1
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Markovitsi D. On the Use of the Intrinsic DNA Fluorescence for Monitoring Its Damage: A Contribution from Fundamental Studies. ACS OMEGA 2024; 9:26826-26837. [PMID: 38947837 PMCID: PMC11209687 DOI: 10.1021/acsomega.4c02256] [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: 03/07/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024]
Abstract
The assessment of DNA damage by means of appropriate fluorescent probes is widely spread. In the specific case of UV-induced damage, it has been suggested to use the emission of dimeric photoproducts as an internal indicator for the efficacy of spermicidal lamps. However, in the light of fundamental studies on the UV-induced processes, outlined in this review, this is not straightforward. It is by now well established that, in addition to photodimers formed via an electronic excited state, photoionization also takes place with comparable or higher quantum yields, depending on the irradiation wavelength. Among the multitude of final lesions, some have been fully characterized, but others remain unknown; some of them may emit, while others go undetected upon monitoring fluorescence, the result being strongly dependent on both the irradiation and the excitation wavelength. In contrast, the fluorescence of undamaged nucleobases associated with emission from ππ* states, localized or excitonic, appearing at wavelengths shorter than 330 nm is worthy of being explored to this end. Despite its low quantum yield, it is readily detected nowadays. Its intensity decreases due to the disappearance of the reacting nucleobases and the loss of exciton coherence provoked by the presence of lesions, independently of their type. Thus, it could potentially provide valuable information about the DNA damage induced, not only by UV radiation but also by other sanitizing or therapeutic agents.
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Affiliation(s)
- Dimitra Markovitsi
- Université Paris-Saclay, CNRS,
Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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2
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Anderson RF, Shinde SS, Andrau L, Leung B, Skene C, White JM, Lobachevsky PN, Martin RF. Chemical Repair of Radical Damage to the GC Base Pair by DNA-Bound Bisbenzimidazoles. J Phys Chem B 2024. [PMID: 38686959 DOI: 10.1021/acs.jpcb.4c01069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The migration of an electron-loss center (hole) in calf thymus DNA to bisbenzimidazole ligands bound in the minor groove is followed by pulse radiolysis combined with time-resolved spectrophotometry. The initially observed absorption spectrum upon oxidation of DNA by the selenite radical is consistent with spin on cytosine (C), as the GC• pair neutral radical, followed by the spectra of oxidized ligands. The rate of oxidation of bound ligands increased with an increase in the ratio (r) ligands per base pair from 0.005 to 0.04. Both the rate of ligand oxidation and the estimated range of hole transfer (up to 30 DNA base pairs) decrease with the decrease in one-electron reduction potential between the GC• pair neutral radical of ca. 1.54 V and that of the ligand radicals (E0', 0.90-0.99 V). Linear plots of log of the rate of hole transfer versus r give a common intercept at r = 0 and a free energy change of 12.2 ± 0.3 kcal mol-1, ascribed to the GC• pair neutral radical undergoing a structural change, which is in competition to the observed hole transfer along DNA. The rate of hole transfer to the ligands at distance, R, from the GC• pair radical, k2, is described by the relationship k2 = k0 exp(constant/R), where k0 includes the rate constant for surmounting a small barrier.
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Affiliation(s)
- Robert F Anderson
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Sujata S Shinde
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Laura Andrau
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Brenda Leung
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Colin Skene
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Jonathan M White
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Pavel N Lobachevsky
- Molecular Radiation Biology, Peter MacCallum Cancer Centre, Melbourne 3052, Australia
| | - Roger F Martin
- School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
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3
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Zhou Q, Guo W, Hu Z, Yan S, Jie J, Su H. Can methylated purine bases act as photoionization hotspots? Photochem Photobiol 2024; 100:368-379. [PMID: 37792888 DOI: 10.1111/php.13862] [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: 05/29/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
The direct photoionization of DNA canonical bases under ultraviolet radiation is difficult due to the high ionization potentials. According to previous quantum chemical calculations, methylation can have great influence on the ionization potential. Are methylated nucleobases prone to photoionization and cause DNA damage? As an important epigenetic modification in transcription, expression, and regulation of genes, it is of great biological significance to explore the effect of methylation on base photoionization from the experimental perspective. Herein, we study the photoionization behavior of methylated purines 6 mA and 6mG at 266 nm using a nanosecond transient UV-Vis spectroscopy. The hydrated electron and methylated base radicals are observed, indicating the occurrence of photoionization for both 6mG and 6 mA. We measured one-photon ionization yields to be (5.0 ± 0.2) × 10-3 and (1.4 ± 0.2) × 10-3 for 6mG and 6 mA, respectively. These are higher than those of (dA)20 and (dA20 )·(dT20 ) previously reported, indicating that methylation significantly promotes base photoionization with a stronger effect than base stacking, consistent with calculations in literature. Given that the hydrated electrons and methylated base radicals from photoionization can trigger a cascade of deleterious reactions, the methylated purine bases may act as hotspots of DNA photoionization damage of living organisms.
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Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Wenwen Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuyi Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing, China
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4
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Ling CCH, Chan WX, Siow JX, Loh ZH. Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment. J Phys Chem A 2024; 128:626-635. [PMID: 38207335 DOI: 10.1021/acs.jpca.3c08232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.
