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DNA as a training platform for photodynamic processes in soft materials

Deliverables

Open-source code for the simulation of pump-probe and 2D electron spectra from quantum-dynamics.

Open-source code for the simulation of pump-probe and 2D electron spectra from quantum-dynamics.

Introduction Week: DNA fundamentals

Introduction Week: DNA fundamentals.

Technology Training Camps

Technology Training Camps, due in M18 and M22. Lead Beneficiaries UNIVIE and POLIMI

Website

Website

Outreach Plan

Outreach Plan

Supervisory and External Advisory Boards established

Supervisory and External Advisory Boards established

Progress report 1

Progress Report 1

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Publications

Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine

Author(s): Nadine Müller, Eveliina Ponkkonen, Thomas Carell, Andriy Khobta
Published in: International Journal of Molecular Sciences, 22, 2021, Page(s) 11025, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222011025

The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis

Author(s): Lara Martínez Fernández, Javier Cerezo, Haritha Asha, Fabrizio Santoro, Sonia Coriani, Roberto Improta
Published in: ChemPhotoChem, 3/9, 2019, Page(s) 846-855, ISSN 2367-0932
Publisher: European Chemical Societies Publishing
DOI: 10.1002/cptc.201900107

Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features

Author(s): Akos Banyasz, Evangelos Balanikas, Lara Martinez-Fernandez, Gérard Baldacchino, Thierry Douki, Roberto Improta, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry B, 123/23, 2019, Page(s) 4950-4957, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.9b02637

Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by G-Quadruplexes and Modify Their Reactivity

Author(s): Behnaz Behmand, Evangelos Balanikas, Lara Martinez-Fernandez, Roberto Improta, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry Letters, 11/4, 2020, Page(s) 1305-1309, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.9b03667

Populations and Dynamics of Guanine Radicals in DNA strands—Direct versus Indirect Generation

Author(s): Evangelos Balanikas, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: Molecules, 24/13, 2019, Page(s) 2347, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules24132347

Directional and regioselective hole injection of spiropyran photoswitches intercalated into A/T-duplex DNA

Author(s): Davide Avagliano, Pedro A. Sánchez-Murcia, Leticia González
Published in: Physical Chemistry Chemical Physics, 21/32, 2019, Page(s) 17971-17977, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp03398j

A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

Author(s): Michael Stadlmeier, Leander Simon Runtsch, Filipp Streshnev, Martin Wühr, Thomas Carell
Published in: ChemBioChem, 21/1-2, 2019, Page(s) 103-107, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201900611

On the stability of a dipole-bound state in the presence of a molecule

Author(s): Maria Elena Castellani, Cate S. Anstöter, Jan R. R. Verlet
Published in: Physical Chemistry Chemical Physics, 21/44, 2019, Page(s) 24286-24290, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp04942h

DNA-binding mechanism of spiropyran photoswitches: the role of electrostatics

Author(s): Davide Avagliano, Pedro A. Sánchez-Murcia, Leticia González
Published in: Physical Chemistry Chemical Physics, 21/17, 2019, Page(s) 8614-8618, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cp07508e

A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding

Author(s): Irene Ponzo, Friederike M. Möller, Herwin Daub, Nena Matscheko
Published in: Molecules, 24/16, 2019, Page(s) 2877, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules24162877

Guanine Radicals Generated in Telomeric G-Quadruplexes by Direct Absorption of Low-Energy UV Photons: Effect of Potassium Ions

Author(s): Evangelos Balanikas, Akos Banyasz, Gérard Baldacchino, Dimitra Markovitsi
Published in: Molecules, 25/9, 2020, Page(s) 2094, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules25092094

Analysis of an Active Deformylation Mechanism of 5‐Formyl‐deoxycytidine (fdC) in Stem Cells

Author(s): Alexander Schön, Ewelina Kaminska, Florian Schelter, Eveliina Ponkkonen, Eva Korytiaková, Sarah Schiffers, Thomas Carell
Published in: Angewandte Chemie International Edition, 59/14, 2020, Page(s) 5591-5594, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202000414

Spiropyran meets guanine quadruplexes: Isomerization mechanism and DNA binding modes of quinolizidine‐substituted spiropyran probes

Author(s): Davide Avagliano, Pedro A. Sánchez-Murcia, Leticia González
Published in: Chemistry – A European Journal, 2020, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202001586

Linear absorption spectra of solvated thiouracils resolved at the hybrid RASPT2/MM level

Author(s): Artur Nenov, Irene Conti, Rocio Borrego-Varillas, Giulio Cerullo, Marco Garavelli
Published in: Chemical Physics, 515, 2018, Page(s) 643-653, ISSN 0301-0104
Publisher: Elsevier BV
DOI: 10.1016/j.chemphys.2018.07.025

Observation of the Sub-100 Femtosecond Population of a Dark State in a Thiobase Mediating Intersystem Crossing

Author(s): Rocío Borrego-Varillas, Danielle C. Teles-Ferreira, Artur Nenov, Irene Conti, Lucia Ganzer, Cristian Manzoni, Marco Garavelli, Ana Maria de Paula, Giulio Cerullo
Published in: Journal of the American Chemical Society, 140/47, 2018, Page(s) 16087-16093, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.8b07057

Vibrations of the guanine–cytosine pair in chloroform: an anharmonic computational study

Author(s): James A. Green, Roberto Improta
Published in: Physical Chemistry Chemical Physics, 22/10, 2020, Page(s) 5509-5522, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cp06373k

Exciton Trapping Dynamics in DNA Multimers

Author(s): Rocio Borrego-Varillas, Giulio Cerullo, Dimitra Markovitsi
Published in: The Journal of Physical Chemistry Letters, 10/7, 2019, Page(s) 1639-1643, ISSN 1948-7185
Publisher: American Chemical Society
DOI: 10.1021/acs.jpclett.9b00450

Triplet‐Induced Lesion Formation at CpT and TpC Sites in DNA

Author(s): Julia Gontcharov, Lizhe Liu, Bert M. Pilles, Thomas Carell, Wolfgang J. Schreier, Wolfgang Zinth
Published in: Chemistry – A European Journal, 25/66, 2019, Page(s) 15164-15172, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201903573

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two‐Dimensional Electronic Spectroscopy

Author(s): Francesco Segatta, Itay Gdor, Julien Réhault, Simone Taioli, Noga Friedman, Mordechai Sheves, Ivan Rivalta, Sanford Ruhman, Giulio Cerullo, Marco Garavelli
Published in: Chemistry – A European Journal, 24/46, 2018, Page(s) 12084-12092, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201803525

Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules

Author(s): R. Borrego-Varillas, A. Nenov, L. Ganzer, A. Oriana, C. Manzoni, A. Tolomelli, I. Rivalta, S. Mukamel, M. Garavelli, G. Cerullo
Published in: Chemical Science, 10/43, 2019, Page(s) 9907-9921, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc03871j