1
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Koga M, Kang DH, Heim ZN, Meyer P, Erickson BA, Haldar N, Baradaran N, Havenith M, Neumark DM. Extreme ultraviolet time-resolved photoelectron spectroscopy of adenine, adenosine and adenosine monophosphate in a liquid flat jet. Phys Chem Chem Phys 2024; 26:13106-13117. [PMID: 38629206 DOI: 10.1039/d4cp00856a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Time-resolved photoelectron spectroscopy using an extreme-ultraviolet (XUV) probe pulse was used to investigate the UV photoinduced dynamics of adenine (Ade), adenosine (Ado), and adenosine-5-monophosphate (AMP) in a liquid water jet. In contrast to previous studies using UV probe pulses, the XUV pulse at 21.7 eV can photoionize all excited states of a molecule, allowing for full relaxation pathways to be addressed after excitation at 4.66 eV. This work was carried out using a gas-dynamic flat liquid jet, resulting in considerably enhanced signal compared to a cylindrical jet. All three species decay on multiple time scales that are assigned based on their decay associated spectra; the fastest decay of ∼100 fs is assigned to ππ* decay to the ground state, while a smaller component with a lifetime of ∼500 fs is attributed to the nπ* state. An additional slower channel in Ade is assigned to the 7H Ade conformer, as seen previously. This work demonstrates the capability of XUV-TRPES to disentangle non-adiabatic dynamics in an aqueous solution in a state-specific manner and represents the first identification of the nπ* state in the relaxation dynamics of adenine and its derivatives.
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Affiliation(s)
- Masafumi Koga
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Do Hyung Kang
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Zachary N Heim
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Philipp Meyer
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801, Germany
| | - Blake A Erickson
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Neal Haldar
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Negar Baradaran
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801, Germany
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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2
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Kufner CL, Crucilla S, Ding D, Stadlbauer P, Šponer J, Szostak JW, Sasselov DD, Szabla R. Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern. Chem Sci 2024; 15:2158-2166. [PMID: 38332835 PMCID: PMC10848779 DOI: 10.1039/d3sc04971j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/27/2023] [Indexed: 02/10/2024] Open
Abstract
Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient self-repair of cyclobutane pyrimidine dimers (CPDs) in specific short DNA oligomers such as the GAT[double bond, length as m-dash]T sequence. The mechanism was characterized as sequential electron transfer through the nucleobase stack which is controlled by the redox potentials of nucleobases and their sequence. Here, we demonstrate that the inverse sequence T[double bond, length as m-dash]TAG promotes self-repair with higher quantum yields (0.58 ± 0.23%) than GAT[double bond, length as m-dash]T (0.44 ± 0.18%) in a comparative study involving UV-irradiation experiments. After extended exposure to UV irradiation, a photostationary equilibrium between self-repair and damage formation is reached at 33 ± 13% for GAT[double bond, length as m-dash]T and at 40 ± 16% for T[double bond, length as m-dash]TAG, which corresponds to the maximum total yield of self-repair. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations allowed us to assign this disparity to better stacking overlap between the G and A bases, which lowers the energies of the key A-˙G+˙ charge transfer state in the dominant conformers of the T[double bond, length as m-dash]TAG tetramer. These conformational differences also hinder alternative photorelaxation pathways of the T[double bond, length as m-dash]TAG tetranucleotide, which otherwise compete with the sequential electron transfer mechanism responsible for CPD self-repair. Overall, we demonstrate that photoinduced electron transfer is strongly dependent on conformation and the availability of alternative photodeactivation mechanisms. This knowledge can be used in the identification and prediction of canonical and modified DNA sequences exhibiting efficient electron transfer. It also further contributes to our understanding of DNA self-repair and its potential role in the photochemical selection of the most photostable sequences on the early Earth.
