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Petropoulos V, Martinez-Fernandez L, Uboldi L, Maiuri M, Cerullo G, Balanikas E, Markovitsi D. Real-time observation of sub-100-fs charge and energy transfer processes in DNA dinucleotides. Chem Sci 2024; 15:12098-12107. [PMID: 39092131 PMCID: PMC11290326 DOI: 10.1039/d4sc02514h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/26/2024] [Indexed: 08/04/2024] Open
Abstract
Using as showcase the DNA dinucleotide 5'-dTpdG-3', in which the thymine (T) is located at the 5' end with respect to the guanine (G), we study the photoinduced electronic relaxation of coupled chromophores in solution with an unprecedented refinement. On the one hand, transient absorption spectra are recorded from 20 fs to 45 ps over the 330-650 nm range with a temporal resolution of 30 fs; on the other hand, quantum chemistry calculations determine the ground state geometry of the 4 possible conformers with stacked nucleobases, the associated Franck-Condon states, and map the relaxation pathways leading to excited state minima. Important spectral changes occurring before 100 fs are correlated with concomitant G+ → T- charge transfer and T → G energy transfer processes. The lifetime of the excited charge transfer state is only 5 ps and the absorption spectrum of a long-lived nπ*T state is detected. Our experimental results match the transient spectral properties computed for the anti-syn conformer of 5'-dTpdG-3', which is characterized by the lowest ground state energy and differs from that encountered in B-form duplexes.
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Affiliation(s)
- Vasilis Petropoulos
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Lara Martinez-Fernandez
- Instituto de Química Física Blas Cabrera, Consejo Superior de Investigaciones Científicas Calle Serrano 119 Madrid 28006 Spain
| | - Lorenzo Uboldi
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Margherita Maiuri
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano Piazza Leonardo da Vinci 32 I-20133 Milano Italy
- Istituto di Fotonica e Nanotecnologie-CNR Piazza Leonardo da Vinci 32 I-20133 Milano Italy
| | - Evangelos Balanikas
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva-4 Switzerland
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000 91405 Orsay France
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2
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Schrödter M, Wagenknecht HA. Natural Epigenetic DNA Modifications Cause Remote DNA Photodamage. J Am Chem Soc 2024. [PMID: 39037865 DOI: 10.1021/jacs.4c03883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
5-Formyl-2'-deoxycytidine, an intermediate during the erasure of epigenetic marker 5-methyl-2'-deoxycytidine, and 5-formyl-2'-deoxyuridine, an oxidative lesion of thymidine, are naturally occurring DNA modifications. The carbonyl groups of these DNA modifications are the smallest possible photosensitizers and have the potential to generate cyclobutane pyrimidine dimers upon irradiation with UV light. To evidence this damaging potential, ternary DNA architectures were used, in which the photosensitizer and the damage site were located at well-defined positions in the sequences. The quantitative and time-dependent analysis revealed not only the high photodamaging potential of both natural DNA modifications but also the mechanisms for this new pathway to photodamage. 5-Formyl-2'-deoxycytidine is more efficiently generating cyclobutane pyrimidine dimers than 5-formyl-2'-deoxyuridine because the latter is also photochemically converted to 5-carboxy-2'-deoxyuridine. This demonstrates for the first time that epigenetic DNA modifications regulating gene expression interact with sunlight and can induce DNA photodamages.
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Affiliation(s)
- Maren Schrödter
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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3
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Cadet J, Angelov D, Di Mascio P, Wagner JR. Contribution of oxidation reactions to photo-induced damage to cellular DNA. Photochem Photobiol 2024. [PMID: 38970297 DOI: 10.1111/php.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/08/2024]
Abstract
This review article is aimed at providing updated information on the contribution of immediate and delayed oxidative reactions to the photo-induced damage to cellular DNA/skin under exposure to UVB/UVA radiations and visible light. Low-intensity UVC and UVB radiations that operate predominantly through direct excitation of the nucleobases are very poor oxidizing agents giving rise to very low amounts of 8-oxo-7,8-dihydroguanine and DNA strand breaks with respect to the overwhelming bipyrimidine dimeric photoproducts. The importance of these two classes of oxidatively generated damage to DNA significantly increases together with a smaller contribution of oxidized pyrimidine bases upon UVA irradiation. This is rationalized in terms of sensitized photooxidation reactions predominantly mediated by singlet oxygen together with a small contribution of hydroxyl radical that appear to also be implicated in the photodynamic effects of the blue light component of visible light. Chemiexcitation-mediated formation of "dark" cyclobutane pyrimidine dimers in UVA-irradiated melanocytes is a recent major discovery that implicates in the initial stage, a delayed generation of reactive oxygen and nitrogen species giving rise to triplet excited carbonyl intermediate and possibly singlet oxygen. High-intensity UVC nanosecond laser radiation constitutes a suitable source of light to generate pyrimidine and purine radical cations in cellular DNA via efficient biphotonic ionization.
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Affiliation(s)
- Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LMBC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University, Balçova, Izmir, Turkey
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - J Richard Wagner
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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4
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Martínez-Fernández L, Green JA, Esposito L, Jouybari MY, Zhang Y, Santoro F, Kohler B, Improta R. The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study. Chem Sci 2024; 15:9676-9693. [PMID: 38939156 PMCID: PMC11206432 DOI: 10.1039/d4sc00910j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024] Open
Abstract
Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - James Alexander Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main Frankfurt am Main Germany
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
| | - Martha Yaghoubi Jouybari
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
- National Research Council of Canada 100 Sussex Drive Ottawa Ontario K1A 0R6 Canada
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
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5
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Lizondo-Aranda P, Gustavsson T, Martínez-Fernández L, Improta R, Lhiaubet-Vallet V. The Excited State Dynamics of a Mutagenic Guanosine Etheno Adduct Investigated by Femtosecond Fluorescence Spectroscopy and Quantum Mechanical Calculations. Chemistry 2024:e202401835. [PMID: 38869969 DOI: 10.1002/chem.202401835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Femtosecond fluorescence upconversion experiments were combined with CASPT2 and time dependent DFT calculations to characterize the excited state dynamics of the mutagenic etheno adduct 1,N2-etheno-2'-deoxyguanosine (ϵdG). This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The ϵdG fluorescence is strongly modified with respect to that of the canonical nucleoside dG, notably by an about 6-fold increase in fluorescence lifetime and quantum yield at neutral pH. In addition, femtosecond fluorescence upconversion experiments reveal the presence of two emission bands with maxima at 335 nm for the shorter-lived and 425 nm for the longer-lived. Quantum mechanical calculations rationalize these findings and provide absorption and fluorescence spectral shapes similar to the experimental ones. Two different bright minima are located on the potential energy surface of the lowest energy singlet excited state. One planar minimum, slightly more stable, is associated with the emission at 335 nm, whereas the other one, with a bent etheno ring, is associated with the red-shifted emission.
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Affiliation(s)
- Paloma Lizondo-Aranda
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de Valencia, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, Valencia, 46022, Spain
| | | | - Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, IQF-CSIC, Calle Serrano 119, 28006, Madrid, Spain
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via De Amicis 95, I-80145, Napoli, Italy
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de Valencia, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, Valencia, 46022, Spain
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6
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Herb D, Rossini M, Ankerhold J. Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence. Phys Rev E 2024; 109:064413. [PMID: 39020927 DOI: 10.1103/physreve.109.064413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/21/2024] [Indexed: 07/20/2024]
Abstract
After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.
