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Petropoulos V, Martinez-Fernandez L, Uboldi L, Maiuri M, Cerullo G, Balanikas E, Markovitsi D. Real-time observation of sub-100-fs charge and energy transfer processes in DNA dinucleotides. Chem Sci 2024; 15:12098-12107. [PMID: 39092131 PMCID: PMC11290326 DOI: 10.1039/d4sc02514h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/26/2024] [Indexed: 08/04/2024] Open
Abstract
Using as showcase the DNA dinucleotide 5'-dTpdG-3', in which the thymine (T) is located at the 5' end with respect to the guanine (G), we study the photoinduced electronic relaxation of coupled chromophores in solution with an unprecedented refinement. On the one hand, transient absorption spectra are recorded from 20 fs to 45 ps over the 330-650 nm range with a temporal resolution of 30 fs; on the other hand, quantum chemistry calculations determine the ground state geometry of the 4 possible conformers with stacked nucleobases, the associated Franck-Condon states, and map the relaxation pathways leading to excited state minima. Important spectral changes occurring before 100 fs are correlated with concomitant G+ → T- charge transfer and T → G energy transfer processes. The lifetime of the excited charge transfer state is only 5 ps and the absorption spectrum of a long-lived nπ*T state is detected. Our experimental results match the transient spectral properties computed for the anti-syn conformer of 5'-dTpdG-3', which is characterized by the lowest ground state energy and differs from that encountered in B-form duplexes.
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Affiliation(s)
- Vasilis Petropoulos
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Lara Martinez-Fernandez
- Instituto de Química Física Blas Cabrera, Consejo Superior de Investigaciones Científicas Calle Serrano 119 Madrid 28006 Spain
| | - Lorenzo Uboldi
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Margherita Maiuri
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
- Istituto di Fotonica e Nanotecnologie-CNR Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Evangelos Balanikas
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva-4 Switzerland
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000 91405 Orsay France
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2
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Martínez-Fernández L, Green JA, Esposito L, Jouybari MY, Zhang Y, Santoro F, Kohler B, Improta R. The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study. Chem Sci 2024; 15:9676-9693. [PMID: 38939156 PMCID: PMC11206432 DOI: 10.1039/d4sc00910j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024] Open
Abstract
Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - James Alexander Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main Frankfurt am Main Germany
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
| | - Martha Yaghoubi Jouybari
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
- National Research Council of Canada 100 Sussex Drive Ottawa Ontario K1A 0R6 Canada
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
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3
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Zhou J, Wang X, Jia M, He X, Pan H, Chen J. Ultrafast spectroscopy study of DNA photophysics after proflavine intercalation. J Chem Phys 2024; 160:124305. [PMID: 38526107 DOI: 10.1063/5.0194608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Proflavine (PF), an acridine DNA intercalating agent, has been widespread applied as an anti-microbial and topical antiseptic agent due to its ability to suppress DNA replication. On the other hand, various studies show that PF intercalation to DNA can increase photogenotoxicity and has potential chances to induce carcinomas of skin appendages. However, the effects of PF intercalation on the photophysical and photochemical properties of DNA have not been sufficiently explored. In this study, the excited state dynamics of the PF intercalated d(GC)9 • d(GC)9 and d(AT)9 • d(AT)9 DNA duplex are investigated in an aqueous buffer solution. Under 267 nm excitation, we observed ultrafast charge transfer (CT) between PF and d(GC)9 • d(GC)9 duplex, generating a CT state with an order of magnitude longer lifetime compared to that of the intrinsic excited state reported for the d(GC)9 • d(GC)9 duplex. In contrast, no excited state interaction was detected between PF and d(AT)9 • d(AT)9. Nevertheless, a localized triplet state with a lifetime over 5 µs was identified in the PF-d(AT)9 • d(AT)9 duplex.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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4
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Wang X, Martínez-Fernández L, Zhang Y, Wu P, Kohler B, Improta R, Chen J. Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation. J Am Chem Soc 2024; 146:1839-1848. [PMID: 38194423 DOI: 10.1021/jacs.3c04567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Peicong Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via De Amicis 95, Napoli I-80145, Italy
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, Shanxi, China
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Petropoulos V, Uboldi L, Maiuri M, Cerullo G, Martinez-Fernandez L, Balanikas E, Markovitsi D. Effect of the DNA Polarity on the Relaxation of Its Electronic Excited States. J Phys Chem Lett 2023; 14:10219-10224. [PMID: 37931204 DOI: 10.1021/acs.jpclett.3c02580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The DNA polarity, i.e., the order in which nucleobases are connected together via the phosphodiester backbone, is crucial for several biological processes. But, so far, there has not been experimental evidence regarding its effect on the relaxation of DNA electronic excited states. Here we examine this aspect for two dinucleotides containing adenine and guanine: 5'-dApdG-3' and 5'-dGpdA-3' in water. We used two different femtosecond transient absorption setups: one providing high temporal resolution and broad spectral coverage (330-650 nm) between 30 fs and 50 ps, and the other recording decays at selected wavelengths until 1.2 ns. The transient absorption spectra corresponding to the minima in the potential energy surface of the first excited state were computed by quantum chemistry methods. Our results show that the excited charge transfer state in 5'-dGpdA-3' is formed with a ∼75% higher quantum yield and exhibits slower decay (170 ± 10 ps vs 112 ± 12 ps) compared to 5'-dApdG-3'.