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Affiliation(s)
- Corinna L Kufner
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Sarah Crucilla
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
- Department of Earth and Planetary Sciences, Harvard University Cambridge Massachusetts 02138 USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital Boston Massachusetts 02114 USA
- Department of Chemistry and Chemical Biology, Harvard University Cambridge Massachusetts 02138 USA
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jack W Szostak
- Howard Hughes Medical Institute, The University of Chicago Chicago IL 60637 USA
- Department of Chemistry, The University of Chicago Chicago Illinois 60637 USA
| | - Dimitar D Sasselov
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Rafał Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 Wrocław 50-370 Poland
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3
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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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4
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Bauer B, Sharma R, Chergui M, Oppermann M. Exciton decay mechanism in DNA single strands: back-electron transfer and ultrafast base motions. Chem Sci 2022; 13:5230-5242. [PMID: 35655577 PMCID: PMC9093102 DOI: 10.1039/d1sc06450a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/09/2022] [Indexed: 12/03/2022] Open
Abstract
The photochemistry of DNA systems is characterized by the ultraviolet (UV) absorption of π-stacked nucleobases, resulting in exciton states delocalized over several bases. As their relaxation sensitively depends on local stacking conformations, disentangling the ensuing electronic and structural dynamics has remained an experimental challenge, despite their fundamental role in protecting the genome from potentially harmful UV radiation. Here we use transient absorption and transient absorption anisotropy spectroscopy with broadband femtosecond deep-UV pulses (250–360 nm) to resolve the exciton dynamics of UV-excited adenosine single strands under physiological conditions. Due to the exceptional deep-UV bandwidth and polarization sensitivity of our experimental approach, we simultaneously resolve the population dynamics, charge-transfer (CT) character and conformational changes encoded in the UV transition dipoles of the π-stacked nucleotides. Whilst UV excitation forms fully charge-separated CT excitons in less than 0.3 ps, we find that most decay back to the ground state via a back-electron transfer. Based on the anisotropy measurements, we propose that this mechanism is accompanied by a structural relaxation of the photoexcited base-stack, involving an inter-base rotation of the nucleotides. Our results finally complete the exciton relaxation mechanism for adenosine single strands and offer a direct view into the coupling of electronic and structural dynamics in aggregated photochemical systems. Despite its key role in DNA photochemistry, the decay mechanism of excitons in stacked bases has remained difficult to resolve. Ultrafast polarization spectroscopy now reveals a back-electron transfer and ultrafast base motions in adenosine strands.![]()
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Affiliation(s)
- Benjamin Bauer
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
| | - Rahul Sharma
- Laboratory for Computation and Visualization in Mathematics and Mechanics, École Polytechnique Fédérale de Lausanne, MATH-FSB CH-1015 Lausanne Switzerland
| | - Majed Chergui
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
| | - Malte Oppermann
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
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5
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Jones NC, Nielsen SB, Hoffmann SV. On the delocalization length in RNA single strands of cytosine: how many bases see the light? Phys Chem Chem Phys 2020; 22:2188-2192. [DOI: 10.1039/c9cp05292e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics.
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Affiliation(s)
- Nykola C. Jones
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
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6
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Reveguk ZV, Khoroshilov EV, Sharkov AV, Pomogaev VA, Buglak AA, Tarnovsky AN, Kononov AI. Exciton Absorption and Luminescence in i-Motif DNA. Sci Rep 2019; 9:15988. [PMID: 31690734 PMCID: PMC6831829 DOI: 10.1038/s41598-019-52242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/17/2019] [Indexed: 11/08/2022] Open
Abstract
We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.
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Affiliation(s)
- Zakhar V Reveguk
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Evgeny V Khoroshilov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991, Moscow, Russia
| | - Andrey V Sharkov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991, Moscow, Russia
| | - Vladimir A Pomogaev
- Department of Physics, Tomsk State University, Tomsk, 634050, Russia
- Department of Chemistry and Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University 1370 Sankyuk-dong, Buk-gu, Daegu, 702-701, Republic of Korea
| | - Andrey A Buglak
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Alexander N Tarnovsky
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Alexei I Kononov
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia.
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7
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Snyder JA, Charnay AP, Kohl FR, Zhang Y, Kohler B. DNA-like Photophysics in Self-Assembled Silver(I)–Nucleobase Nanofibers. J Phys Chem B 2019; 123:5985-5994. [PMID: 31283245 DOI: 10.1021/acs.jpcb.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Joshua A. Snyder
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Aaron P. Charnay
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Forrest R. Kohl
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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8
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Abstract
Using as a model the single adenine strand (dA)20, we study the ultrafast evolution of electronic excitations in DNA with a time resolution of 30 fs. Our transient absorption spectra in the UV and visible spectral domains show that internal conversion among photogenerated exciton states occurs within 100 fs. Subsequently, the ππ* states acquire progressively charge-transfer character before being completely trapped, within 3 ps, by fully developed charge-transfer states corresponding to transfer of an electron from one adenine moiety to another (A+A-).
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Affiliation(s)
- Rocio Borrego-Varillas
- 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
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS , Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
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9
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Bauer B, Oppermann M, Chergui M. Exciton dynamics in DNA oligomers studied by broadband deep-UV transient absorption spectroscopy. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920510006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report broadband transient absorption measurements of adenine strands in the deep-UV (250-370 nm). By varying the strand length we resolve the interplay between inter-base stacking and exciton formation and dynamics in DNA oligomers.
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10
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Stange UC, Temps F. Ultrafast electronic deactivation of UV-excited adenine and its ribo- and deoxyribonucleosides and -nucleotides: A comparative study. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Volkov IL, Reveguk ZV, Serdobintsev PY, Ramazanov RR, Kononov AI. DNA as UV light-harvesting antenna. Nucleic Acids Res 2018; 46:3543-3551. [PMID: 29186575 PMCID: PMC6283424 DOI: 10.1093/nar/gkx1185] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 12/23/2022] Open
Abstract
The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.
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Affiliation(s)
- Ivan L Volkov
- St. Petersburg State University, St. Petersburg 199034, Russia
| | | | - Pavel Yu Serdobintsev
- St. Petersburg State University, St. Petersburg 199034, Russia
- St. Petersburg State Polytechnic University, St. Petersburg 195251, Russia
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12
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Marchetti B, Karsili TNV, Ashfold MNR, Domcke W. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs. Phys Chem Chem Phys 2018; 18:20007-27. [PMID: 26980149 DOI: 10.1039/c6cp00165c] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.