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Affiliation(s)
- Christine Chun Hui Ling
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Wei Xin Chan
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Jing Xuan Siow
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
| | - Zhi-Heng Loh
- School of Chemistry, Chemical Engineering and Biotechnology, and School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
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5
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Wang X, Martínez-Fernández L, Zhang Y, Wu P, Kohler B, Improta R, Chen J. Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation. J Am Chem Soc 2024; 146:1839-1848. [PMID: 38194423 DOI: 10.1021/jacs.3c04567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Peicong Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via De Amicis 95, Napoli I-80145, Italy
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, Shanxi, China
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6
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Masi A, Capobianco A, Bobrowski K, Peluso A, Chatgilialoglu C. Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization. Biomolecules 2023; 13:1493. [PMID: 37892175 PMCID: PMC10605094 DOI: 10.3390/biom13101493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
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Affiliation(s)
- Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
- Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
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7
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Moe MM, Saito T, Tsai M, Liu J. Singlet O 2 Oxidation of the Radical Cation versus the Dehydrogenated Neutral Radical of 9-Methylguanine in a Watson-Crick Base Pair. Consequences of Structural Context. J Phys Chem B 2022; 126:5458-5472. [PMID: 35849846 DOI: 10.1021/acs.jpcb.2c03748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In DNA, guanine is the most susceptible to oxidative damage by exogenously and endogenously produced electronically excited singlet oxygen (1O2). The reaction mechanism and the product outcome strongly depend on the nucleobase ionization state and structural context. Previously, exposure of a monomeric 9-methylguanine radical cation (9MG•+, a model guanosine compound) to 1O2 was found to result in the formation of an 8-peroxide as the initial product. The present work explores the 1O2 oxidation of 9MG•+ and its dehydrogenated neutral form [9MG - H]• within a Watson-Crick base pair consisting of one-electron-oxidized 9-methylguanine-1-methylcytosine [9MG·1MC]•+. Emphasis is placed on entangling the base pair structural context and intra-base pair proton transfer with and consequences thereof on the singlet oxygenation of guanine radical species. Electrospray ionization coupled with guided-ion beam tandem mass spectrometry was used to study the formation and reaction of guanine radical species in the gas phase. The 1O2 oxidation of both 9MG•+ and [9MG - H]• is exothermic and proceeds barrierlessly either in an isolated monomer or within a base pair. Single- and multi-referential theories were tested for treating spin contaminations and multi-configurations occurring in radical-1O2 interactions, and reaction potential energy surfaces were mapped out to support experimental findings. The work provides a comprehensive profile for the singlet oxygenation of guanine radicals in different charge states and in the absence and the presence of base pairing. All results point to an 8-peroxide as the major oxidation product in the experiment, and the oxidation becomes slightly more favorable in a neutral radical form. On the basis of a variety of reaction pathways and product profiles observed in the present and previous studies, the interplay between guanine structure, base pairing, and singlet oxygenation and its biological implications are discussed.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194 Hiroshima, Japan
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Avenue, Long Island City, New York 11101, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
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8
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Moe MM, Benny J, Liu J. Collision-induced dissociation of homodimeric and heterodimeric radical cations of 9-methylguanine and 9-methyl-8-oxoguanine: correlation between intra-base pair proton transfer originating from the N1-H at a Watson-Crick edge and non-statistical dissociation. Phys Chem Chem Phys 2022; 24:9263-9276. [PMID: 35403654 DOI: 10.1039/d2cp00312k] [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
It has been shown previously in protonated, deprotonated and ionized guanine-cytosine base pairs that intra-base pair proton transfer from the N1-H at the Watson-Crick edge of guanine to the complementary nucleobase prompts non-statistical dissociation of the base-pair system, and the dissociation of a proton-transferred base-pair structure is kinetically more favored than that of the starting, conventional base-pair structure. However, the fundamental chemistry underlying this anomalous and intriguing kinetics has not been completely revealed, which warrants the examination of more base-pair systems in different structural contexts in order to derive a generalized base-pair structure-kinetics correlation. The purpose of the present work is to expand the investigation to the non-canonical homodimeric and heterodimeric radical cations of 9-methylguanine (9MG) and 9-methyl-8-oxoguanine (9MOG), i.e., [9MG·9MG]˙+, [9MOG·9MG]˙+ and [9MOG·9MOG]˙+. Experimentally, collision-induced dissociation tandem mass spectrometry coupled with an electrospray ionization (ESI) source was used for the formation of base-pair radical cations, followed by detection of dissociation product ions and cross sections in the collisions with Xe gas under single ion-molecule collision conditions and as a function of the center-of-mass collision energy. Computationally, density functional theory and coupled cluster theory were used to calculate and identify probable base-pair structures and intra-base pair proton transfer and hydrogen transfer reactions, followed by kinetics modeling to explore the properties of dissociation transition states and kinetic factors. The significance of this work is twofold: it provides insight into base-pair opening kinetics in three biologically-important, non-canonical systems upon oxidative and ionization damage; and it links non-statistical dissociation to intra-base pair proton-transfer originating from the N1-H at the Watson-Crick edge of 8-oxoguanine, enhancing understanding towards the base-pair fragmentation assisted by proton transfer.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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9
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Chung Kim Chung K, Mahdavi-Amiri Y, Korfmann C, Hili R. PhOxi-Seq: Single-Nucleotide Resolution Sequencing of N2-Methylation at Guanosine in RNA by Photoredox Catalysis. J Am Chem Soc 2022; 144:5723-5727. [PMID: 35316019 DOI: 10.1021/jacs.2c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical modifications regulate the fate and function of cellular RNAs. Newly developed sequencing methods have allowed a deeper understanding of the biological role of RNA modifications; however, the vast majority of post-transcriptional modifications lack a well-defined sequencing method. Here, we report a photo-oxidative sequencing (PhOxi-seq) approach for guanosine N2-methylation, a common methylation mark seen in N2-methylguanosine (m2G) and N2,N2-dimethylguanosine (m22G). Using visible light-mediated organic photoredox catalysis, m2G and m22G are chemoselectively oxidized in the presence of canonical RNA nucleosides, which results in a strong mutation signature observed during sequencing. PhOxi-seq was demonstrated on various tRNAs and rRNA to reveal N2-methylation with excellent response and markedly improved read-through at m22G sites.
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Affiliation(s)
- Kimberley Chung Kim Chung
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Yasaman Mahdavi-Amiri
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Christopher Korfmann
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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10
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Razskazovskiy Y, Campbell EB, Cutright ZD, Thomas CS, Roginskaya M. One-electron oxidation of guanine derivatives: Detection of 2,5-diaminoimidazolone and novel guanine-guanine cross-links as major end products. Radiat Phys Chem Oxf Engl 1993 2022. [DOI: 10.1016/j.radphyschem.2022.110099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Kumar A, Sevilla MD. Proton-Transfer Reactions in One-Electron-Oxidized G-Quadruplexes: A Density Functional Theory Study. J Phys Chem B 2022; 126:1483-1491. [PMID: 35152699 PMCID: PMC8881324 DOI: 10.1021/acs.jpcb.1c10529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, G-quadruplexes (Gq) formed in B-DNA as secondary structures are found to be important therapeutic targets and material for developing nanodevices. Gq are guanine-rich and thus susceptible to oxidative damage by producing short-lived intermediate radicals via proton-transfer reactions. Understanding the mechanisms of radical formation in Gq is of fundamental interest to understand the early stages of DNA damage. Herein, we used density functional theory including aqueous phase (ωB97XD-PCM/6-31++G**) and considered single layer of Gq [G-quartets (G4): association of four guanines in a cyclic Hoogsteen hydrogen-bonded arrangement (Scheme 1)] to unravel the mechanisms of formation of intermediates by calculating the relative Gibbs free energies and spin density distributions of one-electron-oxidized G4 and its various proton-transfer states: G•+, G(N1-H)•, G(N2-H')•, G(N2-H″)•, G(N1-H)•-(H+O6)G, and G(N2-H)•-(H+N7)G. The present calculation predicts the formation of G(N2-H)•-(H+N7)G, which is only ca. 0.8 kcal/mol higher in energy than the initially formed G•+. The formation of G(N2-H)•-(H+N7)G plays a key role in explaining the formation of 8-OG along with G(N1-H)• formation via tautomerization from G(N2-H)•, as proposed recently.