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Affiliation(s)
- Vasilis Petropoulos
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lorenzo Uboldi
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Evangelos Balanikas
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva-4, Switzerland
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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Pakbin B, Zolghadr L, Rafiei S, Brück WM, Brück TB. FTIR differentiation based on genomic DNA for species identification of Shigella isolates from stool samples. Sci Rep 2022; 12:2780. [PMID: 35177783 PMCID: PMC8854563 DOI: 10.1038/s41598-022-06746-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Shigellosis is one of the major public health concerns in developing and low-income countries caused by four species of Shigella. There is an apparent need to develop rapid, cost-effective, sensitive and specific methods for differentiation of Shigella species to be used in outbreaks and health surveillance systems. We developed a sensitive and specific Fourier-transform infrared spectroscopy (FTIR) based method followed by principal component analysis (PCA) and hierarchical clustering analysis (HCA) assays to differentiate four species of Shigella isolates from stool samples. The FTIR based method was evaluated by differentiation of 91 Shigella species from each other in clinical samples using both gold standards (culture-based and agglutination methods) and developed FTIR assay; eventually, the sensitivity and specificity of the developed method were calculated. In summary, four distinct FTIR spectra associated with four species of Shigella were obtained with wide variations in three definite regions, including 1800–1550 cm−1, 1550–1100 cm−1, and 1100–800 cm−1 distinguish these species from each other. In this study, we found the FTIR method followed by PCA analysis with specificity, sensitivity, differentiation error and correct differentiation rate values of 100, 100, 0 and 100%, respectively, for identification and differentiation of all species of the Shigella in stool samples.
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Affiliation(s)
- Babak Pakbin
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.,Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950, Sion 2, Switzerland
| | - Leila Zolghadr
- Chemistry Department, Imam Khomeini International University, Qazvin, Iran
| | - Shahnaz Rafiei
- Chemistry Department, Imam Khomeini International University, Qazvin, Iran
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950, Sion 2, Switzerland.
| | - Thomas B Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748, Garching bei München, Germany
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7
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Green JA, Yaghoubi Jouybari M, Asha H, Santoro F, Improta R. Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge-Transfer State in the Photoexcited Guanine-Cytosine Pair. J Chem Theory Comput 2021; 17:4660-4674. [PMID: 34270258 DOI: 10.1021/acs.jctc.1c00416] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We introduce a method (FrD-LVC) based on a fragment diabatization (FrD) for the parametrization of a linear vibronic coupling (LVC) model suitable for studying the photophysics of multichromophore systems. In combination with effective quantum dynamics (QD) propagations with multilayer multiconfigurational time-dependent Hartree (ML-MCTDH), the FrD-LVC approach gives access to the study of the competition between intrachromophore decays, like those at conical intersections, and interchromophore processes, like exciton localization/delocalization and the involvement of charge-transfer (CT) states. We used FrD-LVC parametrized with time-dependent density functional theory (TD-DFT) calculations, adopting either CAM-B3LYP or ωB97X-D functionals, to study the ultrafast photoexcited QD of a guanine-cytosine (GC) hydrogen-bonded pair, within a Watson-Crick arrangement, considering up to 12 coupled diabatic electronic states and the effect of all of the 99 vibrational coordinates. The bright excited states localized on C and, especially, on G are predicted to be strongly coupled to the G → C CT state, which is efficiently and quickly populated after an excitation to any of the four lowest energy bright local excited states. Our QD simulations show that more than 80% of the excited population on G and ∼50% of that on C decay to this CT state in less than 50 fs. We investigate the role of vibronic effects in the population of the CT state and show that it depends mainly on its large reorganization energy so that it can occur even when it is significantly less stable than the bright states in the Franck-Condon region. At the same time, we document that the formation of the GC pair almost suppresses the involvement of dark nπ* excited states in the photoactivated dynamics.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
| | - Martha Yaghoubi Jouybari
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Consiglio Nazionale delle Ricerche, SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Haritha Asha
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Consiglio Nazionale delle Ricerche, SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
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8
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Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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9
