1
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Pérez de Carvasal K, Nicollet L, Smietana M, Morvan F. Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:7418-7425. [PMID: 37196178 DOI: 10.1021/acs.langmuir.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,8,4,5-naphthalenetetracarboxylic diimide (NDI) are known to interact through the formation of charge-transfer complexes. The introduction of DAN and NDI into various DNA duplexes and hairpins was investigated by ultraviolet (UV) melting curve analysis. The positioning of the DAN:NDI pair was found to strongly influence the stability of DNA duplex and hairpins. In particular, while the introduction of one DAN/NDI pair in front of each other in the center of a DNA duplex led to a decrease of the thermal stability (ΔTm - 6 °C), the addition of a second pair restored or even increased the stability. In contrast, the introduction of DAN:NDI pairs at the end of a duplex always induced a strong stabilization (ΔTm up to +20 °C). Finally, a DAN:NDI pair positioned in the loop of a hairpin induced a stronger stabilization than a T4 loop (ΔTm + 10 °C). Based on charge-transfer interactions, the strong stabilizations observed allow the preparation of highly stabilized DNA nanostructures opening the way to numerous applications in nanotechnology.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - Laura Nicollet
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - Michael Smietana
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - François Morvan
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
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2
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Liu B, Vonhausen Y, Schulz A, Höbartner C, Würthner F. Peptide Backbone Directed Self‐Assembly of Merocyanine Oligomers into Duplex Structures. Angew Chem Int Ed Engl 2022; 61:e202200120. [PMID: 35194914 PMCID: PMC9401582 DOI: 10.1002/anie.202200120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 11/10/2022]
Abstract
The pseudopeptide backbone provided by N‐(2‐aminoethyl)‐glycine oligomers with attached nucleobases has been widely utilized in peptide nucleic acids (PNAs) as DNA mimics. Here we demonstrate the suitability of this backbone for the formation of structurally defined dye stacks. Toward this goal a series of peptide merocyanine (PMC) dye oligomers connected to a N‐(2‐aminoethyl)‐glycine backbone were prepared through peptide synthesis. Our concentration‐, temperature‐ and solvent‐dependent UV/Vis absorption studies show that under the control of dipole–dipole interactions, smaller‐sized oligomers consisting of one, two or three dyes self‐assemble into defined duplex structures containing two up to six chromophores. In contrast, upon further extension of the oligomer, the chosen peptide backbone cannot direct the formation of a defined duplex architecture anymore due to intramolecular aggregation between the dyes. For all aggregate species a moderate aggregation‐induced emission enhancement is observed.
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Affiliation(s)
- Bin Liu
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Yvonne Vonhausen
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Alexander Schulz
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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3
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Kihal N, Nazemi A, Bourgault S. Supramolecular Nanostructures Based on Perylene Diimide Bioconjugates: From Self-Assembly to Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1223. [PMID: 35407341 PMCID: PMC9000806 DOI: 10.3390/nano12071223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 12/18/2022]
Abstract
Self-assembling π-conjugated systems constitute efficient building blocks for the construction of supramolecular structures with tailored functional properties. In this context, perylene diimide (PDI) has attracted attention owing to its chemical robustness, thermal and photo-stability, and outstanding optical and electronic properties. Recently, the conjugation of PDI derivatives to biological molecules, including oligonucleotides and peptides, has opened new avenues for the design of nanoassemblies with unique structures and functionalities. In the present review, we offer a comprehensive summary of supramolecular bio-assemblies based on PDI. After briefly presenting the physicochemical, structural, and optical properties of PDI derivatives, we discuss the synthesis, self-assembly, and applications of PDI bioconjugates.