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Affiliation(s)
- Anil Kumar
- Corresponding Author: . Tel: +1 248 370 2327, . Tel: +1 248 370 2328
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12
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Denisov SA, Ward S, Shcherbakov V, Stark AD, Kaczmarek R, Radzikowska-Cieciura E, Debnath D, Jacobs T, Kumar A, Sevilla MD, Pernot P, Dembinski R, Mostafavi M, Adhikary A. Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group. J Phys Chem B 2022; 126:430-442. [PMID: 34990129 PMCID: PMC8776618 DOI: 10.1021/acs.jpcb.1c09068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O-)═S)). ESR investigations show that DMTP(O-)═S reacts with Cl2•- to form the σ2σ*1 adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O-)═S to produce [-P-S[Formula: see text]S-P-]-. -P-S[Formula: see text]Cl in G-P(O-)═S undergoes hole transfer to Gua, forming the cation radical (G•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O-)═S forms the thiyl radical (-P-S•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]-. Gua in G-P(O-)═S is oxidized unimolecularly by the -P-S• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.
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Affiliation(s)
- Sergey A. Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Alexander D. Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Ewa Radzikowska-Cieciura
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Michael D. Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Roman Dembinski
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA,Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
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13
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Zhou W, Liu J. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules. Phys Chem Chem Phys 2021; 23:24464-24477. [PMID: 34698322 DOI: 10.1039/d1cp03884b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al., Phys. Chem. Chem. Phys., 2018, 20, 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands (i.e., 9MG˙+·(H2O)1-2) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙+ and are referred to as HAO6 and HAN7, respectively. The primary products of HAO6 and HAN7 reactions, including [9MG + HO6]+/[9MG + HN7]+ and ˙OH, react further to either form [8OH-9MG + HO6]˙+ and [8OH-9MG + HN7]˙+via C8-hydroxylation or form radical cations of 6-enol-guanine (6-enol-G˙+) and 7H-guanine (7HG˙+) via SN2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG+ by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + HN7]˙+ has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy.
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Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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14
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Deprotonation Dynamics of Guanine Radical Cations †. Photochem Photobiol 2021; 98:523-531. [PMID: 34653259 DOI: 10.1111/php.13540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
This review is dedicated to guanine radical cations (G+ )· that are precursors to oxidatively generated damage to DNA. (G+ )· are unstable in neutral aqueous solution and tend to lose a proton. The deprotonation process has been studied by time-resolved absorption experiments in which (G+ )· radicals are produced either by an electron abstraction reaction, using an external oxidant, or by low-energy/low-intensity photoionization of DNA. Both the position of the released proton and the dynamics of the process depend on the secondary DNA structure. While deprotonation in duplex DNA leads to (G-H1)· radicals, in guanine quadruplexes the (G-H2)· analogs are observed. Deprotonation in monomeric guanosine proceeds with a time constant of ˜60 ns; in genomic DNA, it is completed within 2 µs; and in guanine quadruplexes, it spans from at least 30 ns to over 50 µs. Such a deprotonation dynamics in four-stranded structures, extended over more than three decades of times, is correlated with the anisotropic structure of DNA and the mobility of its hydration shell. In this case, commonly used second-order reaction models are inappropriate for its description.
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Affiliation(s)
| | - Akos Banyasz
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France.,Univ Lyon, ENS de Lyon, CNRS, UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, Lyon, F-69342, France
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, Gif-sur-Yvette, F-91191, France
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15
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Peng H, Jie J, Mortimer IP, Ma Z, Su H, Greenberg MM. Reactivity and DNA Damage by Independently Generated 2'-Deoxycytidin- N4-yl Radical. J Am Chem Soc 2021; 143:14738-14747. [PMID: 34467764 DOI: 10.1021/jacs.1c06425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Oxidative stress produces a variety of radicals in DNA, including pyrimidine nucleobase radicals. The nitrogen-centered DNA radical 2'-deoxycytidin-N4-yl radical (dC·) plays a role in DNA damage mediated by one electron oxidants, such as HOCl and ionizing radiation. However, the reactivity of dC· is not well understood. To reduce this knowledge gap, we photochemically generated dC· from a nitrophenyl oxime nucleoside and within chemically synthesized oligonucleotides from the same precursor. dC· formation is confirmed by transient UV-absorption spectroscopy in laser flash photolysis (LFP) experiments. LFP and duplex DNA cleavage experiments indicate that dC· oxidizes dG. Transient formation of the dG radical cation (dG+•) is observed in LFP experiments. Oxidation of the opposing dG in DNA results in hole transfer when the opposing dG is part of a dGGG sequence. The sequence dependence is attributed to a competition between rapid proton transfer from dG+• to the opposing dC anion formed and hole transfer. Enhanced hole transfer when less acidic O6-methyl-2'-deoxyguanosine is opposite dC· supports this proposal. dC· produces tandem lesions in sequences containing thymidine at the 5'-position by abstracting a hydrogen atom from the thymine methyl group. The corresponding thymidine peroxyl radical completes tandem lesion formation by reacting with the 5'-adjacent nucleotide. As dC· is reduced to dC, its role in the process is traceless and is only detectable because of the ability to independently generate it from a stable precursor. These experiments reveal that dC· oxidizes neighboring nucleotides, resulting in deleterious tandem lesions and hole transfer in appropriate sequences.
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Affiliation(s)
- Haihui Peng
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ifor P Mortimer
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Zehan Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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16
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Landi A, Capobianco A, Peluso A. The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study. Molecules 2021; 26:5497. [PMID: 34576968 PMCID: PMC8465834 DOI: 10.3390/molecules26185497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/28/2022] Open
Abstract
The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800-1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.
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Affiliation(s)
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, SA, Italy; (A.L.); (A.P.)