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Baweja S, Kalal B, Maity S. Spectroscopic Characterization of Hydrogen-Bonded 2,7-Diazaindole Water Complex Isolated in the Gas Phase. J Phys Chem A 2024; 128:3329-3338. [PMID: 38652167 DOI: 10.1021/acs.jpca.4c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a systematic experimental analysis of the 1:1 complex of 2,7-diazaindole (27DAI) with water in the gas phase. The complex was characterized by using two-color-resonant two-photon ionization (R2PI), laser-induced fluorescence (LIF), single vibronic level fluorescence (SVLF), and photoionization efficiency (PIE) spectroscopic methods. The 000 band of the S1←S0 electronic transition of the 27DAI-H2O complex was observed at 33,074 cm-1, largely red-shifted by 836 cm-1 compared to that of the bare 27DAI. From the R2PI spectrum, the detected modes at 141 (ν'Tx), 169 (ν'Ty), and 194 (ν'Ry) cm-1 were identified as the internal motions of the H2O molecule in the complex. However, these modes were detected at 115 (ν″Tx), 152 (ν″Ty), and 190 (ν″Ry) cm-1 in the ground state, which suggested a stronger hydrogen bonding interaction in the photo-excited state. The structural determination was aided by the detection of νNH and νOH values in the ground and excited state complexes using the FDIR and IDIR spectroscopies. The detection of νNH at 3414 and νOH at 3447 cm-1 in 27DAI-H2O has shown an excellent correlation with the most stable structure consisting of N(1)-H···O and OH···N(7) hydrogen-bonded bridging water molecule in the ground state. The structure of the complex in the electronic excited state (S1) was confirmed by the corresponding bands at 3210 (νNH) and 3265 cm-1 (νOH). The IR-UV hole-burning spectroscopy confirmed the presence of only one isomer in the molecular beam. The ionization energy (IE) of the 27DAI-H2O complex was obtained as 8.789 ± 0.002 eV, which was significantly higher than the 7AI-H2O complex. The higher IE values of N-rich molecules suggest a higher resistivity of such molecules against photodamage. The obtained structure of the 27DAI-H2O complex has explicitly shown the formation of a cyclic one-solvent bridge incorporating N(1)-H···O and O-H···N(7) hydrogen bonds upon microsolvation. The lower excitation and higher ionization energies of the 27DAI-H2O complex compared to 7AI-H2O established higher stabilization of N-rich molecules. The solvent clusters forming a linear bridge between the hydrogen/proton acceptor and donor sites in the complex can be considered as a stepping stone to investigate the photoinduced deactivation mechanisms in nitrogen containing biologically relevant molecules.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Bhavika Kalal
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Surajit Maity
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
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8
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Chang XP, Wang JL, Peng LY, Cen XJ, Yin BW, Xie BB. Mechanistic photophysics of tellurium-substituted cytosine: Electronic structure calculations and nonadiabatic dynamics simulations. Photochem Photobiol 2024; 100:339-354. [PMID: 37435854 DOI: 10.1111/php.13835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
Previously, the MS-CASPT2 method was performed to study the static and qualitative photophysics of tellurium-substituted cytosine (TeC). To get quantitative information, we used our recently developed QTMF-FSSH dynamics method to simulate the excited-state decay of TeC. The CASSCF method was adopted to reduce the calculation costs, which was confirmed to provide reliable structures and energies as those of MS-CASPT2. A detailed structural analysis showed that only 5% trajectories will hop to the lower triplet or singlet state via the twisted (S2 /S1 /T2 )T intersection, while 67% trajectories will choose the planar intersections of (S2 /S1 /T3 /T2 /T1 )P and (S2 /S1 /T2 /T1 )P but subsequently become twisted in other electronic states. By contrast, ~28% trajectories will maintain in a plane throughout dynamics. Electronic population revealed that the S2 population will ultrafast transfer to the lower triplet or singlet state. Later, the TeC system will populate in the spin-mixed electronic states composed of S1 , T1 and T2 . At the end of 300 fs, most trajectories (~74%) will decay to the ground state and only 17.4% will survive in the triplet states. Our dynamics simulation verified that tellurium substitution will enhance the intersystem crossings, but the very short triplet lifetime (ca. 125 fs) will make TeC a less effective photosensitizer.
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Affiliation(s)
- Xue-Ping Chang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang, China
| | - Jie-Lei Wang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
| | - Ling-Ya Peng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Xu-Jiang Cen
- Ningbo Zhongtian Engineering Co., Ltd., Ningbo, China
| | - Bo-Wen Yin
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou, China
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9
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Ortiz-Rodríguez LA, Caldero-Rodríguez NE, Seth SK, Díaz-González K, Crespo-Hernández CE. Electronic relaxation mechanism of 9-methyl-2,6-diaminopurine and 2,6-diaminopurine-2'-deoxyribose in solution. Photochem Photobiol 2024; 100:393-403. [PMID: 38018292 DOI: 10.1111/php.13887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/16/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023]
Abstract
Prolonged ultraviolet exposure results in the formation of cyclobutane pyrimidine dimers (CPDs) in RNA. Consequently, prebiotic photolesion repair mechanisms should have played an important role in the maintenance of the structural integrity of primitive nucleic acids. 2,6-Diaminopurine is a prebiotic nucleobase that repairs CPDs with high efficiency when incorporated into polymers. We investigate the electronic deactivation pathways of 2,6-diaminopurine-2'-deoxyribose and 9-methyl-2,6-diaminopurine in acetonitrile and aqueous solution to shed light on the photophysical and excited state properties of the 2,6-diaminopurine chromophore. Evidence is presented that both are photostable compounds exhibiting similar deactivation mechanisms upon the population of the S1 (ππ* La ) state at 290 nm. The mechanism involves deactivation through the C2- and C6-reaction coordinates and >99% of the excited state population decays through nonradiative pathways involving two conical intersections with the ground state. The radiative and nonradiative lifetimes are longer in aqueous solution compared to acetonitrile. While τ1 is similar in both derivatives, τ2 is ca. 1.5-fold longer in 2,6-diaminopurine-2'-deoxyribose due to a more efficient trapping in the S1 (ππ* La ) minimum. Therefore, 2,6-diaminopurine could have accumulated in significant quantities during prebiotic times to be incorporated into non-canonical RNA and play a significant role in its photoprotection.
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Affiliation(s)
| | | | - Sourav Kanti Seth
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
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10
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Chen XR, Jiang WJ, Guo QH, Liu XY, Cui G, Li L. Theoretical insights into the photophysics of an unnatural base Z: A MS-CASPT2 investigation. Photochem Photobiol 2024; 100:380-392. [PMID: 38041414 DOI: 10.1111/php.13884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 12/03/2023]
Abstract
We have employed the highly accurate multistate complete active space second-order perturbation theory (MS-CASPT2) method to investigate the photoinduced excited state relaxation properties of one unnatural base, namely Z. Upon excitation to the S2 state of Z, the internal conversion to the S1 state would be dominant. From the S1 state, two intersystem crossing paths leading to the T2 and T1 states and one internal conversion path to the S0 state are possible. However, considering the large barrier to access the S1 /S0 conical intersection and the strong spin-orbit coupling between S1 and T2 states (>40 cm-1 ), the intersystem crossing to the triplet manifolds is predicted to be more preferred. Arriving at the T2 state, the internal conversion to the T1 state and the intersystem crossing back to the S1 state are both possible considering the S1 /T2 /T1 three-state intersection near the T2 minimum. Upon arrival at the T1 state, the deactivation to S0 can be efficient after overcoming a small barrier to access T1 /S0 crossing point, where the spin-orbit coupling (SOC) is as large as 39.7 cm-1 . Our present work not only provides in-depth insights into the photoinduced process of unnatural base Z, but can also help the future design of novel unnatural bases with better photostability.
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Affiliation(s)
- Xin-Rui Chen
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Wen-Jun Jiang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Qian-Hong Guo
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Laicai Li
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, China
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11
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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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12
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Bezabih MS, Kaliakin DS, Blanco-González A, Barneschi L, Tarnovsky AN, Olivucci M. Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories. J Phys Chem B 2023; 127:10871-10879. [PMID: 38055701 DOI: 10.1021/acs.jpcb.3c06433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.
