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DNA-based Oligomeric and Polymeric Functional Materials

English title DNA-based Oligomeric and Polymeric Functional Materials
Applicant Häner Robert
Number 149148
Funding scheme Project funding (Div. I-III)
Research institution Departement für Chemie und Biochemie Universität Bern
Institution of higher education University of Berne - BE
Main discipline Organic Chemistry
Start/End 01.10.2013 - 30.09.2016
Approved amount 600'000.00
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Keywords (8)

supramolecular polymers; light harvesting systems; fluorescence; chromophore; oligonucleotides; DNA; exciplex; polyaromatic hydrocarbons

Lay Summary (German)

Lead
Desoxyribonukleinsäure (DNA) dient als molekulares Gerüst für die Herstellung von Strukturen im Nanometerbereich. Die starre Struktur der Doppelhelix erlaubt es, Farbstoffmoleküle in präzis definierter Geometrie anzuordnen. Im vorliegenden Projekt werden Farbstoff-Aggregate DNA-gesteuert hergestellt und untersucht.
Lay summary

Hintergrund: Durch den Einbau geeigneter Farbstoff-Derivate in Oligonukleotide können Aggregate von verschiedenen aromatischen Verbindungen erzeugt werden. Die präzise Anordnung von Einzelmolekülen zu einem grösseren Verbund wird aufgrund der vorgegebenen molekularen Struktur der DNA-Doppelhelix ermöglicht. Dadurch lassen sich die Eigenschaften von Farbstoff-Aggregaten studieren, die auf andere Weise nur schwer oder gar nicht zugänglich sind. Die mit spektroskopischen Methoden gewonnenen Erkenntnisse dienen dazu, Materialien mit speziellen optischen und elektronischen Eigenschaften zu entdecken. Solche Materialien können Verwendung in optischen Geräten, in Photozellen oder in diagnostischen Methoden finden.

Ziele: Basierend auf den Erkenntnissen, die wir mit der Untersuchung von Pyren-Derivaten und verwandten Aromaten gewonnen haben, verwenden wir DNA-Farbstoff-Konjugate zur Herstellung von mehrsträngigen molekularen Architekturen. Weitere geeignete Farbstoff-Derivate, wie z.B. von Chrysen und Porphyrin, werden hergestellt und auf ihre Eigenschaften untersucht. Von spezieller Bedeutung werden die Kompatibilität der Farbstoff-Moleküle mit der DNA-Synthese und die Fähigkeit der Doppelstrangpaarung sein. Eine weitere Stossrichtung unserer Forschung ist der Herstellung und Untersuchung von supramolekularen Polymeren und lichtsammelnden Komplexen gewidmet.

Bedeutung: Die Verwendung der DNA als intelligentes, molekulares Baugerüst erlaubt die präzise Anordnung von funktionellen Molekülen und kann dadurch Zugang zu neuartigen Materialien mit speziellen elektronischen und physikalischen Eigenschaften verschaffen. Solche Materialien können Verwendung in optischen Geräten, in Photozellen oder in diagnostischen Hilfsmitteln zur frühen Erkennung von Infektions- oder Erbkrankheiten finden.

