1
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Peng J, Pan Y, Zhou Y, Lei X, Guo Y, Lei Y, Kong Q, Cheng S, Yang X. Mechanistic Aspects of Photodegradation of Deoxynucleosides Induced by Triplet State of Effluent Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4751-4760. [PMID: 38324714 DOI: 10.1021/acs.est.3c08782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Excited triplet states of wastewater effluent organic matter (3EfOM*) are known as important photo-oxidants in the degradation of extracellular antibiotic resistance genes (eArGs) in sunlit waters. In this work, we further found that 3EfOM* showed highly selective reactivity toward 2'-deoxyguanosine (dG) sites within eArGs in irradiated EfOM solutions at pH 7.0, while it showed no photosensitizing capacity toward 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxycytidine (the basic structures of eArGs). The 3EfOM* contributed to the photooxidation of dG primarily via one-electron transfer mechanism, with second-order reaction rate constants of (1.58-1.74) × 108 M-1 s-1, forming the oxidation intermediates of dG (dG(-H)•). The formed dG(-H)• could play a significant role in hole hopping and damage throughout eArGs. Using the four deoxynucleosides as probes, the upper limit for the reduction potential of 3EfOM* is estimated to be between 1.47 and 1.94 VNHE. Compared to EfOM, the role of the triplet state of terrestrially natural organic matter (3NOM*) in dG photooxidation was minor (∼15%) mainly due to the rapid reverse reactions of dG(-H)• by the antioxidant moieties of NOM. This study advances our understanding of the difference in the photosensitizing capacity and electron donating capacity between NOM and EfOM and the photodegradation mechanism of eArGs induced by 3EfOM*.
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Affiliation(s)
- Jianglin Peng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Yanheng Pan
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yangjian Zhou
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Xin Lei
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming 650500, P. R. China
| | - Yifan Guo
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Yu Lei
- Key Laboratory of Photochemistry, Institute of Chemistry Chinese Academy of Sciences, Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
| | - Qingqing Kong
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, P. R. 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, P. R. 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, P. R. China
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Wang Y, Liu L, Gao Y, Zhao J, Liu C, Gong L, Yang Z. Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad. Phys Chem Chem Phys 2023; 26:504-516. [PMID: 38084041 DOI: 10.1039/d3cp04357f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The rapid deprotonation of G˙+ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions χ*(r) and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation. The activation energy calculated by the QM method of X˙ is the lowest among other bases in the GGX(8-oxo-G) tetrad, which is supported by the computation of the average electronegativity calculated by ABEEM PFF. By utilizing QM/MM(ABEEM) with a two-way free energy perturbation method, the deprotonation activation energy of X˙ in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol-1, while that of G˙+ in the G-tetrad is 20.7 ± 0.6 kJ mol-1, consistent with the experimental measurement of 20 ± 1.0 kJ mol-1. These results manifest that X˙ in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G˙+ in the G-tetrad, suggesting that the GGX(8-oxo-G) tetrad may serve as a more favorable hole transport carrier. Furthermore, the unequal average electronegativities of bases in the GGX(8-oxo-G) tetrad impede the deprotonation rate. This study provides a potential foundation for investigating the microscopic mechanism of DNA electronic devices.
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Affiliation(s)
- Yue Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Linlin Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yue Gao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Jiayue Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Zhongzhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
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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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Peng J, Pan Y, Zhou Y, Kong Q, Lei Y, Lei X, Cheng S, Zhang X, Yang X. Triplet Photochemistry of Effluent Organic Matter in Degradation of Extracellular Antibiotic Resistance Genes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7230-7239. [PMID: 37114949 DOI: 10.1021/acs.est.2c08036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Wastewater effluent is a major source of extracellular antibiotic resistance genes (eArGs) in the aquatic environment, a threat to human health and biosecurity. However, little is known about the extent to which organic matter in the wastewater effluent (EfOM) might contribute to photosensitized oxidation of eArGs. Triplet states of EfOM were found to dominate the degradation of eArGs (accounting for up to 85%). Photo-oxidation proceeded mainly via proton-coupled electron transfer reactions. They broke plasmid strands and damaged bases. O2•- was also involved, and it coupled with the reactions' intermediate radicals of eArGs. The second-order reaction rates of blaTEM-1 and tet-A segments (209-216 bps) with the triplet state of 4-carboxybenzophenone were calculated to be (2.61-2.75) × 108 M-1 s-1. Besides as photosensitizers, the antioxidant moieties in EfOM also acted as quenchers to revert intermediate radicals back to their original forms, reducing the rate of photodegradation. However, the terrestrial origin natural organic matter was unable to photosensitize because it formed less triplets, especially high-energy triplets, so its inhibitory effects predominated. This study advances our understanding of the role of EfOM in the photo-oxidation of eArGs and the difference between EfOM and terrestrial-origin natural organic matter.
