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Wang Y, Ma L, Wei S. Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study. ACS OMEGA 2024; 9:50730-50741. [PMID: 39741838 PMCID: PMC11683639 DOI: 10.1021/acsomega.4c08956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 12/02/2024] [Accepted: 12/06/2024] [Indexed: 01/03/2025]
Abstract
Due to the lower oxidation potential than natural nucleic acid bases, one-electron oxidation of DNA is usually funneled into the direction of intermediates for oxidized DNA damage like 8-oxo-7,8-dihydroadenine (8-oxoA) leading to a radical cation, which may undergo facile deprotonation. However, compared to the sophisticated studies devoted to natural bases, much less is known about the radical cation degradation behavior of an oxidized DNA base. Inspired by this, a comprehensive theoretical investigation is performed to illuminate the deprotonation of 8-oxoA radical cation (8-oxoA•+) in both free and encumbered context by calculating the pK a value and mapping the energy profiles. The calculative pK a values of active protons in free 8-oxoA•+ follow the order: N7-H < N9-H < N6-H1< N6-H2, suggesting the preference of proton departure in free 8-oxoA•+. To further illustrate the preferred site and mechanism for 8-oxoA•+ deprotonation, energy profiles are constructed to distinguish the possibility from that of all active protons in both contexts. The results show distinctly that 8-oxoA•+ mainly suffers from the loss of proton from N9 due to the lowest energy barrier but deprotonates N7-H in real DNA as the connection of N9 and ribose. The energy barriers for the deprotonation of N7-H from 8-oxoA•+ in free and encumbered contexts are 1.5 and 1.3 kcal/mol, respectively, indicating a fast deprotonation reaction. It is more interestingly that the N9-H proton transfer (PT, toward N3) to adjacent water follows a stepwise fashion rather than a one-step approach as previously reported. Furthermore, the PT behavior of free N9-H toward O8 is dramatically influenced by base pairing T, where it is localized at neighboring water without further PT to adjacent water in free 8-oxoA•+ but migrated directly to adjacent water in the 8-oxoA•+:T base pair. And the deprotonation of N6-H2 in 8-oxoA•+:T is disturbed as the PT to O4 of the pairing T base is inhibited. It is warmly anticipated that these results could provide an in-depth perspective to understand the important role of 8-oxoA in mutation.
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Affiliation(s)
- Yinghui Wang
- College
of Science, Chang’an University, Xi’an 710064, China
| | - Lei Ma
- College
of Science, Chang’an University, Xi’an 710064, China
| | - Simin Wei
- State
Key Laboratory of Research & Development of Characteristic Qin
Medicine Resources (Cultivation), Co-Construction Collaborative Innovation
Center for Chinese Medicine Resources Industrialization by Shaanxi
& Education Ministry, Shaanxi University
of Chinese Medicine, Xianyang 712083, China
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2
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Boaro A, Ramos LD, Bastos EL, Bechara EJH, Bartoloni FH. Comparison of the mechanisms of DNA damage following photoexcitation and chemiexcitation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 262:113070. [PMID: 39657451 DOI: 10.1016/j.jphotobiol.2024.113070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 11/25/2024] [Accepted: 11/27/2024] [Indexed: 12/12/2024]
Abstract
In this review, we compare the mechanisms and consequences of electronic excitation of DNA via photon absorption or photosensitization, as well as by chemically induced generation of excited states. The absorption of UV radiation by DNA is known to produce cyclobutane pyrimidine dimers (CPDs) and thymine pyrimidone photoproducts. Photosensitizers are known to enable such transformations using UV-A and visible light by generating triplet species able to transfer energy to DNA. Conversely, chemiexcitation of DNA is a process related to the formation of high energy peroxides whose decomposition leads to triplet excited species. In practice, both photoexcitation and chemiexcitation produce reactive excited species able to promote some DNA nucleobases to their excited state. We discuss the effect of epigenetic methylation modifications of DNA and the role of endogenous and exogenous photosensitizers on the formation of DNA photoproducts via triplet-triplet energy transfer as well as oxidative DNA damages. The mechanisms of pathogenic pathway involving the generation of CPDs via chemiexcitation (namely dark CPDs, dCPDs) are discussed and compared with photoexcitation considering their spatiotemporal characteristics. Recognition of the multifaceted noxious effects of UV radiation opens new horizons for the development of effective electronically excited quenchers, thereby providing a crucial step toward mitigating DNA photodamage.
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Affiliation(s)
- Andreia Boaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, SP 09210-580, Brazil; Laboratorio de Genetica e Cardiologia Molecular, Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP 05403-000, Brazil.
| | - Luiz Duarte Ramos
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, SP 09210-580, Brazil
| | - Erick Leite Bastos
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, SP 09210-580, Brazil; Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Fernando Heering Bartoloni
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, SP 09210-580, Brazil
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Wang Y, Wei S. Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H +)GC motif. Phys Chem Chem Phys 2024; 26:5683-5692. [PMID: 38288746 DOI: 10.1039/d3cp05885a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
A comprehensive theoretical investigation was performed to illuminate the influence of hydrogen bonds (H-bonds) on the obscure reaction of a hydroxyl radical (HO˙) and guanine (G) by selecting the building block of parallel triplex DNA, C(H+)GC, as the model. By mapping the energy profiles for addition and hydrogen abstraction reactions, the favorable pathway is predicted. The results reveal that in the C(H+)GC context, barrierless hydrogen abstraction from N2 of G leading to a neutral radical G(N2-H)˙ appears to become significant, but electrophilic attack by HO˙ on C8 of G resulting in 8-oxoG is the most thermodynamically favorable course. This shows a strong structural dependence due to the context constrained by the H-bond, which is dramatically different from the situation in unencumbered G. More interestingly, it proves that the stability order of resulting adduct radicals is not altered by H-bonding, but the activity for possible sites of the hydroxylation reaction changes. The significant influence of the H-bond on elementary reactions involved in the reaction is emphasized in the C(H+)GC context but is not restricted to the H-abstraction reaction. It is greatly anticipated that the present study could provide thoughtful insights into the vague hydroxyl radical-induced oxidation chemistry.