Direct link to Lay Summary Last update: 07.10.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Integrating DNA Photonic Wires into Light-Harvesting Supramolecular Polymers
Kownacki Mariusz, Langenegger Simon M., Liu Shi-Xia, Häner Robert (2018), Integrating DNA Photonic Wires into Light-Harvesting Supramolecular Polymers, in Angewandte Chemie International Edition.
Probing Lewis acid–base interactions in single-molecule junctions
Liu Xunshan, Li Xiaohui, Sangtarash Sara, Sadeghi Hatef, Decurtins Silvio, Häner Robert, Hong Wenjing, Lambert Colin J., Liu Shi-Xia (2018), Probing Lewis acid–base interactions in single-molecule junctions, in Nanoscale, 10(38), 18131-18134.
Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties
Bösch Caroline D., Jevric Jovana, Bürki Nutcha, Probst Markus, Langenegger Simon M., Häner Robert (2018), Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties, in Bioconjugate Chemistry, 29(5), 1505-1509.
Formation of Supramolecular Nanotubes by Self-assembly of a Phosphate-linked Dimeric Anthracene in Water
Yu Hao, Sabetti Mattia, Häner Robert (2018), Formation of Supramolecular Nanotubes by Self-assembly of a Phosphate-linked Dimeric Anthracene in Water, in Chemistry - An Asian Journal, 13(8), 968-971.
Self-assembly of a redox-active bolaamphiphile into supramolecular vesicles
Rothenbühler Simon, Bösch Caroline D., Langenegger Simon M., Liu Shi-Xia, Häner Robert (2018), Self-assembly of a redox-active bolaamphiphile into supramolecular vesicles, in Organic & Biomolecular Chemistry, 16(38), 6886-6889.
Silica Mineralization of DNA-Inspired 1D and 2D Supramolecular Polymers
Vybornyi Mykhailo, Vyborna Yuliia, Häner Robert (2017), Silica Mineralization of DNA-Inspired 1D and 2D Supramolecular Polymers, in ChemistryOpen, 6(4), 488-491.
Synthesis of Responsive Two-Dimensional Polymers via Self-Assembled DNA Networks
Yu Hao, Alexander Duncan T. L., Aschauer Ulrich, Häner Robert (2017), Synthesis of Responsive Two-Dimensional Polymers via Self-Assembled DNA Networks, in Angewandte Chemie International Edition, 56(18), 5040-5044.
Functional DNA-grafted supramolecular polymers – chirality, cargo binding and hierarchical organization
Vyborna Yuliia, Vybornyi Mykhailo, Häner Robert (2017), Functional DNA-grafted supramolecular polymers – chirality, cargo binding and hierarchical organization, in Chemical Communications, 53(37), 5179-5181.
Morphological diversity of supramolecular polymers of DNA-containing oligopyrenes – formation of chiroptically active nanosheets
Vyborna Y., Altunbas S., Vybornyi M., Häner R. (2017), Morphological diversity of supramolecular polymers of DNA-containing oligopyrenes – formation of chiroptically active nanosheets, in Chemical Communications, 53(89), 12128-12131.
Pathway Diversity in the Self-Assembly of DNA-Derived Bioconjugates
Vyborna Yuliia, Vybornyi Mykhailo, Häner Robert (2016), Pathway Diversity in the Self-Assembly of DNA-Derived Bioconjugates, in Bioconjugate Chemistry, 27(11), 2755-2761.
Light-Harvesting Nanotubes Formed by Supramolecular Assembly of Aromatic Oligophosphates
Bösch Caroline D., Langenegger Simon M., Häner Robert (2016), Light-Harvesting Nanotubes Formed by Supramolecular Assembly of Aromatic Oligophosphates, in Angewandte Chemie International Edition, 55(34), 9961-9964.
Solution-phase synthesis of 1D tubular polymers via preorganization–polymerization
Yu Hao, Häner Robert (2016), Solution-phase synthesis of 1D tubular polymers via preorganization–polymerization, in Chemical Communications, 52(100), 14396-14399.
Structural Insight into DNA-Assembled Oligochromophores: Crystallographic Analysis of Pyrene- and Phenanthrene-Modified DNA in Complex with BpuJi Endonuclease
M. Probst W. Aeschimann T.T.H. Chau S.M. Langenegger A. Stocker R. Häner (2016), Structural Insight into DNA-Assembled Oligochromophores: Crystallographic Analysis of Pyrene- and Phenanthrene-Modified DNA in Complex with BpuJi Endonuclease, in Nucleic Acids Res., 2016(44), 7079-7089.
Supramolecular Organization of Dye Molecules in Zeolite L Channels: Synthesis, Properties, and Composite Materials
Cao Pengpeng, Khorev Oleg, Devaux André, Sägesser Lucie, Kunzmann Andreas, Ecker Achim, Häner Robert, Brühwiler Dominik, Calzaferri Gion, Belser Peter (2016), Supramolecular Organization of Dye Molecules in Zeolite L Channels: Synthesis, Properties, and Composite Materials, in Chemistry - A European Journal, 22(12), 4046-4060.
