1
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Takezawa Y, Kudo N, Fuse N, Shionoya M. DNA three-way junction structures with amino acid side chains prepared via post-synthetic amide condensation. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-14. [PMID: 38359331 DOI: 10.1080/15257770.2024.2314645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
DNA three-way junction (3WJ) structures with three amino acid side chains in the core have been synthesized via post-synthetic DNA modification. Amide condensation reactions of oligonucleotides containing 2'-aminouridine with activated esters yielded DNA strands modified with His, Cys and Asp side chains to form modified 3WJs. Even a 3WJ with three negatively charged Asp side chains formed stably at room temperature. Furthermore, DNA hybridization alone placed two (His and Asp) and three (His, Cys, and Asp) side chains within the 3WJs, indicating that the DNA 3WJs are a useful platform for spatial arrangement of amino acid side chains.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naofumi Kudo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Fuse
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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2
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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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3
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Mao D, Paluzzi VE, Zhang C, Mao C. DNA conformational equilibrium enables continuous changing of curvatures. NANOSCALE 2023; 15:470-475. [PMID: 36515101 DOI: 10.1039/d2nr05404c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Assembly of complex structures from a small set of tiles is a common theme in biology. For example, many copies of identical proteins make up polyhedron-shaped, viral capsids and tubulin can make long microtubules. This inspired the development of tile-based DNA self-assembly for nanoconstruction, particularly for structures with high symmetries. In the final structure, each type of motif will adopt the same conformation, either rigid or with defined flexibility. For structures that have no symmetry, their assembly remains a challenge from a small set of tiles. To meet this challenge, algorithmic self-assembly has been explored driven by computational science, but it is not clear how to implement this approach to one-dimensional (1D) structures. Here, we have demonstrated that a constant shift of a conformational equilibrium could allow 1D structures to evolve. As shown by atomic force microscopy imaging, one type of DNA tile successfully assembled into DNA spirals and concentric circles, which became less and less curved from the structure's center outward. This work points to a new direction for tile-based DNA assembly.
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Affiliation(s)
- Dake Mao
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Victoria E Paluzzi
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Cuizheng Zhang
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Chengde Mao
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
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4
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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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5
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Takada T, Nishida K, Honda Y, Nakano A, Nakamura M, Fan S, Kawai K, Fujitsuka M, Yamana K. Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions. Chembiochem 2021; 22:2729-2735. [PMID: 34191388 DOI: 10.1002/cbic.202100309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/20/2022]
Abstract
Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.
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Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Koma Nishida
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Yurika Honda
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Aoi Nakano
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazushige Yamana
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
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6
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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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7
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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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8
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Lone MS, Bhat PA, Afzal S, Chat OA, Dar AA. Energy transduction through FRET in self-assembled soft nanostructures based on surfactants/polymers: current scenario and prospects. SOFT MATTER 2021; 17:425-446. [PMID: 33400748 DOI: 10.1039/d0sm01625j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The self-assembled systems of surfactants/polymers, which are capable of supporting energy funneling between fluorophores, have recently gained significant attraction. Surfactant and polymeric micelles form nanoscale structures spanning a radius of 2-10 nm are generally suitable for the transduction of energy among fluorophores. These systems have shown great potential in Förster resonance energy transfer (FRET) due to their unique characteristics of being aqueous based, tendency to remain self-assembled, spontaneous formation, tunable nature, and responsiveness to different external stimuli. This review presents current developments in the field of energy transfer, particularly the multi-step FRET processes in the self-assembled nanostructures of surfactants/polymers. The part one of this review presents a background and brief overview of soft systems and discusses certain aspects of the self-assemblies of surfactants/polymers and their co-solubilization property to bring fluorophores to close proximity to transduce energy. The second part of this review deals with single-step and multi-step FRET in the self-assemblies of surfactants/polymers and links FRET systems with advanced smart technologies including multicolor formation, data encryption, and artificial antenna systems. This review also discusses the diverse examples in the literature to present the emerging applications of FRET. Finally, the prospects regarding further improvement of FRET in self-assembled soft systems are outlined.
