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DNA-assisted self-organization of aromatic chromophores

English title DNA-assisted self-organization of aromatic chromophores
Applicant Häner Robert
Number 132581
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 01.10.2010 - 30.09.2013
Approved amount 480'000.00
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Keywords (8)

nucleic acids; fluorescence; aromatic stacking; self-organization; aromatic hydrocarbons; molecular beacon; supramolecular chemistry; charge transfer

Lay Summary (English)

Lead
Lay summary
Lead:DNA serves as a framework for the construction of well-defined structures on the nanometer scale. The formation and the properties of ordered aggregates of aromatic chromophores in a DNA duplex are investigated.Background:Arrays of various types of aromatic compounds can be generated by inserting segments of suitable derivatives into a DNA framework or by using the double helix as a scaffold for placement of appended chromophores. In addition to opening the way to novel types of materials with potentially useful spectroscopic, electronic or physical properties, oligonucleotide-chromophore conjugates may also lead to improved types of diagnostic tools. The rational formation of aromatic chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess largely different properties than the individual molecules. Due to its repetitive and well-defined structural features DNA is a practical tool for the generation of nanometer-sized structures. Thus, the approach of using nucleic acids as a guiding frame for the formation of highly ordered chromophore assemblies has emerged over the past few years as a new research direction.Goals:Building upon the results obtained in the past with pyrene and related polyaromatic compounds, we are using DNA-chromophore conjugates for the assembly of multi-stranded architectures. The synthesis and evaluation of novel types of non-nucleosidic chromophores will be pursued. While we continue the investigation of additional types of pyrene derivatives we will extend our efforts to the synthesis of quinoxaline and porphyrin derivatives. The newly synthesized compounds will be evaluated for their stacking behaviour as well as their spectroscopic properties. Crucial aspects are the ability to assist hybrid formation, the fluorescence properties, and the compatibility with oligonucleotide synthesis. Additionally, we will extend our investigations of artificial helical systems formed by oligomers of pyrene and other building blocks. The amplification of chirality observed in a system composed of chiral and achiral oligopyrenes suggests that the oligomers undergo supramolecular polymerization. A further goal is the investigation of electron transfer through non-nucleosidic, aromatic building blocks.Significance:The use of DNA as an intelligent scaffold that allows the precise placement of functional molecules may open a way to novel types of materials with potentially useful spectroscopic, electronic or physical properties. In addition, oligonucleotide-chromophore conjugates may lead to improved types of diagnostic tools for the early detection of infective or genetic diseases.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Control of aggregation-induced emission by DNA hybridization
S. Li, S.M. Langenegger, R. Häner (2013), Control of aggregation-induced emission by DNA hybridization, in Chem. Commun., 49, 5835-5837.
J- vs. H-type assembly: pentamethine cyanine (Cy5) as near-IR chiroptical reporter
L.I. Markova, V.L. Malinovskii, L.D. Patsenker, R. Häner (2013), J- vs. H-type assembly: pentamethine cyanine (Cy5) as near-IR chiroptical reporter, in Chem. Commun., 49, 5298-5300.
Supramolecular Organization of Heptapyrenotide Oligomers - an in Depth Investigation by Molecular Dynamics Simulations
F. Simona, A.L. Nussbaumer, R. Häner, M. Cascella (2013), Supramolecular Organization of Heptapyrenotide Oligomers - an in Depth Investigation by Molecular Dynamics Simulations, in J. Phys. Chem. B, 117, 2576-2585.
Temporary Zinc Oxide-Eugenol Cement: Eugenol Quantity in Dentin and Bond Strength of Resin Composite