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Affiliation(s)
- Nadjib Kihal
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec City, QC G1V 0A6, Canada
- Centre Québécois sur les Matériaux Fonctionnels/Québec Centre for Advanced Materials, CQMF/QCAM, Montreal, QC H3A 2A7, Canada
| | - Ali Nazemi
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Centre Québécois sur les Matériaux Fonctionnels/Québec Centre for Advanced Materials, CQMF/QCAM, Montreal, QC H3A 2A7, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec City, QC G1V 0A6, Canada
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4
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Liu B, Vonhausen Y, Schulz A, Höbartner C, Würthner F. Peptide Backbone Directed Self‐Assembly of Merocyanine Oligomers into Duplex Structures. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bin Liu
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Yvonne Vonhausen
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Alexander Schulz
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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5
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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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6
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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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7
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Ucar H, Wagenknecht HA. DNA-templated control of chirality and efficient energy transport in supramolecular DNA architectures with aggregation-induced emission. Chem Sci 2021; 12:10048-10053. [PMID: 34377398 PMCID: PMC8317660 DOI: 10.1039/d1sc02351a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/19/2021] [Indexed: 01/15/2023] Open
Abstract
Two conjugates of tetraphenylethylene with d-2′-deoxyuridine (1d) and l-2′-deoxyuridine (1l) were synthesized to construct new supramolecular DNA-architectures by self-assembly. The non-templated assemblies of 1d and 1l show strong aggregation-induced emission and their chirality is exclusively controlled by the configuration of their sugar part. In contrast, the chirality of the DNA-templated assemblies is governed by the configuration of the DNA, and there is no configuration-selective binding of 1d to d-A20 and 1l to l-A20. The quantum yield of the assembly of 1d along the single-stranded DNA A20 is 0.40; approximately every second available binding site on the DNA template is occupied by 1d. The strong aggregation-induced emission of these DNA architectures can be efficiently quenched and the excitation energy can be transported to Atto dyes at the 5′-terminus. A multistep energy transport “hopping” precedes the final energy transfer to the terminal acceptor. The building block 1d promotes this energy transport as stepping stones. This was elucidated by reference DNA double strands in which 1d was covalently incorporated at two distinct sites in the sequences, one near the Atto dye, and one farther away. This new type of completely self-assembled supramolecular DNA architecture is hierarchically ordered and the DNA template controls not only the binding but also the energy transport properties. The high intensity of the aggregation-induced emission and the excellent energy transport properties make these DNA-based materials promising candidates for optoelectronic applications. DNA architectures with tetraphenylethylene are assembled in a non-covalent way. The strong aggregation-induced emission of the chromophores is quenched and the energy is transported to Atto dyes by a multistep energy “hopping”.![]()
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Affiliation(s)
- Hülya Ucar
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe German
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe German
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8
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Bialas D, Kirchner E, Röhr MIS, Würthner F. Perspectives in Dye Chemistry: A Rational Approach toward Functional Materials by Understanding the Aggregate State. J Am Chem Soc 2021; 143:4500-4518. [DOI: 10.1021/jacs.0c13245] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David Bialas
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eva Kirchner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Merle I. S. Röhr
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Frank Würthner
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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9
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Röthlisberger P, Levi-Acobas F, Leumann CJ, Hollenstein M. Enzymatic synthesis of biphenyl-DNA oligonucleotides. Bioorg Med Chem 2020; 28:115487. [PMID: 32284226 DOI: 10.1016/j.bmc.2020.115487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022]
Abstract
The incorporation of nucleotides equipped with C-glycosidic aromatic nucleobases into DNA and RNA is an alluring strategy for a number of practical applications including fluorescent labelling of oligonucleotides, expansion of the genetic alphabet for the generation of aptamers and semi-synthetic organisms, or the modulation of excess electron transfer within DNA. However, the generation of C-nucleoside containing oligonucleotides relies mainly on solid-phase synthesis which is quite labor intensive and restricted to short sequences. Here, we explore the possibility of constructing biphenyl-modified DNA sequences using enzymatic synthesis. The presence of multiple biphenyl-units or biphenyl residues modified with electron donors and acceptors permits the incorporation of a single dBphMP nucleotide. Moreover, templates with multiple abasic sites enable the incorporation of up to two dBphMP nucleotides, while TdT-mediated tailing reactions produce single-stranded DNA oligonucleotides with four biphenyl residues appended at the 3'-end.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France.
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10
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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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11
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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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12
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Röthlisberger P, Levi-Acobas F, Sarac I, Ricoux R, Mahy JP, Herdewijn P, Marlière P, Hollenstein M. Incorporation of a minimal nucleotide into DNA. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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13
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Berdnikova DV, Sosnin NI, Fedorova OA, Ihmels H. Governing the DNA-binding mode of styryl dyes by the length of their alkyl substituents – from intercalation to major groove binding. Org Biomol Chem 2018; 16:545-554. [DOI: 10.1039/c7ob02736b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The length of alkyl substituents governs the DNA binding mode of mono- and bis-chromophoric styryl dyes.