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Abstract
The intrinsic fluorescence of nucleic acids is extremely weak compared to that of the fluorescent labels used to probe their structural and functional behavior. Thus, for technical reasons, the investigation of the intrinsic DNA fluorescence was limited for a long time. But with the improvement in spectroscopic techniques, the situation started to change around the turn of the century. During the past two decades, various factors modulating the static and dynamic properties of the DNA fluorescence have been determined; it was shown that, under certain conditions, quantum yields may be up 100 times higher than what was known so far. The ensemble of these studies opened up new paths for the development of label-free DNA fluorescence for biochemical applications. In parallel, these studies have shed new light on the primary processes leading to photoreactions that damage DNA when it absorbs UV radiation.We have been studying a variety of DNA systems, ranging from the monomeric nucleobases to double-stranded and four-stranded structures using fluorescence spectroscopy. The specificity of our work resides in the quantitative association of the steady-state fluorescence spectra with time-resolved data recorded from the femtosecond to the nanosecond timescales, made possible by the development of specific methodologies.Among others, our fluorescence studies provide information on the energy and the polarization of electronic transitions. These are valuable indicators for the evolution of electronic excitations in complex systems, where the electronic coupling between chromophores plays a key role. Highlighting collective effects that originate from electronic interactions in DNA multimers is the objective of the present Account.In contrast to the monomeric chromophores, whose fluorescence decays within a few picoseconds, that of DNA multimers persists on the nanosecond timescale. Even if long-lived states represent only a small fraction of electronic excitations, they may be crucial to the DNA photoreactivity because the probability to reach reactive conformations increases over time, owing to the incessant structural dynamics of nucleic acids.Our femtosecond studies have revealed that an ultrafast excitation energy transfer takes place among the nucleobases within duplexes and G-quadruplexes. Such an ultrafast process is possible when collective states are populated directly upon photon absorption. At much longer times, we discovered an unexpected long-lived high-energy emission stemming from what was coined "HELM excitons". These collective states, whose emission increases with the duplex size, could be responsible for the delayed fluorescence of ππ* states observed for genomic DNA.Most studies dealing with excited-state relaxation in DNA were carried out with excitation in the absorption band peaking at around 260 nm. We went beyond this and also performed the first time-resolved study with excitation in the UVA spectral range, where a very weak absorption tail is present. The resulting fluorescence decays are much slower and the fluorescence quantum yields are much higher than for UVC excitation. We showed that the base pairing of DNA strands enhances the UVA fluorescence and, in parallel, increases the photoreactivity because it modifies the nature of the involved collective excited states.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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10
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Yaghoubi Jouybari M, Liu Y, Improta R, Santoro F. Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study. J Chem Theory Comput 2020; 16:5792-5808. [PMID: 32687360 DOI: 10.1021/acs.jctc.0c00455] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The nonadiabatic quantum dynamics (QD) of cytosine and 1-methylcytosine in the gas phase is simulated for 250 fs after a photoexcitation to one of the first two bright states. The nuclear wavepacket is propagated on the coupled diabatic potential energy surfaces of the lowest seven excited states, including ππ*, nπ*, and Rydberg states along all the vibrational degrees of freedom. We focus in particular on the interplay between the bright and the dark nπ* states, not considering the decay to the ground electronic state. To run these simulations, we implemented an automatic general procedure to parametrize linear vibronic coupling (LVC) models with time-dependent density functional theory (DFT) computations and interfaced it with Gaussian package. The wavepacket was propagated with the multilayer version of the multiconfigurational time dependent Hartree method. Two different density functionals, PBE0 and CAM-B3LYP, which provide a different description of the relative stability of the lowest energy dark states, were used to parametrize the LVC Hamiltonian. Part of the photoexcited population on lowest HOMO-LUMO transition (πHπL*) decays within less than 100 fs to a nπ* state which mainly involves a promotion of an electron from the oxygen lone pair to the LUMO (nOπL*). The population of the second ππ* state decays almost completely, in <100 fs, not only to πHπL* and to nOπL* states but also to another nπL* state involving the nitrogen lone pair. The efficiency of the adopted protocol allowed us to check the accuracy of the predictions by repeating the QD simulations with different LVC Hamiltonians parametrized either at the ground-state minimum or at stationary structures of different relevant excited states.