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Affiliation(s)
- Barbara Marchetti
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Tolga N V Karsili
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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13
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Segarra-Martí J, Jaiswal VK, Pepino AJ, Giussani A, Nenov A, Mukamel S, Garavelli M, Rivalta I. Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates. Faraday Discuss 2018; 207:233-250. [DOI: 10.1039/c7fd00201g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.
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Affiliation(s)
- Javier Segarra-Martí
- Univ Lyon, Ens de Lyon, CNRS
- Université Claude Bernard Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
| | - Vishal K. Jaiswal
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Ana Julieta Pepino
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Angelo Giussani
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Shaul Mukamel
- Department of Chemistry
- University of California
- Irvine
- USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Ivan Rivalta
- Univ Lyon, Ens de Lyon, CNRS
- Université Claude Bernard Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
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14
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Remington JM, Philip AM, Hariharan M, Kohler B. On the origin of multiexponential fluorescence decays from 2-aminopurine-labeled dinucleotides. J Chem Phys 2017; 145:155101. [PMID: 27782452 DOI: 10.1063/1.4964718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The fluorescent probe 2-aminopurine (2Ap) has been used for decades to study local conformational fluctuations in DNA. Steady-state and time-resolved measurements of 2Ap fluorescence have been used to predict specific conformational states through suitable modeling of the quenching of the fluorescence of a 2Ap residue incorporated site-specifically into a DNA strand. The success of this approach has been limited by a lack of understanding of the precise factors responsible for the complex, multiexponential decays observed experimentally. In this study, dinucleotides composed of 2Ap and adenine were studied by the time-correlated single-photon counting technique to investigate the causes of heterogeneous emission kinetics. Contrary to previous reports, we argue that emission from 2Ap that is stacked with a neighboring base contributes negligibly to the emission signals recorded more than 50 ps after excitation, which are instead dominated by emission from unstacked 2Ap. We find that the decay kinetics can be modeled using a continuous lifetime distribution, which arises from the inherent distance dependence of electron transfer rates without the need to postulate a small number of discrete states with decay times derived from multiexponential fits. These results offer a new perspective on the quenching of 2Ap fluorescence and expand the information that can be obtained from experiments.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
| | - Abbey M Philip
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Sreekaryam, Thiruvananthapuram, Kerala 695016, India
| | - Bern Kohler
- Department of Chemistry, Montana State University, Bozeman, Montana 59715, USA
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15
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Pola M, Kochman MA, Picchiotti A, Prokhorenko VI, Miller RJD, Thorwart M. Linear photoabsorption spectra and vertical excitation energies of microsolvated DNA nucleobases in aqueous solution. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [Formula: see text]-type states. Apart from a systematic blue shift of around [Formula: see text][Formula: see text]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [Formula: see text] and partial [Formula: see text] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.
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Affiliation(s)
- Martina Pola
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michal A. Kochman
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alessandra Picchiotti
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Valentyn I. Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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16
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Saha S, Quiney HM. Solvent effects on the excited state characteristics of adenine–thymine base pairs. RSC Adv 2017. [DOI: 10.1039/c7ra03244g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.
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Affiliation(s)
- S. Saha
- ARC Centre of Excellence for Advanced Molecular Imaging
- Theoretical Condensed Matter Physics Group
- School of Physics
- The University of Melbourne
- Australia
| | - H. M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging
- Theoretical Condensed Matter Physics Group
- School of Physics
- The University of Melbourne
- Australia
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17
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Prokhorenko VI, Picchiotti A, Pola M, Dijkstra AG, Miller RJD. New Insights into the Photophysics of DNA Nucleobases. J Phys Chem Lett 2016; 7:4445-4450. [PMID: 27786479 DOI: 10.1021/acs.jpclett.6b02085] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report the results of an extended time-resolved study of DNA nucleobases in aqueous solutions conducted in the deep UV using broad-band femtosecond transient absorption and electronic two-dimensional spectroscopies. We found that the photodeactivation in all DNA nucleobases occurs in two steps: fast relaxation (500-700 fs) from the excited state ππ* to a "dark" state and its depopulation to the ground state within 1-2 ps. Our experimental observations and performed theoretical modeling allow us to conclude that this dark state can be associated with the nπ* electronic state, which is connected to the excited and ground states via conical intersections.
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Affiliation(s)
- Valentyn I Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alessandra Picchiotti
- Max Planck Institute for the Structure and Dynamics of Matter , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Martina Pola
- Institute for Theoretical Physics, University of Hamburg , Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Arend G Dijkstra
- Max Planck Institute for the Structure and Dynamics of Matter , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter , Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry and Department of Physics, University of Toronto , 80 St. George Street, Toronto, Canada M5S 1H6
- The Hamburg Center for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
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18
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Skowron DJ, Zhang Y, Beckstead AA, Remington JM, Strawn M, Kohler B. Subnanosecond Emission Dynamics of AT DNA Oligonucleotides. Chemphyschem 2016; 17:3558-3569. [PMID: 27582073 DOI: 10.1002/cphc.201600566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/30/2016] [Indexed: 01/16/2023]
Abstract
UV radiation creates excited electronic states in DNA that can decay to mutagenic photoproducts. When excited states return to the electronic ground state, photochemical injury is avoided. Understanding of the available relaxation pathways has advanced rapidly during the past decade, but there has been persistent uncertainty, and even controversy, over how to compare results from transient absorption and time-resolved emission experiments. Here, emission from single- and double-stranded AT DNA compounds excited at 265 nm was studied in aqueous solution using the time-correlated single photon counting technique. There is quantitative agreement between the emission lifetimes ranging from 50 to 200 ps and ones measured in transient absorption experiments, demonstrating that both techniques probe the same excited states. The results indicate that excitations with lifetimes of more than a few picoseconds are weakly emissive excimer and charge transfer states. Only a minute fraction of excitations persist beyond 1 ns in AT DNA strands at room temperature.