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Affiliation(s)
- Daria V. Berdnikova
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
- Department of Chemistry–Biology and Center of Micro and Nanochemistry and Engineering
| | - Nikolai I. Sosnin
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Olga A. Fedorova
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Heiko Ihmels
- Department of Chemistry–Biology and Center of Micro and Nanochemistry and Engineering
- University of Siegen
- 57068 Siegen
- Germany
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14
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Abendroth JM, Nakatsuka N, Ye M, Kim D, Fullerton EE, Andrews AM, Weiss PS. Analyzing Spin Selectivity in DNA-Mediated Charge Transfer via Fluorescence Microscopy. ACS NANO 2017; 11:7516-7526. [PMID: 28672111 DOI: 10.1021/acsnano.7b04165] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding spin-selective interactions between electrons and chiral molecules is critical to elucidating the significance of electron spin in biological processes and to assessing the potential of chiral assemblies for organic spintronics applications. Here, we use fluorescence microscopy to visualize the effects of spin-dependent charge transport in self-assembled monolayers of double-stranded DNA on ferromagnetic substrates. Patterned DNA arrays provide background regions for every measurement to enable quantification of substrate magnetization-dependent fluorescence due to the chiral-induced spin selectivity effect. Fluorescence quenching of photoexcited dye molecules bound within DNA duplexes is dependent upon the rate of charge separation/recombination upon photoexcitation and the efficiency of DNA-mediated charge transfer to the surface. The latter process is modulated using an external magnetic field to switch the magnetization orientation of the underlying ferromagnetic substrates. We discuss our results in the context of the current literature on the chiral-induced spin selectivity effect across various systems.
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Affiliation(s)
| | | | | | - Dokyun Kim
- Center for Memory and Recording Research, University of California, San Diego , La Jolla, California 92093, United States
| | - Eric E Fullerton
- Center for Memory and Recording Research, University of California, San Diego , La Jolla, California 92093, United States
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15
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Mishra AK, Weissman H, Krieg E, Votaw KA, McCullagh M, Rybtchinski B, Lewis FD. Self‐Assembly of Perylenediimide–Single‐Strand‐DNA Conjugates: Employing Hydrophobic Interactions and DNA Base‐Pairing To Create a Diverse Structural Space. Chemistry 2017; 23:10328-10337. [DOI: 10.1002/chem.201700752] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 01/05/2023]
Affiliation(s)
| | - Haim Weissman
- Department of Organic ChemistryWeizmann Institute of Science Rehovot 76100 Israel
| | - Elisha Krieg
- Department of Organic ChemistryWeizmann Institute of Science Rehovot 76100 Israel
| | - Kevin A. Votaw
- Department of ChemistryColorado State University Fort Collins Colorado 80523 USA
| | - Martin McCullagh
- Department of ChemistryColorado State University Fort Collins Colorado 80523 USA
| | - Boris Rybtchinski
- Department of Organic ChemistryWeizmann Institute of Science Rehovot 76100 Israel
| | - Frederick D. Lewis
- Department of ChemistryNorthwestern University Evanston Illinois 60208-3113 USA
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16
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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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17
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Xiang Y, Zhang Q, Li Z, Chen H. Role of electrostatic complementarity between perylenediimide and porphyrin in highly stabilized GNA. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 70:1156-1162. [DOI: 10.1016/j.msec.2016.03.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/03/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
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18
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Takada T, Ido M, Ashida A, Nakamura M, Yamana K. DNA-Templated Synthesis of Perylenediimide Stacks Utilizing Abasic Sites as Binding Pockets and Reactive Sites. Chembiochem 2016; 17:2230-2233. [DOI: 10.1002/cbic.201600454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Misa Ido
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Akane Ashida
- 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
| | - Kazushige Yamana
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
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19
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Wardrip AG, Mazaheripour A, Hüsken N, Jocson J, Bartlett A, Lopez RC, Frey N, Markegard CB, Kladnik G, Cossaro A, Floreano L, Verdini A, Burke AM, Dickson MN, Kymissis I, Cvetko D, Morgante A, Sharifzadeh S, Nguyen HD, Gorodetsky AA. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angew Chem Int Ed Engl 2016; 55:14267-14271. [DOI: 10.1002/anie.201605411] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Austin G. Wardrip
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Nina Hüsken
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Robert C. Lopez
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Nathan Frey
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Cade B. Markegard
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Gregor Kladnik
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
| | | | | | | | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Ioannis Kymissis
- Department of Electrical Engineering Columbia University New York NY 10027 USA
| | - Dean Cvetko
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
- Institut J. Stefan Jamova 39 1000 Ljubljana Slovenia
| | - Alberto Morgante
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Department of Physics University of Trieste Trieste 34128 Italy
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Alon A. Gorodetsky
