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Sequence-Defined Oligophosphates - From Modified DNA to Supramolecular Precision Materials

English title Sequence-Defined Oligophosphates - From Modified DNA to Supramolecular Precision Materials
Applicant Häner Robert
Number 188468
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 01.04.2020 - 31.03.2024
Approved amount 963'591.00
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Keywords (6)

chromophore; phosphodiester; light harvesting systems; energy transfer; supramolecular polymers; DNA

Lay Summary (German)

Desoxyribonukleinsäure (DNA) dient als molekulares Gerüst für die Herstellung von Strukturen im Nanometerbereich. Die starre Struktur der Doppelhelix erlaubt es, funktionelle Moleküle in präzis definierter Geometrie anzuordnen. Im vorliegenden Projekt werden einerseits DNA-basierte Farbstoff-Aggregate hergestellt und untersucht. Andererseits dient die DNA Doppelhelix als Leitmotiv für die Herstellung von 1- und 2-dimensionalen Polymeren, sowie von unilamellaren Vesikeln im Nanometerbereich. Die Bausteine dieser Polymere sind, wie in der DNA, über anionische Phosphodiester-Brücken verknüpft. Die Kombination von negativer Ladung und aromatischen Chromophoren gewährleistet einerseits eine gute Löslichkeit in Wasser und erlaubt gleichzeitig die effiziente Bildung von Aggregaten durch aromatische Molekülstapelung.
Lay summary

Hintergrund: 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 Multi-Chromophoren studieren, die auf andere Weise nur schwer oder gar nicht zugänglich sind. Auf diese Weise gewonnene Erkenntnisse werden in einem weiteren Schritt dazu verwendet, entsprechende Chromophor-Aggregate ohne DNA-Gerüst herzustellen. Insbesondere lassen sich so Polymere mit speziellen optischen und elektronischen Eigenschaften synthetisieren.

Ziele: Basierend auf den Erkenntnissen, die wir mit der Untersuchung von DNA-Farbstoff-Konjugaten gewonnen haben, werden supramolekulare Polymere mit speziellen strukturellen und elektronischen Eigenschaften hergestellt. Von besonderer Bedeutung sind hierbei Polymere mit lichtsammelnden Eigenschaften. Ein besonderer Aspekt besteht in der Herstellung von Nano-Strukturen, deren Gestalt und elektronische Eigenschaften sich kontrolliert ändern lassen, z.B. durch Bestrahlung mit Licht oder Änderung des pH-Wertes.

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 in der Zukunft zur Energiegewinnung eingesetzt werden, z.B.  in Form von lichtsammelnden Komplexen. Andererseits können sie auch Verwendung finden in optischen Geräten, in Photozellen oder in diagnostischen Hilfsmitteln zur frühen Erkennung von Infektions- oder Erbkrankheiten. Erkenntnisse, die mit Hilfe von DNA gewonnen werden, lassen sich auch auf chemisch einfachere Bausteine anwenden und führen so zur Entwicklung von bio-inspirierten Materialien.
Direct link to Lay Summary Last update: 23.10.2019

Responsible applicant and co-applicants


Associated projects

Number Title Start Funding scheme
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)


The research topic of ‘sequence-defined oligophosphates’ has lately evolved from the vast area of nucleic acids nanotechnology. Whereas the potential of DNA for applications in the material sciences is amply documented, the exploration of phosphodiester-linked oligomers of non-nucleosidic building blocks is still in its early phase. Our group is well positioned to play a significant role in the coming years due to our combined experience in nucleic acids technology as well as synthetic organic chemistry. This allows us to directly address newly arising questions by chemical synthesis of novel types of building blocks and their incorporation into oligomers. Over the past 5-10 years, the use of polycyclic aromatic hydrocarbons (PAHs) as building blocks for oligomers (oligoarenotides) has become the core area of our research. Such oligomers, even very short ones (e.g. trimers), were shown to form different types of supramolecular polymers (SPs) via self-assembly in water. We reported the assembly of 1- and 2-dimensional (1D and 2D) objects, such as fibers, sheets, tubes and also spherical objects. More recently, we were able to demonstrate some potential applications of these SPs in the context of artificial light-harvesting complexes (LHCs). In the future, we will expand and diversify our projects by entering adjacent fields. Major opportunities for the near future exist in the development of oligomers that self-assemble into supramolecular polymers of different dimensionality, in the development of functionalized supramolecular platforms and in the design of shape-shifting supramolecular polymers.In the future, a major focus will be set on the assembly of oligomers containing different types of functional groups (e.g. photo-reactive groups, carbohydrates, oligonucleotides). So far, we have only been able to use linear SPs as templates for arranging additional functionalities (Au-nanoparticles and fluorophores) and the decoration of 2D objects (nanosheets) with functionalities remains a major goal. A first step in this direction is the incorporation of mannose units into oligopyrenotides. Other, simpler chemical modifications will also be pursued and should provide access to functionalized platforms, e.g. via click-type chemistry.Photochemically reactive building blocks will be pursued intensively. This should enable the assembly of ‘caged’ SPs that can respond to an external stimulus which, in turn, may lead to changes in the SP morphology (shape-shifting SPs). Alternatively, the incorporation of photo-cleavable linkers into an SP may result in its complete disassembly or, in yet another scenario, facilitate the release of a cargo attached to the SP. The different responses to such a light-trigger stimulus may be controlled by the positioning of the photo-cleavable unit in the oligomer. Suitable photo-cleavable phosphoramidites have been explored for different reasons in the past and were shown to be perfectly compatible with oligonucleotide synthesis.Furthermore, we intend to concentrate on the investigation of SPs with aggregation-induced emission (AIE) properties. The study of chromophores that exhibit aggregation-induced emission behavior has become a field of high interest. Using TPE (tetraphenylethylene) modified DNA we were previously able to show that AIE can be controlled via DNA hybridization. We will further expand this work to the assembly of TPE-derived SPs. We will follow our well-established pattern for preparing TPE-oligomers and testing their folding and assembly behavior in water. Intramolecular folding and supramolecular polymerization should both result in a significant increase in luminescence.Finally, we will continue our efforts devoted to the synthesis and self-assembly of cationic oligomers. In contrast to phosphodiester-based oligomers, such oligomers cannot be assembled via automated synthesis and require different synthetic approaches. We have achieved the synthesis of a short oligomer (a 3,6-disubstituted phenanthrene trimer), which also possesses self-assembly properties in aqueous medium. We will expand these efforts to the synthesis of 1,6-disubstituted cationic pyrene oligomers, which can be expected to self-assemble into nanosheets. The goal of this project consists in the construction of layered supramolecular structures, i.e. via layer-by-layer assembly of negatively and positively charged nanosheets.