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Affiliation(s)
- David J Skowron
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Ashley A Beckstead
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Jacob M Remington
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Madison Strawn
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
| | - Bern Kohler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717-3400, USA
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19
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Spata VA, Matsika S. Photophysical deactivation pathways in adenine oligonucleotides. Phys Chem Chem Phys 2016; 17:31073-83. [PMID: 26536353 DOI: 10.1039/c5cp04254b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work we study deactivation processes in adenine oligomers after absorption of UV radiation using Quantum Mechanics combined with Molecular Mechanics (QM/MM). Correlated electronic structure methods appropriate for describing the excited states are used to describe a π-stacked dimer of adenine bases incorporated into (dA)20(dT)20. The results of these calculations reveal three different types of excited state minima which play a role in deactivation processes. Within this set of minima there are minima where the excited state is localized on one adenine (monomer-like) as well as minima where the excited state is delocalized on two adenines, forming different types of excimers and bonded excimers of varying but inter-related character. The proximity of their energies reveals that the minima can decay into one another along a flat potential energy surface dependent on the interbase separation. Additionally, analysis of the emissive energies and other physical properties, including theoretical anisotropy calculations, and comparison with fluorescence experiments, provides evidence that excimers play an important role in long-lived signals in adenine oligonucleotides while the subpicosecond decay is attributed to monomer-like minima. The necessity for a close approach of the nucleobases reveals that the deactivation mechanism is tied to macro-molecular motion.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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20
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Benda Z, Szalay PG. Characterization of the excited states of DNA building blocks: a coupled cluster computational study. Phys Chem Chem Phys 2016; 18:23596-606. [PMID: 27506397 DOI: 10.1039/c6cp02969h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DNA building blocks consisting of up to four nucleobases are investigated using the EOM-CCSD and CC2-LR methods in two B-DNA-like arrangements of a poly-adenine:poly-thymine (poly-A:poly-T) system. Excitation energies and oscillator strengths are presented and the characteristics of the excited states are discussed. Excited states of single-stranded poly-A systems are highly delocalized, especially the spectroscopically bright states, where delocalization over up to four fragments can be observed. In the case of poly-T systems, the states are somewhat less delocalized, extending to maximally about three fragments. A single A:T Watson-Crick pair has highly localized states, while delocalization over base pairs can be observed for some excited states of the (A)2:(T)2 system, but intrastrand delocalization is more pronounced in this case, as well. As for the characteristics of the simulated UV absorption spectra, a significant decrease of intensity can be observed in the case of single strands with increasing chain length; this is due to the stacking interactions and is in accordance with previous results. On the other hand, the breaking of H-bonds between the two strands does not alter the spectral intensity considerably, it only causes a redshift of the absorption band, thus it is unable to explain the experimentally observed DNA hyperchromism on its own, and stacking interactions need to be considered for the description of this effect as well.
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Affiliation(s)
- Zsuzsanna Benda
- Institute of Chemistry, Eötvös University, H-1518 Budapest, P.O. Box 32, Hungary.
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21
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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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22
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Li Q, Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Voityuk AA, Mukamel S, Roca-Sanjuán D, Garavelli M, Blancafort L. Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate. Chemistry 2016; 22:7497-507. [PMID: 27113273 PMCID: PMC5021121 DOI: 10.1002/chem.201505086] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 02/04/2023]
Abstract
The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.
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Affiliation(s)
- Quansong Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, 100081, Beijing, P.R. China
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Ivan Rivalta
- Univ Lyon, >Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France
| | - Alexander A Voityuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilvi, 17071, Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California, 92697-2025, USA
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, 46071, Valencia, Spain
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, 40126, Bologna, Italy.
- Univ Lyon, >Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France.
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilvi, 17071, Girona, Spain.