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
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20
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Wardrip AG, Mazaheripour A, Hüsken N, Jocson J, Bartlett A, Lopez RC, Frey N, Markegard CB, Kladnik G, Cossaro A, Floreano L, Verdini A, Burke AM, Dickson MN, Kymissis I, Cvetko D, Morgante A, Sharifzadeh S, Nguyen HD, Gorodetsky AA. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Austin G. Wardrip
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Nina Hüsken
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Robert C. Lopez
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Nathan Frey
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Cade B. Markegard
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Gregor Kladnik
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
| | | | | | | | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Ioannis Kymissis
- Department of Electrical Engineering Columbia University New York NY 10027 USA
| | - Dean Cvetko
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
- Institut J. Stefan Jamova 39 1000 Ljubljana Slovenia
| | - Alberto Morgante
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Department of Physics University of Trieste Trieste 34128 Italy
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Alon A. Gorodetsky
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
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21
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Kim KT, Choi TS, Kim KY, Kim HI, Kim BH. Disassembly of Chromophore-Guided DNA Duplexes through Site-Selective Binding of Coralyne to Pyrene-Modified Adenine Bases. Chempluschem 2016; 81:590-593. [DOI: 10.1002/cplu.201600230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ki Tae Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Tae Su Choi
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
- Department of Chemistry; Korea University; Seoul 02841 Republic of Korea
| | - Ka Young Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Hugh I. Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
- Department of Chemistry; Korea University; Seoul 02841 Republic of Korea
| | - Byeang Hyean Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
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22
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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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23
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Markegard CB, Mazaheripour A, Jocson JM, Burke AM, Dickson MN, Gorodetsky AA, Nguyen HD. Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates. J Phys Chem B 2015; 119:11459-65. [DOI: 10.1021/acs.jpcb.5b03874] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cade B. Markegard
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Jonah-Micah Jocson
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Alon A. Gorodetsky
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
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24
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Würthner F, Saha-Möller CR, Fimmel B, Ogi S, Leowanawat P, Schmidt D. Perylene Bisimide Dye Assemblies as Archetype Functional Supramolecular Materials. Chem Rev 2015; 116:962-1052. [PMID: 26270260 DOI: 10.1021/acs.chemrev.5b00188] [Citation(s) in RCA: 963] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Frank Würthner
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Chantu R Saha-Möller
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Benjamin Fimmel
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Soichiro Ogi
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Pawaret Leowanawat
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - David Schmidt
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
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25
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Moradpour Hafshejani S, Watson SMD, Tuite EM, Pike AR. Click Modification of Diazido Acridine Intercalators: A Versatile Route towards Decorated DNA Nanostructures. Chemistry 2015. [DOI: 10.1002/chem.201501836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Gershberg J, Radić Stojković M, Škugor M, Tomić S, Rehm TH, Rehm S, Saha-Möller CR, Piantanida I, Würthner F. Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes. Chemistry 2015; 21:7886-95. [DOI: 10.1002/chem.201500184] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 12/12/2022]
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27
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Weiser M, Wagenknecht HA. Dynamic DNA architectures: spontaneous DNA strand exchange and self-sorting driven by perylene bisimide interactions. Chem Commun (Camb) 2015; 51:16530-3. [DOI: 10.1039/c5cc06491k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Three differently bay-substituted perylene bisimides together with the conventional unsubstituted chromophore were synthetically incorporated as homodimers in DNA double strands and undergo spontaneous strand exchange if mixed together.
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Affiliation(s)
- Martin Weiser
- Institute of Organic Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
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28
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Xu Z, Guo K, Yu J, Sun H, Tang J, Shen J, Müllen K, Yang W, Yin M. A unique perylene-based DNA intercalator: localization in cell nuclei and inhibition of cancer cells and tumors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4087-4092. [PMID: 24976526 DOI: 10.1002/smll.201401262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 05/22/2014] [Indexed: 06/03/2023]
Abstract
To date, perylene derivatives have not been explored as DNA intercalator to inhibit cancer cells by intercalating into the base pairs of DNA. Herein, a water-soluble perylene bisimide (PBDI) that efficiently intercalates into the base pairs of DNA is synthesized. Excitingly, PBDI is superior to the commercial DNA intercalator, amonafide, for specific nuclear accumulation and effective suppression of cancer cells and tumors.