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Affiliation(s)
- Meseret Simachew Bezabih
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Danil S Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Leonardo Barneschi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Alexander N Tarnovsky
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
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13
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Cuéllar-Zuquin J, Pepino AJ, Fdez. Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size. J Chem Theory Comput 2023; 19:8258-8272. [PMID: 37882796 PMCID: PMC10851440 DOI: 10.1021/acs.jctc.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
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Affiliation(s)
- Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Ana Julieta Pepino
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Francesco Aquilante
- Theory
and Simulation of Materials (THEOS), and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
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14
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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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15
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Crucilla SJ, Ding D, Lozano GG, Szostak JW, Sasselov DD, Kufner CL. UV-driven self-repair of cyclobutane pyrimidine dimers in RNA. Chem Commun (Camb) 2023; 59:13603-13606. [PMID: 37899697 DOI: 10.1039/d3cc04013e] [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: 10/31/2023]
Abstract
Nucleic acids can be damaged by ultraviolet (UV) irradiation, forming structural photolesions such as cyclobutane-pyrimidine-dimers (CPD). In modern organisms, sophisticated enzymes repair CPD lesions in DNA, but to our knowledge, no RNA-specific enzymes exist for CPD repair. Here, we show for the first time that RNA can protect itself from photolesions by an intrinsic UV-induced self-repair mechanism. This mechanism, prior to this study, has exclusively been observed in DNA and is based on charge transfer from CPD-adjacent bases. In a comparative study, we determined the quantum yields of the self-repair of the CPD-containing RNA sequence, GAU = U to GAUU (0.23%), and DNA sequence, d(GAT = T) to d(GATT) (0.44%), upon 285 nm irradiation via UV/Vis spectroscopy and HPLC analysis. After several hours of irradiation, a maximum conversion yield of ∼16% for GAU = U and ∼33% for d(GAT = T) was reached. We examined the dynamics of the intermediate charge transfer (CT) state responsible for the self-repair with ultrafast UV pump - IR probe spectroscopy. In the dinucleotides GA and d(GA), we found comparable quantum yields of the CT state of ∼50% and lifetimes on the order of several hundred picoseconds. Charge transfer in RNA strands might lead to reactions currently not considered in RNA photochemistry and may help understanding RNA damage formation and repair in modern organisms and viruses. On the UV-rich surface of the early Earth, these self-stabilizing mechanisms likely affected the selection of the earliest nucleotide sequences from which the first organisms may have developed.
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Affiliation(s)
- Sarah J Crucilla
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 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
| | - Gabriella G Lozano
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
| | - Jack W Szostak
- 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
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Dimitar D Sasselov
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
| | - Corinna L Kufner
- Harvard-Smithsonian Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138, USA.
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16
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Iwata T, Kurahashi Y, Wijaya IMM, Kandori H. Spectroscopic Investigation of Na +-Dependent Conformational Changes of a Cyclobutane Pyrimidine Dimer-Repairing Deoxyribozyme. ACS OMEGA 2023; 8:37274-37281. [PMID: 37841180 PMCID: PMC10569015 DOI: 10.1021/acsomega.3c05083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
UV1C is an enzymatically active DNA sequence (deoxyribozyme, DNAzyme) that functions as a cyclobutane pyrimidine dimer (CPD) photolyase. UV1C forms parallel guanine quadruplexes (G-quadruplexes) with a DNA substrate in the presence of 240 mM Na+, the structure of which is important for the enzymatic activity. To investigate the repair mechanism of CPD by UV1C, we designed light-induced Fourier transform infrared (FTIR) spectroscopy. Prior to FTIR measurements, circular dichroism (CD) spectroscopy was conducted to determine the Na+ concentration at which the most G-quadruplexes were formed. We found that UV1C also forms a hybrid G-quadruplex structure at over 500 mM Na+. By assuming a concentration equilibrium between G-quadruplexes and Na+, 1.3 and 1.8 Na+ were found to bind to parallel and hybrid G-quadruplexes, respectively. The hybrid G-quadruplex form of UV1C was also suggested to exhibit photolyase activity. Light-induced FTIR spectra recorded upon the photorepair of CPD by UV1C were compared for parallel G-quadruplex-rich and hybrid G-quadruplex-rich samples. Spectral variations were indicative of structural differences in parallel and hybrid G-quadruplexes before and after CPD cleavage. Differences were also observed when compared to the CPD repair spectrum by CPD photolyase. The spectral differences during CPD repair by either protein or DNAzyme suggest the local environment of the substrates, the surrounding protein, or the aqueous solution.
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Affiliation(s)
- Tatsuya Iwata
- Department
of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yuhi Kurahashi
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - I Made Mahaputra Wijaya
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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17
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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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18
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Jin P, Wang JN, Wang X, Jia M, Pan H, Mei Y, Chen J. Tracking the Early Stage of Triplet-Induced Photodamage in a DNA Dimer and Oligomer Containing 5-Methylcytosine. J Phys Chem B 2023; 127:6878-6886. [PMID: 37490365 DOI: 10.1021/acs.jpcb.3c02454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Methylation at the C5 position of cytosine, a naturally occurring epigenetic modification on DNA, shows a high correlation with mutational hotspots in disease such as skin cancer. Due to its essential biological relevance, numerous studies were devoted to confirming that the methylated sites favor the formation of the cyclobutane pyrimidine dimer (CPD), a well-known UV-induced lesion. However, photophysical and photochemical properties of dinucleotides and polynucleotides containing 5-methylcytosine (5mC) remain elusive. Herein, a charge transfer (CT) triplet state, generated via intersystem crossing (ISC) from a CT singlet state that enhanced after methylation on cytosine, is directly observed by using femtosecond transient absorption (TA) and time-resolved mid-infrared (TRIR) spectroscopy together with quantum chemical calculations for the first time in the T5mC dimer. Such an ISC process is quenched due to limitations of the ground-state geometries in 5mC-containing single-strand oligomer d(T5mC)9. This mechanistic information is important for understanding the early stage of triplet state-induced CPD formation in 5mC containing DNA.
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Affiliation(s)
- Peipei Jin
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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19
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Improta R. Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations. Int J Mol Sci 2023; 24:12614. [PMID: 37628797 PMCID: PMC10454157 DOI: 10.3390/ijms241612614] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.
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Affiliation(s)
- Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
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20
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Carr EC, Barton Q, Grambo S, Sullivan M, Renfro CM, Kuo A, Pangilinan J, Lipzen A, Keymanesh K, Savage E, Barry K, Grigoriev IV, Riekhof WR, Harris SD. Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche. G3 (BETHESDA, MD.) 2023; 13:jkad110. [PMID: 37221014 PMCID: PMC10411609 DOI: 10.1093/g3journal/jkad110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/25/2023]
Abstract
Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primar yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.
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Affiliation(s)
- Erin C Carr
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Quin Barton
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Sarah Grambo
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Mitchell Sullivan
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Cecile M Renfro
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Keykhosrow Keymanesh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Wayne R Riekhof
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Steven D Harris
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, USA
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21
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Jarupula R, Khodia S, Shabeeb M, Maity S. A combined spectroscopic and computational investigation on the solvent-to-chromophore excited-state proton transfer in the 2,2'-pyridylbenzimidazole-methanol complex. Phys Chem Chem Phys 2023. [PMID: 37337710 DOI: 10.1039/d3cp01742g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
This article demonstrates experimental proof of excited state 'solvent-to-chromophore' proton transfer (ESPT) in the isolated gas phase PBI (2,2'-pyridylbenzimidazole)-CH3OH complex, aided by computational calculations. The binary complexes of PBI with CH3OH/CH3OD were produced in a supersonic jet-cooled molecular beam and the energy barrier of the photo-excited process was determined using resonant two-colour two-photon ionization spectroscopy (R2PI). The ESPT process in the PBI-CH3OH complex was confirmed by the disappearance of the Franck-Condon active vibrational transitions above 000 + 390 cm-1. In the PBI-CH3OD complex, the reappearance of the Franck-Condon transitions till 000 + 800 cm-1 confirmed the elevation of the ESPT barrier upon isotopic substitution due to the lowering of the zero-point vibrational energy. The ESPT energy barrier in PBI-CH3OH was bracketed as 410 ± 20 cm-1 (4.91 ± 0.23 kJ mol-1) by comparing the spectra of PBI-CH3OH and PBI-CH3OD. The solvent-to-chromophore proton transfer was confirmed based on the significantly decreased quantum tunnelling of the solvent proton in the PBI-CH3OD complex. The computational investigation resulted in an energy barrier of 6.0 kJ mol-1 for the ESPT reaction in the PBI-CH3OH complex, showing excellent agreement with the experimental value. Overall, the excited state reaction progressed through an intersection of ππ* and nπ* states before being deactivated to the ground state via internal conversion. The present investigation reveals a novel reaction pathway for the deactivation mechanism of the photo-excited N-containing biomolecules in the presence of protic-solvents.