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17
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Zhang LQ, Xu XM, Li XY, Guo J, Wang HZ, Sun JY, Cai JP. Urinary 8-oxo-7,8-dihydroguanosine levels are elevated in HCV-infected patients. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:884-895. [PMID: 34379042 DOI: 10.1080/15257770.2021.1961272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
HCV patients are usually under substantial oxidative stress because of viral infection. A total of 177 patients with HCV infection and 198 age- and sex-matched healthy controls were enrolled in this study. We evaluated the urinary levels of 8-oxo-7, 8-dihydro-2'deoxyguanosine (8-oxodGuo) and 8-oxo-7, 8-dihydroguanosine (8-oxoGuo) in patients with HCV infection and explored the factors affecting the urinary 8-oxodGuo or 8-oxoGuo levels. Biomarkers of liver function, cancer, and inflammation were determined. Nonparametric correlations were used to evaluate the correlation between 8-oxoGuo or 8-oxodGuo and various laboratory biochemical indicators. Results showed that the levels of urinary 8-oxoGuo both in male and female patients with HCV infection were significantly higher than those in healthy controls (both p < 0.0001), while the urinary 8-oxodGuo levels only in male patients with HCV infection were significantly higher than those in healthy controls (p < 0.01). Urinary 8-oxoGuo was significantly associated with the white blood cell count, C-reactive protein level, and 8-oxodGuo level (p = 0.016, p = 0.003, and p = 0.000, respectively). Urinary 8-oxodGuo was significantly associated with the white blood cell count and 8-oxoGuo level (p = 0.018 and p = 0.000, respectively). A regression equation of urinary 8-oxoGuo or 8-oxodGuo was also established using the biomarkers in plasma. The results suggested that patients with a high C-reactive protein level are likely to have high urinary 8-oxoGuo levels as well, which may be useful for assessing the level of inflammation and oxidative stress in HCV patients.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.1961272 .
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Affiliation(s)
- Li-Qun Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Beijing, P.R. China.,Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xin-Min Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China
| | - Xiang-Yu Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Beijing, P.R. China.,Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Jie Guo
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China
| | - Hui-Zhu Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China
| | - Ji-Yun Sun
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Beijing, P.R. China.,Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
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18
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The Two Faces of the Guanyl Radical: Molecular Context and Behavior. Molecules 2021; 26:molecules26123511. [PMID: 34207639 PMCID: PMC8227002 DOI: 10.3390/molecules26123511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.
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19
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Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Moe MM, Benny J, Sun Y, Liu J. Experimental and theoretical assessment of protonated Hoogsteen 9-methylguanine-1-methylcytosine base-pair dissociation: kinetics within a statistical reaction framework. Phys Chem Chem Phys 2021; 23:9365-9380. [PMID: 33885080 DOI: 10.1039/d0cp06682f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We investigated the collision-induced dissociation (CID) reactions of a protonated Hoogsteen 9-methylguanine-1-methylcytosine base pair (HG-[9MG·1MC + H]+), which aims to address the mystery of the literature reported "anomaly" in product ion distributions and compare the kinetics of a Hoogsteen base pair with its Watson-Crick isomer WC-[9MG·1MC + H]+ (reported recently by Sun et al.; Phys. Chem. Chem. Phys., 2020, 22, 24986). Product ion cross sections and branching ratios were measured as a function of center-of-mass collision energy using guided-ion beam tandem mass spectrometry, from which base-pair dissociation energies were determined. Product structures and energetics were assessed using various theories, of which the composite DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97XD/6-311++G(d,p) was adopted as the best-performing method for constructing a reaction potential energy surface. The statistical Rice-Ramsperger-Kassel-Marcus theory was found to provide a useful framework for rationalizing the dominating abundance of [1MC + H]+ over [9MG + H]+ in the fragment ions of HG-[9MG·1MC + H]+. The kinetics analysis proved the necessity for incorporating into kinetics modeling not only the static properties of reaction minima and transition states but more importantly, the kinetics of individual base-pair conformers that have formed in collisional activation. The analysis also pinpointed the origin of the statistical kinetics of HG-[9MG·1MC + H]+vs. the non-statistical behavior of WC-[9MG·1MC + H]+ in terms of their distinctively different intra-base-pair hydrogen-bonds and consequently the absence of proton transfer between the N1 position of 9MG and the N3' of 1MC in the Hoogsteen base pair. Finally, the Hoogsteen base pair was examined in the presence of a water ligand, i.e., HG-[9MG·1MC + H]+·H2O. Besides the same type of base-pair dissociation as detected in dry HG-[9MG·1MC + H]+, secondary methanol elimination was observed via the SN2 reaction of water with nucleobase methyl groups.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA.
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21
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Sun Y, Tsai M, Moe MM, Liu J. Dynamics and Multiconfiguration Potential Energy Surface for the Singlet O2 Reactions with Radical Cations of Guanine, 9-Methylguanine, 2′-Deoxyguanosine, and Guanosine. J Phys Chem A 2021; 125:1564-1576. [DOI: 10.1021/acs.jpca.1c00095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College 31-10 Thomson Avenue, Long Island City, New York 11101, United States
| | - May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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22
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Zhu Y, Zhu M, Xie J, Hu Y, Liu Y, Zhu C. Photochemical reaction kinetics and mechanism of bisphenol A with K 2S 2O 8 in aqueous solution: a laser flash photolysis study. CAN J CHEM 2021. [DOI: 10.1139/cjc-2019-0485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The photochemical reaction kinetics and mechanism of bisphenol A (BPA) with potassium persulfate (K2S2O8) were investigated by using 266 nm laser flash photolysis and gas chromatography mass spectrum (GC-MS) technique. Sulfate radical (SO4•−), generated upon K2S2O8 photolysis, reacted with BPA with the overall rate constant of (1.61 ± 0.15) × 109 L mol−1 s−1, and two main reaction mechanisms were involved. One was addition channel to generate BPA–SO4•− adduct with a specific second-order rate constant of (1.09 ± 0.15) × 109 L mol−1 s−1. Molecular oxygen was involved in the decay of the BPA–SO4•− adduct with a rate constant of (1.28 ± 0.14) × 108 L mol−1 s−1. Another channel was the formation of BPA’s phenoxyl radical, likely derived from a deprotonation of the cation radical (BPA•+) generated from single electron transfer reactions. The specific rate constant of BPA’s phenoxyl radical formation was determined to be (6.16 ± 0.08) × 108 L mol−1 s−1. The overall rate constant was in line with the sum of aforementioned two specific rate constants for two main reaction channels. By comparing these rate constants, it was indicated that SO4•− addition channel accounted for ∼65% (1.09/1.61) to the overall reaction, and phenoxyl radical formation accounted for only ∼35% (0.62/1.61). The transformation products of BPA were identified by using GC-MS including 4-isopropylphenol, 4-isopropenylphenol, and 2,4-di-tert-butylphenol, and the reaction mechanism was proposed. These results may provide microscopic kinetics and mechanism information on BPA degradation using SO4•−-based advanced oxidation processes.