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Affiliation(s)
- Mohd Sajid Lone
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| | - Parvaiz Ahmad Bhat
- Department of Chemistry, Government Degree College, Pulwama-192301, J&K, India.
| | - Saima Afzal
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| | - Oyais Ahmad Chat
- Department of Chemistry, Government Degree College, Pulwama-192301, J&K, India.
| | - Aijaz Ahmad Dar
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
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9
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Mishra A, Dhiman S, George SJ. ATP‐Driven Synthetic Supramolecular Assemblies: From ATP as a Template to Fuel. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Shikha Dhiman
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Subi J. George
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
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10
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Mishra A, Dhiman S, George SJ. ATP‐Driven Synthetic Supramolecular Assemblies: From ATP as a Template to Fuel. Angew Chem Int Ed Engl 2020; 60:2740-2756. [DOI: 10.1002/anie.202006614] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Shikha Dhiman
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Subi J. George
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
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11
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Jevric J, Langenegger SM, Häner R. Light-Harvesting Supramolecular Polymers: Energy Transfer to Various Polyaromatic Acceptors. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jovana Jevric
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Simon M. Langenegger
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
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12
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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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13
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Evenou P, Rossignol J, Pembouong G, Gothland A, Colesnic D, Barbeyron R, Rudiuk S, Marcelin AG, Ménand M, Baigl D, Calvez V, Bouteiller L, Sollogoub M. Bridging β-Cyclodextrin Prevents Self-Inclusion, Promotes Supramolecular Polymerization, and Promotes Cooperative Interaction with Nucleic Acids. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Pierre Evenou
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Julien Rossignol
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Gaëlle Pembouong
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Adélie Gothland
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Dmitri Colesnic
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Renaud Barbeyron
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Sergii Rudiuk
- PASTEUR; Département de chimie; École normale supérieure; PSL University; Sorbonne Université; CNRS; 75005 Paris France
| | - Anne-Geneviève Marcelin
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Mickaël Ménand
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Damien Baigl
- PASTEUR; Département de chimie; École normale supérieure; PSL University; Sorbonne Université; CNRS; 75005 Paris France
| | - Vincent Calvez
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Laurent Bouteiller
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Matthieu Sollogoub
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
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14
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Evenou P, Rossignol J, Pembouong G, Gothland A, Colesnic D, Barbeyron R, Rudiuk S, Marcelin AG, Ménand M, Baigl D, Calvez V, Bouteiller L, Sollogoub M. Bridging β-Cyclodextrin Prevents Self-Inclusion, Promotes Supramolecular Polymerization, and Promotes Cooperative Interaction with Nucleic Acids. Angew Chem Int Ed Engl 2018; 57:7753-7758. [DOI: 10.1002/anie.201802550] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Pierre Evenou
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Julien Rossignol
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Gaëlle Pembouong
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Adélie Gothland
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Dmitri Colesnic
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Renaud Barbeyron
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Sergii Rudiuk
- PASTEUR; Département de chimie; École normale supérieure; PSL University; Sorbonne Université; CNRS; 75005 Paris France
| | - Anne-Geneviève Marcelin
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Mickaël Ménand
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Damien Baigl
- PASTEUR; Département de chimie; École normale supérieure; PSL University; Sorbonne Université; CNRS; 75005 Paris France
| | - Vincent Calvez
- Sorbonne Université; INSERM; Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR 1136; 83 boulevard de l'hôpital 75652 Paris cedex 13 France
| | - Laurent Bouteiller
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
| | - Matthieu Sollogoub
- Sorbonne Université; CNRS; Institut Parisien de Chimie Moléculaire; UMR 8232; 4 place Jussieu 75005 Paris France
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15
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Lai G, Luh TY. Polynorbornene-based Template for Polymer Synthesis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Guoqiao Lai
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Tien-Yau Luh
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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16
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Photomodulation of DNA-Templated Supramolecular Assemblies. Chemistry 2017; 24:706-714. [DOI: 10.1002/chem.201704538] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/22/2022]
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17
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Guo Z, Wang K, Yu P, Zhang S, Sun K, Li Z. Role of intrinsic hydrogen bonds in the assembly of perylene imide derivatives in solution and at the liquid–solid interface. Phys Chem Chem Phys 2017; 19:23007-23014. [DOI: 10.1039/c7cp04928e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The impact of hydrogen bond formation on the supramolecular assembly of two perylene imide-based derivatives was systematically investigated.