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23
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Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Tolomelli A, Mukamel S, Garavelli M. Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1867-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Spata VA, Lee W, Matsika S. Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides. J Phys Chem Lett 2016; 7:976-984. [PMID: 26911276 DOI: 10.1021/acs.jpclett.5b02756] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Wook Lee
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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25
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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26
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Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF, Mukamel S, Garavelli M. Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations. Faraday Discuss 2015; 177:345-62. [PMID: 25607949 DOI: 10.1039/c4fd00175c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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27
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Nenov A, Giussani A, Segarra-Martí J, Jaiswal VK, Rivalta I, Cerullo G, Mukamel S, Garavelli M. Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy. J Chem Phys 2015; 142:212443. [PMID: 26049463 DOI: 10.1063/1.4921016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pump-probe electronic spectroscopy using femtosecond laser pulses has evolved into a standard tool for tracking ultrafast excited state dynamics. Its two-dimensional (2D) counterpart is becoming an increasingly available and promising technique for resolving many of the limitations of pump-probe caused by spectral congestion. The ability to simulate pump-probe and 2D spectra from ab initio computations would allow one to link mechanistic observables like molecular motions and the making/breaking of chemical bonds to experimental observables like excited state lifetimes and quantum yields. From a theoretical standpoint, the characterization of the electronic transitions in the visible (Vis)/ultraviolet (UV), which are excited via the interaction of a molecular system with the incoming pump/probe pulses, translates into the determination of a computationally challenging number of excited states (going over 100) even for small/medium sized systems. A protocol is therefore required to evaluate the fluctuations of spectral properties like transition energies and dipole moments as a function of the computational parameters and to estimate the effect of these fluctuations on the transient spectral appearance. In the present contribution such a protocol is presented within the framework of complete and restricted active space self-consistent field theory and its second-order perturbation theory extensions. The electronic excited states of adenine have been carefully characterized through a previously presented computational recipe [Nenov et al., Comput. Theor. Chem. 1040-1041, 295-303 (2014)]. A wise reduction of the level of theory has then been performed in order to obtain a computationally less demanding approach that is still able to reproduce the characteristic features of the reference data. Foreseeing the potentiality of 2D electronic spectroscopy to track polynucleotide ground and excited state dynamics, and in particular its expected ability to provide conformational dependent fingerprints in dimeric systems, the performances of the selected reduced level of calculations have been tested in the construction of 2D electronic spectra for the in vacuo adenine monomer and the unstacked adenine homodimer, thereby exciting the Lb/La transitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Vishal K Jaiswal
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Ivan Rivalta
- Université de Lyon, CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo Da Vinci 32, IT-20133 Milano, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
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28
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Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate. Front Chem 2015; 3:29. [PMID: 25941671 PMCID: PMC4403598 DOI: 10.3389/fchem.2015.00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023] Open
Abstract
The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.
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Affiliation(s)
| | | | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
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29
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Zhang Y, Dood J, Beckstead AA, Li XB, Nguyen KV, Burrows CJ, Improta R, Kohler B. Photoinduced Electron Transfer in DNA: Charge Shift Dynamics Between 8-Oxo-Guanine Anion and Adenine. J Phys Chem B 2015; 119:7491-502. [PMID: 25660103 DOI: 10.1021/jp511220x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Femtosecond time-resolved IR spectroscopy is used to investigate the excited-state dynamics of a dinucleotide containing an 8-oxoguanine anion at the 5'-end and neutral adenine at the 3'-end. UV excitation of the dinucleotide transfers an electron from deprotonated 8-oxoguanine to its π-stacked neighbor adenine in less than 1 ps, generating a neutral 8-oxoguanine radical and an adenine radical anion. These species are identified by the excellent agreement between the experimental and calculated IR difference spectra. The quantum efficiency of this ultrafast charge shift reaction approaches unity. Back electron transfer from the adenine radical anion to the 8-oxguanine neutral radical occurs in 9 ps, or approximately 6 times faster than between the adenine radical anion and the 8-oxoguanine radical cation (Zhang, Y. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 11612-11617). The large asymmetry in forward and back electron transfer rates is fully rationalized by semiclassical nonadiabatic electron transfer theory. Forward electron transfer is ultrafast because the driving force is nearly equal to the reorganization energy, which is estimated to lie between 1 and 2 eV. Back electron transfer is highly exergonic and takes place much more slowly in the Marcus inverted region.
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Affiliation(s)
- Yuyuan Zhang
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, 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
| | - Xi-Bo Li
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Khiem V Nguyen
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Cynthia J Burrows
- ‡Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Roberto Improta
- §CNR-Consiglio Nazionale delle Ricerche Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, 80136 Napoli, Italy
| | - Bern Kohler
- †Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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30
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Conti I, Nenov A, Höfinger S, Flavio Altavilla S, Rivalta I, Dumont E, Orlandi G, Garavelli M. Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back. Phys Chem Chem Phys 2015; 17:7291-302. [DOI: 10.1039/c4cp05546b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
La and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Siegfried Höfinger
- Zentraler Informatikdienst
- Technische Universität Wien
- 1040 Wien, Austria
- Department of Physics
- Michigan Technological University
| | | | - Ivan Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07, France
| | - Elise Dumont
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
- Lyon, France
| | - Giorgio Orlandi
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
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31
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Lin SH, Fujitsuka M, Ishikawa M, Majima T. Driving force dependence of charge separation and recombination processes in dyads of nucleotides and strongly electron-donating oligothiophenes. J Phys Chem B 2014; 118:12186-91. [PMID: 25265410 DOI: 10.1021/jp509691f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Charge transfer in DNA has attracted great attention of scientists because of its importance in biological processes. However, our knowledge on excess-electron transfer in DNA still remains limited in comparison to numerous studies of hole transfer in DNA. To clarify the dynamics of excess-electron transfer in DNA by photochemical techniques, new electron-donating photosensitizers should be developed. Herein, a terthiophene and two 3,4-ethylenedioxythiophene oligomers were used as photosensitizers in dyads including natural nucleobases as electron acceptors. The charge separation and recombination processes in the dyads were investigated by femtosecond laser flash photolysis, and the driving force dependence of these rate constants was discussed on the basis of the Marcus theory. From this study, the conformation effect on charge recombination process was found. We expect that 3,4-ethylenedioxythiophene oligomers are useful in investigation of excess-electron-transfer dynamics in DNA.