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Affiliation(s)
- Yongchao Zhu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, P.R. China
- Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, P.R. China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, P.R. China
| | - Mengyu Zhu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, P.R. China
- Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, P.R. China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, P.R. China
| | - Jingjing Xie
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, P.R. China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, P.R. China
| | - Yadong Hu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, P.R. China
- Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, P.R. China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, P.R. China
| | - Ying Liu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, P.R. China
- Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, P.R. China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, P.R. China
| | - Chengzhu Zhu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, P.R. China
- Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, P.R. China
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, P.R. China
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23
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Wei S, Zhang Z, Liu S, Wang Y. Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation. NEW J CHEM 2021. [DOI: 10.1039/d1nj01653a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The pKa values of reactive protons in 8-oxoG˙+ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.
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Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Zhenhua Zhang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Shijun Liu
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Yinghui Wang
- College of Science
- Chang’an University
- Xi’an 710064
- China
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24
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Landi A, Capobianco A, Peluso A. Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA. J Phys Chem Lett 2020; 11:7769-7775. [PMID: 32830977 PMCID: PMC8154848 DOI: 10.1021/acs.jpclett.0c01996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the framework of a multistep mechanism in which environmental motion triggers comparatively faster elementary electron-transfer steps and stabilizes hole-transfer products, microscopic coherence is crucial for rationalizing the observed yield ratios of oxidative damage to DNA. Interference among probability amplitudes of indistinguishable electron-transfer paths is able to drastically change the final outcome of charge transport, even in DNA oligomers constituted by similar building blocks, and allows for reconciling apparently discordant experimental observations. Properly tailored DNA oligomers appear to be a promising workbench for studying tunneling in the presence of dissipation at the macroscopic level.
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25
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Balanikas E, Banyasz A, Douki T, Baldacchino G, Markovitsi D. Guanine Radicals Induced in DNA by Low-Energy Photoionization. Acc Chem Res 2020; 53:1511-1519. [PMID: 32786340 DOI: 10.1021/acs.accounts.0c00245] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Guanine (G) radicals are precursors to DNA oxidative damage, correlated with carcinogenesis and aging. During the past few years, we demonstrated clearly an intriguing effect: G radicals can be generated upon direct absorption of UV radiation with energy significantly lower than the G ionization potential. Using nanosecond transient absorption spectroscopy, we studied the primary species, ejected electrons and guanine radicals, which result from photoionization of various DNA systems in aqueous solution.The DNA propensity to undergo electron detachment at low photon energies greatly depends on its secondary structure. Undetected for monomers or unstacked oligomers, this propensity may be 1 order of magnitude higher for G-quadruplexes than for duplexes. The experimental results suggest nonvertical processes, associated with the relaxation of electronic excited states. Theoretical studies are required to validate the mechanism and determine the factors that come into play. Such a mechanism, which may be operative over a broad excitation wavelength range, explains the occurrence of oxidative damage observed upon UVB and UVA irradiation.Quantification of G radical populations and their time evolution questions some widespread views. It appears that G radicals may be generated with the same probability as pyrimidine dimers, which are considered to be the major lesions induced upon absorption of low-energy UV radiation by DNA. As most radical cations undergo deprotonation, the vast majority of the final reaction products is expected to stem from long-lived deprotonated radicals. Consequently, when G radical cations are involved, the widely used oxidation marker 8-oxodG is not representative of the oxidative damage.Beyond the biological consequences, photogeneration of electron holes in G-quadruplexes may inspire applications in nanoelectronics; although four-stranded structures are currently studied as molecular wires, their behavior as photoconductors has not been explored so far.In the present Account, after highlighting some key experimental issues, we first describe the photoionization process, and then, we focus on radicals. We use as show-cases new results obtained for genomic DNA and Oxytricha G-quadruplexes. Generation and reaction dynamics of G radicals in these systems provide a representative picture of the phenomena reported previously for duplexes and G-quadruplexes, respectively.
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Affiliation(s)
| | - Akos Banyasz
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble France
| | - Gérard Baldacchino
- 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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Huang SR, Tureček F. Cation Radicals of Hachimoji Nucleobases. Canonical Purine and Noncanonical Pyrimidine Forms Generated in the Gas Phase and Characterized by UV–Vis Photodissociation Action Spectroscopy. J Phys Chem A 2020; 124:7101-7112. [DOI: 10.1021/acs.jpca.0c06227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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27
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Zhang X, Jie J, Song D, Su H. Deprotonation of Guanine Radical Cation G •+ Mediated by the Protonated Water Cluster. J Phys Chem A 2020; 124:6076-6083. [PMID: 32585092 DOI: 10.1021/acs.jpca.0c03748] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H2O-PCM, 4H2O-PCM, 5H2O-PCM, and 7H2O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G•+.
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Affiliation(s)
- Xianwang Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100048, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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28
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Sobek J, Schmidt M, Grossmann J, Rehrauer H, Schmidt L, Schlapbach R. Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence. Methods Appl Fluoresc 2020; 8:035010. [PMID: 32428873 DOI: 10.1088/2050-6120/ab947d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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29
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Jie J, Xia Y, Huang CH, Zhao H, Yang C, Liu K, Song D, Zhu BZ, Su H. Sulfur-centered hemi-bond radicals as active intermediates in S-DNA phosphorothioate oxidation. Nucleic Acids Res 2020; 47:11514-11526. [PMID: 31724721 PMCID: PMC7145531 DOI: 10.1093/nar/gkz987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/10/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
Phosphorothioate (PS) modifications naturally appear in bacteria and archaea genome and are widely used as antisense strategy in gene therapy. But the chemical effects of PS introduction as a redox active site into DNA (S-DNA) is still poorly understood. Herein, we perform time-resolved spectroscopy to examine the underlying mechanisms and dynamics of the PS oxidation by potent radicals in free model, in dinucleotide, and in S-oligomer. The crucial sulphur-centered hemi-bonded intermediates -P–S∴S–P- were observed and found to play critical roles leading to the stable adducts of -P–S–S–P-, which are backbone DNA lesion products. Moreover, the oxidation of the PS moiety in dinucleotides d[GPSG], d[APSA], d[GPSA], d[APSG] and in S-oligomers was monitored in real-time, showing that PS oxidation can compete with adenine but not with guanine. Significantly, hole transfer process from A+• to PS and concomitant -P–S∴S–P- formation was observed, demonstrating the base-to-backbone hole transfer unique to S-DNA, which is different from the normally adopted backbone-to-base hole transfer in native DNA. These findings reveal the distinct backbone lesion pathway brought by the PS modification and also imply an alternative -P–S∴S–P-/-P–S–S–P- pathway accounting for the interesting protective role of PS as an oxidation sacrifice in bacterial genome.
