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García Coll J, Ulrich S. Nucleic-Acid-Templated Synthesis of Smart Polymer Vectors for Gene Delivery. Chembiochem 2023; 24:e202300333. [PMID: 37401911 DOI: 10.1002/cbic.202300333] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/12/2023] [Accepted: 07/04/2023] [Indexed: 07/05/2023]
Abstract
Nucleic acids are information-rich and readily available biomolecules, which can be used to template the polymerization of synthetic macromolecules. Here, we highlight the control over the size, composition, and sequence one can nowadays obtain by using this methodology. We also highlight how templated processes exploiting dynamic covalent polymerization can, in return, result in therapeutic nucleic acids fabricating their own dynamic delivery vector - a biomimicking concept that can provide original solutions for gene therapies.
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Affiliation(s)
- José García Coll
- IBMM, Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095, Montpellier, France
| | - Sébastien Ulrich
- IBMM, Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095, Montpellier, France
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2
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Takada T, Shimobaki N, Naruo M, Nakamura M, Yamana K. Photoresponsive porphyrin‐DNA complexes constructed through intercalation‐like binding. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tadao Takada
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry 2167 Shosha 671-2280 Himeji, Hyogo JAPAN
| | - Nao Shimobaki
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Moe Naruo
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Mitsunobu Nakamura
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Kazushige Yamana
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
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3
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Ucar H, Wagenknecht HA. Aggregation-induced emission by sequence-selective assembly of cyanolytated distyrylbenzene in supramolecular DNA architectures. Chem Commun (Camb) 2022; 58:6437-6440. [DOI: 10.1039/d2cc01161a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cyanolated distyrylbenzene conjugated to 2’-deoxyuridine is a new building block for supramolecular DNA architectures combining aggregation-induced emission and sequence-selective binding. A high number of binding sites at the DNA...
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4
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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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5
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Müller S, Manger F, Graf von Reventlow L, Colsmann A, Wagenknecht HA. Molecular Chromophore-DNA Architectures With Fullerenes: Optical Properties and Solar Cells. Front Chem 2021; 9:645006. [PMID: 33708761 PMCID: PMC7941155 DOI: 10.3389/fchem.2021.645006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/01/2021] [Indexed: 01/06/2023] Open
Abstract
Supramolecular chemistry allows the construction of complex molecular architectures and the design of collective photophysical properties. DNA is an attractive template to build such supramolecular architectures due to its helical structure, the defined distances between the bases and the canonical base pairing that results in precise control of the chromophore position. The tailored properties of DNA-templated supramolecules eventually allow their implementation into optoelectronic applications. For the generation of free charge carriers from photo-generated excitons, fullerenes can be utilized. We synthesized two fullerene derivates, one of which binds by electrostatic interactions to single-stranded DNA, while the other contains two 2'-deoxyuridine moieties and assembles specifically along oligo-2'-deoxyadenosines (dA20) as DNA template. The DNA-directed assembly of both fullerenes in aqueous solution was investigated by UV/Vis absorbance and circular dichroism (CD) spectroscopy. The specific interactions with DNA make fullerenes with the 2'-deoxyuridine moieties a significantly better component for supramolecular DNA architectures. We studied the fluorescence quenching of both fullerenes with a DNA chromophore assembly. To investigate one of the key properties for optoelectronic applications, that is the supramolecular structure of the DNA-based assemblies in the solid phase, we characterized the CD of supramolecular chromophore-DNA architectures in thin films. Remarkably, the helical chirality of the chromophore assemblies that is induced by the DNA template is conserved even in the solid state. Upon implementation into organic solar cells, the external quantum efficiency measurements showed charge carrier generation on all three chromophore components of the DNA assemblies. The fullerenes with the 2'-deoxyuridine moieties enhance the quantum efficiency of the conversion process significantly, demonstrating the potential of DNA as structural element for ordering chromophores into functional π-systems, which may be employed in future organic solar cells.