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Affiliation(s)
- Jianglin Peng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanheng Pan
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yangjian Zhou
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Qingqing Kong
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - 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
| | - Xin 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
| | - Xinran Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, 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
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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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6
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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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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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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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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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Zhou Q, Wang Y, Dai X, Yang C, Jie J, Su H. One-electron oxidation of TAT-motif triplex DNA and the ensuing Hoogsteen hydrogen-bonding dissociation. J Chem Phys 2020; 152:035101. [PMID: 31968979 DOI: 10.1063/1.5135769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One-electron oxidation of adenine (A) leads initially to the formation of adenine radical cation (A•+). Subsequent deprotonation of A•+ can provoke deoxyribonucleic acid (DNA) damage, which further causes senescence, cancer formation, and even cell death. However, compared with considerable reports on A•+ reactions in free deoxyadenosine (dA) and duplex DNA, studies in non-B-form DNA that play critical biological roles are rare at present. It is thus of vital importance to explore non-B-form DNA, among which the triplex is an emerging topic. Herein, we investigate the deprotonation behavior of A•+ in the TAT triplex with continuous A bases by time-resolved laser flash photolysis. The rate constants for the one-oxidation of triplex 8.4 × 108 M-1 s-1 and A•+ deprotonation 1.3 × 107 s-1 are obtained. The kinetic isotope effect of A•+ deprotonation in the TAT triplex is 1.8, which is characteristic of a direct release of the proton into the solvent similar to free base dA. It is thus elucidated that the A•+ proton bound with the third strand is most likely to be released into the solvent because of the weaker Hoogsteen H-bonding interaction and the presence of the highly mobile hydration waters within the third strand. Additionally, it is confirmed through Fourier transform infrared spectroscopy that the deprotonation of A•+ results in the dissociation of the third strand and disruption of the secondary structure of the triplex. These results provide valuable kinetic data and in-depth mechanistic insights for understanding the adenine oxidative DNA damage in the triplex.
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Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Yinghui Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Xiaojuan Dai
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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16
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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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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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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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25
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Lewis FD, Young RM, Wasielewski MR. Tracking Photoinduced Charge Separation in DNA: from Start to Finish. Acc Chem Res 2018; 51:1746-1754. [PMID: 30070820 DOI: 10.1021/acs.accounts.8b00090] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The initial studies of the dynamics of photoinduced charge separation conducted in our laboratories 20 years ago found strongly distance-dependent rate constants over short distances but failed to detect intermediates in the transport of positive charge (holes). These observations were consistent with the single-step superexchange or tunneling mechanism that had been observed for numerous donor-bridge-acceptor systems at that time. Subsequent studies found weak distance dependence for hole transport over longer distances in DNA, characteristic of incoherent hopping of either localized or delocalized holes. The introduction of synthetic DNA capped hairpin constructs possessing hole donor and acceptor chromophores (or purine bases) at opposite ends of a base-pair domain made it possible to determine the time required for transit of charge from one chromophore to the other and, in some cases, to distinguish between the transit time and the much faster initial charge injection time. These studies eliminated conventional tunneling as a viable mechanism for charge transport in DNA except at very short donor-acceptor separations; however, they did not establish the presence or nature of intermediates in the charge separation process. Recent studies in our laboratories have succeeded in identifying key intermediates as well as untangling the dynamics and efficiency of the charge separation process from start to finish. The dynamics of the initial charge injection process is dependent upon both its free energy and the stacking of the hole donor chromophore and adjacent purine base. The transport of positive charge (holes) over multiple base pairs in duplex DNA occurs most efficiently via repeating adenine bases, known as A-tracts. The transit time across an A-tract is strongly dependent upon the free energy for hole injection, whereas the efficiency of charge separation depends on the competition between charge delocalization and charge recombination in the contact radical ion pair. The guanine cation radical has been detected both by femtosecond transient absorption and by stimulated Raman spectroscopies when the guanine is located near the chromophore employed for hole injection into an A-tract. Replacement of guanine by its derivative 8-phenylethynylguanine (EG), permits tracking of hole transport across longer poly(purine) sequences as a consequence of the stronger transient absorption and stimulated Raman scattering for EG+• vs G+•. We have recently obtained evidence based on femtosecond transient absorption spectroscopy for the formation of delocalized A-polarons in A-tracts possessing four or more A-T base pairs. Similar methods have been used to track hole transport across less-common DNA structures including diblock and triblock poly(purines), locked nucleic acids, three-way junctions, and G-quadruplexes. Similar methods are have been applied to the study of photoinduced electron transport in DNA.
