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Laughery MF, Wilson HE, Sewell A, Stevison S, Wyrick JJ. The Surprising Diversity of UV-Induced Mutations. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300205. [PMID: 38884048 PMCID: PMC11170076 DOI: 10.1002/ggn2.202300205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/22/2024] [Indexed: 06/18/2024]
Abstract
Ultraviolet (UV) light is the most pervasive environmental mutagen and the primary cause of skin cancer. Genome sequencing of melanomas and other skin cancers has revealed that the vast majority of somatic mutations in these tumors are cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which, together with tandem CC>TT substitutions, comprise the canonical UV mutation "signature". These mutation classes are caused by DNA damage directly induced by UV absorption, namely cyclobutane pyrimidine dimers (CPDs) or 6-4 pyrimidine-pyrimidone photoproducts (6-4PP), which form between neighboring pyrimidine bases. However, many of the key driver mutations in melanoma do not fit this mutation signature, but instead are caused by T>A, T>C, C>A, or AC>TT substitutions, frequently occurring in non-dipyrimidine sequence contexts. This article describes recent studies indicating that UV light causes a more diverse spectrum of mutations than previously appreciated, including many of the mutation classes observed in melanoma driver mutations. Potential mechanisms for these diverse mutation signatures are discussed, including UV-induced pyrimidine-purine photoproducts and indirect DNA damage induced by UVA light. Finally, the article reviews recent findings indicating that human DNA polymerase eta normally suppresses these non-canonical UV mutation classes, which can potentially explain why canonical C>T substitutions predominate in human skin cancers.
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Affiliation(s)
- Marian F Laughery
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - Hannah E Wilson
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - Allysa Sewell
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - Scott Stevison
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - John J Wyrick
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
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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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Banyasz A, Martínez-Fernández L, Improta R, Ketola TM, Balty C, Markovitsi D. Radicals generated in alternating guanine-cytosine duplexes by direct absorption of low-energy UV radiation. Phys Chem Chem Phys 2018; 20:21381-21389. [PMID: 30101268 DOI: 10.1039/c8cp02588f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent studies have evidenced that oxidatively damaged DNA, which potentially leads to carcinogenic mutations and aging, may result from the direct absorption of low-energy photons (>250 nm). Herein, the primary species, i.e., ejected electrons and base radicals associated with such damage in duplexes with an alternating guanine-cytosine sequence are quantified by nanosecond transient absorption spectroscopy. The one-photon ionization quantum yield at 266 nm is 1.2 × 10-3, which is similar to those reported previously for adenine-thymine duplexes. This means that the simple presence of guanine, the nucleobase with the lowest ionization potential, does not affect photo-ionization. The transient species detected after 3 μs are identified as deprotonated guanine radicals, which decay with a half-time of 2.5 ms. Spectral assignment is made with the help of quantum chemistry calculations (TD-DFT), which for the first time, provide reference absorption spectra for guanine radicals in duplexes. In addition, our computed spectra predict the changes in transient absorption expected for hole localization as well as deprotonation (to cytosine and bulk water) and hydration of the radical cation.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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Martínez-Fernández L, Improta R. Novel adenine/thymine photodimerization channels mapped by PCM/TD-DFT calculations on dApT and TpdA dinucleotides. Photochem Photobiol Sci 2018. [PMID: 28640303 DOI: 10.1039/c7pp00154a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite the biological relevance of AT-rich DNA sequences, the excited state paths associated with the photochemical reactions involving adenine and thymine stacked pairs have never been characterized, and the structure of the most abundant photoproduct in DNA is unknown. PCM/TD-M052X calculations on dApT and TpdA unveil the paths leading to the main photoproduct in TpdA, provide new insights into the reasons why it is not formed in dApT and show the existence of a new photochemical path, which could produce the precursor of the most abundant genomic AT/TA photoproduct. Our calculations confirm that anti/anti conformers are photochemically active and show that the dynamical solvation effects could significantly modulate the reaction yields.
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Affiliation(s)
- Lara Martínez-Fernández
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80134 Naples, Italy
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Banyasz A, Martínez-Fernández L, Balty C, Perron M, Douki T, Improta R, Markovitsi D. Absorption of Low-Energy UV Radiation by Human Telomere G-Quadruplexes Generates Long-Lived Guanine Radical Cations. J Am Chem Soc 2017; 139:10561-10568. [PMID: 28737902 DOI: 10.1021/jacs.7b05931] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Telomeres, which are involved in cell division, carcinogenesis, and aging and constitute important therapeutic targets, are prone to oxidative damage. This propensity has been correlated with the presence of guanine-rich sequences, capable of forming four-stranded DNA structures (G-quadruplexes). Here, we present the first study on oxidative damage of human telomere G-quadruplexes without mediation of external molecules. Our investigation has been performed for G-quadruplexes formed by folding of GGG(TTAGGG)3 single strands in buffered solutions containing Na+ cations (TEL21/Na+). Associating nanosecond time-resolved spectroscopy and quantum mechanical calculations (TD-DFT), it focuses on the primary species, ejected electrons and guanine radicals, generated upon absorption of UV radiation directly by TEL21/Na+. We show that, at 266 nm, corresponding to an energy significantly lower than the guanine ionization potential, the one-photon ionization quantum yield is 4.5 × 10-3. This value is comparable to that of cyclobutane thymine dimers (the major UV-induced lesions) in genomic DNA; the quantum yield of these dimers in TEL21/Na+ is found to be (1.1 ± 0.1) × 10-3. The fate of guanine radicals, generated in equivalent concentration with that of ejected electrons, is followed over 5 orders of magnitude of time. Such a quantitative approach reveals that an important part of radical cation population survives up to a few milliseconds, whereas radical cations produced by chemical oxidants in various DNA systems are known to deprotonate, at most, within a few microseconds. Under the same experimental conditions, neither one-photon ionization nor long-lived radical cations are detected for the telomere repeat TTAGGG in single-stranded configuration, showing that secondary structure plays a key role in these processes. Finally, two types of deprotonated radicals are identified: on the one hand, (G-H2)• radicals, stable at early times, and on the other hand, (G-H1)• radicals, appearing within a few milliseconds and decaying with a time constant of ∼50 ms.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Lara Martínez-Fernández
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Clémence Balty
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Marion Perron
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Thierry Douki
- CEA, INAC-SyMMES Laboratoire des Lésions des Acides Nucléiques, F-38000 Grenoble, France
| | - Roberto Improta
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France.,Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
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Role of base arrangements and intermolecular hydrogen bonding in charge-transfer states of thymine-adenine dinucleotide in aqueous solution. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Asgatay S, Martinez A, Coantic-Castex S, Harakat D, Philippe C, Douki T, Clivio P. UV-induced TA photoproducts: formation and hydrolysis in double-stranded DNA. J Am Chem Soc 2010; 132:10260-1. [PMID: 20662506 DOI: 10.1021/ja1023173] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrolysis of TA photoproduct leads to two derivatives presenting different formation kinetic profiles depending on the oligomer content. The formation efficiency of TA photoproducts in UV-C-irradiated DNA slightly exceeds the formation of the trans,syn cyclobutane pyrimidine dimer at TT sites.
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Affiliation(s)
- Saâdia Asgatay
- Institut de Chimie Moléculaire de Reims, CNRS UMR 6229, UFR de Pharmacie, Université de Reims Champagne Ardenne, 51 rue Cognacq-Jay, F-51096 Reims Cedex, France
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