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Affiliation(s)
- Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ye Xia
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Chun-Hua Huang
- State Key Lab of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Kunhui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ben-Zhan Zhu
- State Key Lab of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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30
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Huang SR, Liu Y, Tureček F. UV–vis Photodissociation Action Spectroscopy Reveals Cytosine–Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Reduction. J Phys Chem B 2020; 124:3505-3517. [DOI: 10.1021/acs.jpcb.0c01693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Yue Liu
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
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31
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Interactions of Single Particle with Organic Matters: A Facile Bottom-Up Approach to Low Dimensional Nanostructures. QUANTUM BEAM SCIENCE 2020. [DOI: 10.3390/qubs4010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A particle induces a pack of chemical reactions in nanospace: chemical reactions confined into extremely small space provide an ultimate technique for the nanofabrication of organic matter with a variety of functions. Since the discovery of particle accelerators, an extremely high energy density can be deposited, even by a single isolated particle with MeV-ordered kinetic energy. However, this was considered to cause severe damages to organic molecules due to its relatively small bond energies, and lack of ability to control the reactions precisely to form the structures while retaining physico-chemical molecular functionalities. Practically, the severely damaged area along a particle trajectory: a core of a particle track has been simply visualized for the detection/dosimetry of an incident particle to the matters, or been removed to lead nanopores and functionalized by refilling/grafting of fresh organic/inorganic materials. The use of intra-track reactions in the so-called “penumbra” or “halo” area of functional organic materials has been realized and provided us with novel and facile protocols to provide low dimensional nano-materials with perfect size controllability in the 21st century. These protocols are now referred to as single particle nanofabrication technique (SPNT) and/or single particle triggered linear polymerization technique (STLiP), paving the way towards a new approach for nanomaterials with desired functionalities from original molecules. Herein, we report on the extremely wide applicability of SPNT/STLiP protocols for the future development of materials for opto-electronic, catalytic, and biological applications among others.
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32
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Anderson RF, Shinde SS, Maroz A, Reynisson J. The reduction potential of the slipped GC base pair in one-electron oxidized duplex DNA. Phys Chem Chem Phys 2020; 22:642-646. [PMID: 31822872 DOI: 10.1039/c9cp05544d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Redox equilibrium between the low potential aniline radical cation and the guanine in the GC base pair of duplex DNA has been established using pulse radiolysis. We relate the measurement of a radical one-electron reduction potential, E0', of 1.01 ± 0.03 V to the perturbation of the GC base pair to accommodate the neutral guanyl radical in an energetically more stable 'slipped' structure. The formation of the 'slipped' structure is exothermic by -11.4 kcal mol-1 as calculated by DFT, which is inline with our experimental results.
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Affiliation(s)
- Robert F Anderson
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
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33
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Sun Y, Moe MM, Liu J. Is non-statistical dissociation a general feature of guanine–cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine–1-methylcytosine Watson–Crick base pair, and comparison with its deprotonated and radical cation analogues. Phys Chem Chem Phys 2020; 22:24986-25000. [DOI: 10.1039/d0cp04243a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Non-statistical dissociation of a protonated guanine–cytosine Watson–Crick base pair.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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34
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Liu Y, Huang SR, Tureček F. Guanine–adenine interactions in DNA tetranucleotide cation radicals revealed by UV/vis photodissociation action spectroscopy and theory. Phys Chem Chem Phys 2020; 22:16831-16842. [DOI: 10.1039/d0cp02362k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen-rich cation radicals (GATT + 2H)+˙ and (AGTT + 2H)+˙ represent oligonucleotide models of charged hydrogen atom adducts to DNA.
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Affiliation(s)
- Yue Liu
- Department of Chemistry
- University of Washington
- Seattle
- USA
| | - Shu R. Huang
- Department of Chemistry
- University of Washington
- Seattle
- USA
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35
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Sun Y, Moe MM, Liu J. Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand. Phys Chem Chem Phys 2020; 22:14875-14888. [DOI: 10.1039/d0cp01788d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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36
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Bhunia S, Kumar A, Ojha AK. Tuning of structural and magnetic properties by intriguing radical-radical interaction by double electron oxidation in U-A-U′ triplex formation. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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38
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Cercola R, Uleanya KO, Dessent CEH. Electron detachment dynamics of the iodide-guanine cluster: does ionization occur from the iodide or from guanine? Mol Phys 2019. [DOI: 10.1080/00268976.2019.1679402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Lei Y, Cheng S, Luo N, Yang X, An T. Rate Constants and Mechanisms of the Reactions of Cl • and Cl 2•- with Trace Organic Contaminants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11170-11182. [PMID: 31483622 DOI: 10.1021/acs.est.9b02462] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cl• and Cl2•- radicals contribute to the degradation of trace organic contaminants (TrOCs) such as pharmaceutical and personal care products and endocrine-disrupting chemicals. However, little is known about their reaction rate constants and mechanisms. In this study, the reaction rate constants of Cl• and Cl2•- with 88 target compounds were determined using laser flash photolysis. Decay kinetics, product buildup kinetics, and competition kinetics were applied to track the changes in their transient spectra. Cl• exhibited quite high reactivity toward TrOCs with reaction rate constants ranging from 3.10 × 109 to 4.08 × 1010 M-1 s-1. Cl2•- was less reactive but more selective, with reaction rate constants varying from <1 × 106 to 2.78 × 109 M-1 s-1. Three QSAR models were developed, which were capable of predicting the reaction rate constants of Cl2•- with TrOCs bearing phenol, alkoxy benzene, and aniline groups. The detection of Cl•-adducts of many TrOCs suggested that Cl• addition was an important reaction mechanism. Single electron transfer (SET) predominated in reactions of Cl• with TrOCs bearing electron-rich moieties (e.g., sulfonamides), and their cation radicals were observed. Cl• might also abstract hydrogen atoms from phenolic compounds to generate phenoxyl radicals. Moreover, Cl• could react with TrOCs through multiple pathways since more than one transient intermediate was detected simultaneously. SET was the major reaction mechanism of Cl2•- reactions with TrOCs bearing phenols, alkoxy benzenes, and anilines groups. Cl2•- was found to play an important role in TrOC degradation, though it has been often neglected in previous studies. The results improve the understanding of halogen radical-involved chemistry in TrOC degradation.