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Affiliation(s)
- Shih-Hsun Lin
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University , Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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32
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Spata VA, Matsika S. Role of excitonic coupling and charge-transfer states in the absorption and CD spectra of adenine-based oligonucleotides investigated through QM/MM simulations. J Phys Chem A 2014; 118:12021-30. [PMID: 25184994 DOI: 10.1021/jp507520c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this work, we study the photophysical properties of an adenine-based oligonucleotide using an ensemble of about 200 configurations obtained from molecular dynamics simulations. Specifically, a QM/MM approach is used to obtain the excited-state energies and properties of (dA)20(dT)20 with a dimer of π-stacked adenine bases included in the quantum region. The absorption and circular dichroism spectra are computed and analyzed using the algebraic diagrammatic construction through second order level of theory method (ADC(2)) combined with classical mechanics. We find that the experimentally observed red-shifted shoulder in the absorption spectrum is due to excitonic interactions, while charge-transfer states are present within the absorption band at the higher-energy end of the spectrum. More importantly, low-energy states with charge-transfer mixing exist, which could lead to excimers and bonded excimers. These observations suggest that mixing between charge-transfer and excitonic states plays an important role in the photophysics of oligonucleotides. They also highlight the importance of taking into account the conformational flexibility of the oligonucleotide when investigating photophysical properties.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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33
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Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide. Proc Natl Acad Sci U S A 2014; 111:11612-7. [PMID: 25071180 DOI: 10.1073/pnas.1404411111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
During the early evolution of life, 8-oxo-7,8-dihydro-2'-deoxyguanosine (O) may have functioned as a proto-flavin capable of repairing cyclobutane pyrimidine dimers in DNA or RNA by photoinduced electron transfer using longer wavelength UVB radiation. To investigate the ability of O to act as an excited-state electron donor, a dinucleotide mimic of the FADH2 cofactor containing O at the 5'-end and 2'-deoxyadenosine at the 3'-end was studied by femtosecond transient absorption spectroscopy in aqueous solution. Following excitation with a UV pulse, a broadband mid-IR pulse probed vibrational modes of ground-state and electronically excited molecules in the double-bond stretching region. Global analysis of time- and frequency-resolved transient absorption data coupled with ab initio quantum mechanical calculations reveal vibrational marker bands of nucleobase radical ions formed by electron transfer from O to 2'-deoxyadenosine. The quantum yield of charge separation is 0.4 at 265 nm, but decreases to 0.1 at 295 nm. Charge recombination occurs in 60 ps before the O radical cation can lose a deuteron to water. Kinetic and thermodynamic considerations strongly suggest that all nucleobases can undergo ultrafast charge separation when π-stacked in DNA or RNA. Interbase charge transfer is proposed to be a major decay pathway for UV excited states of nucleic acids of great importance for photostability as well as photoredox activity.
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34
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Chen J, Kohler B. Base stacking in adenosine dimers revealed by femtosecond transient absorption spectroscopy. J Am Chem Soc 2014; 136:6362-72. [PMID: 24735123 DOI: 10.1021/ja501342b] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Excitons formed in DNA by UV absorption decay via poorly understood pathways that can culminate in mutagenic photoproducts. In order to gain insight into how base stacking influences UV excited states in DNA, five dinucleosides composed of adenosine or 2'-deoxyadenosine units joined by flexible linkers were studied by femtosecond transient absorption spectroscopy. In aqueous solution, transient absorption signals recorded at pump and probe wavelengths of 267 and 250 nm, respectively, show that UV absorption produces excimer states in all dimers that decay orders of magnitude more slowly than excitations in a single adenine nucleotide. Adding methanol as a cosolvent disrupts π-π stacking of the adenine moieties and causes the excimer states in all five dinucleosides to vanish for a methanol concentration of 80% by volume. These observations confirm that base stacking is an essential requirement for the slow decay channel seen in these and other DNA model compounds. This channel appears to be insensitive to the precise stacking conformation at the instant of photon absorption as long as the bases are cofacially stacked. Notably, circular dichroism (CD) spectra of several of the dinucleosides are weak and monomer-like and lack the exciton coupling that has been emphasized in the past as an indicator of base-stacked structure. For these dimers, the coupled transition dipole moments of the two adenines are proposed to adopt left- and right-handed arrangements upon stacking with roughly equal probability. Although the mechanism behind slow nonradiative decay in DNA is still uncertain, these results show that the signature of these states in transient absorption experiments can be a more reliable diagnostic of base stacking than the occurrence of exciton-coupled CD signals. These observations also draw attention to the important role the backbone plays in producing structures with axial (helical) chirality.