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Affiliation(s)
- Sara Müller
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Felix Manger
- Material Research Center for Energy Systems, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Light Technology Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Lorenz Graf von Reventlow
- Material Research Center for Energy Systems, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Light Technology Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander Colsmann
- Material Research Center for Energy Systems, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Light Technology Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
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6
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Coste M, Kotras C, Bessin Y, Gervais V, Dellemme D, Leclercq M, Fossépré M, Richeter S, Clément S, Surin M, Ulrich S. Synthesis, Self‐Assembly, and Nucleic Acid Recognition of an Acylhydrazone‐Conjugated Cationic Tetraphenylethene Ligand. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Maëva Coste
- IBMM Université de Montpellier, CNRS, ENSCM Montpellier France
| | - Clément Kotras
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Yannick Bessin
- IBMM Université de Montpellier, CNRS, ENSCM Montpellier France
| | - Virginie Gervais
- CNRS Institut de Pharmacologie et de Biologie Structurale (IPBS) Université de Toulouse, UPS 205 route de Narbonne 31077 Toulouse France
| | - David Dellemme
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Sébastien Richeter
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
| | - Sébastien Clément
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
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7
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Tufenkjian E, Kahlfuss C, Kyritsakas N, Hosseini MW, Bulach V. Synthesis of Porphyrins Di‐ and Tetra‐Functionalized with Nucleobases. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elsa Tufenkjian
- Institution Department Chemistry of Complex Matter laboratory, UMR 7140 University of Strasbourg, Institut Le Bel 67000 Strasbourg France
| | - Christophe Kahlfuss
- Institution Department Chemistry of Complex Matter laboratory, UMR 7140 University of Strasbourg, Institut Le Bel 67000 Strasbourg France
| | - Nathalie Kyritsakas
- Institution Department Chemistry of Complex Matter laboratory, UMR 7140 University of Strasbourg, Institut Le Bel 67000 Strasbourg France
| | - Mir Wais Hosseini
- Institution Department Chemistry of Complex Matter laboratory, UMR 7140 University of Strasbourg, Institut Le Bel 67000 Strasbourg France
| | - Véronique Bulach
- Institution Department Chemistry of Complex Matter laboratory, UMR 7140 University of Strasbourg, Institut Le Bel 67000 Strasbourg France
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8
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Müller S, Fritz Y, Wagenknecht H. Control of Energy Transfer Between Pyrene- and Perylene-Nucleosides by the Sequence of DNA-Templated Supramolecular Assemblies. ChemistryOpen 2020; 9:389-392. [PMID: 32257746 PMCID: PMC7110160 DOI: 10.1002/open.201900346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/09/2020] [Indexed: 12/18/2022] Open
Abstract
DNA was used as supramolecular scaffold to order chromophores and control their optical properties. Ethynylpyrene as energy donor was attached to 2'-desoxy-2-aminoadenosine that binds selectively to thymidines (T) in the template. Ethynylperylene as acceptor was attached to 2'-desoxyuridine that is complementary to 2'-desoxyadenosine (A). This donor-acceptor pair was assembled along single-stranded DNA templates of different A-T sequences to investigate the sequence control of the energy transfer between the chromophores. The fluorescence intensities increase in the mixed assemblies along the DNA templates from A10T10 over (AATT)5 to (AT)10, although these templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This shows that the sequence selective assembly of the two building blocks along DNA templates is programmable and alters the fluorescence readout. Such sequence-controlled supramolecular chemistry represents the key element for future functional π-systems in materials for light harvesting of solar energy.
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Affiliation(s)
- Sara Müller
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Yannic Fritz
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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9
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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10
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Hofsäβ R, Ensslen P, Wagenknecht HA. Control of helical chirality in supramolecular chromophore-DNA architectures. Chem Commun (Camb) 2019; 55:1330-1333. [PMID: 30638231 DOI: 10.1039/c8cc08887j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Four different d- and l-configured chromophore-2'-deoxyuridine conjugates were applied to elucidate the helical chirality of their non-covalent assemblies along the d- and l-configured DNA templates by optical spectroscopy. There is no configuration-selective recognition between these nucleosides and the DNA templates. The helicity of the DNA assemblies is either controlled by the configuration of the DNA template or by the nucleoside configuration.
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Affiliation(s)
- Robert Hofsäβ
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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11
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Hofsäß R, Sinn S, Biedermann F, Wagenknecht HA. Programmable and Sequence-Selective Supramolecular Assembly of Two Different Chromophores along DNA Templates. Chemistry 2018; 24:16257-16261. [DOI: 10.1002/chem.201804314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Robert Hofsäß
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan Sinn
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Frank Biedermann
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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12
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Trévisan M, Fossépré M, Paolantoni D, Rubio-Magnieto J, Dumy P, Ulrich S, Surin M. Self-assembly and chiroptical properties in supramolecular complexes of adenosine phosphates and guanidinium-bispyrene. Chirality 2018; 30:719-729. [PMID: 29578614 DOI: 10.1002/chir.22852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 11/10/2022]
Abstract
Supramolecular systems that respond to the hydrolysis of adenosine phosphates (APs) are attractive for biosensing and to fabricate bioinspired self-assembled materials. Here, we report on the formation of supramolecular complexes between an achiral guanidinium derivative bearing two pyrene moieties, with each of the three adenosine phosphates: AMP, ADP, and ATP. By combining results from circular dichroism spectroscopy and molecular modeling simulations, we explore the induced chirality, the dynamics of the complexes, and the interactions at play, which altogether provide insights into the supramolecular self-assembly between APs and the guanidinium-bispyrene. Finally, we identify the chiroptical signals of interest in mixtures of the guanidinium derivative with the three APs in different proportions. This study constitutes a basis to evolve toward a chiroptical detection of the hydrolysis of APs based on organic supramolecular probes.
