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Dietzsch J, Bialas D, Bandorf J, Würthner F, Höbartner C. Tuning Exciton Coupling of Merocyanine Nucleoside Dimers by RNA, DNA and GNA Double Helix Conformations. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116783] [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)
- Julia Dietzsch
- Institute of Organic Chemistry University of Würzburg Germany
| | - David Bialas
- Institute of Organic Chemistry University of Würzburg Germany
- Center for Nanosystems Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | | | - Frank Würthner
- Institute of Organic Chemistry University of Würzburg Germany
- Center for Nanosystems Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry University of Würzburg Germany
- Center for Nanosystems Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
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Dietzsch J, Bialas D, Bandorf J, Würthner F, Höbartner C. Tuning exciton coupling of merocyanine nucleoside dimers by RNA, DNA and GNA double helix conformations. Angew Chem Int Ed Engl 2021; 61:e202116783. [PMID: 34937127 PMCID: PMC9302137 DOI: 10.1002/anie.202116783] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 12/02/2022]
Abstract
Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π–π‐stacking and hydrogen‐bonding interactions. The realized supramolecular motifs include hydrogen‐bonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.
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Affiliation(s)
- Julia Dietzsch
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - David Bialas
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - Johannes Bandorf
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - Frank Würthner
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - Claudia Höbartner
- Universität Würzburg, Institute für Organische Chemie, Am Hubland, 97074, Würzburg, GERMANY
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Takada T, Nishida K, Honda Y, Nakano A, Nakamura M, Fan S, Kawai K, Fujitsuka M, Yamana K. Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions. Chembiochem 2021; 22:2729-2735. [PMID: 34191388 DOI: 10.1002/cbic.202100309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/20/2022]
Abstract
Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.
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Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Koma Nishida
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Yurika Honda
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Aoi Nakano
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazushige Yamana
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
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Kamiya Y, Kamimoto H, Zhu H, Asanuma H. Development and Modification of Pre-miRNAs with a FRET Dye Pair for the Intracellular Visualization of Processing Intermediates That Are Generated in Cells. SENSORS (BASEL, SWITZERLAND) 2021; 21:1785. [PMID: 33806517 PMCID: PMC7961592 DOI: 10.3390/s21051785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 01/02/2023]
Abstract
microRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs), which regulate gene expression via the RNA interference (RNAi) system. miRNAs have attracted enormous interest because of their biological significance and disease relationship. In cell systems, the generation of miRNA is regulated by multiple steps: the transfer of primary miRNA from the nucleus to the cytosol, the generation of the precursor-miRNA (pre-miRNA), the production of double-stranded RNA from pre-miRNA by the Dicer, the interaction with protein argonaute-2 (AGO2), and the subsequent release of one strand to form miRISC with AGO2. In this study, we attempt to visualize the intermediates that were generated in the miRNA-maturation step in the cells to acquire a detailed understanding of the maturation process of miRNA. To achieve this, we developed pre-miRNAs labeling with a Dicer- or AGO2-responsible fluorescence resonance energy transfer (FRET) dye pair. We observed that modifications with the dye at suitable positions did not interfere with the biological activities of pre-miRNAs. Further, imaging analyses employing these pre-miRNAs demonstrated that the processing of pre-miRNA promoted the accumulation of miRNA at the specific foci in the cytosol. The FRET-labeled pre-miRNA would further elucidate the mechanisms of the RNAi process and provide the basis for development of nucleic acid drugs working in the RNAi system.
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Affiliation(s)
- Yukiko Kamiya
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; (H.K.); (H.Z.)
| | | | | | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; (H.K.); (H.Z.)
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Asanuma H, Murayama K, Kamiya Y, Kashida H. The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180278] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Keiji Murayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yukiko Kamiya
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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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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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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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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Asanuma H, Kashida H, Kamiya Y. De novo design of functional oligonucleotides with acyclic scaffolds. CHEM REC 2014; 14:1055-69. [PMID: 25171046 DOI: 10.1002/tcr.201402040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 01/20/2023]
Abstract
In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs-wedge, interstrand-wedge, dimer, and cluster-have been prepared from natural DNA or RNA and functional base surrogates prepared from d-threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence-specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d-threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.
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Affiliation(s)
- Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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Kamiya Y, Ito A, Ito H, Urushihara M, Takai J, Fujii T, Liang X, Kashida H, Asanuma H. Selective labeling of mature RISC using a siRNA carrying fluorophore–quencher pair. Chem Sci 2013. [DOI: 10.1039/c3sc51197a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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