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Affiliation(s)
- Zongxia Guo
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department
- School of Polymer Science and Engineering
- Qingdao University of Science and Technology (QUST)
- Qingdao 266042
| | - Kun Wang
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department
- School of Polymer Science and Engineering
- Qingdao University of Science and Technology (QUST)
- Qingdao 266042
| | - Ping Yu
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department
- School of Polymer Science and Engineering
- Qingdao University of Science and Technology (QUST)
- Qingdao 266042
| | - Shengyue Zhang
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department
- School of Polymer Science and Engineering
- Qingdao University of Science and Technology (QUST)
- Qingdao 266042
| | - Kai Sun
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Zhibo Li
- Key Laboratory of Biobased Polymer Materials
- Shandong Provincial Education Department
- School of Polymer Science and Engineering
- Qingdao University of Science and Technology (QUST)
- Qingdao 266042
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18
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Pandeeswar M, Senanayak SP, Govindaraju T. Nanoarchitectonics of Small Molecule and DNA for Ultrasensitive Detection of Mercury. ACS APPLIED MATERIALS & INTERFACES 2016; 8:30362-30371. [PMID: 27753489 DOI: 10.1021/acsami.6b10527] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reliable and ultrasensitive detection of mercury ions is of paramount importance for toxicology assessment, environmental protection, and human health. Herein, we present a novel optoelectronic approach based on nanoarchitectonics of small-molecule templated DNA system that consists of an adenine (A)-conjugated small organic semiconductor (BNA) and deoxyribo-oligothymidine (dTn). This mutually templated dynamic chiral coassembly system (BNAn-dTn) with tunable chiroptical, morphological, and electrical properties is tapped in to enable ultrasensitive and selective detection of inorganic and organometallic mercury in water. We observe a rapid transformation of the BNAn-dTn coassembly into a metallo-DNA duplex [dT-Hg-dT]n in the presence of mercury, which is utilized for a chiro-optical and conductivity-based rapid and subnanomolar sensitivity (≥0.1 nM, 0.02 ppb) to mercury ions in water (∼100 times lower than United States Environmental Protection Agency tolerance limit). This ultrasensitive detection of inorganic and organometallic mercury is driven by a novel chemical design principle that allows strong mercury thymine interaction. This study is anticipated to inspire the development of future templated DNA nanotechnology-based optoelectronic devices for the rapid and ultrasensitive detection of numerous other toxic analytes.
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Affiliation(s)
- M Pandeeswar
- Bioorganic Chemistry Laboratory, New Chemistry Unit and ‡Molecular Electronics Lab, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Satyaprasad P Senanayak
- Bioorganic Chemistry Laboratory, New Chemistry Unit and ‡Molecular Electronics Lab, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - T Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and ‡Molecular Electronics Lab, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bengaluru 560064, Karnataka, India
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19
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Besenius P. Controlling supramolecular polymerization through multicomponent self-assembly. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/pola.28385] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Pol Besenius
- Institute of Organic Chemistry, Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 Mainz 55128 Germany
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20
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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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21
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Iwaura R, Kanai Y, Ohnishi-Kameyama M. Investigation of Supramolecular Nanofibers Formed from Multicomponent Nucleotide-Appended Bolaamphiphiles and Heteropolymeric DNA as a Template. Chempluschem 2016; 81:1230-1236. [PMID: 31964101 DOI: 10.1002/cplu.201600348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Indexed: 12/13/2022]
Abstract
A novel DNA-templated multicomponent self-assembly of well-defined, molecular-level-controlled nanostructures in aqueous solution is demonstrated by using a thermal cycling procedure. The strategy uses four building blocks comprising 1,18-nucleotide-appended bolaamphiphiles (3'-phosphorylated adenosine, thymidine, guanosine, or cytidine connected to each end of an oligomethylene chain) and a heteropolymeric 58-mer containing a palindromic sequence as the template DNA. Atomic force microscopic observations, circular dichroism, and temperature-dependent absorption spectra revealed that the multicomponent self-assembly of the four nucleotide bolaamphiphiles and template DNA formed right-handed helical nanofibers with complementary base pairs during thermal cycling. Nanofibers were not formed if one of the four nucleotide bolaamphiphiles was missing, suggesting that construction of the helical nanofiber resulted from self-assembly of all four bolaamphiphiles to form matched base pairs sorted according to the sequence of the template DNA.