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Affiliation(s)
- Frederick D. Lewis
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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26
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Merta TJ, Geacintov NE, Shafirovich V. Generation of 8-oxo-7,8-dihydroguanine in G-Quadruplexes Models of Human Telomere Sequences by One-electron Oxidation. Photochem Photobiol 2018; 95:244-251. [PMID: 29679477 PMCID: PMC6196120 DOI: 10.1111/php.12926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022]
Abstract
The mechanistic aspects of one-electron oxidation of G-quadruplexes in the basket (Na+ ions) and hybrid (K+ ions) conformations were investigated by transient absorption laser kinetic spectroscopy and HPLC detection of the 8-oxo-7,8-dihydroguanine (8-oxoG) oxidation product. The photo-induced one-electron abstraction from G-quadruplexes was initiated by sulfate radical anions (SO4 ˙- ) derived from the photolysis of persulfate ions by 308 nm excimer laser pulses. In neutral aqueous solutions (pH 7.0), the transient absorbance of neutral guanine radicals, G(-H)˙, is observed following the complete decay of SO4 ˙- radicals (~10 μs after the actinic laser flash). In both basket and hybrid conformations, the G(-H)˙ decay is biphasic with one component decaying with a lifetime of ~0.1 ms, and the other with a lifetime of 20-30 ms. The fast decay component (~0.1 ms) in G-quadruplexes is correlated with the formation of 8-oxoG lesions. We propose that in G-quadruplexes, G(-H)˙ radicals retain radical cation character by sharing the N1-proton with the O6 -atom of G in the [G˙+ : G] Hoogsteen base pair; this [G(-H)˙: H+ G <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>⇄</mml:mo></mml:math> G˙+ : G] leads to the hydration of G˙+ radical cation within the millisecond time domain, and is followed by the formation of the 8-oxoG lesions.
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Affiliation(s)
- Tomasz J Merta
- Chemistry Program, NYU Shanghai, Pudong Xinqu, Shanghai Shi, China
| | - Nicholas E Geacintov
- Chemistry Program, NYU Shanghai, Pudong Xinqu, Shanghai Shi, China.,Chemistry Department, New York University, New York, NY
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27
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Yang Y, Yang W, Su H, Fang W, Chen X. Mechanistic insights into the photogeneration and quenching of guanine radical cation via one-electron oxidation of G-quadruplex DNA. Phys Chem Chem Phys 2018; 20:13598-13606. [DOI: 10.1039/c8cp01718b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Selectivity of activation site for the photogeneration and quenching of guanine radical cation was elucidated by the analysis of the relaxation paths of one-electron oxidation of G-quadruplex DNA.
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Affiliation(s)
- Yumei Yang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Wenjing Yang
- College of Material Science & Engineering
- Taiyuan University of Technology
- People's Republic of China
| | - Hongmei Su
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Xuebo Chen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education
- Department of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
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28
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Sun Y, Zhou W, Moe MM, Liu J. Reactions of water with radical cations of guanine, 9-methylguanine, 2′-deoxyguanosine and guanosine: keto–enol isomerization, C8-hydroxylation, and effects of N9-substitution. Phys Chem Chem Phys 2018; 20:27510-27522. [DOI: 10.1039/c8cp05453c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactions of D2O with guanine radical cations in nucleobases and nucleosides were studied in the gas phase using the guided-ion-beam experiment and computational modeling.