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Affiliation(s)
- Jinquan Chen
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717-3400, United States
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35
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Charge separation and charge delocalization identified in long-living states of photoexcited DNA. Proc Natl Acad Sci U S A 2014; 111:4369-74. [PMID: 24616517 DOI: 10.1073/pnas.1323700111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Base stacking in DNA is related to long-living excited states whose molecular nature is still under debate. To elucidate the molecular background we study well-defined oligonucleotides with natural bases, which allow selective UV excitation of one single base in the strand. IR probing in the picosecond regime enables us to dissect the contribution of different single bases to the excited state. All investigated oligonucleotides show long-living states on the 100-ps time scale, which are not observable in a mixture of single bases. The fraction of these states is well correlated with the stacking probabilities and reaches values up to 0.4. The long-living states show characteristic absorbance bands that can be assigned to charge-transfer states by comparing them to marker bands of radical cation and anion spectra. The charge separation is directed by the redox potential of the involved bases and thus controlled by the sequence. The spatial dimension of this charge separation was investigated in longer oligonucleotides, where bridging sequences separate the excited base from a sensor base with a characteristic marker band. After excitation we observe a bleach of all involved bases. The contribution of the sensor base is observable even if the bridge is composed of several bases. This result can be explained by a charge delocalization along a well-stacked domain in the strand. The presence of charged radicals in DNA strands after light absorption may cause reactions--oxidative or reductive damage--currently not considered in DNA photochemistry.
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36
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Chatterley AS, West CW, Roberts GM, Stavros VG, Verlet JRR. Mapping the Ultrafast Dynamics of Adenine onto Its Nucleotide and Oligonucleotides by Time-Resolved Photoelectron Imaging. J Phys Chem Lett 2014; 5:843-848. [PMID: 26274076 DOI: 10.1021/jz500264c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The intrinsic photophysics of nucleobases and nucleotides following UV absorption presents a key reductionist step toward understanding the complex photodamage mechanisms occurring in DNA. The decay mechanism of adenine in particular has been the focus of intense investigation, as has how these correlate to those of its more biologically relevant nucleotide and oligonucleotides in aqueous solution. Here, we report on time-resolved photoelectron imaging of the deprotonated 3'-deoxy-adenosine-5'-monophosphate nucleotide and the adenosine di- and trinucleotides. Through a comparison of gas- and solution-phase experiments and available theoretical studies, the dynamics of the base are shown to be relatively insensitive to the surrounding environment. The decay mechanism primarily involves internal conversion from the initially populated (1)ππ* states to the ground state. The relaxation dynamics of the adenosine oligonucleotides are similar to those of the nucleobase, in contrast to the aqueous oligonucleotides, where a fraction of the ensemble forms long-lived excimer states.
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Affiliation(s)
- Adam S Chatterley
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christopher W West
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
| | - Gareth M Roberts
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vasilios G Stavros
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jan R R Verlet
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
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37
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Law YK, Forties RA, Liu X, Poirier MG, Kohler B. Sequence-dependent thymine dimer formation and photoreversal rates in double-stranded DNA. Photochem Photobiol Sci 2014; 12:1431-9. [PMID: 23727985 DOI: 10.1039/c3pp50078k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The kinetics of thymine-thymine cyclobutane pyrimidine dimer (TT-CPD) formation was studied at 23 thymine-thymine base steps in two 247-base pair DNA sequences irradiated at 254 nm. Damage was assayed site-specifically and simultaneously on both the forward and reverse strands by detecting emission from distinguishable fluorescent labels at the 5'-termini of fragments cleaved at CPD sites by T4 pyrimidine dimer glycosylase and separated by gel electrophoresis. The total DNA strand length of nearly 1000 bases made it possible to monitor damage at all 9 tetrads of the type XTTY, where X and Y are non-thymine bases. TT-CPD yields for different tetrads were found to vary by as much as an order of magnitude, but similar yields were observed at all instances of a given tetrad. Kinetic analysis of CPD formation at 23 distinct sites reveals that both the formation and reversal photoreactions depend sensitively on the identity of the nearest-neighbour bases on the 5' and the 3' side of a photoreactive TT base step. The lowest formation and reversal rates occur when two purine bases flank a TT step, while the highest formation and reversal rates are observed for tetrads with at least one flanking C. Overall, the results show that the probabilities of CPD formation and photoreversal depend principally on interactions with nearest-neighbour bases.
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Affiliation(s)
- Yu Kay Law
- Biophysics Program, The Ohio State University, Columbus, OH, USA
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38
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Nielsen LM, Hoffmann SV, Nielsen SB. Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated. Photochem Photobiol Sci 2014; 12:1273-85. [PMID: 23545881 DOI: 10.1039/c3pp25438k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.