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Affiliation(s)
- Marie Trévisan
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
| | - Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jenifer Rubio-Magnieto
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
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13
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Chiral multichromophoric supramolecular nanostructures assembled by single stranded DNA and RNA templates. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Hwang YM, Kwon N, Kim SK, Jang YJ. Chiral Selective Stacking of a Cationic Porphyrin along Z-Form Poly[d(A-T) 2]. J Phys Chem B 2017; 121:2104-2110. [PMID: 28218531 DOI: 10.1021/acs.jpcb.7b00228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, the binding mode of porphyrin-free single-stranded poly[d(AT)] and trans-BMPyP was observed in the Z-form trans-BMPyP-poly[d(A-T)2] complex induced by extensive stacking depending on the temperature and concentration through circular dichroism (CD). The Z-form trans-BMPyP-poly[d(A-T)2] complex (R = 0.30) retained the Z-form DNA structure at a low temperature (20 °C) by the trans-BMPyP molecules. When the temperature was increased to 60 °C, the DNA was almost unfolded as a single-stranded poly[d(AT)], but the extensive stacking binding mode of trans-BMPyP was maintained and the shape of the porphyrin Soret band was symmetrically changed in comparison with the shape of the Z-form DNA. However, when the temperature was raised to 80 °C, the extensive stacking binding mode of trans-BMPyP was also unfolded almost completely. The binding mode of the trans-BMPyP-single-stranded poly[d(AT)] complex was very similar to the already known binding mode of porphyrins and a double-stranded DNA. The binding mode was dependent on the concentration ratio ([porphyrin]/[DNA]): a monomeric binding mode at a concentration ratio of 0.04, a moderate groove binding mode at a concentration ratio between 0.08 and 0.16, and extensive stacking at a concentration ratio between 0.20 and 0.30. The same result was obtained when the temperature of the Z-form DNA (R = 0.30) was increased to 60 °C. However, those binding modes were not found in cis-BMPyP, which was because, in the extensive stacking of trans-BMPyP along the DNA skeleton, the distance between the two positive methylpyridine ions at the trans site and thymine, one of the DNA bases, is decreased, creating a much more hydrophobic environment. In addition, the poly AT sequences found from the CD spectra for the binding of trans-BMPyP-poly[d(A-T)2] and trans-BMPyP-poly[d(AT)] (R = 0.30) showed that both of them underwent effective extensive stacking and that the chirality of extensive stacking was dependent on the form of DNA.
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Affiliation(s)
- Yoon Mo Hwang
- Department of Chemistry and ‡College of Basic Education, Yeungnam University , Dae-dong, Gyeongsan 38541, Gyeong-buk, Republic of Korea
| | - Nayoung Kwon
- Department of Chemistry and ‡College of Basic Education, Yeungnam University , Dae-dong, Gyeongsan 38541, Gyeong-buk, Republic of Korea
| | - Seog K Kim
- Department of Chemistry and ‡College of Basic Education, Yeungnam University , Dae-dong, Gyeongsan 38541, Gyeong-buk, Republic of Korea
| | - Yoon Jung Jang
- Department of Chemistry and ‡College of Basic Education, Yeungnam University , Dae-dong, Gyeongsan 38541, Gyeong-buk, Republic of Korea
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15
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Surin M. From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers. Polym Chem 2016. [DOI: 10.1039/c6py00480f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel Materials
- Center for Innovation and Research in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
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16
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Rubio-Magnieto J, Kumar M, Brocorens P, Idé J, George SJ, Lazzaroni R, Surin M. Chiral supramolecular organization and cooperativity in DNA-templated assemblies of ZnII–chromophore complexes. Chem Commun (Camb) 2016; 52:13873-13876. [DOI: 10.1039/c6cc07414f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Templated cooperative binding induced assembly of chromophores is achieved via interactions between Zn-complexes and the DNA phosphodiester backbone.