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Affiliation(s)
- Martha Yaghoubi Jouybari
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Yanli Liu
- School of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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11
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Zhang Y, de La Harpe K, Kohl FR, Kohler B. Isotopic substitution affects excited state branching in a DNA duplex in aqueous solution. Chem Commun (Camb) 2019; 55:4174-4177. [PMID: 30895979 DOI: 10.1039/c9cc01105f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changing the solvent from H2O to D2O dramatically affects the branching of the initial excited electronic states in an alternating G·C DNA duplex into two distinct decay channels. The slower, multisite PCET channel that deactivates more than half of all excited states in D2O becomes six times weaker in H2O.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA.
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12
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Francés-Monerris A, Gattuso H, Roca-Sanjuán D, Tuñón I, Marazzi M, Dumont E, Monari A. Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA. Chem Sci 2018; 9:7902-7911. [PMID: 30450180 PMCID: PMC6202918 DOI: 10.1039/c8sc03252a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.
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Affiliation(s)
| | - Hugo Gattuso
- Theoretical Physical Chemistry , Research Unit Molecular Systems (UR MOLSYS) , University of Liège , 4000 Liège , Belgium
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular , Universitat de València , Apartado 22085 , ES-46071 Paterna , Spain
| | - Iñaki Tuñón
- Departamento de Química Física , Universitat de València , 46100 Burjassot , Spain
| | - Marco Marazzi
- Departamento de Química , Centro de Investigación en Síntesis Química (CISQ) , Universidad de La Rioja , 26006 Logroño , Spain
| | - Elise Dumont
- Univ. Lyon , ENS de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F69342 , Lyon , France
| | - Antonio Monari
- Université de Lorraine , CNRS , LPCT , Nancy F-54000 , France . ;
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13
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Martinez-Fernandez L, Prampolini G, Cerezo J, Liu Y, Santoro F, Improta R. Solvent effect on the energetics of proton coupled electron transfer in guanine-cytosine pair in chloroform by mixed explicit and implicit solvation models. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Banyasz A, Martínez-Fernández L, Improta R, Ketola TM, Balty C, Markovitsi D. Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation. Phys Chem Chem Phys 2018; 20:21381-21389. [PMID: 30101268 DOI: 10.1039/c8cp02588f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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15
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The optical properties of adenine cation in different oligonucleotides: a PCM/TD-DFT study. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2223-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Martinez-Fernandez L, Improta R. Photoactivated proton coupled electron transfer in DNA: insights from quantum mechanical calculations. Faraday Discuss 2018; 207:199-216. [DOI: 10.1039/c7fd00195a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect.
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Affiliation(s)
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche
- Istituto di Biostrutture e Bioimmagini
- 80136 Naples
- Italy
- LIDYL
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17
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Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
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18
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Lee J, Challa JR, McCamant DW. Ultraviolet Light Makes dGMP Floppy: Femtosecond Stimulated Raman Spectroscopy of 2'-Deoxyguanosine 5'-Monophosphate. J Phys Chem B 2017; 121:4722-4732. [PMID: 28412810 DOI: 10.1021/acs.jpcb.7b01694] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultrafast dynamics of 2'-deoxyguanosine 5'-monophosphate after excitation with ultraviolet light has been studied with femtosecond transient absorption (TA) and femtosecond stimulated Raman spectroscopy (FSRS). TA kinetics and transient anisotropy spectra reveal a rapid relaxation from the Franck-Condon region, producing an extremely red-shifted stimulated emission band at ∼440 nm that is formed after 200 fs and subsequent relaxation for 0.8-1.5 ps, consistent with prior studies. Viscosity dependence shows that the initial relaxation, before 0.5 ps, is the same in water or viscous glycerol/water mixtures, but after 0.5 ps the dynamics significantly slow down in a viscous solution. This indicates that large amplitude structural changes occur after 0.5 ps following photoexcitation. FSRS obtained with both 480 and 600 nm Raman pump pulses observe very broad Raman peaks at 509 and 1530 cm-1, as well as a narrower peak at 1179 cm-1. All of the Raman peaks decay with 0.7-1.3 ps time constants. The 1530 cm-1 peak also shows an increasing inhomogeneous linewidth over the first 0.3 ps. Our TA and FSRS data are consistent with a structurally inhomogeneous population in the S1 (La) state and, in particular, with previous theoretical models in which out-of-plane distortion at C2 and the amine move the molecule toward a conical intersection with the ground state. These FSRS data are the first to directly observe the structural inhomogeneity imparted upon the excited-state population by the broad, flat potential energy surface of the S1 (La) state.