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39
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Plasser F, Lischka H. Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution. Photochem Photobiol Sci 2014; 12:1440-52. [PMID: 23737069 DOI: 10.1039/c3pp50032b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The excited states and potential surfaces of the adenine dinucleotide are analyzed in gas phase and in solution using a correlated ab initio methodology in a QM/MM framework. In agreement with previous studies, a rather flat S1 surface with a number of minima of different character is found. Specifically, our results suggest that exciplexes with remarkably short intermolecular separation down to ~2.0 Å are formed. A detailed analysis shows that due to strong orbital interactions their character differs significantly from any states present in the Franck-Condon region. The lowest S1 energy minimum is a ππ* exciplex with only a small amount of charge transfer. It possesses appreciable oscillator strength with a polarization almost perpendicular to the planes of the two adenine molecules.
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Affiliation(s)
- Felix Plasser
- Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria.
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40
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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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41
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Stuhldreier MC, Temps F. Ultrafast photo-initiated molecular quantum dynamics in the DNA dinucleotide d(ApG) revealed by broadband transient absorption spectroscopy. Faraday Discuss 2013; 163:173-88; discussion 243-75. [PMID: 24020202 DOI: 10.1039/c3fd00003f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ultrafast photo-initiated quantum dynamics of the adenine-guanine dinucleotide d(ApG) in aqueous solution (pH 7) has been studied by femtosecond time-resolved spectroscopy after excitation at lambda = 260 nm. The results reveal a hierarchy of processes on time scales from tau < 100 fs to tau > 100 ps. Characteristic spectro-temporal signatures are observed indicating the transformation of the molecules in the electronic relaxation from the photo-excited state to a long-lived exciplex. In particular, broadband UV/VIS excited-state absorption (ESA) measurements detected a distinctive absorption by the excited dinucleotide around lambda = 335 nm, approximately 0.5 eV to the blue compared to the maximum of the broad and unstructured ESA spectrum after excitation of an equimolar mixture of the mononucleotides dAMP and dGMP. A similar feature has been identified as signature of the excimer in the dynamics of the adenine dinucleotide d(ApA). The lifetime of the d(ApG) exciplex was found to be tau = 124 +/- 4 ps both from the ESA decay time and from the ground-state recovery time, far longer than the sub-picosecond lifetimes of excited dAMP or dGMP. Fluorescence-time profiles measured by the up-conversion technique indicate that the exciplex state is reached around approximately 6 ps after excitation. Very weak residual fluorescence at longer times red-shifted to the emission from the photo-excited state shows that the exciplex is almost optically dark, but still has enough oscillator strength to give rise to the dual fluorescence of the dinucleotide in the static fluorescence spectrum.
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Affiliation(s)
- Mayra C Stuhldreier
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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42
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D'Abramo M, Castellazzi CL, Orozco M, Amadei A. On the nature of DNA hyperchromic effect. J Phys Chem B 2013; 117:8697-704. [PMID: 23799235 DOI: 10.1021/jp403369k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A combined theoretical-experimental study of the hyperchromic effect as occurring in the denaturation of a double stranded polyA-polyT is presented. Our theoretical/computational procedure allows us to reproduce the essential features of the experimental spectra and to characterize those molecular interactions responsible for the changes in the UV absorbance. We found that although excitonic intrastrand interactions strongly affect the absorbance, they are almost fully maintained in the single-stranded DNA. Our data indicate that hyperchromic effect originates from the higher delocalization of the excitonic states in the denaturated DNA with respect to the double-stranded conformation.
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43
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Chen J, Thazhathveetil AK, Lewis FD, Kohler B. Ultrafast Excited-State Dynamics in Hexaethyleneglycol-Linked DNA Homoduplexes Made of A·T Base Pairs. J Am Chem Soc 2013; 135:10290-3. [DOI: 10.1021/ja4049459] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jinquan Chen
- Department of Chemistry and
Biochemistry, Montana State University,
P.O. Box 173400, Bozeman, Montana 59717, United States
| | - Arun K. Thazhathveetil
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Bern Kohler
- Department of Chemistry and
Biochemistry, Montana State University,
P.O. Box 173400, Bozeman, Montana 59717, United States
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44
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Spata VA, Matsika S. Bonded Excimer Formation in π-Stacked 9-Methyladenine Dimers. J Phys Chem A 2013; 117:8718-28. [DOI: 10.1021/jp4033194] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vincent A. Spata
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
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45
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Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT. Excimer formation by stacking G-quadruplex blocks. Chemphyschem 2013; 14:2667-71. [PMID: 23780713 DOI: 10.1002/cphc.201300481] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Nguyen Thuan Dao
- School of Physical and Mathematical Science, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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46
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Santoro F, Improta R, Avila F, Segado M, Lami A. The interplay between neutral exciton and charge transfer states in single-strand polyadenine: a quantum dynamical investigation. Photochem Photobiol Sci 2013; 12:1527-43. [DOI: 10.1039/c3pp50111f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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47
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Voityuk AA. Effects of dynamic disorder on exciton delocalization and photoinduced charge separation in DNA. Photochem Photobiol Sci 2013; 12:1303-9. [DOI: 10.1039/c2pp25389e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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48
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Nielsen LM, Hoffmann SV, Brøndsted Nielsen S. Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments. Chem Commun (Camb) 2012; 48:10425-7. [PMID: 22983199 DOI: 10.1039/c2cc35201j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circular dichroism spectra (176-330 nm) of RNA adenine oligomers, (rA)(n) (n = 1-10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands.
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49
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