1
|
Detection of the thietane precursor in the UVA formation of the DNA 6-4 photoadduct. Nat Commun 2020; 11:3599. [PMID: 32680990 PMCID: PMC7368040 DOI: 10.1038/s41467-020-17333-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
Notwithstanding the central biological role of the (6-4) photoadduct in the induction of skin cancer by sunlight, crucial mechanistic details about its formation have evaded characterization despite efforts spanning more than half a century. 4-Thiothymidine (4tT) has been widely used as an important model system to study its mechanism of formation, but the excited-state precursor, the intermediate species, and the time scale leading to the formation of the (6-4) photoadduct have remained elusive. Herein, steady-state and time-resolved spectroscopic techniques are combined with new and reported quantum-chemical calculations to demonstrate the excited state leading to the formation of the thietane intermediate, its rate, and the formation of the (6-4) photoadduct using the 5’-TT(4tT)T(4tT)TT-3’ DNA oligonucleotide. Efficient, sub-1 ps intersystem crossing leads to the population of a triplet minimum of the thietane intermediate in as short as 3 ps, which intersystem crosses to its ground state and rearranges to form the (6-4) photoadduct. The mechanisms of formation of the (6-4) photoproducts in DNA damage by sunlight is still debated. Here the authors show, by optical spectroscopies and computations, the details of the formation of a (6-4) photoadduct via the thietane intermediate in a single-stranded DNA oligonucleotide.
Collapse
|
2
|
Giussani A, Worth GA. On the Intrinsically Low Quantum Yields of Pyrimidine DNA Photodamages: Evaluating the Reactivity of the Corresponding Minimum Energy Crossing Points. J Phys Chem Lett 2020; 11:4984-4989. [PMID: 32490676 DOI: 10.1021/acs.jpclett.0c01264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The low quantum yield of photoformation of cyclobutane pyrimidine dimers and pyrimidine-pyrimidone (6-4) adducts in DNA bases is usually associated with the presence of more favorable nonreactive decay paths and with the unlikeliness of exciting the system in a favorable conformation. Here, we prove that the ability of the reactive conical intersection to bring the system either back to the absorbing conformation or to the photoproduct must be considered as a fundamental factor in the low quantum yields of the mentioned photodamage. In support of the proposed model, the one order of magnitude difference in the quantum yield of formation of the cyclobutane thymine dimer with respect to the thymine-thymine (6-4) adduct is rationalized here by comparing the reactive ability of the seam of intersections leading respectively to the cyclobutane thymine dimer and the oxetane precursor of the thymine-thymine (6-4) adduct at the CASPT2 level of theory.
Collapse
Affiliation(s)
- Angelo Giussani
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Graham A Worth
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| |
Collapse
|
3
|
Wang X, Yu H. The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6-4) dimer formation. J Mol Model 2018; 24:319. [PMID: 30353277 DOI: 10.1007/s00894-018-3863-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Density functional theory calculations were carried out to investigate the formation mechanism of the thymine-thymine (6-4) dimer ((6-4)TT), which is one of the main DNA lesions induced by ultraviolet radiation and is closely related to skin cancers. The DNA backbone was found to have nonnegligible effects on the triplet reaction pathway, particularly the reaction steps involving substantial base rotations. The mechanism for the isomerization from (6-4)TT to its Dewar valence isomer (DewarTT) was also explored, confirming the necessity of absorbing a second photon. In addition, the solvation effects were examined and showed considerable influence on the potential energy surface. Graphical Abstract DFT calculations on the influence of DNA backbone on the mechanism of UV-induced thymine-thymine (6-4) dimer formation.
Collapse
Affiliation(s)
- Xingyong Wang
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia.
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| |
Collapse
|
4
|
Giussani A, Conti I, Nenov A, Garavelli M. Photoinduced formation mechanism of the thymine–thymine (6–4) adduct in DNA; a QM(CASPT2//CASSCF):MM(AMBER) study. Faraday Discuss 2018; 207:375-387. [DOI: 10.1039/c7fd00202e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Out-of-plane puckering of the C4′ atom forming a new CC bond seems essential for oxetane formation.
Collapse
Affiliation(s)
- Angelo Giussani
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| |
Collapse
|
5
|
Jian Y, Maximowitsch E, Liu D, Adhikari S, Li L, Domratcheva T. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. Chemistry 2017; 23:7526-7537. [PMID: 28370554 DOI: 10.1002/chem.201700045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.
Collapse
Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,School of Chemistry & Chemical Engineering, Shaanxi Normal University (SNNU), No. 620, West Chang'an Avenue, Xi'an, Shaanxi, 710119, P. R. China
| | - Egle Maximowitsch
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| |
Collapse
|
6
|
Wang HX, Pu M, Ding YC. Density functional theoretical studies on the ring-opening polymerization mechanism of oxetane cation series compounds. RSC Adv 2017. [DOI: 10.1039/c7ra09317a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanism of ring-opening polymerization of oxetane cation series compounds was investigated using the B3LYP and MP2 methods of density functional theory andab initiomethods, at the basis set levels of 6-31G(d,p) and 6-311++G(d,p).
Collapse
Affiliation(s)
- Hai-Xia Wang
- School of Science
- Xi'an Jiaotong University
- Xi'an 700049
- P. R. China
| | - Min Pu
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Yu-Cheng Ding
- School of Mechanic Engineering
- Xi'an Jiaotong University
- Xi'an 700049
- P. R. China
| |
Collapse
|
7
|
Huang X, Zhang R. A Theoretical Rationale why Furan-side Monoadduct is More Favorable Toward Diadduct Formation in 8-Methoxypsoralen and Thymine Complexes. Photochem Photobiol 2013; 89:891-9. [DOI: 10.1111/php.12067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/26/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Xuebin Huang
- Key Laboratory of Cluster Science; School of Chemistry; Beijing Institute of Technology; Beijing; China
| | - Rubo Zhang
- Key Laboratory of Cluster Science; School of Chemistry; Beijing Institute of Technology; Beijing; China
| |
Collapse
|
8
|
Giussani A, Serrano-Andrés L, Merchán M, Roca-Sanjuán D, Garavelli M. Photoinduced formation mechanism of the thymine-thymine (6-4) adduct. J Phys Chem B 2013; 117:1999-2004. [PMID: 23339629 DOI: 10.1021/jp307200g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.
Collapse
Affiliation(s)
- Angelo Giussani
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain.
| | | | | | | | | |
Collapse
|