T. Koch, A. Peutzfeld, V.L. Malinovskii, S. Flury, R. Häner, A. Lussi (2013), Temporary Zinc Oxide-Eugenol Cement: Eugenol Quantity in Dentin and Bond Strength of Resin Composite, in Eur. J. Oral. Sci., 121, 363-369.
2,1,3-Benzothiadiazole-Modified DNA
Garo F, Haner R (2012), 2,1,3-Benzothiadiazole-Modified DNA, in EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, (14), 2801-2808.
A DNA-Based Light-Harvesting Antenna
Garo F, Haner R (2012), A DNA-Based Light-Harvesting Antenna, in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 51(4), 916-919.
Cooperative and Non-Cooperative Assembly of Oligopyrenotides Resolved by Atomic Force Microscopy
A.V. Rudnev V.L. Malinovskii A.L. Nussbaumer A. Mishchenko R. Häner T. Wandlowski (2012), Cooperative and Non-Cooperative Assembly of Oligopyrenotides Resolved by Atomic Force Microscopy, in Macromol., 2012(45), 5986-5992.
DNA Triplex-Mediated Assembly of Polyaromatic Chromophores
S.M. Biner, R. Häner (2012), DNA Triplex-Mediated Assembly of Polyaromatic Chromophores, in Chem&Biodivers, 9(11), 2485-2493.
Influence of a GC base pair on excitation energy transfer in DNA-assembled phenantherene p-stacks
F. Garo, R. Häner (2012), Influence of a GC base pair on excitation energy transfer in DNA-assembled phenantherene p-stacks, in Bioconjug. Chem., 23, 2105-2113.
Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly
Malinovskii VL, Nussbaumer AL, Haner R (2012), Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly, in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 51(20), 4905-4908.
Photon harvesting by excimer-forming multichromophores
Adeyemi OO, Malinovskii VL, Biner SM, Calzaferri G, Haner R (2012), Photon harvesting by excimer-forming multichromophores, in CHEMICAL COMMUNICATIONS, 48(77), 9589-9591.
Supramolecular polymerization of oligopyrenotides - stereochemical control by single, natural nucleotides
Nussbaumer AL, Samain F, Malinovskii VL, Haner R (2012), Supramolecular polymerization of oligopyrenotides - stereochemical control by single, natural nucleotides, in ORGANIC & BIOMOLECULAR CHEMISTRY, 10(25), 4891-4898.
Synthesis and Properties of Squaraine-Modified DNA
L.I. Markowa, V.L. Malinovskii, L.D. Patsenker, R. Häner (2012), Synthesis and Properties of Squaraine-Modified DNA, in Org. Biomol. Chem., 10, 8944-8947.
The DNA three-way junction as a mould for tripartite chromophore assembly
Probst M, Wenger D, Biner SM, Haner R (2012), The DNA three-way junction as a mould for tripartite chromophore assembly, in ORGANIC & BIOMOLECULAR CHEMISTRY, 10(4), 755-759.
A Two-Color, Self-Controlled Molecular Beacon
Biner SM, Haner R (2011), A Two-Color, Self-Controlled Molecular Beacon, in CHEMBIOCHEM, 12(18), 2733-2736.
Amplification of Chirality by Supramolecular Polymerization of Pyrene Oligomers
Nussbaumer Alina L., Studer Daniel, Malinovskii Vladimir L., Häner Robert (2011), Amplification of Chirality by Supramolecular Polymerization of Pyrene Oligomers, in Angew. Chem. Int. Ed., 24, 5490-5494.
Modulation of Chiroptical Properties by DNA-guided Assembly of Fluorenes
Wenger Daniel, Malinovskii Vladimir L., Häner Robert (2011), Modulation of Chiroptical Properties by DNA-guided Assembly of Fluorenes, in Chem. Commun., 47, 3168-3170.
Signal Control by Self-Assembly of Fluorophores in a Molecular Beacon – A Model Study.
Biner Sarah M., Kummer Dominic, Malinovskii Vladimir L., Häner Robert (2011), Signal Control by Self-Assembly of Fluorophores in a Molecular Beacon – A Model Study., in Org. Biomol. Chem., 9, 2628-2633.
Formation of Two-Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers
M. Vybornyi, A.V. Rudnev, S.M. Langenegger, T. Wandlowski, G. Calzaferri, R. Häner, Formation of Two-Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers, in Angew. Chem. Int. Ed., 52.
Self-Absorption and Luminescence Quantum Yields of Dye-Zeolite L Composites
A. Devaux, G. Calzaferri, I. Miletto, P. Cao, P. Belser, D. Brühwiler, O. Khorev, R. Häner, A. Kunzmann, Self-Absorption and Luminescence Quantum Yields of Dye-Zeolite L Composites, in J. Phys. Chem. C.