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Affiliation(s)
- Yinghui Wang
- College of Science, Chang'an University, Xi'an 710064, China.
| | - Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang 712083, China.
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4
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Wei S, He Q, Duan J, Zheng H, Ma L, Wang Y. An Exploration of the Transformation of the 8-Oxo-7,8-Dihydroguanine Radical Cation to Protonated 2-Amino-5-Hydroxy-7,9-Dihydropurine-6,8-Dione in a Base Pair. Chemphyschem 2023; 24:e202200625. [PMID: 36175389 DOI: 10.1002/cphc.202200625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Indexed: 02/04/2023]
Abstract
A theoretical investigation was performed to disclose the transformation mechanism of 8-oxo-7,8-dihydroguanine radical cation (8-oxoG⋅+ ) to protonated 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-8-oxoG) in base pair. The energy profiles for three possible pathways of the events were mapped. It is shown that direct loss of H7 from base paired 8-oxoG⋅+ is the only energetically favorable pathway to generate neutral radical, 8-oxoG(-H7)⋅. Further oxidation of 8-oxoG(-H7)⋅ : C to 8-oxoG(-H7)+ : C is exothermic. However, the 8-oxoG(-H7)+ : C deprotonation from all possible active sites is infeasible, indicating the inaccessible second proton loss and the lack of essential intermediate 2-amino-7,9-dihydropurine-6,8-dione (8-oxoGOX ). This makes 8-oxoG(-H7)+ act as the precursor of hydration leading to the generation of protonated 5-HO-8-oxoG by stepwise fashion in base pair, which would initiate the step down guanidinohydantoin (Gh) pathway. These results clearly specify the structure-dependent transformation for 8-oxoG⋅+ and verify the emergence of protonated 5-HO-8-oxoG in base pair.
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Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang, 712083, China
| | - Qihao He
- Institution Shaanxi Transportation Holding Group Co., Ltd., Xi'an, 710065, China
| | - Jinwei Duan
- College of Science, Chang'an University, Xi'an, 710064, China
| | - Huayu Zheng
- College of Science, Chang'an University, Xi'an, 710064, China
| | - Lei Ma
- College of Science, Chang'an University, Xi'an, 710064, China
| | - Yinghui Wang
- College of Science, Chang'an University, Xi'an, 710064, China
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Jiao Z, Yang C, Zhou Q, Hu Z, Jie J, Zhang X, Su H. Sequence-specific binding behavior of coralyne toward triplex DNA: An ultrafast time-resolved fluorescence spectroscopy study. J Chem Phys 2023; 158:045101. [PMID: 36725513 DOI: 10.1063/5.0133913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Triplex DNA structure has potential therapeutic application in inhibiting the expression of genes involved in cancer and other diseases. As a DNA-targeting antitumor and antibiotic drug, coralyne shows a remarkable binding propensity to triplex over canonical duplex and thus can modulate the stability of triplex structure, providing a prospective gene targeting strategy. Much less is known, however, about coralyne-binding interactions with triplex. By combining multiple steady-state spectroscopy with ultrafast fluorescence spectroscopy, we have investigated the binding behaviors of coralyne with typical triplexes. Upon binding with a G-containing triplex, the fluorescence of coralyne is markedly quenched owing to the photoinduced electron transfer (PET) of coralyne with the G base. Systematic studies show that the PET rates are sensitive to the binding configuration and local microenvironment, from which the coexisting binding modes of monomeric (full and partial) intercalation and aggregate stacking along the sugar-phosphate backbone are distinguished and their respective contributions are determined. It shows that coralyne has preferences for monomeric intercalation within CGG triplex and pure TAT triplex, whereas CGC+ triplex adopts mainly backbone binding of coralyne aggregates due to charge repulsion, revealing the sequence-specific binding selectivity. The triplex-DNA-induced aggregation of coralyne could be used as a probe for recognizing the water content in local DNA structures. The strong π-π stacking of intercalated coralyne monomer with base-triplets plays an important role in stabilizing the triplex structure. These results provide mechanistic insights for understanding the remarkable propensity of coralyne in selective binding to triplex DNA and shed light on the prospective applications of coralyne-triplex targeted anti-gene therapeutics.
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Affiliation(s)
- Zeqing Jiao
- 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
| | - Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Zheng Hu
- 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
| | - Xianwang Zhang
- 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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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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7
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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8
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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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9
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Ye Z, Du Y, Pan X, Zheng X, Xue J. Electron transfer from guanosine to the lowest triplet excited state of 4-nitroindole through hydrogen-bonded complex. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Wei S, Zhang Z, Liu S, Wang Y. Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation. NEW J CHEM 2021. [DOI: 10.1039/d1nj01653a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The pKa values of reactive protons in 8-oxoG˙+ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.
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Affiliation(s)
- Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Zhenhua Zhang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Shijun Liu
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation)
- Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry
- Shaanxi University of Chinese Medicine
- Xianyang 712083
- China
| | - Yinghui Wang
- College of Science
- Chang’an University
- Xi’an 710064
- China
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11
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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: 0.4] [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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