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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
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - 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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29
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Brown KE, Singh APN, Wu YL, Mishra AK, Zhou J, Lewis FD, Young RM, Wasielewski MR. Tracking Hole Transport in DNA Hairpins Using a Phenylethynylguanine Nucleobase. J Am Chem Soc 2017; 139:12084-12092. [DOI: 10.1021/jacs.7b06998] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kristen E. Brown
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arunoday P. N. Singh
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Yi-Lin Wu
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Jiawang Zhou
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry,
Argonne-Northwestern Solar Energy Research (ANSER) Center, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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30
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Banyasz A, Martínez-Fernández L, Balty C, Perron M, Douki T, Improta R, Markovitsi D. Absorption of Low-Energy UV Radiation by Human Telomere G-Quadruplexes Generates Long-Lived Guanine Radical Cations. J Am Chem Soc 2017; 139:10561-10568. [PMID: 28737902 DOI: 10.1021/jacs.7b05931] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Telomeres, which are involved in cell division, carcinogenesis, and aging and constitute important therapeutic targets, are prone to oxidative damage. This propensity has been correlated with the presence of guanine-rich sequences, capable of forming four-stranded DNA structures (G-quadruplexes). Here, we present the first study on oxidative damage of human telomere G-quadruplexes without mediation of external molecules. Our investigation has been performed for G-quadruplexes formed by folding of GGG(TTAGGG)3 single strands in buffered solutions containing Na+ cations (TEL21/Na+). Associating nanosecond time-resolved spectroscopy and quantum mechanical calculations (TD-DFT), it focuses on the primary species, ejected electrons and guanine radicals, generated upon absorption of UV radiation directly by TEL21/Na+. We show that, at 266 nm, corresponding to an energy significantly lower than the guanine ionization potential, the one-photon ionization quantum yield is 4.5 × 10-3. This value is comparable to that of cyclobutane thymine dimers (the major UV-induced lesions) in genomic DNA; the quantum yield of these dimers in TEL21/Na+ is found to be (1.1 ± 0.1) × 10-3. The fate of guanine radicals, generated in equivalent concentration with that of ejected electrons, is followed over 5 orders of magnitude of time. Such a quantitative approach reveals that an important part of radical cation population survives up to a few milliseconds, whereas radical cations produced by chemical oxidants in various DNA systems are known to deprotonate, at most, within a few microseconds. Under the same experimental conditions, neither one-photon ionization nor long-lived radical cations are detected for the telomere repeat TTAGGG in single-stranded configuration, showing that secondary structure plays a key role in these processes. Finally, two types of deprotonated radicals are identified: on the one hand, (G-H2)• radicals, stable at early times, and on the other hand, (G-H1)• radicals, appearing within a few milliseconds and decaying with a time constant of ∼50 ms.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Lara Martínez-Fernández
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Clémence Balty
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Marion Perron
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Thierry Douki
- CEA, INAC-SyMMES Laboratoire des Lésions des Acides Nucléiques, F-38000 Grenoble, France
| | - Roberto Improta
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France.,Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
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31
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Jie J, Liu K, Wu L, Zhao H, Song D, Su H. Capturing the radical ion-pair intermediate in DNA guanine oxidation. SCIENCE ADVANCES 2017; 3:e1700171. [PMID: 28630924 PMCID: PMC5457143 DOI: 10.1126/sciadv.1700171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/06/2017] [Indexed: 05/28/2023]
Abstract
Although the radical ion pair has been frequently invoked as a key intermediate in DNA oxidative damage reactions and photoinduced electron transfer processes, the unambiguous detection and characterization of this species remain formidable and unresolved due to its extremely unstable nature and low concentration. We use the strategy that, at cryogenic temperatures, the transient species could be sufficiently stabilized to be detectable spectroscopically. By coupling the two techniques (the cryogenic stabilization and the time-resolved laser flash photolysis spectroscopy) together, we are able to capture the ion-pair transient G+•⋯Cl- in the chlorine radical-initiated DNA guanine (G) oxidation reaction, and provide direct evidence to ascertain the intricate type of addition/charge separation mechanism underlying guanine oxidation. The unique spectral signature of the radical ion-pair G+•⋯Cl- is identified, revealing a markedly intense absorption feature peaking at 570 nm that is distinctive from G+• alone. Moreover, the ion-pair spectrum is found to be highly sensitive to the protonation equilibria within guanine-cytosine base pair (G:C), which splits into two resolved bands at 480 and 610 nm as the acidic proton transfers along the central hydrogen bond from G+• to C. We thus use this exquisite sensitivity to track the intrabase-pair proton transfer dynamics in the double-stranded DNA oligonucleotides, which is of critical importance for the description of the proton-coupled charge transfer mechanisms in DNA.