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Affiliation(s)
- Yu Lei
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology , Sun Yat-sen University , Guangzhou 510275 , China
| | - Shuangshuang Cheng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology , Sun Yat-sen University , Guangzhou 510275 , China
| | - Na Luo
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control , Guangdong University of Technology , Guangzhou 510006 , China
| | - Xin Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology , Sun Yat-sen University , Guangzhou 510275 , China
| | - Taicheng An
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control , Guangdong University of Technology , Guangzhou 510006 , China
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40
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Lee YA, Cho HY, Kim SK. Neighboring base sequence effect on DNA damage. J Biomol Struct Dyn 2019; 38:3188-3195. [PMID: 31432766 DOI: 10.1080/07391102.2019.1659186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Guanine is the most strongly oxidized base in DNA; generation of a guanine radical cation as an intermediate in an oxidation reaction leads to migration through a resulting cationic hole in the DNA π-stack until it is trapped by irreversible reaction with water or other free radicals. In the case of normal sequences, the primary position of Guanine oxidations by one-electron oxidants such as carbonate radical anions, BPT(7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene), and riboflavin are 5'-G in GG doublets and the central G in a GGG triplet. According to results, the properties of guanine oxidation on abasic site containing sequences are independent from the position of AP(apurinic/apyrimidinic) site in the presence of carbonate radical anions under a short irradiation time, although this radical is exposed to solvent by the existence of an abasic site. The lack of abasic site effect on guanine oxidative damage by the carbonate radical may be due to a sequence-independent property of the initial electron transfer rate in the hole injection step, or may relate to an electron transfer mechanism with large reorganization energy dependency. Consequently, the carbonate radical anions may easily migrate to another single G in the charge re-distribution step. Meanwhile, there is a strong dependency on the presence of an AP(apurinic/apyrimidinic) site in the cleavage patterns of guanine oxidations by physically large oxidizing agents, such as BPT(7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene) and riboflavin. These radicals show strong AP(apurinic/apyrimidinic) site dependency and clear G-site selectivity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
| | - Ha Young Cho
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
| | - Seog K Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
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41
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Balanikas E, Banyasz A, Baldacchino G, Markovitsi D. Populations and Dynamics of Guanine Radicals in DNA strands-Direct versus Indirect Generation. Molecules 2019; 24:molecules24132347. [PMID: 31247883 PMCID: PMC6651618 DOI: 10.3390/molecules24132347] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 01/17/2023] Open
Abstract
Guanine radicals, known to be involved in the damage of the genetic code and aging, are studied by nanosecond transient absorption spectroscopy. They are generated in single, double and four-stranded structures (G-quadruplexes) by one and two-photon ionization at 266 nm, corresponding to a photon energy lower than the ionization potential of nucleobases. The quantum yield of the one-photon process determined for telomeric G-quadruplexes (TEL25/Na+) is (5.2 ± 0.3) × 10−3, significantly higher than that found for duplexes containing in their structure GGG and GG sequences, (2.1 ± 0.4) × 10−3. The radical population is quantified in respect of the ejected electrons. Deprotonation of radical cations gives rise to (G-H1)• and (G-H2)• radicals for duplexes and G-quadruplexes, respectively. The lifetimes of deprotonated radicals determined for a given secondary structure strongly depend on the base sequence. The multiscale non-exponential dynamics of these radicals are discussed in terms of inhomogeneity of the reaction space and continuous conformational motions. The deviation from classical kinetic models developed for homogeneous reaction conditions could also be one reason for discrepancies between the results obtained by photoionization and indirect oxidation, involving a bi-molecular reaction between an oxidant and the nucleic acid.
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Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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42
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Banyasz A, Balanikas E, Martinez-Fernandez L, Baldacchino G, Douki T, Improta R, Markovitsi D. Radicals Generated in Tetramolecular Guanine Quadruplexes by Photoionization: Spectral and Dynamical Features. J Phys Chem B 2019; 123:4950-4957. [PMID: 31117607 DOI: 10.1021/acs.jpcb.9b02637] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplexes are four-stranded DNA structures playing a key role in many biological functions and are promising for applications in the field of nanoelectronics. Characterizing the generation and fate of radical cations (electron holes) within these systems is important in relation to the DNA oxidative damage and/or conductivity issues. This study focuses on guanine radicals in G-quadruplexes formed by association of four TGGGGT strands in the presence of Na+ cations, (TG4T)4/Na+. Using nanosecond transient spectroscopy with 266 nm excitation, we quantitatively characterize hydrated ejected electrons and three types of guanine radicals. We show that, at an energy lower by 2.7 eV than the guanine ionization potential, one-photon ionization occurs with quantum yield of (3.5 ± 0.5) × 10-3. Deprotonation of the radical cations is completed within 20 μs, leading to the formation of (G-H2)• radicals, following a strongly nonexponential decay pattern. Within 10 ms, the latter undergoes tautomerization to deprotonated (G-H1)• radicals. The dynamics of the various radicals determined for (TG4T)4/Na+, in connection to those reported previously for telomeric G-quadruplexes TEL21/Na+, is correlated with energetic factors computed by quantum chemical methods. The faster deprotonation of radical cations in (TG4T)4/Na+ compared to TEL21/Na+ explains that irradiation of the former does not generate 8-oxodGuo, which is readily detected by high-performance liquid chromatography/mass spectrometry in the case of TEL21/Na+.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.,Univ Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , F-69342 Lyon , France
| | | | - Lara Martinez-Fernandez
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France.,Departamento de Química , Universidad Autónoma de Madrid , c/ Francisco Tomás y Valiente 7, Cantoblanco , 28049 Madrid , Spain
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
| | - Thierry Douki
- Univ. Grenoble-Alpes, CEA, CNRS, SyMMES UMR , 5819 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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43
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Choi J, Tojo S, Ahn DS, Fujitsuka M, Miyamoto S, Kobayashi K, Ihee H, Majima T. Proton Transfer Accompanied by the Oxidation of Adenosine. Chemistry 2019; 25:7711-7718. [PMID: 30957282 DOI: 10.1002/chem.201900732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Indexed: 11/07/2022]
Abstract
Despite numerous experimental and theoretical studies, the proton transfer accompanying the oxidation of 2'-deoxyadenosine 5'-monophosphate 2'-deoxyadenosine 5'-monophosphate (5'-dAMP, A) is still under debate. To address this issue, we have investigated the oxidation of A in acidic and neutral solutions by using transient absorption (TA) and time-resolved resonance Raman (TR3 ) spectroscopic methods in combination with pulse radiolysis. The steady-state Raman signal of A was significantly affected by the solution pH, but not by the concentration of adenosine (2-50 mm). More specifically, the A in acidic and neutral solutions exists in its protonated (AH+ (N1+H+ )) and neutral (A) forms, respectively. On the one hand, the TA spectral changes observed at neutral pH revealed that the radical cation (A.+ ) generated by pulse radiolysis is rapidly converted into A. (N6-H) through the loss of an imino proton from N6. In contrast, at acidic pH (<4), AH.2+ (N1+H+ ) generated by pulse radiolysis of AH+ (N1+H+ ) does not undergo the deprotonation process owing to the pKa value of AH.2+ (N1+H+ ), which is higher than the solution pH. Furthermore, the results presented in this study have demonstrated that A, AH+ (N1+H+ ), and their radical species exist as monomers in the concentration range of 2-50 mm. Compared with the Raman bands of AH+ (N1+H+ ), the TR3 bands of AH.2+ (N1+H+ ) are significantly down-shifted, indicating a decrease in the bond order of the pyrimidine and imidazole rings due to the resonance structure of AH.2+ (N1+H+ ). Meanwhile, A. (N6-H) does not show a Raman band corresponding to the pyrimidine+NH2 scissoring vibration due to diprotonation at the N6 position. These results support the final products generated by the oxidation of adenosine in acidic and neutral solutions being AH.2+ (N1+H+ ) and A. (N6-H), respectively.