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Affiliation(s)
- Joohyun Lee
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - J Reddy Challa
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David W McCamant
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
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19
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Zhang Y, Li XB, Fleming AM, Dood J, Beckstead AA, Orendt AM, Burrows CJ, Kohler B. UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes. J Am Chem Soc 2016; 138:7395-401. [DOI: 10.1021/jacs.6b03216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yuyuan Zhang
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Xi-Bo Li
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Aaron M. Fleming
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Jordan Dood
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ashley A. Beckstead
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Anita M. Orendt
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
- Center
for High Performance Computing, University of Utah, Salt Lake City, Utah 84112-0190, United States
| | - Cynthia J. Burrows
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Bern Kohler
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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20
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Zhang Y, de La Harpe K, Beckstead AA, Martínez-Fernández L, Improta R, Kohler B. Excited-State Dynamics of DNA Duplexes with Different H-Bonding Motifs. J Phys Chem Lett 2016; 7:950-954. [PMID: 26886244 DOI: 10.1021/acs.jpclett.6b00074] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The excited-state dynamics of three distinct forms of the d(GC)9·d(GC)9 DNA duplex were studied by combined time-resolved infrared experiments and quantum mechanical calculations. In the B- and Z-forms, bases on opposite strands form Watson-Crick (WC) base pairs but stack differently because of salt-induced changes in backbone conformation. At low pH, the two strands associate by Hoogsteen (HG) base pairing. Ultraviolet-induced intrastrand electron transfer (ET) triggers interstrand proton transfer (PT) in the B- and Z-forms, but the PT pathway is blocked in the HG duplex. Despite the different decay mechanisms, a common excited-state lifetime of ∼ 30 ps is observed in all three duplex forms. The ET-PT pathway in the WC duplexes and the solely intrastrand ET pathway in the HG duplex yield the same pair of π-stacked radicals on one strand. Back ET between these radicals is proposed to be the rate-limiting step behind excited-state deactivation in all three duplexes.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Kimberly de La Harpe
- Department of Physics, United States Air Force Academy , USAF Academy, Colorado 80840, United States
| | - Ashley A Beckstead
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
| | - Lara Martínez-Fernández
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini , 80136 Naples, Italy
| | - Roberto Improta
- Consiglio Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini , 80136 Naples, Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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21
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Vayá I, Brazard J, Huix-Rotllant M, Thazhathveetil AK, Lewis FD, Gustavsson T, Burghardt I, Improta R, Markovitsi D. High-Energy Long-Lived Mixed Frenkel-Charge-Transfer Excitons: From Double Stranded (AT)n to Natural DNA. Chemistry 2016; 22:4904-14. [PMID: 26928984 DOI: 10.1002/chem.201504007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 01/07/2023]
Abstract
The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV-induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine-thymine double-stranded structures (AT)n . Fluorescence measurements on (AT)n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time-dependent (TD)-DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine-to-thymine charge-transfer states. Emission from such high-energy long-lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π-π* states (≥0.1). An increase in the size of the system quenches π-π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π-π* and charge-transfer states. Subsequently, we identify the common features between the HELM states of (AT)n structures with those reported previously for alternating (GC)n : high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π-π* states, giving rise to delayed fluorescence.
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Affiliation(s)
- Ignacio Vayá
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France
| | - Johanna Brazard
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France
| | - Miquel Huix-Rotllant
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France.,Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | | | - Frederick D Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, USA.
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France
| | - Irene Burghardt
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche, Via mezzocannone 16, 80136, Napoli, Italy.
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris Saclay, 91191, Gif-sur-Yvette, France.
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22
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Martinez-Fernandez L, Zhang Y, de La Harpe K, Beckstead AA, Kohler B, Improta R. Photoinduced long-lived charge transfer excited states in AT-DNA strands. Phys Chem Chem Phys 2016; 18:21241-5. [DOI: 10.1039/c6cp04550b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The IR spectrum of a charge transfer (CT) excited electronic state in DNA has been computed for the first time, enabling assignment of the long-lived component of the transient IR spectrum of a d(AT)9 single strand to an A → T CT state.