Assembly of Extra-Large Nanosheets by Supramolecular Polymerization of Amphiphilic Pyrene Oligomers in Aqueous Solution
Vybornyi Mykhailo, Rudnev Alexander, Haener Robert (2015), Assembly of Extra-Large Nanosheets by Supramolecular Polymerization of Amphiphilic Pyrene Oligomers in Aqueous Solution, in CHEMISTRY OF MATERIALS, 27(4), 1426-1431.
DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers
Vyborna Yuliia, Vybornyi Mykhailo, Rudnev Alexander V., Haener Robert (2015), DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers, in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54(27), 7934-7938.
Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks
Winiger Christian B., Langenegger Simon M., Calzaferri Gion, Haener Robert (2015), Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks, in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54(12), 3643-3647.
From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers
Vyborna Yuliia, Vybornyi Mykhailo, Haener Robert (2015), From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers, in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137(44), 14051-14054.
Hydrodynamic and Thermophoretic Effects on the Supramolecular Chirality of Pyrene-Derived Nanosheets
Micali Norberto, Vybornyi Mykhailo, Mineo Placido, Khorev Oleg, Haener Robert, Villari Valentina (2015), Hydrodynamic and Thermophoretic Effects on the Supramolecular Chirality of Pyrene-Derived Nanosheets, in CHEMISTRY-A EUROPEAN JOURNAL, 21(26), 9505-9513.
Tubes or sheets: divergent aggregation pathways of an amphiphilic 2,7-substituted pyrene trimer
Vybornyi Mykhailo, Hechevarria Yamileidi Bur-Cecilio, Glauser Marlene, Rudnev Alexander V., Haener Robert (2015), Tubes or sheets: divergent aggregation pathways of an amphiphilic 2,7-substituted pyrene trimer, in CHEMICAL COMMUNICATIONS, 51(90), 16191-16193.
A modular LHC built on the DNA three-way junction
Probst Markus, Langenegger Simon M., Haener Robert (2014), A modular LHC built on the DNA three-way junction, in CHEMICAL COMMUNICATIONS, 50(2), 159-161.
Assembling Multiporphyrin Stacks Inside the DNA Double Helix
Vybornyi Mykhailo, Nussbaumer Alia L., Langenegger Simon M., Haener Robert (2014), Assembling Multiporphyrin Stacks Inside the DNA Double Helix, in BIOCONJUGATE CHEMISTRY, 25(10), 1785-1793.
Influence of perylenediimide-pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity
Winiger Christian B., Langenegger Simon M., Khorev Oleg, Haener Robert (2014), Influence of perylenediimide-pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity, in BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY, 10, 1589-1595.
Long-Distance Electronic Energy Transfer in Light-Harvesting Supramolecular Polymers
Winiger Christian B., Li Shaoguang, Kumar Ganesh R., Langenegger Simon M., Haener Robert (2014), Long-Distance Electronic Energy Transfer in Light-Harvesting Supramolecular Polymers, in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 53(49), 13609-13613.
Observation of the rare chrysene excimer
Khorev Oleg, Boesch Caroline D., Probst Markus, Haener Robert (2014), Observation of the rare chrysene excimer, in CHEMICAL SCIENCE, 5(4), 1506-1512.
Control of aggregation-induced emission by DNA hybridization
Li Shaoguang, Langenegger Simon M., Haener Robert (2013), Control of aggregation-induced emission by DNA hybridization, in CHEMICAL COMMUNICATIONS, 49(52), 5835-5837.
Formation of Two-Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers
Vybornyi Mykhailo, Rudnev Alexander V., Langenegger Simon M., Wandlowski Thomas, Calzaferri Gion, Haener Robert (2013), Formation of Two-Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers, in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 52(44), 11488-11493.
J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter
Markova Larysa I., Malinovskii Vladimir L., Patsenker Leonid D., Haener Robert (2013), J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter, in CHEMICAL COMMUNICATIONS, 49(46), 5298-5300.
Supramolecular Organization of Heptapyrenotide Oligomers-An in Depth Investigation by Molecular Dynamics Simulations
Simona Fabio, Nussbaumer Alina L., Haener Robert, Cascella Michele (2013), Supramolecular Organization of Heptapyrenotide Oligomers-An in Depth Investigation by Molecular Dynamics Simulations, in JOURNAL OF PHYSICAL CHEMISTRY B, 117(8), 2576-2585.