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Affiliation(s)
- Zejun Xu
- State Key Laboratory of Chemical Resource Engineering, Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education Beijing, University of Chemical Technology, 100029, Beijing, China
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29
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Takada T, Yamaguchi K, Tsukamoto S, Nakamura M, Yamana K. Light-up fluorescent probes utilizing binding behavior of perylenediimide derivatives to a hydrophobic pocket within DNA. Analyst 2014; 139:4016-21. [DOI: 10.1039/c4an00493k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Takada T, Ashida A, Nakamura M, Fujitsuka M, Majima T, Yamana K. Photocurrent Generation Enhanced by Charge Delocalization over Stacked Perylenediimide Chromophores Assembled within DNA. J Am Chem Soc 2014; 136:6814-7. [DOI: 10.1021/ja501535z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Tadao Takada
- Department
of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Akane Ashida
- Department
of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Mitsunobu Nakamura
- Department
of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Mamoru Fujitsuka
- The
Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The
Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazushige Yamana
- Department
of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
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31
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Nguyen T, Håkansson P, Edge R, Collison D, Goodman BA, Burns JR, Stulz E. EPR based distance measurement in Cu-porphyrin–DNA. NEW J CHEM 2014. [DOI: 10.1039/c4nj00673a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.
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Affiliation(s)
- ThaoNguyen Nguyen
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Pär Håkansson
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Ruth Edge
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - David Collison
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - Bernard A. Goodman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning 530005, China
| | - Jonathan R. Burns
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Eugen Stulz
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
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32
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Takada T, Ashida A, Nakamura M, Yamana K. Cationic perylenediimide as a specific fluorescent binder to mismatch containing DNA. Bioorg Med Chem 2013; 21:6011-4. [PMID: 23953688 DOI: 10.1016/j.bmc.2013.07.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 11/15/2022]
Abstract
Small ligand molecules, which can recognize thermodynamically unstable site within DNA, such as mismatch base pair, abasic site, and single-bulge, have attracted much attention because of their potential diagnostics and biological applications. In this paper, we describe the binding of cationic perylenediimide (cPDI) molecules to thymine-containing mismatch base pair in DNA and the formation of cPDI dimer at the mismatch site. The cPDI dimer exhibits a characteristic excimer emission at 650nm. For T/T mismatch containing DNA, the switching behavior from the PDI dimer (650nm) to the monomer (550nm) emission in specific response to Hg(2+) ion was observed.
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Affiliation(s)
- Tadao Takada
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
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33
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Sezi S, Wagenknecht HA. DNA-templated formation of fluorescent self-assembly of ethynyl pyrenes. Chem Commun (Camb) 2013; 49:9257-9. [DOI: 10.1039/c3cc44733b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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34
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Fujii T, Hara Y, Osawa T, Kashida H, Liang X, Yoshida Y, Asanuma H. Bulge-like Asymmetric Heterodye Clustering in DNA Duplex Results in Efficient Quenching of Background Emission Based on the Maximized Excitonic Interaction. Chemistry 2012; 18:10865-72. [DOI: 10.1002/chem.201201365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Indexed: 11/08/2022]
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35
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Takada T, Otsuka Y, Nakamura M, Yamana K. Molecular Arrangement and Assembly Guided by Hydrophobic Cavities inside DNA. Chemistry 2012; 18:9300-4. [DOI: 10.1002/chem.201201469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Indexed: 11/07/2022]
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36
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Wang S, Guo J, Ono T, Kool ET. DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems. Angew Chem Int Ed Engl 2012; 51:7176-80. [PMID: 22684777 DOI: 10.1002/anie.201201928] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/16/2012] [Indexed: 11/07/2022]
Abstract
Dye-ing to live: Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. The development of a multispectral set of improved DNA-scaffolded fluorophores is described. Their use in multicolor cellular imaging (see scheme) and in tracking of biological motions on the subsecond timescale is demonstrated.
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Affiliation(s)
- Shenliang Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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37
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Wang S, Guo J, Ono T, Kool ET. DNA Polyfluorophores for Real-Time Multicolor Tracking of Dynamic Biological Systems. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Asanuma H, Fujii T, Kato T, Kashida H. Coherent interactions of dyes assembled on DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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39
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Görl D, Zhang X, Würthner F. Molecular assemblies of perylene bisimide dyes in water. Angew Chem Int Ed Engl 2012; 51:6328-48. [PMID: 22573415 DOI: 10.1002/anie.201108690] [Citation(s) in RCA: 395] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Indexed: 01/28/2023]
Abstract
Perylene bisimides are among the most valuable functional dyes and have numerous potential applications. As a result of their chemical robustness, photostability, and outstanding optical and electronic properties, these dyes have been applied as pigments, fluorescence sensors, and n-semiconductors in organic electronics and photovoltaics. Moreover, the extended quadrupolar π system of this class of dyes has facilitated the construction of numerous supramolecular architectures with fascinating photophysical properties. However, the supramolecular approach to the formation of perylene bisimide aggregates has been restricted mostly to organic media. Pleasingly, considerable progress has been made in the last few years in developing water-soluble perylene bisimides and their application in aqueous media. This Review provides an up-to-date overview on the self-assembly of perylene bisimides through π-π interactions in aqueous media. Synthetic strategies for the preparation of water-soluble perylene bisimides and the influence of water on the π-π stacking of perylene bisimides as well as the resulting applications are discussed.