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Affiliation(s)
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry
- Montana State University
- Bozeman
- USA
| | | | | | - Bern Kohler
- Department of Chemistry and Biochemistry
- Montana State University
- Bozeman
- USA
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche
- I-80134 Napoli
- Italy
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23
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Zhang Y, de La Harpe K, Beckstead AA, Improta R, Kohler B. UV-Induced Proton Transfer between DNA Strands. J Am Chem Soc 2015; 137:7059-62. [DOI: 10.1021/jacs.5b03914] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yuyuan Zhang
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kimberly de La Harpe
- Department
of Physics, United States Air Force Academy, USAF Academy, Colorado 80840, United States
| | - Ashley A. Beckstead
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Roberto Improta
- Consiglio
Nationale delle Ricerche, Istituto di Biostrutture e Bioimmagini, Via Mezzocannone
16, 80136 Naples, Italy
| | - Bern Kohler
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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24
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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25
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Richter M, Mai S, Marquetand P, González L. Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics. Phys Chem Chem Phys 2014; 16:24423-36. [PMID: 25301389 PMCID: PMC4391640 DOI: 10.1039/c4cp04158e] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/03/2014] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxation to the singlet ground state and instead privileges transitions from the low-lying nπ* state (S1) to a ππ* triplet state (T2) followed by rapid internal conversion to the lowest triplet state.
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Affiliation(s)
- Martin Richter
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Sebastian Mai
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Philipp Marquetand
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Leticia González
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
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26
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Bucher DB, Schlueter A, Carell T, Zinth W. Watson-Crick Base Pairing Controls Excited-State Decay in Natural DNA. Angew Chem Int Ed Engl 2014; 53:11366-9. [DOI: 10.1002/anie.201406286] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/22/2014] [Indexed: 11/11/2022]
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27
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Bucher DB, Schlueter A, Carell T, Zinth W. In natürlicher DNA wird der Zerfall des angeregten Zustands durch Watson-Crick-Basenpaarung bestimmt. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406286] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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29
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Chen J, Zhang Y, Kohler B. Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:39-87. [DOI: 10.1007/128_2014_570] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Devereux SJ, Keane PM, Vasudevan S, Sazanovich IV, Towrie M, Cao Q, Sun XZ, George MW, Cardin CJ, Kane-Maguire NAP, Kelly JM, Quinn SJ. Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods. Dalton Trans 2014; 43:17606-9. [DOI: 10.1039/c4dt01989j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excited-state quenching of DNA intercalated [Cr(phen)2(dppz)]3+ by guanine proceeds by rapid forward and back electron transfer of <3 ps.
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Affiliation(s)
- Stephen J. Devereux
- School of Chemistry and Chemical Biology
- Centre for Synthesis and Chemical Biology
- University College Dublin
- Dublin 4, Ireland
| | - Páraic M. Keane
- School of Chemistry
- Trinity College Dublin
- Dublin 2, Ireland
- Department of Chemistry
- University of Reading
| | - Suni Vasudevan
- School of Chemistry
- Trinity College Dublin
- Dublin 2, Ireland
| | - Igor V. Sazanovich
- Central Laser Facility
- Research Complex at Harwell
- Science & Technology Facilities Council
- Rutherford Appleton Laboratory
- Didcot, UK
| | - Michael Towrie
- Central Laser Facility
- Research Complex at Harwell
- Science & Technology Facilities Council
- Rutherford Appleton Laboratory
- Didcot, UK
| | - Qian Cao
- Department of Chemistry
- University of Nottingham
- , UK
| | | | | | | | | | - John M. Kelly
- School of Chemistry
- Trinity College Dublin
- Dublin 2, Ireland
| | - Susan J. Quinn
- School of Chemistry and Chemical Biology
- Centre for Synthesis and Chemical Biology
- University College Dublin
- Dublin 4, Ireland
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31
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Sauri V, Gobbo JP, Serrano-Pérez JJ, Lundberg M, Coto PB, Serrano-Andrés L, Borin AC, Lindh R, Merchán M, Roca-Sanjuán D. Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism. J Chem Theory Comput 2012; 9:481-96. [DOI: 10.1021/ct3006166] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vicenta Sauri
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - João P. Gobbo
- Instituto de Química,
Universidade de São Paulo and NAP-PhotoTech, the USP Consortium
for Photochemical Technology, Av. Prof. Lineu Prestes, 748, 05508-900,
São Paulo, SP, Brazil
| | - Juan J. Serrano-Pérez
- Department of Chemistry, Imperial
College London, Exhibition Road, London, SW7 2AZ, United Kingdom
| | - Marcus Lundberg
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
| | - Pedro B. Coto
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
- Institut
für Theoretische
Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg,
Staudtstraβe 7, 91058 Erlangen, Germany
- Departamento de Química-Física,
Universidad de Alcalá de Henares, Ctra. Madrid-Barcelona (Autovía
A2) Km. 33.600, 28871 Alcalá de Henares, Spain
| | - Luis Serrano-Andrés
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - Antonio C. Borin
- Instituto de Química,
Universidade de São Paulo and NAP-PhotoTech, the USP Consortium