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Affiliation(s)
- Jialong Jie
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunhui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lidan Wu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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32
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Zhang S, Liu H, Cheng P, Ren D, Gong X. Analysis of the [CuL n ]2+ and [CuG n ]2+ (n = 2–4) complex structures: Comparison with CID experiment and DFT calculation. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416130173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Harris MA, Mishra AK, Young RM, Brown KE, Wasielewski MR, Lewis FD. Direct Observation of the Hole Carriers in DNA Photoinduced Charge Transport. J Am Chem Soc 2016; 138:5491-4. [DOI: 10.1021/jacs.6b00702] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michelle A. Harris
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Kristen E. Brown
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
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34
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Young RM, Singh APN, Thazhathveetil AK, Cho VY, Zhang Y, Renaud N, Grozema FC, Beratan DN, Ratner MA, Schatz GC, Berlin YA, Lewis FD, Wasielewski MR. Charge Transport across DNA-Based Three-Way Junctions. J Am Chem Soc 2015; 137:5113-22. [DOI: 10.1021/jacs.5b00931] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Ryan M. Young
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
- Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Arunoday P. N. Singh
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Arun K. Thazhathveetil
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Vincent Y. Cho
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Yuqi Zhang
- Departments
of Chemistry, Biochemistry, and Physics, Duke University
, Durham, North Carolina
27708, United States
| | - Nicolas Renaud
- DelftChemTech, Delft University of Technology
, Julianalaan 136, 2628 BL
Delft, The Netherlands
| | - Ferdinand C. Grozema
- DelftChemTech, Delft University of Technology
, Julianalaan 136, 2628 BL
Delft, The Netherlands
| | - David N. Beratan
- Departments
of Chemistry, Biochemistry, and Physics, Duke University
, Durham, North Carolina
27708, United States
| | - Mark A. Ratner
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Yuri A. Berlin
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Northwestern University
, Evanston, Illinois
60208-3113, United States
- Argonne-Northwestern
Solar Energy Research (ANSER) Center, Northwestern University
, Evanston, Illinois
60208-3113, United States
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35
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Wu L, Liu K, Jie J, Song D, Su H. Direct observation of guanine radical cation deprotonation in G-quadruplex DNA. J Am Chem Soc 2014; 137:259-66. [PMID: 25506785 DOI: 10.1021/ja510285t] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Although numerous studies have been devoted to the charge transfer through double-stranded DNA (dsDNA), one of the major problems that hinder their potential applications in molecular electronics is the fast deprotonation of guanine cation (G(+•)) to form a neutral radical that can cause the termination of hole transfer. It is thus of critical importance to explore other DNA structures, among which G-quadruplexes are an emerging topic. By nanosecond laser flash photolysis, we report here the direct observation and findings of the unusual deprotonation behavior (loss of amino proton N2-H instead of imino proton N1-H) and slower (1-2 orders of magnitude) deprotonation rate of G(+•) within G-quadruplexes, compared to the case in the free base dG or dsDNA. Four G-quadruplexes AG3(T2AG3)3, (G4T4G4)2, (TG4T)4, and G2T2G2TGTG2T2G2 (TBA) are measured systematically to examine the relationship of deprotonation with the hydrogen-bonding surroundings. Combined with in depth kinetic isotope experiments and pKa analysis, mechanistic insights have been further achieved, showing that it should be the non-hydrogen-bonded free proton to be released during deprotonation in G-quadruplexes, which is the N2-H exposed to solvent for G bases in G-quartets or the free N1-H for G base in the loop. The slower N2-H deprotonation rate can thus ensure less interruption of the hole transfer. The unique deprotonation features observed here for G-quadruplexes open possibilities for their interesting applications as molecular electronic devices, while the elucidated mechanisms can provide illuminations for the rational design of G-quadruplex structures toward such applications and enrich the fundamental understandings of DNA radical chemistry.