Collaboration

Group / person Country
Types of collaboration
Prof. L. Patsenker, University of Karkhov Ukraine (Europe)
- in-depth/constructive exchanges on approaches, methods or results
KTI-Project with Prof. P. Belser, University of Fribourg Switzerland (Europe)
- Industry/business/other use-inspired collaboration
Prof. M. Cascella, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. T. Feurer, Prof. A. Cannizzo, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. T. Wandlowski, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. K. Nakatani, Osaka University Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Easter Lecture Individual talk Organizing Chromophores the DNA Way: How we drifted into Materials Research 28.03.2013 Genf, Switzerland Häner Robert;
Nucleic Acid Center - Seminar Individual talk Organizing Chromophores the DNA Way: How we drifted into Materials Research 12.02.2013 Odense, Denmark Häner Robert;
Berner Chemische Gesellschaft Talk given at a conference Organizing Chromophores the DNA Way: How we drifted into Materials Research 21.11.2012 Bern, Switzerland Häner Robert;
Telluride Workshop on Nucleic Acids Chemistry Talk given at a conference Organizing Chromophores the DNA Way 30.07.2012 Telluride, Colorado, United States of America Häner Robert;


Self-organised

Title Date Place
3rd International Symposium on DNA-encoded chemical libraries 20.08.2012 Zürich, Switzerland

Communication with the public

Communication Title Media Place Year
Other activities Biochemie am Samstag German-speaking Switzerland 2011

Associated projects

Number Title Start Funding scheme
149148 DNA-based Oligomeric and Polymeric Functional Materials 01.10.2013 Project funding (Div. I-III)
149148 DNA-based Oligomeric and Polymeric Functional Materials 01.10.2013 Project funding (Div. I-III)
117617 DNA-Like Architectures with Polyaromatic Hydrocarbons 01.10.2007 Project funding (Div. I-III)
139078 1.7 mm Micro-Probehead for small volume NMR Spectroscopic Investigations 01.03.2012 R'EQUIP

Abstract

The construction and investigation of nucleic acid-guided, supramolecular structures is proposed. Building upon the results obtained in the past with pyrene and related polyaromatic compounds, we will use DNA-chromophore conjugates for the assembly of multi-stranded architectures. The synthesis and evaluation of novel types of non-nucleosidic chromophores will be pursued. At the same time, the spectroscopic and structural characterization of extended chromophore arrays is becoming a major aspect of our reserach.In a first part, we will explore new classes of aromatic building blocks. While we continue the investigation of additional types of pyrene derivatives we will extend our efforts to the synthesis of quinoxaline and porphyrin derivatives. The newly synthesized compounds will be evaluated for their stacking behaviour1,2 as well as their spectroscopic properties. Crucial aspects are the ability to assist hybrid formation, the fluorescence properties, and the compatibility with oligonucleotide synthesis. The proposed quinoxaline derivatives will provide an easy access to an extended library of compounds. Preliminary analysis of the spectroscopic properties of a first member of the series showed promising properties (high extinction coefficient and good quantum yield). The synthesis of the porphyrin derivatives as well as their incorporation into oligonucleotides is considerably more challenging. Considering the unique electronic properties of the porphyrins, the preparation of covalently linked stacks of defined length and composition is a worthy endeavour, however.3,4Secondly, we will extend our investigations of artificial helical systems formed by oligomers of pyrene and other building blocks. The amplification of chirality observed in a system composed of an achiral oligopyrene and traces of a (chiral) pyrene oligomer containing a single deoxynucleotide suggests that, under certain conditions, the oligomers form supramolecular polymers. The properties of these macromolecular assemblies will be further investigated with the different spectroscopic methods available. Along the same lines, we will explore the rational formation of molecular nanowires with bi-segmental oligomers composed of DNA and artificial building blocks (pyrene or PDI). Potential insight into the nature of these polymeric structures may be obtained through a collaborative effort with the group of T. Wandlowski of our department.Thirdly, the possibility of chemical ligation and template-assisted chain elongation of oligopyrenotides will be investigated. The formation of multi-stranded hybrids by oligopyrene strands via interstrand stacking interactions opens the opportunity of testing the formation of phosphodiester bonds from activated phosphate esters on (oligopyrene) template strands. Although not as efficient as enzymatic phosphodiester bond formation by enzymatic means and with natural substrates, such type of a templated oligomerization might provide a way to primitive, self-reproducing systems, especially if more than one type of building block were used.In a further part we will prepare modified hybrids that will allow the investigation of the efficiency of electron transfer through pi-stacks of non-nucleosidic, aromatic building blocks. For this purpose, oligomers containing pyrene (electron acceptor) and a quencher (electron donor) which are separated by a polyaromatic building block (e.g. phenanthrene) will be prepared. The determination of the relative fluorescence quantum yields will give information on the photo-induced electron transfer process.In addition to the above mentioned activities we will continue our efforts with the development of excimer based molecular beacons. In collaboration with the Department of Clinical Research (Prof. R. Jaggi), we will test differently designed beacon stems for their suitability for PCR and other applications.
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