for Photochemical Technology, Av. Prof. Lineu Prestes, 748, 05508-900,
São Paulo, SP, Brazil
| | - Roland Lindh
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
| | - Manuela Merchán
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - Daniel Roca-Sanjuán
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
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32
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Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P. UV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase. J Phys Chem A 2012; 116:5383-91. [DOI: 10.1021/jp302468x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frédéric Rosu
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Valérie Gabelica
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Edwin De Pauw
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Rodolphe Antoine
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Michel Broyer
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Philippe Dugourd
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
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33
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Keane PM, Wojdyla M, Doorley GW, Kelly JM, Clark IP, Parker AW, Greetham GM, Towrie M, Magno LM, Quinn SJ. Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state. Phys Chem Chem Phys 2012; 14:6307-11. [PMID: 22358255 DOI: 10.1039/c2cp23774a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The decay pathways of UV-excited cytosine polymers are investigated using picosecond time-resolved infrared spectroscopy. Similar yields of a non-emissive (1)nπ* state are found in the single-stranded dC(30) polymer as in the dCMP monomer, but with a longer lifetime in the polymer (80 ps vs. 39 ps). A longer lifetime is also found in the d(CpC) dinucleotide. No evidence of excimer states is observed, suggesting that localised (1)nπ* excited states are the most significant intermediates present on the picosecond timescale.
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Affiliation(s)
- Páraic M Keane
- School of Chemistry and Centre for Synthesis and Chemical Biology, Trinity College, Dublin 2, Ireland
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Biemann L, Kovalenko SA, Kleinermanns K, Mahrwald R, Markert M, Improta R. Excited State Proton Transfer Is Not Involved in the Ultrafast Deactivation of Guanine–Cytosine Pair in Solution. J Am Chem Soc 2011; 133:19664-7. [DOI: 10.1021/ja2089734] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lars Biemann
- Department of Physical Chemistry, Heinrich-Heine University, University-str. 1, D-40225 Düsseldorf, Germany
| | - Sergey A. Kovalenko
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Karl Kleinermanns
- Department of Physical Chemistry, Heinrich-Heine University, University-str. 1, D-40225 Düsseldorf, Germany
| | - Rainer Mahrwald
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Morris Markert
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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Keane PM, Wojdyla M, Doorley GW, Watson GW, Clark IP, Greetham GM, Parker AW, Towrie M, Kelly JM, Quinn SJ. A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives. J Am Chem Soc 2011; 133:4212-5. [PMID: 21384855 DOI: 10.1021/ja1106089] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The role of N1-substitution in controlling the deactivation processes in photoexcited cytosine derivatives has been explored using picosecond time-resolved IR spectroscopy. The simplest N1-substituted derivative, 1-methylcytosine, exhibits relaxation dynamics similar to the cytosine nucleobase and distinct from the biologically relevant nucleotide and nucleoside analogues, which have longer-lived excited-state intermediates. It is suggested that this is the case because the sugar group either facilitates access to the long-lived (1)n(O)π* state or retards its crossover to the ground state.
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Affiliation(s)
- Páraic M Keane
- School of Chemistry and Centre for Synthesis and Chemical Biology, Trinity College, Dublin 2, Ireland
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Yang M, Szyc Ł, Röttger K, Fidder H, Nibbering ETJ, Elsaesser T, Temps F. Dynamics and Couplings of N−H Stretching Excitations of Guanosine−Cytidine Base Pairs in Solution. J Phys Chem B 2011; 115:5484-92. [DOI: 10.1021/jp110561d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ming Yang
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Łukasz Szyc
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Katharina Röttger
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Henk Fidder
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Erik T. J. Nibbering
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
| | - Friedrich Temps
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
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37
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Parker AW, Lin CY, George MW, Towrie M, Kuimova MK. Infrared characterization of the guanine radical cation: finger printing DNA damage. J Phys Chem B 2010; 114:3660-7. [PMID: 20175506 DOI: 10.1021/jp9106958] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxidation of DNA represents a major pathway of genetic mutation. We have applied infrared spectroscopy in 77 K glass with supporting density functional theory (DFT) calculations (EDF1/6-31+G*) to provide an IR signature of the guanine radical cation G(+*), formed as a result of 193 nm photoionization of DNA. Deprotonation of this species to produce the neutral radical G(-H)(*) does not occur in 77 K glass. DFT calculations indicate that the formation of G(+*) within the double helix does not significantly perturb the geometry of the G/C pair, even though there is a significant movement of the N(1) proton away from G toward C. However, this is in stark contrast to drastic changes that are expected if full deprotonation of G/C occurs, producing the G(-H)(*)/C pair. These results are discussed in light of solution-phase time-resolved IR spectroscopic studies and demonstrate the power of IR to follow dynamics of DNA damage in natural environments.