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Affiliation(s)
- Ramesh Jarupula
- Indian Institute of Technology Hyderabad, Department of Chemistry, Sangareddy, Telangana, 502284, India.
| | - Saurabh Khodia
- Indian Institute of Technology Hyderabad, Department of Chemistry, Sangareddy, Telangana, 502284, India.
| | - Muhammed Shabeeb
- Indian Institute of Technology Hyderabad, Department of Chemistry, Sangareddy, Telangana, 502284, India.
| | - Surajit Maity
- Indian Institute of Technology Hyderabad, Department of Chemistry, Sangareddy, Telangana, 502284, India.
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22
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Gonçalves LCP, Angelé-Martinez C, Premi S, Palmatier MA, Prado FM, Di Mascio P, Bastos EL, Brash DE. Chemiexcited Neurotransmitters and Hormones Create DNA Photoproducts in the Dark. ACS Chem Biol 2023; 18:484-493. [PMID: 36775999 PMCID: PMC10276651 DOI: 10.1021/acschembio.2c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
In DNA, electron excitation allows adjacent pyrimidine bases to dimerize by [2 + 2] cycloaddition, creating chemically stable but lethal and mutagenic cyclobutane pyrimidine dimers (CPDs). The usual cause is ultraviolet radiation. Alternatively, CPDs can be made in the dark (dCPDs) via chemically mediated electron excitation of the skin pigment melanin, after it is oxidized by peroxynitrite formed from the stress-induced radicals superoxide and nitric oxide. We now show that the dark process is not limited to the unusual structural molecule melanin: signaling biomolecules such as indolamine and catecholamine neurotransmitters and hormones can also be chemiexcited to energy levels high enough to form dCPDs. Oxidation of serotonin, dopamine, melatonin, and related biogenic amines by peroxynitrite created triplet-excited species, evidenced by chemiluminescence, energy transfer to a triplet-state reporter, or transfer to O2 resulting in singlet molecular oxygen. For a subset of these signaling molecules, triplet states created by peroxynitrite or peroxidase generated dCPDs at levels comparable to ultraviolet (UV). Neurotransmitter catabolism by monoamine oxidase also generated dCPDs. These results reveal a large class of signaling molecules as electronically excitable by biochemical reactions and thus potential players in deviant mammalian metabolism in the absence of light.
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Affiliation(s)
- Leticia C. P. Gonçalves
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520-8040, USA
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, SP, Brazil
- Present address: Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
| | - Carlos Angelé-Martinez
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520-8040, USA
| | - Sanjay Premi
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520-8040, USA
- Present address: Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Meg A. Palmatier
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520-8040, USA
| | - Fernanda Manso Prado
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, SP, Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, SP, Brazil
| | - Erick L. Bastos
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, SP, Brazil
| | - Douglas E. Brash
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520-8040, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, 06520-8028, USA
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23
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Chang XP, Zhao G, Zhang TS, Xie BB. Quantum mechanics/molecular mechanics studies on mechanistic photophysics of cytosine aza-analogues: 2,4-diamino-1,3,5-triazine and 2-amino-1,3,5-triazine in aqueous solution. Phys Chem Chem Phys 2023; 25:7669-7680. [PMID: 36857660 DOI: 10.1039/d2cp05639a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The excited-state properties and photophysics of cytosine aza-analogues, i.e., 2,4-diamino-1,3,5-triazine (2,4-DT) and 2-amino-1,3,5-triazine (2-AT) in solution have been systematically explored using the QM(MS-CASPT2//CASSCF)/MM approach. The excited-state nonradiative relaxation mechanisms for the initially photoexcited S1(ππ*) state decay back to the S0 state are proposed in terms of the present computed minima, surface crossings (conical intersections and singlet-triplet crossings), and excited-state decay paths in the S1, S2, T1, T2, and S0 states. Upon photoexcitation to the bright S1(ππ*) state, 2,4-DT quickly relaxes to its S1 minimum and then overcomes a small energy barrier of 5.1 kcal mol-1 to approach a S1/S0 conical intersection, where the S1 system hops to the S0 state through S1 → S0 internal conversion (IC). In addition, at the S1 minimum, the system could partially undergo intersystem crossing (ISC) to the T1 state, followed by further ISC to the S0 state via the T1/S0 crossing point. In the T1 state, an energy barrier of 7.9 kcal mol-1 will trap 2,4-DT for a while. In parallel, for 2-AT, the system first relaxes to the S1 minimum and then S1 → S0 IC or S1 → T1 → S0 ISCs take place to the S0 state by surmounting a large barrier of 15.3 kcal mol-1 or 11.9 kcal mol-1, respectively, which heavily suppress electronic transition to the S0 state. Different from 2,4-DT, upon photoexcitation in the Franck-Condon region, 2-AT can quickly evolve in an essentially barrierless manner to nearby S2/S1 conical intersection, where the S2 and T1 states can be populated. Once it hops to the S2 state, the system will overcome a relatively small barrier (6.6 kcal mol-1vs. 15.3 kcal mol-1) through IC to the S0 state. Similarly, an energy barrier of 11.9 kcal mol-1 heavily suppresses the T1 state transformation to the S0 state. The present work manifests that the amination/deamination of the triazine rings can affect some degree of different vertical and adiabatic excitation energies and nonradiative decay pathways in solution. It not only rationalizes excited-state decay dynamics of 2,4-DT and 2-AT in aqueous solution but could also provide insights into the understanding of the photophysics of aza-nucleobases.
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Affiliation(s)
- Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China.
| | - Geng Zhao
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China.
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou 311231, China
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24
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Ultrafast Photo-Ion Probing of the Relaxation Dynamics in 2-Thiouracil. Molecules 2023; 28:molecules28052354. [PMID: 36903604 PMCID: PMC10005304 DOI: 10.3390/molecules28052354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
In this work, we investigate the relaxation processes of 2-thiouracil after UV photoexcitation to the S2 state through the use of ultrafast, single-colour, pump-probe UV/UV spectroscopy. We place focus on investigating the appearance and subsequent decay signals of ionized fragments. We complement this with VUV-induced dissociative photoionisation studies collected at a synchrotron, allowing us to better understand and assign the ionisation channels involved in the appearance of the fragments. We find that all fragments appear when single photons with energy > 11 eV are used in the VUV experiments and hence appear through 3+ photon-order processes when 266 nm light is used. We also observe three major decays for the fragment ions: a sub-autocorrelation decay (i.e., sub-370 fs), a secondary ultrafast decay on the order of 300-400 fs, and a long decay on the order of 220 to 400 ps (all fragment dependent). These decays agree well with the previously established S2 → S1 → Triplet → Ground decay process. Results from the VUV study also suggest that some of the fragments may be created by dynamics occurring in the excited cationic state.