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Affiliation(s)
- Rika Iwaura
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Yoshikazu Kanai
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Mayumi Ohnishi-Kameyama
- Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
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22
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Mejías SH, López-Andarias J, Sakurai T, Yoneda S, Erazo KP, Seki S, Atienza C, Martín N, Cortajarena AL. Repeat protein scaffolds: ordering photo- and electroactive molecules in solution and solid state. Chem Sci 2016; 7:4842-4847. [PMID: 29732049 PMCID: PMC5905405 DOI: 10.1039/c6sc01306f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/23/2016] [Indexed: 01/15/2023] Open
Abstract
The precise control over the organization of photoactive components at the nanoscale is one of the main challenges for the generation of new and sophisticated macroscopically ordered materials with enhanced properties. In this work we present a novel bioinspired approach using protein-based building blocks for the arrangement of photo- and electroactive porphyrin derivatives. We used a designed repeat protein scaffold with demonstrated unique features that allow for the control of their structure, functionality, and assembly. Our designed domains act as exact biomolecular templates to organize porphyrin molecules at the required distance. The hybrid conjugates retain the structure and assembly properties of the protein scaffold and display the spectroscopic features of orderly aggregated porphyrins along the protein structure. Finally, we achieved a solid ordered bio-organic hybrid thin film with anisotropic photoconductivity.
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Affiliation(s)
- Sara H Mejías
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
| | - Javier López-Andarias
- Departamento de Química Orgánica I , Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain .
| | - Tsuneaki Sakurai
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , Japan
| | - Satoru Yoneda
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , Japan
| | - Kevin P Erazo
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
| | - Shu Seki
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , Japan
| | - Carmen Atienza
- Departamento de Química Orgánica I , Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain .
| | - Nazario Martín
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
- Departamento de Química Orgánica I , Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain .
| | - Aitziber L Cortajarena
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
- CIC biomaGUNE , Paseo de Miramón 182 , E-20009 Donostia-San Sebastian , Spain
- Ikerbasque , Basque Foundation for Science , Ma Díaz de Haro 3 , E-48013 Bilbao , Spain
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23
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Narayanaswamy N, Suresh G, Priyakumar UD, Govindaraju T. Double zipper helical assembly of deoxyoligonucleotides: mutual templating and chiral imprinting to form hybrid DNA ensembles. Chem Commun (Camb) 2016; 51:5493-6. [PMID: 25233941 DOI: 10.1039/c4cc06759b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, the conventional and unconventional hydrogen bonding potential of adenine in APA for double zipper helical assembly of deoxyoligonucleotides is demonstrated under ambient conditions. The quantum mechanical calculations supported the formation of hybrid DNA ensembles.
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Affiliation(s)
- Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India.
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24
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Krieg E, Bastings MMC, Besenius P, Rybtchinski B. Supramolecular Polymers in Aqueous Media. Chem Rev 2016; 116:2414-77. [DOI: 10.1021/acs.chemrev.5b00369] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Pol Besenius
- Institute
of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Mainz 55128, Germany
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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25
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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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26
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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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27
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Kocsis I, Rotaru A, Legrand YM, Grosu I, Barboiu M. Supramolecular rulers enabling selective detection of pure short ssDNA via chiral self-assembly. Chem Commun (Camb) 2016; 52:386-9. [DOI: 10.1039/c5cc08283h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
TPA propellers appear to be compatible with the general requirements for amplified chiral supramolecular rulers used to determine the number of base pairs of short ssDNAs.