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Affiliation(s)
- Lidan Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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36
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Rokhlenko Y, Cadet J, Geacintov NE, Shafirovich V. Mechanistic aspects of hydration of guanine radical cations in DNA. J Am Chem Soc 2014; 136:5956-62. [PMID: 24689701 PMCID: PMC4004273 DOI: 10.1021/ja412471u] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The mechanistic aspects of hydration of guanine radical cations, G(•+) in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G(•+) radical one-electron oxidation products were generated by SO4(•-) radical anions derived from the photolysis of S2O8(2-) anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4(•-) radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)(•) with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)(•) radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)(•) decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G(-H)(•) radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)(•) radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G(•+):C] base pair. This [G(-H)(•):H(+)C ⇆ G(•+):C] equilibrium allows for the hydration of G(•+) followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G(•+) and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally.
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Affiliation(s)
- Yekaterina Rokhlenko
- Chemistry Department, New York University , 31 Washington Place, New York, New York 10003-5180, United States
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37
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Cadet J, Wagner JR, Shafirovich V, Geacintov NE. One-electron oxidation reactions of purine and pyrimidine bases in cellular DNA. Int J Radiat Biol 2014; 90:423-32. [PMID: 24369822 DOI: 10.3109/09553002.2013.877176] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE The aim of this survey is to critically review the available information on one-electron oxidation reactions of nucleobases in cellular DNA with emphasis on damage induced through the transient generation of purine and pyrimidine radical cations. Since the indirect effect of ionizing radiation mediated by hydroxyl radical is predominant in cells, efforts have been made to selectively ionize bases using suitable one-electron oxidants that consist among others of high intensity UVC laser pulses. Thus, the main oxidation product in cellular DNA was found to be 8-oxo-7,8-dihydroguanine as a result of direct bi-photonic ionization of guanine bases and indirect formation of guanine radical cations through hole transfer reactions from other base radical cations. The formation of 8-oxo-7,8-dihydroguanine and other purine and pyrimidine degradation products was rationalized in terms of the initial generation of related radical cations followed by either hydration or deprotonation reactions in agreement with mechanistic pathways inferred from detailed mechanistic studies. The guanine radical cation has been shown to be implicated in three other nucleophilic additions that give rise to DNA-protein and DNA-DNA cross-links in model systems. Evidence was recently provided for the occurrence of these three reactions in cellular DNA. CONCLUSION There is growing evidence that one-electron oxidation reactions of nucleobases whose mechanisms have been characterized in model studies involving aqueous solutions take place in a similar way in cells. It may also be pointed out that the above cross-linked lesions are only produced from the guanine radical cation and may be considered as diagnostic products of the direct effect of ionizing radiation.
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Affiliation(s)
- Jean Cadet
- Institut Nanosciences & Cryogénie, CEA/Grenoble , Grenoble , France
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38
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Lin Y, Wang H, Wu Y, Gao S, Schaefer III HF. Proton-transfer in hydrogenated guanine–cytosine trimer neutral species, cations, and anions embedded in B-form DNA. Phys Chem Chem Phys 2014; 16:6717-25. [DOI: 10.1039/c3cp54904f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Zhao J, Wang M, Yang H, Zhang M, Liu P, Bu Y. Radical–Radical Interactions among Oxidized Guanine Bases Including Guanine Radical Cation and Dehydrogenated Guanine Radicals. J Phys Chem B 2013; 117:10698-710. [DOI: 10.1021/jp4042149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Zhao
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Mei Wang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Hongfang Yang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Meng Zhang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Ping Liu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Yuxiang Bu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
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40
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Hsu SCN, Wang TP, Kao CL, Chen HF, Yang PY, Chen HY. Theoretical Study of the Protonation of the One-Electron-Reduced Guanine–Cytosine Base Pair by Water. J Phys Chem B 2013; 117:2096-105. [DOI: 10.1021/jp400299v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sodio C. N. Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hui-Fen Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Po-Yu Yang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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41