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25
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Gustavsson T, Markovitsi D. The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes. J Phys Chem Lett 2023; 14:2141-2147. [PMID: 36802626 DOI: 10.1021/acs.jpclett.2c03884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
During the past few years, several studies reported that a significant part of the intrinsic fluorescence of DNA duplexes decays with surprisingly long lifetimes (1-3 ns) at wavelengths shorter than the ππ* emission of their monomeric constituents. This high-energy nanosecond emission (HENE), hardly discernible in the steady-state fluorescence spectra of most duplexes, was investigated by time-correlated single-photon counting. The ubiquity of HENE contrasts with the paradigm that the longest-lived excited states correspond to low-energy excimers/exciplexes. Interestingly, the latter were found to decay faster than the HENE. So far, the excited states responsible for HENE remain elusive. In order to foster future studies for their characterization, this Perspective presents a critical summary of the experimental observations and the first theoretical approaches. Moreover, some new directions for further work are outlined. Finally, the obvious need for computations of the fluorescence anisotropy considering the dynamic conformational landscape of duplexes is stressed.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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26
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Brash DE, Goncalves LCP. Chemiexcitation: Mammalian Photochemistry in the Dark †. Photochem Photobiol 2023; 99:251-276. [PMID: 36681894 PMCID: PMC10065968 DOI: 10.1111/php.13781] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/18/2023] [Indexed: 01/23/2023]
Abstract
Light is one way to excite an electron in biology. Another is chemiexcitation, birthing a reaction product in an electronically excited state rather than exciting from the ground state. Chemiexcited molecules, as in bioluminescence, can release more energy than ATP. Excited states also allow bond rearrangements forbidden in ground states. Molecules with low-lying unoccupied orbitals, abundant in biology, are particularly susceptible. In mammals, chemiexcitation was discovered to transfer energy from excited melanin, neurotransmitters, or hormones to DNA, creating the lethal and carcinogenic cyclobutane pyrimidine dimer. That process was initiated by nitric oxide and superoxide, radicals triggered by ultraviolet light or inflammation. Several poorly understood chronic diseases share two properties: inflammation generates those radicals across the tissue, and cells that die are those containing melanin or neuromelanin. Chemiexcitation may therefore be a pathogenic event in noise- and drug-induced deafness, Parkinson's disease, and Alzheimer's; it may prevent macular degeneration early in life but turn pathogenic later. Beneficial evolutionary selection for excitable biomolecules may thus have conferred an Achilles heel. This review of recent findings on chemiexcitation in mammalian cells also describes the underlying physics, biochemistry, and potential pathogenesis, with the goal of making this interdisciplinary phenomenon accessible to researchers within each field.
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Affiliation(s)
- Douglas E. Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520-8028, USA
| | - Leticia C. P. Goncalves
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA
- Institut de Chimie de Nice CNRS UMR7272, Université Côte d’Azur, 28 Avenue Valrose 06108 Nice, France
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27
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Kufner CL, Krebs S, Fischaleck M, Philippou-Massier J, Blum H, Bucher DB, Braun D, Zinth W, Mast CB. Sequence dependent UV damage of complete pools of oligonucleotides. Sci Rep 2023; 13:2638. [PMID: 36788271 PMCID: PMC9929323 DOI: 10.1038/s41598-023-29833-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the sequence-dependent DNA damage formation requires probing a complete pool of sequences over a wide dose range of the damage-causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA to ultraviolet radiation at 266 nm and doses of up to 500 absorbed photons per base. At the dimer level, our results confirm existing literature values of photodamage, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow us to predict their abundance in high-UV environments.
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Affiliation(s)
- Corinna L. Kufner
- grid.38142.3c000000041936754XHarvard-Smithsonian Center for Astrophysics, Department of Astronomy, Harvard University, 60 Garden Street, Cambridge, MA 02138 USA
| | - Stefan Krebs
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Marlis Fischaleck
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Julia Philippou-Massier
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Helmut Blum
- grid.5252.00000 0004 1936 973XLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dominik B. Bucher
- grid.6936.a0000000123222966Chemistry Department, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Dieter Braun
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Wolfgang Zinth
- grid.5252.00000 0004 1936 973XBiomolecular Optics and Center for Integrated Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
| | - Christof B. Mast
- grid.5252.00000 0004 1936 973XSystems Biophysics, Ludwig Maximilians University Munich, Amalienstr. 54, 80799 Munich, Germany
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28
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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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29
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Heim ZN, Neumark DM. Nonadiabatic Dynamics Studied by Liquid-Jet Time-Resolved Photoelectron Spectroscopy. Acc Chem Res 2022; 55:3652-3662. [PMID: 36480155 DOI: 10.1021/acs.accounts.2c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of the liquid microjet technique by Faubel and co-workers has enabled the investigation of high vapor pressure liquids and solutions utilizing high-vacuum methods. One such method is photoelectron spectroscopy (PES), which allows one to probe the electronic properties of a sample through ionization in a state-specific manner. Liquid microjets consisting of pure solvents and solute-solvent systems have been studied with great success utilizing PES and, more recently, time-resolved PES (TRPES). Here, we discuss progress made over recent years in understanding the solvation and excited state dynamics of the solvated electron and nucleic acid constituents (NACs) using these methods, as well as the prospect for their future.The solvated electron is of particular interest in liquid microjet experiments as it represents the simplest solute system. Despite this simplicity, there were still many unresolved questions about its binding energy and excited state relaxation dynamics that are ideal problems for liquid microjet PES. In the work discussed in this Account, accurate binding energies were measured for the solvated electron in multiple high vapor pressure solvents. The advantages of liquid jet PES were further highlighted in the femtosecond excited state relaxation studies on the solvated electron in water where a 75 ± 20 fs lifetime attributable to internal conversion from the excited p-state to a hot ground state was measured, supporting a nonadiabatic relaxation mechanism.Nucleic acid constituents represent a class of important solutes with several unresolved questions that the liquid microjet PES method is uniquely suited to address. As TRPES is capable of tracking dynamics with state-specificity, it is ideal for instances where there are multiple excited states potentially involved in the dynamics. Time-resolved studies of NAC relaxation after excitation using ultraviolet light identified relaxation lifetimes from multiple excited states. The state-specific nature of the TRPES method allowed us to identify the lack of any signal attributable to the 1nπ* state in thymine derived NACs. The femtosecond time resolution of the technique also aided in identifying differences between the excited state lifetimes of thymidine and thymidine monophosphate. These have been interpreted, aided by molecular dynamics simulations, as an influence of conformational differences leading to a longer excited state lifetime in thymidine monophosphate.Finally, we discuss advances in tabletop light sources extending into the extreme ultraviolet and soft X-ray regimes that allow expansion of liquid jet TRPES to full valence band and potentially core level studies of solutes and pure liquids in liquid microjets. As most solutes have ground state binding energies in the range of 10 eV, observation of both excited state decay and ground state recovery using ultraviolet pump-ultraviolet probe TRPES has been intractable. With high-harmonic generation light sources, it will be possible to not only observe complete relaxation pathways for valence level dynamics but to also track dynamics with element specificity by probing core levels of the solute of interest.
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Affiliation(s)
- Zachary N Heim
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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30
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Photobiochemical mechanisms of biomolecules relevant to germicidal ultraviolet irradiation at 222 and 254 nm. Sci Rep 2022; 12:18217. [PMID: 36309578 PMCID: PMC9617911 DOI: 10.1038/s41598-022-22969-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/21/2022] [Indexed: 12/31/2022] Open
Abstract
To inactivate viruses and microorganisms, ultraviolet light in the short wavelength region is a promising candidate for mitigating the infection of disease. Germicidal mercury lamps emitting at 254 nm and KrCl excimer lamps emitting at 222 nm have sterilisation properties. In this work, wavelength dependence of the photobiochemical mechanisms was investigated with 222- and 254-nm irradiation to analyze the underlying damage mechanisms of DNA/RNA and proteins, using Escherichia coli, a protease, an oligopeptide, amino acids, plasmid DNA and nucleosides. The photorepair of damaged DNA and the "dark" reversion of the hydrates of uracil phosphoramidite coupling blocks were also investigated.