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Affiliation(s)
- Istvan Kocsis
- Adaptive Supramolecular Nanosystems Group
- Institut Européen des Membranes
- University of Montpellier/ENSCM/CNRS 5635
- Pl. Eugène Bataillon
- 34095 Montpellier, Cedex 5
| | - Alexandru Rotaru
- “Petru Poni” Institute of Macromolecular Chemistry of Romanian Academy – 41A
- Iasi
- Romania
| | - Yves-Marie Legrand
- Adaptive Supramolecular Nanosystems Group
- Institut Européen des Membranes
- University of Montpellier/ENSCM/CNRS 5635
- Pl. Eugène Bataillon
- 34095 Montpellier, Cedex 5
| | - Ion Grosu
- Chemistry Department
- Babeş-Bolyai University
- 400028 Cluj -Napoca
- Romania
| | - Mihail Barboiu
- Adaptive Supramolecular Nanosystems Group
- Institut Européen des Membranes
- University of Montpellier/ENSCM/CNRS 5635
- Pl. Eugène Bataillon
- 34095 Montpellier, Cedex 5
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28
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Designed Repeat Proteins as Building Blocks for Nanofabrication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 940:61-81. [DOI: 10.1007/978-3-319-39196-0_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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De Coen LM, Heugebaert TSA, García D, Stevens CV. Synthetic Entries to and Biological Activity of Pyrrolopyrimidines. Chem Rev 2015; 116:80-139. [DOI: 10.1021/acs.chemrev.5b00483] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laurens M. De Coen
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Thomas S. A. Heugebaert
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Daniel García
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Christian V. Stevens
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
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30
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Ensslen P, Gärtner S, Glaser K, Colsmann A, Wagenknecht HA. A DNA-Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA-Based Solar Cells. Angew Chem Int Ed Engl 2015; 55:1904-8. [DOI: 10.1002/anie.201509332] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/23/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Philipp Ensslen
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stefan Gärtner
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Konstantin Glaser
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Alexander Colsmann
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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31
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Ensslen P, Gärtner S, Glaser K, Colsmann A, Wagenknecht HA. Ein DNA-Fulleren-Konjugat als Templat für supramolekulare Chromophorstapel: Auf dem Weg zu DNA-basierten Solarzellen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Philipp Ensslen
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Stefan Gärtner
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Konstantin Glaser
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Alexander Colsmann
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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32
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Pan D, Sun J, Jin H, Li Y, Li L, Wu Y, Zhang L, Yang Z. Supramolecular assemblies of novel aminonucleoside phospholipids and their bonding to nucleic acids. Chem Commun (Camb) 2015; 51:469-72. [PMID: 25383905 DOI: 10.1039/c4cc07538b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A novel class of aminonucleoside phospholipids has been developed. These molecules could spontaneously assemble into supramolecular structures including multilamellar organization, hydrogels, superhelical strands, and vesicles. Their ability to bind to DNA by hydrogen bonding and π-π stacking interactions was investigated by many means.
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Affiliation(s)
- Delin Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road 38, Beijing 100191, China.
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33
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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: 958] [Impact Index Per Article: 106.4] [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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34
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Meng YF, Wei J, Gao PC, Jiang Y. Self-assembling amphiphilic poly(propargyl methacrylate) grafted DNA copolymers into multi-strand helices. SOFT MATTER 2015; 11:5610-5613. [PMID: 26096216 DOI: 10.1039/c5sm01325a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
DNA was covalently grafted onto poly(propargyl methacrylate) (PPMA) via "click" chemistry to synthesize the amphiphilic polymer brush. The PPMA-g-DNA brush could assemble into a primary structure of a nanofiber, which can be compactly spun into a multiple-strand helix in micron-length. The brush could also self-assemble with DNA labelled gold nanoparticles.
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Affiliation(s)
- Yi-Fan Meng
- School of Chemistry and Chemical Engineering, Southeast University, No. 2 Dongnandaxue Road, Jiangning District, Nanjing, Jiangsu 211189, P. R. China.
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35
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Peng HQ, Niu LY, Chen YZ, Wu LZ, Tung CH, Yang QZ. Biological Applications of Supramolecular Assemblies Designed for Excitation Energy Transfer. Chem Rev 2015; 115:7502-42. [DOI: 10.1021/cr5007057] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hui-Qing Peng
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Li-Ya Niu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- Key
Laboratory of Radiopharmaceuticals, Ministry of Education, College
of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yu-Zhe Chen
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Li-Zhu Wu
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Chen-Ho Tung
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Qing-Zheng Yang
- Key
Laboratory of Photochemical Conversion and Optoelectronic Materials,
Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- Key
Laboratory of Radiopharmaceuticals, Ministry of Education, College
of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
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36
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015; 54:7934-8. [DOI: 10.1002/anie.201502066] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 03/31/2015] [Indexed: 12/31/2022]
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37
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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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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Takada T, Ido M, Ashida A, Nakamura M, Fujitsuka M, Kawai K, Majima T, Yamana K. Photocurrent Generation through Charge-Transfer Processes in Noncovalent Perylenediimide/DNA Complexes. Chemistry 2015; 21:6846-51. [DOI: 10.1002/chem.201406592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 12/30/2022]
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Paolantoni D, Cantel S, Dumy P, Ulrich S. A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies. Int J Mol Sci 2015; 16:3609-25. [PMID: 25667976 PMCID: PMC4346916 DOI: 10.3390/ijms16023609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 12/16/2022] Open
Abstract
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.