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Affiliation(s)
- Anthony W Parker
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX, UK.
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Powe AM, Das S, Lowry M, El-Zahab B, Fakayode SO, Geng ML, Baker GA, Wang L, McCarroll ME, Patonay G, Li M, Aljarrah M, Neal S, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2010; 82:4865-94. [DOI: 10.1021/ac101131p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Aleeta M. Powe
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Susmita Das
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Mark Lowry
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Bilal El-Zahab
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Sayo O. Fakayode
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Maxwell L. Geng
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Gary A. Baker
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Lin Wang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Matthew E. McCarroll
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Gabor Patonay
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Min Li
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Mohannad Aljarrah
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Sharon Neal
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
| | - Isiah M. Warner
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208, Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department
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Vayá I, Miannay FA, Gustavsson T, Markovitsi D. High-Energy Long-Lived Excited States in DNA Double Strands. Chemphyschem 2010; 11:987-9. [DOI: 10.1002/cphc.201000027] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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de La Harpe K, Crespo-Hernández CE, Kohler B. Deuterium isotope effect on excited-state dynamics in an alternating GC oligonucleotide. J Am Chem Soc 2010; 131:17557-9. [PMID: 19950991 DOI: 10.1021/ja9076364] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotope effects on the excited-state dynamics of single- and double-stranded GC-containing DNAs were studied by femtosecond transient absorption spectroscopy. A pronounced deuterium isotope effect was observed in alternating d(GC)(9).d(GC)(9), but none was seen in the nonalternating or single-stranded variations investigated. These findings demonstrate that an interstrand process involving proton-coupled electron transfer contributes to the excited-state dynamics in DNAs having an appropriate base sequence.
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Affiliation(s)
- Kimberly de La Harpe
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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41
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de la Harpe K, Crespo-Hernández CE, Kohler B. The excited-state lifetimes in a G x C DNA duplex are nearly independent of helix conformation and base-pairing motif. Chemphyschem 2009; 10:1421-5. [PMID: 19301308 DOI: 10.1002/cphc.200900004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA photophysics: Femtosecond transient absorption experiments reveal that excited states produced by UV light in a duplex DNA oligonucleotide decay at essentially the same rate in B and Z helix conformers (see figure).
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Affiliation(s)
- Kimberly de la Harpe
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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Towrie M, Doorley GW, George MW, Parker AW, Quinn SJ, Kelly JM. ps-TRIR covers all the bases--recent advances in the use of transient IR for the detection of short-lived species in nucleic acids. Analyst 2009; 134:1265-73. [PMID: 19562188 DOI: 10.1039/b902108f] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent developments of the picosecond transient absorption infrared technique and its ability to elucidate the nature and kinetic behaviour of transient species formed upon pulsed laser excitation of nucleic acids are described.
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Affiliation(s)
- Michael Towrie
- Central Laser Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK OX11 0QX
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43
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McGovern DA, Doorley GW, Whelan AM, Parker AW, Towrie M, Kelly JM, Quinn SJ. A study of the pH dependence of electronically excited guanosine compounds by picosecond time-resolved infrared spectroscopy. Photochem Photobiol Sci 2009; 8:542-8. [PMID: 19337669 DOI: 10.1039/b817756b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photophysical properties of 5'-guanosine monophosphate (5'-GMP) and polyguanylic acid {poly(G)} in D(2)O solutions of varying pH have been studied using picosecond transient infrared absorption spectroscopy. Whereas in neutral or weakly alkaline solution only the vibrationally excited electronic ground state of 5'-GMP is observed, in acidic solution the relatively long-lived (229 +/- 20 ps) electronic excited state of protonated 5'-GMP, which possesses strong absorptions at 1517 and 1634 cm(-1), could be detected. The picosecond transient behaviour of polyguanylic acid in acidic solution is also very different from that of the polynucleotide in neutral solution due not only to the protonation of guanine moieties yielding the protonated excited state but because of the disruption of the guanine stacks which are present in the species in neutral solution.
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Affiliation(s)
- David A McGovern
- Centre for Chemical Synthesis and Chemical Biology, Trinity College, Dublin 2, Ireland
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