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31
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Wu P, Wang X, Pan H, Chen J. Direct Observation of Excitation Wavelength-Dependent Ultrafast Intersystem Crossing in Cytosine Nucleoside Solution. J Phys Chem B 2022; 126:7975-7980. [PMID: 36179273 DOI: 10.1021/acs.jpcb.2c05865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A triplet excited state can lead to different DNA photolesions, especially in cytosine and its nucleoside/nucleotide as they are hotspots for DNA mutations. However, the triplet state generation mechanism is in controversy, and experimental evidence of ultrafast intersystem crossing (ISC) has not been registered in these molecules. In this work, ultrafast ISC is directly observed in 2'-deoxycytidine (dCyd) solution by using femtosecond transient absorption spectroscopy. Surprisingly, we demonstrate that ISC in dCyd is sensitive to the excitation wavelength, and a spin-vibronic ISC mechanism is proposed. This finding is the last piece of the dCyd excited-state deactivation mechanism puzzle and sets the base for further investigation of triplet state-involved photophysics and photochemistry in dCyd-containing DNA.
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Affiliation(s)
- Peicong Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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32
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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33
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Vayá I, Gustavsson T, Markovitsi D. High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes. Molecules 2022; 27:molecules27113558. [PMID: 35684495 PMCID: PMC9181881 DOI: 10.3390/molecules27113558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
The publication deals with polymeric pA●pT and oligomeric A20●T20 DNA duplexes whose fluorescence is studied by time-correlated single photon counting. It is shown that their emission on the nanosecond timescale is largely dominated by high-energy components peaking at a wavelength shorter than 305 nm. Because of their anisotropy (0.02) and their sensitivity to base stacking, modulated by the duplex size and the ionic strength of the solution, these components are attributed to mixed ππ*/charge transfer excitons. As high-energy long-lived excited states may be responsible for photochemical reactions, their identification via theoretical studies is an important challenge.
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Affiliation(s)
- Ignacio Vayá
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain;
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Correspondence:
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34
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Asban S, Keefer D, Chernyak VY, Mukamel S. Sensing ultrashort electronic coherent beating at conical intersections by single-electron pulses. Proc Natl Acad Sci U S A 2022; 119:e2205510119. [PMID: 35609200 PMCID: PMC9295798 DOI: 10.1073/pnas.2205510119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceIn a theoretical study, we present an ultrafast technique for probing time-dependent molecular charge densities. An ultrafast optical pump first brings the molecule into an electronic nonstationary state. This is followed by coherent inelastic scattering of a broadband single-electron probe pulse with a variable delay T, which is detected spectrally. The technique is applied to reveal phase-sensitive background-free coherent electron beating in the conical intersection passage in uracil and reveals the otherwise elusive coherent beating of strongly coupled electrons and nuclei.
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Affiliation(s)
- Shahaf Asban
- Department of Chemistry, University of California, Irvine, CA 92697-2025
- Department of Physics & Astronomy, University of California, Irvine, CA 92697-2025
| | - Daniel Keefer
- Department of Chemistry, University of California, Irvine, CA 92697-2025
- Department of Physics & Astronomy, University of California, Irvine, CA 92697-2025
| | - Vladimir Y. Chernyak
- Department of Chemistry, Wayne State University, Detroit, MI 48202
- Department of Mathematics, Wayne State University, Detroit, MI 48202
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA 92697-2025
- Department of Physics & Astronomy, University of California, Irvine, CA 92697-2025
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35
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Ashfold MNR, Kim SK. Non-Born-Oppenheimer effects in molecular photochemistry: an experimental perspective. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200376. [PMID: 35341307 DOI: 10.1098/rsta.2020.0376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 06/14/2023]
Abstract
Non-adiabatic couplings between Born-Oppenheimer (BO)-derived potential energy surfaces are now recognized as pivotal in describing the non-radiative decay of electronically excited molecules following photon absorption. This opinion piece illustrates how non-BO effects provide photostability to many biomolecules when exposed to ultraviolet radiation, yet in many other cases are key to facilitating 'reactive' outcomes like isomerization and bond fission. The examples are presented in order of decreasing molecular complexity, spanning studies of organic sunscreen molecules in solution, through two families of heteroatom containing aromatic molecules and culminating with studies of isolated gas phase H2O molecules that afford some of the most detailed insights yet available into the cascade of non-adiabatic couplings that enable the evolution from photoexcited molecule to eventual products. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.
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Affiliation(s)
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
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36
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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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37
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Xie BB, Jia PK, Wang KX, Chen WK, Liu XY, Cui G. Generalized Ab Initio Nonadiabatic Dynamics Simulation Methods from Molecular to Extended Systems. J Phys Chem A 2022; 126:1789-1804. [PMID: 35266391 DOI: 10.1021/acs.jpca.1c10195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonadiabatic dynamics simulation has become a powerful tool to describe nonadiabatic effects involved in photophysical processes and photochemical reactions. In the past decade, our group has developed generalized trajectory-based ab initio surface-hopping (GTSH) dynamics simulation methods, which can be used to describe a series of nonadiabatic processes, such as internal conversion, intersystem crossing, excitation energy transfer and charge transfer of molecular systems, and photoinduced nonadiabatic carrier dynamics of extended systems with and without spin-orbit couplings. In this contribution, we will first give a brief introduction to our recently developed methods and related numerical implementations at different computational levels. Later, we will present some of our latest applications in realistic systems, which cover organic molecules, biological proteins, organometallic compounds, periodic organic and inorganic materials, etc. Final discussion is given to challenges and outlooks of ab initio nonadiabatic dynamics simulations.
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Affiliation(s)
- Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Ke-Xin Wang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, Sichuan, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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38
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Wang D, Wang X, Jiang Y, Cao S, Jin P, Pan H, Sun H, Sun Z, Chen J. Excited State Dynamics of Methylated Guanosine Derivatives Revealed by Femtosecond Time-resolved Spectroscopy. Photochem Photobiol 2022; 98:1008-1016. [PMID: 35203108 DOI: 10.1111/php.13612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/20/2022] [Indexed: 11/28/2022]
Abstract
Methylated DNA/RNA nucleobases are important epigenetic marks in living species and play an important role for targeted therapies. Moreover, they could bring significant changes to the photo-stability of nucleic acid, leading these sites become mutational hotspots for disease such as skin cancer. While a number of studies have demonstrated the relationship between excited state dynamics and the biological function of methylated cytosine in DNA, investigations aimed at unraveling the excited state dynamics of methylated guanosine in RNA have been largely overlooked. In this work, influence of methylation on the excited state dynamics of guanosine is studied by using femtosecond time-resolved spectroscopy. Our results suggest that the effect of methyl substitution on the photophysical properties of guanosine is position sensitive. N1-methylguanosine shows very similar excited state dynamics as that in guanosine, while almost one order of magnitude longer lifetime of the La state is observed in N2, N2-dimethylguanosine. Notably, N7-methylation can lead to a new minimum on the La state, which shows a two orders of magnitude longer excited state lifetime compared with guanosine. These findings not only help understanding excited state dynamics of methylated guanosines, but also lay the foundation for further studying DNA/RNA strands incorporated with these bases.
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Affiliation(s)
- Danhong Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Peipei Jin
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China
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39
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Fedotov DA, Paul AC, Koch H, Santoro F, Coriani S, Improta R. Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study. Phys Chem Chem Phys 2022; 24:4987-5000. [PMID: 35142309 DOI: 10.1039/d1cp04340d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, namely, equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the ππ* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying nπ* state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effects by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the nπ* state. Finally, ESA spectra have been computed from the minima of the lowest energy ππ* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.
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Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Alexander C Paul
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri, 7, I-56126, Pisa, Italy.
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, I-56124 Pisa, Italy.
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. .,Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, I-80134 Napoli, Italy.