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Affiliation(s)
- Jungkweon Choi
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Republic of Korea
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Sachiko Tojo
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Doo-Sik Ahn
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Republic of Korea
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Shunichi Miyamoto
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazuo Kobayashi
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, 305-701, Republic of Korea
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
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Landi A, Borrelli R, Capobianco A, Peluso A. Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires. J Phys Chem Lett 2019; 10:1845-1851. [PMID: 30939015 DOI: 10.1021/acs.jpclett.9b00650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.
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Affiliation(s)
- Alessandro Landi
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science , University of Torino , Via Leonardo da Vinci 44 , I-10095 Grugliasco , Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia , Università di Salerno , I-84084 Fisciano , Salerno , Italy
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Kumar A, Sevilla MD. Excited States of One-Electron Oxidized Guanine-Cytosine Base Pair Radicals: A Time Dependent Density Functional Theory Study. J Phys Chem A 2019; 123:3098-3108. [PMID: 30896952 DOI: 10.1021/acs.jpca.9b00906] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One-electron oxidized guanine (G•+) in DNA generates several short-lived intermediate radicals via proton transfer reactions resulting in the formation of neutral guanine radicals. The identification of these radicals in DNA is of fundamental interest to understand the early stages of DNA damage. Herein, we used time-dependent density functional theory (TD-ωB97XD-PCM/6-31G(3df,p)) to calculate the vertical excitation energies of one-electron oxidized G and G-cytosine (C) base pair in various protonation states: G•+, G(N1-H)•, and G(N2-H)•, as well as G•+-C, G(N1-H)•-(H+)C, G(N1-H)•-(N4-H+)C), G(N1-H)•-C, and G(N2-H)•-C in aqueous phase. The calculated UV-vis spectra of these radicals are in good agreement with the experiment for the G radical species when the calculated values are red-shifted by 40-70 nm. The present calculations show that the lowest energy transitions of proton transfer species (G(N1-H)•-(H+)C, G(N1-H)•-(N4-H+)C, and G(N1-H)•-C) are substantially red-shifted in comparison to the spectrum of G•+-C. The calculated spectrum of G(N2-H)•-C shows intense absorption (high oscillator strength), which matches the strong absorption in the experimental spectra of G(N2-H)• at 600 nm. The present calculations predict the lowest charge transfer transition of C → G•+ is π → π* in nature and lies in the UV region (3.4-4.3 eV) with small oscillator strength.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry , Oakland University , Rochester , Michigan 48309 , United States
| | - Michael D Sevilla
- Department of Chemistry , Oakland University , Rochester , Michigan 48309 , United States
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Dang A, Liu Y, Tureček F. UV–Vis Action Spectroscopy of Guanine, 9-Methylguanine, and Guanosine Cation Radicals in the Gas Phase. J Phys Chem A 2019; 123:3272-3284. [DOI: 10.1021/acs.jpca.9b01542] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Andy Dang
- Department of Chemistry, University of Washington, Bagley Hall,
Box 351700, Seattle, Washington 98195-1700, United States
| | - Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall,
Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall,
Box 351700, Seattle, Washington 98195-1700, United States
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Wang Y, Zhao H, Zhou Q, Dai X, Liu K, Song D, Su H. Monitoring the Structure-Dependent Reaction Pathways of Guanine Radical Cations in Triplex DNA: Deprotonation Versus Hydration. J Phys Chem B 2019; 123:2853-2863. [PMID: 30834754 DOI: 10.1021/acs.jpcb.9b00608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exposure of DNA to one-electron oxidants leads initially to the formation of guanine radical cations (G•+), which may degrade by deprotonation or hydration and ultimately cause strand breaks or 8-oxoG lesions. As the structure is dramatically changed by binding of the third strand in the major groove of the target duplex, it makes the triplex an interesting DNA structure to be examined and compared with the duplex on the G•+ degradation pathways. Here, we report for the first time the time-resolved spectroscopy study on the G•+ reaction dynamics in triplex DNA together with the Fourier transform infrared characterization of steady-state products, from which structural effects on the reactivity of G•+ are unraveled. For an antiparallel triplex-containing GGC motif, G•+ mainly suffers from fast deprotonation (9.8 ± 0.2) × 106 s-1, featuring release of both N1-H and N2-H of G in the third strand directly into bulk water. The much faster and distinct deprotonation behavior compared to the duplex should be related to long-resident water spines in the third strand. The G•+ hydration product 8-oxoG is negligible for an antiparallel triplex; instead, the 5-HOO-(G-H) hydroperoxide formed after G•+ deprotonation is identified by its vibrational marker band. In contrast, in a parallel triplex (C+GC), the deprotonation of G•+ occurs slowly (6.0 ± 0.3) × 105 s-1 with the release of N1-H, while G•+ hydration becomes the major pathway with yields of 8-oxoG larger than in the duplex. The increased positive charge brought by the third strand makes the G radical in the parallel triplex sustain more cation character and prone for hydration. These results indicate that non-B DNA (triplex) plays an important role in DNA damage formation and provide mechanistic insights to rationalize why triplex structures might become hot spots for mutagenesis.
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Affiliation(s)
- Yinghui Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Qian Zhou
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Xiaojuan Dai
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Kunhui Liu
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Di Song
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Hongmei Su
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
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48
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Wang Y, Zhao H, Yang C, Jie J, Dai X, Zhou Q, Liu K, Song D, Su H. Degradation of Cytosine Radical Cations in 2′-Deoxycytidine and in i-Motif DNA: Hydrogen-Bonding Guided Pathways. J Am Chem Soc 2019; 141:1970-1979. [DOI: 10.1021/jacs.8b10743] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yinghui Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
- University of Chinese Academy of Science, Beijing 100049, P. R. China
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiaojuan Dai
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Kunhui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Di Song
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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49
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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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50
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Menachery SPM, Nguyen TP, Gopinathan P, Aravind UK, Aravindakumar CT. Exploring the mechanism of diphenylmethanol oxidation: A combined experimental and theoretical approach. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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