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Affiliation(s)
- Jenifer Rubio-Magnieto
- Laboratory for Chemistry of Novel Materials
- Center for Innovation in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
| | - Mohit Kumar
- Supramolecular Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
- Bangalore
- India
| | - Patrick Brocorens
- Laboratory for Chemistry of Novel Materials
- Center for Innovation in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
| | - Julien Idé
- Laboratory for Chemistry of Novel Materials
- Center for Innovation in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
| | - Subi J. George
- Supramolecular Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
- Bangalore
- India
| | - Roberto Lazzaroni
- Laboratory for Chemistry of Novel Materials
- Center for Innovation in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials
- Center for Innovation in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
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17
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Kumari R, Singh S, Monisha M, Bhowmick S, Roy A, Das N, Das P. Hierarchical coassembly of DNA-triptycene hybrid molecular building blocks and zinc protoporphyrin IX. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:697-707. [PMID: 27335759 PMCID: PMC4901925 DOI: 10.3762/bjnano.7.62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/29/2016] [Indexed: 05/06/2023]
Abstract
Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)-DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA-organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5'-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA-TPA molecular building blocks as well as a model guest molecule within the DNA-TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA-TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA-DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA-TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.
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Affiliation(s)
- Rina Kumari
- Department of Chemistry, IIT Patna, Bihata 801118, India
| | - Sumit Singh
- Department of Chemistry, IIT Patna, Bihata 801118, India
| | - Mohan Monisha
- Department of Biotechnology, IIT Hyderabad, Hyderabad, 502205, India
| | | | - Anindya Roy
- Department of Biotechnology, IIT Hyderabad, Hyderabad, 502205, India
| | - Neeladri Das
- Department of Chemistry, IIT Patna, Bihata 801118, India
| | - Prolay Das
- Department of Chemistry, IIT Patna, Bihata 801118, India
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18
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Ensslen P, Wagenknecht HA. One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting. Acc Chem Res 2015; 48:2724-33. [PMID: 26411920 DOI: 10.1021/acs.accounts.5b00314] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.
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Affiliation(s)
- Philipp Ensslen
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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20
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Lourenço LMO, Iglesias BA, Pereira PMR, Girão H, Fernandes R, Neves MGPMS, Cavaleiro JAS, Tomé JPC. Synthesis, characterization and biomolecule-binding properties of novel tetra-platinum(ii)-thiopyridylporphyrins. Dalton Trans 2015; 44:530-8. [DOI: 10.1039/c4dt02697g] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
New tetra-platinum(ii)-thiopyridylporphyrin complexes and their DNA binding studies.
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Affiliation(s)
| | | | - Patrícia M. R. Pereira
- QOPNA and Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
- Laboratory of Pharmacology and Experimental Therapeutics
| | - Henrique Girão
- Centre of Ophthalmology and Vision Sciences
- IBILI
- Faculty of Medicine of University of Coimbra
- 3000-548 Coimbra
- Portugal
| | - Rosa Fernandes
- Laboratory of Pharmacology and Experimental Therapeutics
- IBILI
- Faculty of Medicine
- University of Coimbra
- 3000-548 Coimbra
| | | | | | - João P. C. Tomé
- QOPNA and Department of Chemistry
- University of Aveiro
- 3810-193 Aveiro
- Portugal
- Department of Organic Chemistry
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21
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Takada T, Otsuka Y, Nakamura M, Yamana K. Formation of a charge transfer complex within a hydrophobic cavity in DNA. RSC Adv 2014. [DOI: 10.1039/c4ra11761a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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22
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Ensslen P, Fritz Y, Wagenknecht HA. Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates. Org Biomol Chem 2014; 13:487-92. [PMID: 25374296 DOI: 10.1039/c4ob01860e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.