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40
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Caldero-Rodríguez NE, Ortiz-Rodríguez LA, Gonzalez AA, Crespo-Hernández CE. Photostability of 2,6-diaminopurine and its 2'-deoxyriboside investigated by femtosecond transient absorption spectroscopy. Phys Chem Chem Phys 2022; 24:4204-4211. [PMID: 35119441 DOI: 10.1039/d1cp05269a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet radiation (UVR) from the sun is essential for the prebiotic syntheses of nucleotides, but it can also induce photolesions such as the cyclobutane pyrimidine dimers (CPDs) to RNA or DNA oligonucleotide in prebiotic Earth. 2,6-Diaminopurine (26DAP) has been proposed to repair CPDs in high yield under prebiotic conditions and be a key component in enhancing the photostability of higher-order prebiotic DNA structures. However, its electronic relaxation pathways have not been studied, which is necessary to know whether 26DAP could have survived the intense UV fluxes of the prebiotic Earth. We investigate the electronic relaxation mechanism of both 26DAP and its 2'-deoxyribonucleoside (26DAP-d) in aqueous solution using steady-state and femtosecond transient absorption measurements that are complemented with electronic-structure calculations. The results demonstrate that both purine derivatives are significantly photostable to UVR. It is shown that upon excitation at 287 nm, the lowest energy 1ππ* state is initially populated. The population then branches following two relaxation coordinates in the 1ππ* potential energy surface, which are identified as the C2- and C6-relaxation coordinates. The population following the C6-coordinate internally converts to the ground state nonradiatively through a nearly barrierless conical intersection within 0.7 ps in 26DAP or within 1.1 ps in 26DAP-d. The population that follows the C2-relaxation coordinate decays back to the ground state by a combination of nonradiative internal conversion via a conical intersection and fluorescence emission from the 1ππ* minimum in 43 ps and 1.8 ns for the N9 and N7 tautomers of 26DAP, respectively, or in 70 ps for 26DAP-d. Fluorescence quantum yields of 0.037 and 0.008 are determined for 26DAP and 26DAP-d, respectively. Collectively, it is demonstrated that most of the excited state population in 26DAP and 26DAP-d decays back to the ground state via both nonradiative and radiative relaxation pathways. This result lends support to the idea that 26DAP could have accumulated in large enough quantities during the prebiotic era to participate in the formation of prebiotic RNA or DNA oligomers and act as a key component in the protection of the prebiotic genetic alphabet.
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Affiliation(s)
| | | | - Andres A Gonzalez
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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41
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Jabeen G, Ahmad MH, Aslam M, Riaz S, Hayat A, Nawaz MH. N-Doped graphene quantum dots (N-GQDs) as fluorescent probes for detection of UV induced DNA damage. RSC Adv 2022; 12:22458-22464. [PMID: 36105959 PMCID: PMC9366598 DOI: 10.1039/d2ra04462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
UV induced DNA damage can lead to the development of skin cancer, skin aging and cell death. In this study, we fabricated a fluorescence-based biosensor that can be applied to the detection of DNA damage caused by UV radiation with the help of nitrogen doped graphene quantum dots (N-GQDs) as the probe material. In this paper, N-GQDs with good fluorescence efficiency have been synthesized by the hydrothermal method and were used as a fluorescent probe for the detection of UV damaged DNA. The fluorescence intensity of N-GQDs was quenched by the static quenching of UV damaged DNA through the formation of a N-GQD/UV damaged DNA complex. Moreover, the effects of different values of pH, NaCl and glucose on analytical performances of the sensor were also studied. Thus, using a fluorescence based approach, we demonstrated a quite simple, rapid, and inexpensive biosensor for the detection of DNA damage caused by UV radiation. UV induced DNA damage can lead to the development of skin cancer, skin aging and cell death.![]()
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Affiliation(s)
- Gulshan Jabeen
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore, 54000, Pakistan
| | - Muhammad Hassan Ahmad
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
| | - Muhammad Aslam
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore, 54000, Pakistan
| | - Sara Riaz
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
| | - Akhtar Hayat
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
| | - Mian Hasnain Nawaz
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, 54000, Pakistan
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42
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Stark B, Poon GM, Wyrick JJ. Molecular mechanism of UV damage modulation in nucleosomes. Comput Struct Biotechnol J 2022; 20:5393-5400. [PMID: 36212527 PMCID: PMC9529667 DOI: 10.1016/j.csbj.2022.08.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Exposure to ultraviolet (UV) light causes the formation of mutagenic cyclobutane pyrimidine dimers (CPDs) in cellular DNA. Previous studies have revealed that CPD formation in nucleosomes, the building blocks of chromatin, shows a striking ∼10 base pair (bp) periodic pattern. CPD formation is suppressed at positions where the DNA minor groove faces toward the histone octamer (minor-in) and elevated CPD formation at positions where the minor groove faces away from the histone octamer (minor-out). However, the molecular mechanism underlying this nucleosome photofootprint is unclear. Here, we analyzed ∼180 high-resolution nucleosome structures to characterize whether differences in DNA mobility or conformation are responsible for the CPD modulation in nucleosomes. Our results indicate that differences in DNA mobility cannot explain CPD modulation in nucleosome. Instead, we find that the sharp DNA bending around the histone octamer results in DNA conformations with structural parameters more susceptible to UV damage formation at minor-out positions and more resistant to CPD formation at minor-in positions. This analysis reveals the molecular mechanism responsible for periodic modulation of CPD formation and UV mutagenesis in nucleosomal DNA.
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43
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Huang X, Lao W, Zhou Y, Sun Y, Wang Q. Glutamate dehydrogenase enables Salmonella to survive under oxidative stress and escape from clearance in macrophages. FEBS Lett 2022; 596:81-94. [PMID: 34855205 DOI: 10.1002/1873-3468.14247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 11/06/2022]
Abstract
Oxidative stress and the production of reactive oxygen species (ROS) are a biological threat to bacteria, which induce the synthesis of proteins and production of antioxidants to combat it. Herein, we report that glutamate dehydrogenase (GDH) of Salmonella can assimilate ammonium into glutamate and promote the generation of glutathione (GSH) to combat oxidative damage. Oxidation induces the transcription of gdhA, which encodes GDH, and activates the enzymatic activity of GDH. The ΔgdhA mutant Salmonella strain showed decreased levels of GSH and reduced survival in macrophages, and this growth deficiency could be partially restored by overexpression of GDH and complementation with its downstream metabolites. Therefore, GDH plays a critical role in the growth of Salmonella in oxidative environments, especially under low energy supply.
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Affiliation(s)
- Xi Huang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, China
| | - Wenji Lao
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, China
| | - Youci Zhou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, China
| | - Yunwei Sun
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, China
| | - Qijun Wang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, China
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44
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Sivapragasam S, Stark B, Albrecht AV, Bohm KA, Mao P, Emehiser RG, Roberts SA, Hrdlicka PJ, Poon GMK, Wyrick JJ. CTCF binding modulates UV damage formation to promote mutation hot spots in melanoma. EMBO J 2021; 40:e107795. [PMID: 34487363 DOI: 10.15252/embj.2021107795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 12/29/2022] Open
Abstract
Somatic mutations in DNA-binding sites for CCCTC-binding factor (CTCF) are significantly elevated in many cancers. Prior analysis has suggested that elevated mutation rates at CTCF-binding sites in skin cancers are a consequence of the CTCF-cohesin complex inhibiting repair of UV damage. Here, we show that CTCF binding modulates the formation of UV damage to induce mutation hot spots. Analysis of genome-wide CPD-seq data in UV-irradiated human cells indicates that formation of UV-induced cyclobutane pyrimidine dimers (CPDs) is primarily suppressed by CTCF binding but elevated at specific locations within the CTCF motif. Locations of CPD hot spots in the CTCF-binding motif coincide with mutation hot spots in melanoma. A similar pattern of damage formation is observed at CTCF-binding sites in vitro, indicating that UV damage modulation is a direct consequence of CTCF binding. We show that CTCF interacts with binding sites containing UV damage and inhibits repair by a model repair enzyme in vitro. Structural analysis and molecular dynamic simulations reveal the molecular mechanism for how CTCF binding modulates CPD formation.