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Affiliation(s)
- Daniel Görl
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry, Am Hubland, 97074 Würzburg, Germany
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40
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Görl D, Zhang X, Würthner F. Molekülverbände von Perylenbisimid-Farbstoffen in Wasser. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108690] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Neelakandan PP, McCullagh M, Schatz GC, Lewis FD. Electronic interactions in helical stacked arrays of the modified DNA base pyrrolocytosine. J Phys Chem B 2012; 116:5199-204. [PMID: 22486518 DOI: 10.1021/jp302385c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The thermal stability and ultraviolet and circular dichroism spectra of nine synthetic DNA hairpins possessing one or more (P)C-G base pairs ((P)C = pyrrolocytosine) have been investigated. One group of hairpins possess 1-5 sequential (P)C-G base pairs while another group possess two (P)C-G base pairs separated by 1-3 A-T base pairs. The first group displays a nearly linear dependence of UV and exciton-coupled circular dichroism (EC-CD) band intensity upon the number of neighboring chromophores, whereas the second group shows weak EC-CD only at the shortest distances between non-neighboring chromophores. This result stands in marked contrast to the exciton coupling seen between stilbene chromophores separated by as many as a dozen base pairs. The weak exciton coupling between non-neighboring (P)C chromophores, like that of the natural nucelobases, is attributed to their relatively weak electronic transition dipoles.
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Affiliation(s)
- Prakash P Neelakandan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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42
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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43
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Probst M, Wenger D, Biner SM, Häner R. The DNA three-way junction as a mould for tripartite chromophore assembly. Org Biomol Chem 2012; 10:755-9. [DOI: 10.1039/c1ob06400b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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44
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Kashida H, Asanuma H. Preparation of supramolecular chromophoric assemblies using a DNA duplex. Phys Chem Chem Phys 2012; 14:7196-204. [DOI: 10.1039/c2cp40520b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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45
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Nakamura M, Fukuda M, Takada T, Yamana K. Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence. Org Biomol Chem 2012; 10:9620-6. [DOI: 10.1039/c2ob26773j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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46
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Rehm TH, Stojković MR, Rehm S, Škugor M, Piantanida I, Würthner F. Interaction of spermine-alanine functionalized perylene bisimide dye aggregates with ds-DNA/RNA secondary structure. Chem Sci 2012. [DOI: 10.1039/c2sc20825c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Franceschin M, Borbone N, Oliviero G, Casagrande V, Scuotto M, Coppola T, Borioni S, Mayol L, Ortaggi G, Bianco A, Amato J, Varra M. Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate. Bioconjug Chem 2011; 22:1309-19. [PMID: 21688831 DOI: 10.1021/bc100526q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.
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Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
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Menacher F, Wagenknecht HA. Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100519] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Burns JR, Zekonyte J, Siligardi G, Hussain R, Stulz E. Directed formation of DNA nanoarrays through orthogonal self-assembly. Molecules 2011; 16:4912-22. [PMID: 21677604 PMCID: PMC6264196 DOI: 10.3390/molecules16064912] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 05/31/2011] [Accepted: 06/10/2011] [Indexed: 01/12/2023] Open
Abstract
We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II) and Ni(II) induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.
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Affiliation(s)
- Jonathan R. Burns
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Jurgita Zekonyte
- National Centre for Advanced Tribology, School of Engineering Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Giuliano Siligardi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Rohanah Hussain
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Eugen Stulz
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Author to whom correspondence should be addressed; ; Tel +44-2380-599369
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Menacher F, Wagenknecht HA. Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution. Photochem Photobiol Sci 2011; 10:1275-8. [PMID: 21547330 DOI: 10.1039/c1pp05091e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular beacons with an excitonically interacting perylene bisimide base pair show the presence of the complementary olignucleotide sequence by both absorption and fluorescence changes.
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Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany
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