Collaboration

Group / person Country
Types of collaboration
Prof. Andrea Cannizzo / Institut of Applied Physics, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Dr. Valentina Villari / CNR-IPCF Istituto per i Processi Chimico-Fisici, Viale F. Stagno d'Alcontres Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Prof. Antonio Monari / Theory-Modeling-Simulation SRSMC, Université de Lorraine & CNRS France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
PD. Dr. Achim Stocker / Dept. Chemie und Biochemie, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Prof. Gion Calzaferri / Dept. Chemie und Biochemie, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Leonid Patsenker, University of Karkhov Ukraine (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Prof. Thomas Feurer / Institut of Applied Physics, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Awards

Title Year
"CEMS Rising Star Award" for the best poster presentation at CEMSupra 2016 International Symposium on Supramolecular Chemistry and Functional Materials, Tokyo, Japan 2016
Best Poster Award 80th Prague Meeting on Macromolecules Prag, July 10-14, 2016 2016
1st Year Graduate Symposium Award, Department of Chemistry and Biochemistry, University ob Bern 2015
Best Poster Award SCS Fall Meeting 2015
Chemistry Travel Award by SCNAT, SCS and SSFEC 2015
Fakultätspreis der Phil. nat. Fakultät, Universität Bern 'Beste Dissertation in Chemie und Biochemie' 2015
Poster Award, 7th International Conference on Molecular Electronics, Strasbourg, France 2014

Associated projects

Number Title Start Funding scheme
132581 DNA-assisted self-organization of aromatic chromophores 01.10.2010 Project funding (Div. I-III)
132581 DNA-assisted self-organization of aromatic chromophores 01.10.2010 Project funding (Div. I-III)
169030 From DNA-Assembled Oligochromophores to Supramolecular Polymers: Aromatic Oligophosphates as Versatile Building Blocks for Functional Materials 01.01.2017 Project funding (Div. I-III)

Abstract

The construction and investigation of DNA-based supramolecular structures is proposed. Novel types of chromophoric building blocks that are compatible with oligonucleotide synthesis will be synthesized and incorporated into DNA strands. The obtained hybrids will be investigated for their structural and electronic properties. The formation and spectroscopic characterization of multi-chromophoric aggregates will be the central aspect of our research.A major effort will be dedicated to deepen our understanding of supramolecular polymerization events with phosphodiester-linked pyrene oligomers. Building on the results obtained with 1,8-pyrene-dicarboxamide units, we will explore the behavior of oligomers composed of building blocks that are different with regard to substitution geometry (1,6-disubstitution) and linker type (alkynyl derived linkers). It will be interesting to see if the effects of amplification of chirality observed in the cases studied so far will change with different types of building blocks.Secondly, we will extend our work related to the construction and study of DNA-based light harvesting antenna systems. The use of phenanthrene and pyrene chromophores appears as an excellent combination for collecting UV light. We will study the use of higher order structures (e.g. the three way junction) for the suitability of collecting and concentrating photonic energy. Furthermore, we will also study the process of excitation energy transfer in these systems in collaboration with the group of T. Feurer, institute of applied physics of our university (NCCR Molecular Ultrafast Science and Technology).A further part of our efforts will be directed at the synthesis and exploration of new types of chromophoric building blocks. While we continue the investigation of additional types of pyrene derivatives, we will broaden our efforts to the synthesis of porphyrin, perylene and anthanthrene derivatives. The newly synthesized compounds will be evaluated for their stacking behaviour as well as their spectroscopic properties. Of major importance in this regard will be the compatibility of the new derivatives with oligonucleotide synthesis, the ability to support the formation of multi-stranded hybrids and, most importantly, the changes in electronic properties upon formation of multi-chromophoric aggregates. We will continue these ongoing efforts with high priority.
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