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Wang M, Zhao J, Bu Y. Theoretical exploration of structures and electronic properties of double-electron oxidized guanine–cytosine base pairs with intriguing radical–radical interactions. Phys Chem Chem Phys 2013; 15:18453-63. [DOI: 10.1039/c3cp52745j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Choi J, Park J, Tanaka A, Park MJ, Jang YJ, Fujitsuka M, Kim SK, Majima T. Hole Trapping of G-Quartets in a G-Quadruplex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201208149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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43
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Choi J, Park J, Tanaka A, Park MJ, Jang YJ, Fujitsuka M, Kim SK, Majima T. Hole Trapping of G-Quartets in a G-Quadruplex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/anie.201208149] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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44
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Liu Y, Liu Z, Geacintov NE, Shafirovich V. Proton-coupled hole hopping in nucleosomal and free DNA initiated by site-specific hole injection. Phys Chem Chem Phys 2012; 14:7400-10. [PMID: 22526555 DOI: 10.1039/c2cp40759k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Nucleosomes were reconstituted from recombinant histones and a 147-mer DNA sequence containing the damage reporter sequence 5'-…d([2AP]T[GGG](1)TT[GGG](2)TTT[GGG](3)TAT)… with 2-aminopurine (2AP) at position 27 from the dyad axis. Footprinting studies with ˙OH radicals reflect the usual effects of "in" and "out" rotational settings, while, interestingly, the guanine oxidizing one-electron oxidant CO(3)(˙-) radical does not. Site-specific hole injection was achieved by 308 nm excimer laser pulses to produce 2AP(˙+) cations, and superoxide via the trapping of hydrated electrons. Rapid deprotonation (~100 ns) and proton coupled electron transfer generates neutral guanine radicals, G(-H)˙ and hole hopping between the three groups of [GGG] on micro- to millisecond time scales. Hole transfer competes with hole trapping that involves the combination of O(2)(˙-) with G(-H)˙ radicals to yield predominantly 2,5-diamino-4H-imidazolone (Iz) and minor 8-oxo-7,8-dihydroguanine (8-oxoG) end-products in free DNA (Misiaszek et al., J. Biol. Chem. 2004, 279, 32106). Hole migration is less efficient in nucleosomal than in the identical protein-free DNA by a factor of 1.2-1.5. The Fpg/piperidine strand cleavage ratio is ~1.0 in free DNA at all three GGG sequences and at the "in" rotational settings [GGG](1,3) facing the histone core, and ~2.3 at the "out" setting at [GGG](2) facing away from the histone core. These results are interpreted in terms of competitive reaction pathways of O(2)(˙-) with G(-H)˙ radicals at the C5 (yielding Iz) and C8 (yielding 8-oxoG) positions. These differences in product distributions are attributed to variations in the local nucleosomal B-DNA base pair structural parameters that are a function of surrounding sequence context and rotational setting.
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Affiliation(s)
- Yang Liu
- Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China
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45
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Rokhlenko Y, Geacintov NE, Shafirovich V. Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions. J Am Chem Soc 2012; 134:4955-62. [PMID: 22329445 DOI: 10.1021/ja212186w] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(•+), its deptotonation product G(-H)(•), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(•-) and SO(4)(•-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ∼20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(•+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(•), which, at best, reacts only slowly with H(2)O and lives for ∼70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(•) can be oxidized further by reaction with CO(3)(•-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.
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Affiliation(s)
- Yekaterina Rokhlenko
- Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, United States
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46
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Cerón-Carrasco JP, Jacquemin D. Interplay between hydroxyl radical attack and H-bond stability in guanine–cytosine. RSC Adv 2012. [DOI: 10.1039/c2ra22389a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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47
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ZHANG LIDONG, PAN YANG, QI FEI. THEORETICAL STUDIES ON PHOTOIONIZATION OF GUANINE TAUTOMERS AND INTERCONVERSION OF CATION RADICALS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609005404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The G3MP2B3 and P3 methods have been used to calculate the adiabatic and vertical ionization potentials (IPs) of the eight most stable tautomers of guanine. The calculated energy discrepancy between adiabatic and vertical IPs are in good agreement with the changes in geometry from neutral ground state to stable cation radicals. The geometries of imino-oxo form tautomers have no obvious change in the ionization process, which results in less energy discrepancy between vertical and adiabatic IPs. In the ionization process, the geometries of the amino-oxo and amino-hydroxy form tautomers change from nonplanar to planar structures. Hence the amino-oxo and amino-hydroxy form tautomers have larger energy discrepancy between vertical and adiabatic IPs. Further studies on the interconversion of the cation radicals shed further light on the transition process between the cation radicals and the main pathways are the hydrogen migrations and internal rotations of hydroxy (OH) and imino (NH) groups. The barriers of hydrogen rotations are lower than those of hydrogen migrations. Furthermore, the barriers for the hydrogen migrations between two rings are higher, which are about 3.0 eV.