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Affiliation(s)
- Philipp Ensslen
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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23
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24
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Paolantoni D, Rubio-Magnieto J, Cantel S, Martinez J, Dumy P, Surin M, Ulrich S. Probing the importance of π-stacking interactions in DNA-templated self-assembly of bisfunctionalized guanidinium compounds. Chem Commun (Camb) 2014; 50:14257-60. [DOI: 10.1039/c4cc05706f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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Choi JK, Reed A, Balaz M. Chiroptical properties, binding affinity, and photostability of a conjugated zinc porphyrin dimer complexed with left-handed Z-DNA and right-handed B-DNA. Dalton Trans 2014; 43:563-7. [PMID: 24129690 DOI: 10.1039/c3dt52210e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the UV-vis absorption and chiroptical properties, binding affinity and photostability of a conjugated positively charged butadiyne-linked Zn(ii) porphyrin dimer bound to DNA sequence poly(dG-dC)2. Right-handed B-DNA, spermine-induced Z-DNA and Co(iii)-induced Z-DNA have been explored. Resonance light scattering (RLS) spectra showed formation of porphyrin aggregates in the presence of all DNA forms with the largest aggregates formed with B-DNA. The porphyrin dimer gave rise to induced bisignate circular dichroism (CD) signals in the presence of the left-handed Z-DNA conformations. On the other hand, the dimer stayed nearly chiroptically silent when complexed with the B-form of poly(dG-dC)2. Our results indicated that the conjugated Zn(ii) porphyrin dimer can be used as a sensor for the chiroptical detection of Z-DNA in the visible (400-500 nm) and near-infrared region of the electromagnetic spectrum (700-800 nm). The helicity of DNA had little effect on the dimer binding affinities. The photostability of the porphyrin dimer complexed with any form of DNA was higher than that of the free molecule. The porphyrin dimer bound to Z-DNA exhibited slower photobleaching than the B-DNA dimer complex.
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Affiliation(s)
- Jung Kyu Choi
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA.
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26
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Wellner C, Wagenknecht HA. Synthesis of DNA conjugates with metalated tetracationic porphyrins by postsynthetic cycloadditions. Org Lett 2014; 16:1692-5. [PMID: 24606171 DOI: 10.1021/ol500364j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Tetracationic porphyrins of the TMPP (meso-tetra-(4-N-methylpyridyl)porphyrin) type, metalated with Cu(II) or with Au(III), were conjugated covalently to oligonucleotides. The Cu(I)-catalyzed cycloaddition (between an azide and an ethynyl group) and the Diels-Alder cycloaddition (between a furan and a maleimide functionality) were successfully applied as two alternative postsynthetic methods to modify the 2'-position of an internal uridine. Melting temperatures and UV/vis absorption properties were compared. CD measurements indicated that the type of conjugation chemistry determines the grade of intercalation of the attached and positively charged porphyrins.
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Affiliation(s)
- Christian Wellner
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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27
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Sargsyan G, Leonard BM, Kubelka J, Balaz M. Supramolecular ssDNA Templated Porphyrin and Metalloporphyrin Nanoassemblies with Tunable Helicity. Chemistry 2014; 20:1878-92. [DOI: 10.1002/chem.201304153] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 01/01/2023]
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Vybornyi M, Rudnev AV, Langenegger SM, Wandlowski T, Calzaferri G, Häner R. Formation of Two-Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers. Angew Chem Int Ed Engl 2013; 52:11488-93. [DOI: 10.1002/anie.201307029] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 01/25/2023]
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29
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Vybornyi M, Rudnev AV, Langenegger SM, Wandlowski T, Calzaferri G, Häner R. Formation of Two-Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307029] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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30
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Sensitive electrochemical monitoring of nucleic acids coupling DNA nanostructures with hybridization chain reaction. Anal Chim Acta 2013; 783:17-23. [PMID: 23726095 DOI: 10.1016/j.aca.2013.04.049] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/20/2013] [Accepted: 04/24/2013] [Indexed: 01/24/2023]
Abstract
Methods based on metal nanotags have been developed for metallobioassay of nucleic acids, but most involve complicated labeling or stripping procedures and are unsuitable for routine use. Herein, we report the proof-of-concept of a novel and label-free metallobioassay for ultrasensitive electronic determination of human immunodeficiency virus (HIV)-related gene fragments at an ultralow concentration based on target-triggered long-range self-assembled DNA nanostructures and DNA-based hybridization chain reaction (HCR). The signal is amplified by silver nanotags on the DNA duplex. The assay mainly consists of capture probe, detection probe, and two different DNA hairpins. In the presence of target DNA, the capture probe immobilized on the sensor sandwiches target DNA with the 3' end of detection probe. Another exposed part of detection probe at the 5' end opens two alternating DNA hairpins in turn, and propagates a chain reaction of hybridization events to form a nicked double-helix. Finally, numerous silver nanotags are immobilized onto the long-range DNA nanostructures, each of which produces a strong electronic signal within the applied potentials. Under optimal conditions, the target-triggered long-range DNA nanostructures present good electrochemical behaviors for the detection of HIV DNA at a concentration as low as 0.5 fM. Importantly, the outstanding sensitivity can make this approach a promising scheme for development of next-generation DNA sensors without the need of enzyme labeling or fluorophore labeling.
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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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