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Affiliation(s)
- Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Bastian Stark
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | | | - Kaitlynne A Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA.,Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | | | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | | | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA.,Center for Reproductive Biology, Washington State University, Pullman, WA, USA
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45
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Scutelnic V, Tsuru S, Pápai M, Yang Z, Epshtein M, Xue T, Haugen E, Kobayashi Y, Krylov AI, Møller KB, Coriani S, Leone SR. X-ray transient absorption reveals the 1A u (nπ*) state of pyrazine in electronic relaxation. Nat Commun 2021; 12:5003. [PMID: 34408141 PMCID: PMC8373973 DOI: 10.1038/s41467-021-25045-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Electronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized 1B2u (ππ*) (S2) and 1B3u (nπ*) (S1) states, the participation of the optically dark 1Au (nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computations. Despite 1Au (nπ*) and 1B3u (nπ*) states having similar energies at relaxed geometry, their X-ray absorption spectra differ largely in transition energy and oscillator strength. The 1Au (nπ*) state is populated in 200 ± 50 femtoseconds after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state.
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Affiliation(s)
- Valeriu Scutelnic
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Shota Tsuru
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.,Ruhr-Universität, Bochum, Germany
| | - Mátyás Pápai
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.,Wigner Research Centre for Physics, Budapest, Hungary
| | - Zheyue Yang
- Department of Chemistry, University of California, Berkeley, CA, USA.,, Shanghai, China
| | - Michael Epshtein
- Department of Chemistry, University of California, Berkeley, CA, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,, Beer-Sheva, Israel
| | - Tian Xue
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Eric Haugen
- Department of Chemistry, University of California, Berkeley, CA, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuki Kobayashi
- Department of Chemistry, University of California, Berkeley, CA, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Klaus B Møller
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stephen R Leone
- Department of Chemistry, University of California, Berkeley, CA, USA. .,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Physics, University of California, Berkeley, CA, USA.
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Yu XF, Fu TH, Xiao B, Yu HY, Li Q. A theoretical study on the excited-state deactivation paths for the A-5FU dimer. Phys Chem Chem Phys 2021; 23:16089-16106. [PMID: 34291779 DOI: 10.1039/d1cp00030f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.
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Affiliation(s)
- Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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Zhu YH, Zhang TS, Tang XF, Xie BB, Cui G. MS-CASPT2 studies on the mechanistic photophysics of tellurium-substituted guanine and cytosine. Phys Chem Chem Phys 2021; 23:12421-12430. [PMID: 34028476 DOI: 10.1039/d1cp01142a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfur-substituted nucleobases are highly promising photosensitizers that are widely used in photodynamic therapy, and there are numerous studies exploring their unique photophysical behaviors. However, relevant photophysical investigations on selenium and tellurium substitutions are still rare. Herein, the high-level multistate complete-active-space second-order perturbation (MS-CASPT2) method was performed for the first time to explore the excited-state relaxation processes of tellurium-substituted guanine (TeG) and cytosine (TeC). Based on the electronic state properties in the Franck-Condon (FC) region, we found that the lowest five (S0, S1, S2, T1, and T2) and six (S0, S1, S2, T1, T2 and T3) states will participate in the nonadiabatic transition processes of TeG and TeC systems, respectively. In these electronic states, two kinds of minimum and intersection structures (i.e., planar and twisted structures) were obtained for both TeG and TeC systems. The linearly interpolated internal coordinate (LIIC) paths and spin-orbit coupling (SOC) constants revealed several possible planar and twisted excited-state decay channels, which could lead the systems to the lowest reactive triplet state of T1. Small energy barriers in the T1 state will trap the TeG and TeC systems for a while before they finally populate to the ground state. Although tellurium substitution would further redshift the absorption wavelength and enhance the intersystem crossing (ISC) rate to the T1 state compared with sulfur and selenium substitutions, the rapid ISC process of T1 → S0 may make it a less effective photosensitizer to sensitize the molecular oxygen. We believe our present work will provide important mechanistic insights into the photophysics of tellurium-substituted nucleobases.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | - Teng-Shuo Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, P. R. China
| | - Xiu-Fang Tang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China.
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China.
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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Lu C, Gutierrez-Bayona NE, Taylor JS. The effect of flanking bases on direct and triplet sensitized cyclobutane pyrimidine dimer formation in DNA depends on the dipyrimidine, wavelength and the photosensitizer. Nucleic Acids Res 2021; 49:4266-4280. [PMID: 33849058 PMCID: PMC8096240 DOI: 10.1093/nar/gkab214] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/15/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the major products of DNA produced by direct absorption of UV light, and result in C to T mutations linked to human skin cancers. Most recently a new pathway to CPDs in melanocytes has been discovered that has been proposed to arise from a chemisensitized pathway involving a triplet sensitizer that increases mutagenesis by increasing the percentage of C-containing CPDs. To investigate how triplet sensitization may differ from direct UV irradiation, CPD formation was quantified in a 129-mer DNA designed to contain all 64 possible NYYN sequences. CPD formation with UVB light varied about 2-fold between dipyrimidines and 12-fold with flanking sequence and was most frequent at YYYR and least frequent for GYYN sites in accord with a charge transfer quenching mechanism. In contrast, photosensitized CPD formation greatly favored TT over C-containing sites, more so for norfloxacin (NFX) than acetone, in accord with their differing triplet energies. While the sequence dependence for photosensitized TT CPD formation was similar to UVB light, there were significant differences, especially between NFX and acetone that could be largely explained by the ability of NFX to intercalate into DNA.
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Affiliation(s)
- Chen Lu
- Department of Chemistry, Washington University, One Brookings Dr., St. Louis, MO 63130, USA
| | | | - John-Stephen Taylor
- Department of Chemistry, Washington University, One Brookings Dr., St. Louis, MO 63130, USA
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Abstract
The intrinsic fluorescence of nucleic acids is extremely weak compared to that of the fluorescent labels used to probe their structural and functional behavior. Thus, for technical reasons, the investigation of the intrinsic DNA fluorescence was limited for a long time. But with the improvement in spectroscopic techniques, the situation started to change around the turn of the century. During the past two decades, various factors modulating the static and dynamic properties of the DNA fluorescence have been determined; it was shown that, under certain conditions, quantum yields may be up 100 times higher than what was known so far. The ensemble of these studies opened up new paths for the development of label-free DNA fluorescence for biochemical applications. In parallel, these studies have shed new light on the primary processes leading to photoreactions that damage DNA when it absorbs UV radiation.We have been studying a variety of DNA systems, ranging from the monomeric nucleobases to double-stranded and four-stranded structures using fluorescence spectroscopy. The specificity of our work resides in the quantitative association of the steady-state fluorescence spectra with time-resolved data recorded from the femtosecond to the nanosecond timescales, made possible by the development of specific methodologies.Among others, our fluorescence studies provide information on the energy and the polarization of electronic transitions. These are valuable indicators for the evolution of electronic excitations in complex systems, where the electronic coupling between chromophores plays a key role. Highlighting collective effects that originate from electronic interactions in DNA multimers is the objective of the present Account.In contrast to the monomeric chromophores, whose fluorescence decays within a few picoseconds, that of DNA multimers persists on the nanosecond timescale. Even if long-lived states represent only a small fraction of electronic excitations, they may be crucial to the DNA photoreactivity because the probability to reach reactive conformations increases over time, owing to the incessant structural dynamics of nucleic acids.Our femtosecond studies have revealed that an ultrafast excitation energy transfer takes place among the nucleobases within duplexes and G-quadruplexes. Such an ultrafast process is possible when collective states are populated directly upon photon absorption. At much longer times, we discovered an unexpected long-lived high-energy emission stemming from what was coined "HELM excitons". These collective states, whose emission increases with the duplex size, could be responsible for the delayed fluorescence of ππ* states observed for genomic DNA.Most studies dealing with excited-state relaxation in DNA were carried out with excitation in the absorption band peaking at around 260 nm. We went beyond this and also performed the first time-resolved study with excitation in the UVA spectral range, where a very weak absorption tail is present. The resulting fluorescence decays are much slower and the fluorescence quantum yields are much higher than for UVC excitation. We showed that the base pairing of DNA strands enhances the UVA fluorescence and, in parallel, increases the photoreactivity because it modifies the nature of the involved collective excited states.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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