Using DNA as a training playground to study the dynamical interaction between light and soft-material.

Transcription

1 Using DNA as a training playground to study the dynamical interaction between light and soft-material. Going from the study of the interaction between DNA and Light to the use of light as a powerful tool to study the interaction between Biomacromolecules Training the ESR both in experimental and computational tools

2 No. Consortium Member Legal Entity Short Name Academic Awards PhDs Country Department/ Division/ Laboratory Nonacademic Scientistin-Charge Expertise & Role (C = Computational, E = Experimental) Beneficiaries B1 Consiglio Nazionale delle Ricerche B2 B3 B4 B5 B6 B7 Centre National de la Recherche Scientifique University of Durham National Institute of Chemistry Ludwig- Maximilians- Universität München Masaryk University Politecnico di Milano CNR ü * CNRS ü * UDUR ü ü KI ü * LMUM ü ü MUNI ü ü POLIMI ü ü FR UK SI DE CZ Institute for Biostructures and Bioimaging (IBB) Institute of Chemistry of Organometallic Compounds (ICCOM) Lasers, Interactions and Dynamics Laboratory Chemistry Slovenian NMR Centre Chemistry Structure and Dynamics of Nucleic Acids Physics Dr. Roberto Improta Dr. Fabrizio Santoro Dr. Dimitra Markovitsi Prof. Jan Verlet Prof. Janez Plavec Prof. Thomas Carell Prof. Jiří Šponer Prof. Giulio Cerullo C: DFT, TD-DFT Simulation of Steady state and time-resolved spectra. Quantum dynamics Photochemistry of DNA E: Time resolved spectroscopy, electronic circular dichroism. Photophysics of G- quadruplex. E: Photoelectron spectroscopy in gas phase. Photophysics of oligonucleotides E: Nuclear magnetic resonance spectroscopy, biophysics of G-quadruplex E: HPLC-MS, fluorimetry, synthesis of DNA lesions. Epigenetic bases. C: Force Field developments, Molecular dynamics. Conformational study of oligonucleotides E: 1D/2D UV electronic spectroscopy.

3 B6 B7 B8 B9 Maximilians- Universität München Masaryk University Politecnico di Milano University College Dublin Università di Bologna MUNI ü ü POLIMI ü ü UCD ü ü UNIBO ü ü B10 Universität Wien UNIVIE ü ü B11 AstraZeneca AZ Limited B12 Baseclick GmbH Baseclick B13 Dynamic Biosensors GmbH DBS ü ü ü DE Chemistry Thomas Carell CZ IL AT UK DE DE Structure and Dynamics of Nucleic Acids Physics School of Chemistry and Chemical Biology Industrial Chemistry Toso Montanari Institute for Theoretical Chemistry Prof. Jiří Šponer Prof. Giulio Cerullo Dr. Susan Quinn Prof. Marco Garavelli Prof. Leticia González Reagents & Assay Dr. Kara Development Herlihy Prof. Thomas Frischmuth Biochemistry Dr. Ralf Strasser synthesis of DNA lesions. Epigenetic bases. C: Force Field developments, Molecular dynamics. Conformational study of oligonucleotides E: 1D/2D UV electronic spectroscopy. Photochemistry of DNA E: Time resolved Infrared spectroscopy, dye/quadruplexes interaction by optical spectroscopy C: QM and QM/ MM calculations. Simulation of 1D/2D spectra. Photochemistry of DNA C: Quantum mechanical calculations, Semi-classical dynamics. Interaction of DNA and small molecules. E: DNA/protein interaction for therapeutic research. E: Click chemistry, synthesis of spiropyran dyes and derivatives, DNA purification E: Biophysical measurements on DNAchips. Building of G- quadruplex chips

4 Figure 1.1b: The LightDyNAmics approach

5 ESR 4 In practice: LightDyNAmics. Grant Number Sigend. Starting 1st April years network. Coordinator. R. Improta (IBB-CNR) 15 ESR (Ph.D) 10 Academic Members + 3 Companies (Full beneficiaries) + 3 Additional Companies for training Half of the money to ESR (Ph.D. ca 3500 euros per month X 3 years) Half of the money to the Group: Training cost + Money for researches. Ca 3000 euros X month LightDynamics Total budget: ca Euros 15 independent yet related research projects Host: CNR; Supervisor: R. Improta (CNR-IBB) Co-Supervisors: F. Santoro (CNR), D. Markovitsi (CNRS) PhD: Yes (see partner list) Start: M4-7 Duration: 36 months Deliverables: D1.3, 1.4, 2.2, 2.6, 3.2, 3.3 Title & WPs: Exciton and charge separation: computational models (WPs 1, 2, 3) Objectives: Science: 1. Investigation of the structural and electronic information embedded in the lineshape of electronic spectra of G-quadruplexes 2. Develop effective mixed quantum/classical computational strategies for the simulation of electronic spectra and the dynamics of excitation energy (EET) and charge transfers (CT). Training: DFT/TD-DFT, exciton models, quantum dynamical and quantum/classical dynamical simulations, simulation of electronic spectra. Expected Results: 1. To simulate the ECD spectra of G-quadruplexes and extract detailed information from their lineshape. 2. To investigate the coupled EET and CT dynamics in G-quadruplexes unveiling the dynamical effects of the solvent, of the fluctuation of interchromophoric distances and orientations and of the intra-chromophore vibrations. Secondments: 1) H: CNRS; T: M6; L: 3m; P: Basics of CD spectroscopy; 2) H: UCD; T: M18; L: 3m; P: Basics of Time Resolved IR spectroscopy ; 3) H: MDL; T: M24; L: 2m; P: Chemometric approach to drug/dna interaction.

6 Three Work-Packages: The methods: New experimental and computational methods for multi-chromophoric systems. G. Cerullo Objectives: To develop and refine a set of experimental time-resolved spectroscopy methods for investigating photoinduced processes in strongly coupled multi-chromophore systems, enabling to disentangle the manifold of excited electronic states and their dynamics from the sub-ps to the ms timescale. To develop and refine a suite of theoretical methods to allow the direct simulation of time-resolved spectra and, by coupling quantum and classical approaches, to follow the excited state dynamics up to the ms time scale. DNA systems of different complexity will be used as training platform for these developments. The system: Light activated dynamics in DNA. D. Markovitsi Ojectives: To describe the photoactivated processes in DNA, from photon absorption to formation of lesions leading to carcinogenic mutations. Photons are absorbed either directly by DNA or by interacting ligands used either as probes for the local DNA environment or as pharmaceutical agents. Systems of increasing complexity (single bases, stacked pairs, single and double helices, I-motifs, DNA-protein complexes) will be studied by several experimental and computational methods. Particular focus will be devoted to guanine quadruplexes, which are targets for cancer therapy and considered as promising structures for applications in electronic devices. The processes:light induced processes in Multichromophore Architectures. S. Quinn Objectives: To investigate the chemical physical effects ruling the main processes triggered by UV light absorption in soft multichromophore materials using DNA as a platform. To identify the spectroscopic signatures associated to these processes. To assess the interplay of the different factors influencing their yield and dynamics, combining experiments and calculations to investigate systems of increasing complexity from gas to condensed phase and up to chipimmobilised structures. To predict and control the final outcome of these processes.