102700] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Indexed: 12/30/2022]
Abstract
Despite recent extensive studies on mechanochromic luminescence (MCL), rational control over the magnitude of the emission-wavelength shift in response to mechanical stimuli remains challenging. In the present study, a two-component donor-acceptor approach has been applied to create a variety of organic MCL composites that exhibit remarkable emission-wavelength switching. Dibenzofuran-based bis(1-pyrenylmethyl)diamine and typical organic fluorophores have been employed as donor and acceptor dyes, respectively. Outstanding wide-range MCL with an emission-wavelength shift of over 300 nm has been achieved by mixing the diamine with 3,4,9,10-perylenetetracarboxylic diimide. Unprecedented two-step MCL in response to mechanical stimuli of different intensity has also been realized for a two-component mixture with 9,10-anthraquinone. Fluorescence microscopy observations at the single-particle level revealed that the segregation and mixing of the two-component dyes contribute to the stimuli-responsive emission-color switching of the MCL composites.
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Affiliation(s)
- Suguru Ito
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Ryohei Sekine
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Masayasu Munakata
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Maho Yamashita
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Takashi Tachikawa
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.,Molecular Photoscience Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
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5
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Kashida H, Kawai H, Azuma H, Araki Y, Wada T, Asanuma H. Quantitative Analyses of Förster Resonance Energy Transfer between Identical Pyrene Chromophores (Homo‐FRET) In DNA Scaffolds. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hidenori Azuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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6
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Nakamura M, Takada T, Yamana K. Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions. Chembiochem 2019; 20:2949-2954. [DOI: 10.1002/cbic.201900350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Kazushige Yamana
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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7
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Nakamura M, Matsui Y, Takada T, Yamana K. Chromophore Arrays Constructed in the Major Groove of DNA Duplexes Using a Post-Synthetic Strategy. ChemistrySelect 2019. [DOI: 10.1002/slct.201803464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Yuki Matsui
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
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8
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Kashida H, Kawai H, Maruyama R, Kokubo Y, Araki Y, Wada T, Asanuma H. Quantitative evaluation of energy migration between identical chromophores enabled by breaking symmetry. Commun Chem 2018. [DOI: 10.1038/s42004-018-0093-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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9
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Kashida H, Kurihara A, Kawai H, Asanuma H. Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes. Nucleic Acids Res 2017; 45:e105. [PMID: 28369626 PMCID: PMC5499647 DOI: 10.1093/nar/gkx200] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/17/2017] [Indexed: 12/18/2022] Open
Abstract
Differences in structures and flexibilities of DNA duplexes play important roles on recognition by DNA-binding proteins. We herein describe a novel method for structural analyses of DNA duplexes by using orientation dependence of Förster resonance energy transfer (FRET). We first analyzed canonical B-form duplex and correct structural parameters were obtained. The experimental FRET efficiencies were in excellent agreement with values theoretically calculated by using determined parameters. We then investigated DNA duplexes with nick and gaps, which are key intermediates in DNA repair systems. Effects of gap size on structures and flexibilities were successfully revealed. Since our method is facile and sensitive, it could be widely used to analyze DNA structures containing damages and non-natural molecules.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ayako Kurihara
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hayato Kawai
- 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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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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KASHIDA H, ASANUMA H. Development of Pseudo Base Pairs Which Show High DNA Duplex Stabilities and Orthogonality. KOBUNSHI RONBUNSHU 2017. [DOI: 10.1295/koron.2017-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiromu KASHIDA
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University
- PRESTO, Japan Science and Technology Agency
| | - Hiroyuki ASANUMA
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University
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12
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Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds. Polym J 2016. [DOI: 10.1038/pj.2016.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Kashida H, Morimoto K, Asanuma H. A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2016; 17:267-273. [PMID: 27877879 PMCID: PMC5101869 DOI: 10.1080/14686996.2016.1182412] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 05/26/2023]
Abstract
We herein report a stem-less probe for the detection of RNA that depends on pairing between Cy3 and nitro methyl red. In our design, two Cy3 residues and two nitro methyl red residues were introduced into an oligonucleotide. In the absence of the target, these dyes formed a complex, and emission of Cy3 was efficiently quenched. Hybridization with the target RNA disrupted this interaction and resulted in Cy3 emission. Under optimized conditions, the signal to background ratio was as high as 180. We demonstrated specific detection of target RNA in cells using a wash-free FISH protocol.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama332-0012, Japan
| | - Kazuhiro Morimoto
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan
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14
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Asanuma H, Niwa R, Akahane M, Murayama K, Kashida H, Kamiya Y. Strand-invading linear probe combined with unmodified PNA. Bioorg Med Chem 2016; 24:4129-4137. [PMID: 27394693 DOI: 10.1016/j.bmc.2016.06.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022]
Abstract
Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration.
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Affiliation(s)
- Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Rie Niwa
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mariko Akahane
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yukiko Kamiya
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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