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Affiliation(s)
- LIDONG ZHANG
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - YANG PAN
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - FEI QI
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
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48
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Bonin J, Robert M. Photoinduced Proton-Coupled Electron Transfers in Biorelevant Phenolic Systems. Photochem Photobiol 2011; 87:1190-203. [DOI: 10.1111/j.1751-1097.2011.00996.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Lee YA, Liu Z, Dedon PC, Geacintov NE, Shafirovich V. Solvent exposure associated with single abasic sites alters the base sequence dependence of oxidation of guanine in DNA in GG sequence contexts. Chembiochem 2011; 12:1731-9. [PMID: 21656632 PMCID: PMC3517150 DOI: 10.1002/cbic.201100140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 12/12/2022]
Abstract
The effect of exposure of guanine in double-stranded oligonucleotides to aqueous solvent during oxidation by one-electron oxidants was investigated by introducing single synthetic tetrahydrofuran-type abasic sites (Ab) either adjacent to or opposite tandem GG sequences. The selective oxidation of guanine was initiated by photoexcitation of the aromatic sensitizers riboflavin and a pyrene derivative, and by the relatively small negatively charged carbonate radical anion. The relative rates of oxidation of the 5'- and 3' side G in runs of 5'⋅⋅⋅GG⋅⋅⋅ (evaluated by standard hot alkali treatment of the damaged DNA strand followed by high resolution gel electrophoresis of the cleavage fragments) are markedly affected by adjacent abasic sites either on the same or opposite strand. For example, in fully double-stranded DNA or one with an Ab adjacent to the 5'-G, the 5'-G/3'-G damage ratio is ≥4, but is inverted (<1.0) with the Ab adjacent to the 3'-G. These striking effects of Ab are attributed to the preferential localization of the "hole" on the most solvent-exposed guanine regardless of the size, charge, or reduction potential of the oxidizing species.
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Affiliation(s)
- Young-Ae Lee
- Department of Chemistry, Kyungpook National University, Daegu 702-701 (Korea)
| | - Zhi Liu
- Chemistry Department, 31 Washington Place, New York University, New York, NY 10003- 5180 (USA)
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139 (USA)
| | - Nicholas E. Geacintov
- Chemistry Department, 31 Washington Place, New York University, New York, NY 10003- 5180 (USA)
| | - Vladimir Shafirovich
- Chemistry Department, 31 Washington Place, New York University, New York, NY 10003- 5180 (USA)
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50
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Khanduri D, Adhikary A, Sevilla MD. Highly oxidizing excited states of one-electron-oxidized guanine in DNA: wavelength and pH dependence. J Am Chem Soc 2011; 133:4527-37. [PMID: 21381665 PMCID: PMC3063320 DOI: 10.1021/ja110499a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Excited states of one-electron-oxidized guanine in DNA are known to induce hole transfer to the sugar moiety and on deprotonation result in neutral sugar radicals that are precursors of DNA strand breaks. This work carried out in a homogeneous aqueous glass (7.5 M LiCl) at low temperatures (77-175 K) shows the extent of photoconversion of one-electron-oxidized guanine and the associated yields of individual sugar radicals are crucially controlled by the photon energy, protonation state, and strandedness of the oligomer. In addition to sugar radical formation, highly oxidizing excited states of one-electron-oxidized guanine are produced with 405 nm light at pH 5 and below that are able to oxidize chloride ion in the surrounding solution to form Cl(2)(•-) via an excited-state hole transfer process. Among the various DNA model systems studied in this work, the maximum amount of Cl(2)(•-) is produced with ds (double-stranded) DNA, where the one-electron-oxidized guanine exists in its cation radical form (G(•+):C). Thus, via excited-state hole transfer, the dsDNA is apparently able to protect itself from cation radical excited states by transfer of damage to the surrounding environment.
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Affiliation(s)
- Deepti Khanduri
- Department of Chemistry Oakland University Rochester, MI 48309
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