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Affiliation(s)
- Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
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41
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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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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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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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44
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Guo Z, Gong R, Mu Y, Wang X, Wan X. Oligopeptide-Assisted Self-Assembly of Oligothiophenes: Co-Assembly and Chirality Transfer. Chem Asian J 2014; 9:3245-50. [DOI: 10.1002/asia.201402646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Indexed: 10/24/2022]
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45
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Kamps AC, Cativo MHM, Chen XJ, Park SJ. Self-Assembly of DNA-Coupled Semiconducting Block Copolymers. Macromolecules 2014. [DOI: 10.1021/ma500509u] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Amanda C. Kamps
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ma. Helen M. Cativo
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Xi-Jun Chen
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - So-Jung Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry and Nano Science, Global Top 5 Program, Ewha Womans University, 52 Ewhayeodae-gil,
Seodaemun-gu, Seoul 120-750, Korea
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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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47
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Kumar M, Venkata Rao K, George SJ. Supramolecular charge transfer nanostructures. Phys Chem Chem Phys 2014; 16:1300-13. [DOI: 10.1039/c3cp54190h] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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48
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Iwaura R, Yui H, Someya Y, Ohnishi-Kameyama M. Construction of energy transfer pathways self-assembled from DNA-templated stacks of anthracene. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 130:199-204. [PMID: 24342131 DOI: 10.1016/j.jphotobiol.2013.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 11/30/2022]
Abstract
We describe optical properties of anthracene stacks formed from single-component self-assembly of thymidylic acid-appended anthracene 2,6-bis[5-(3'-thymidylic acid)pentyloxy] anthracene (TACT) and the binary self-assembly of TACT and complementary 20-meric oligoadenylic acid (TACT/dA20) in an aqueous buffer. UV-Vis and emission spectra for the single-component self-assembly of TACT and the binary self-assembly of TACT/dA20 were very consistent with stacked acene moieties in both self-assemblies. Interestingly, time-resolved fluorescence spectra from anthracene stacks exhibited very different features of the single-component and binary self-assemblies. In the single-component self-assembly of TACT, a dynamic Stokes shift (DSS) and relatively short fluorescence lifetime (τ=0.35ns) observed at around 450nm suggested that the anthracene moieties were flexible. Moreover, a broad emission at 530nm suggested the formation of an excited dimer (excimer). In the binary self-assembly of TACT/dA20, we detected a broad, red-shifted emission component at 534nm with a lifetime (τ=0.4ns) shorter than that observed in the TACT single-component self-assembly. Combining these results with the emission spectrum of the binary self-assembly of TACT/5'-HEX dA20, we concluded that the energy transfer pathway was constructed by columnar anthracene stacks formed from the DNA-templated self-assembly of TACT.
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Affiliation(s)
- Rika Iwaura
- National Food Research Institute (NFRI), National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
| | - Hiroharu Yui
- Department of Chemistry, Faculty of Science, Tokyo University of Science (TUS), 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Yuu Someya
- Department of Chemistry, Faculty of Science, Tokyo University of Science (TUS), 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Mayumi Ohnishi-Kameyama
- National Food Research Institute (NFRI), National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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Guo Z, Song Y, Gong R, Mu Y, Jiang Y, Li M, Wan X. Assembly of peptide–thiophene conjugates: the influence of peptide content and location. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.844810] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Zongxia Guo
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
| | - Yubao Song
- Department of Chemistry, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong Province 266042, P. R. China
| | - Ruiying Gong
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
| | - Youbing Mu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
| | - Yi Jiang
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
| | - Ming Li
- Department of Chemistry, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong Province 266042, P. R. China
| | - Xiaobo Wan
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
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Ehrenschwender T, Schmucker W, Wellner C, Augenstein T, Carl P, Harmer J, Breher F, Wagenknecht HA. Development of a Metal-Ion-Mediated Base Pair for Electron Transfer in DNA. Chemistry 2013; 19:12547-52. [DOI: 10.1002/chem.201300593] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Indexed: 01/01/2023]
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