2
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Hu Z, Zhou Q, Jiao Z, Qin P, Wang F, Xia Y, Zhang T, Jie J, Su H. Low Energy Photoionization of Phosphorothioate DNA-Oligomers and Ensuing Hole Transfer. J Phys Chem B 2022; 126:8699-8707. [PMID: 36259641 DOI: 10.1021/acs.jpcb.2c05521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Phosphorothioate (PS) modified oligonucleotides (S-DNA) naturally exist in bacteria and archaea genome and are widely used as an antisense strategy in gene therapy. However, the introduction of PS as a redox active site may trigger distinct UV photoreactions. Herein, by time-resolved spectroscopy, we observe that 266 nm excitation of S-DNA d(Aps)20 and d(ApsA)10 leads to direct photoionization on the PS moiety to form hemi-bonded -P-S∴S-P- radicals, in addition to A base ionization to produce A+•/A(-H)•. Fluorescence spectroscopy and global analysis indicate that an unusual charge transfer state (CT) between the A and PS moiety might populate in competition with the common CT state among bases as key intermediate states responsible for S-DNA photoionization. Significantly, the photoionization bifurcating to PS and A moieties of S-DNA is discovered, suggesting that the PS moiety could capture the oxidized site and protect the remaining base against ionization lesion, shedding light on the understanding of its existence in living organisms.
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Affiliation(s)
- Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Zeqing Jiao
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Peixuan Qin
- University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Fei Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ye Xia
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Tianfeng Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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3
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Denisov SA, Ward S, Shcherbakov V, Stark AD, Kaczmarek R, Radzikowska-Cieciura E, Debnath D, Jacobs T, Kumar A, Sevilla MD, Pernot P, Dembinski R, Mostafavi M, Adhikary A. Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group. J Phys Chem B 2022; 126:430-442. [PMID: 34990129 PMCID: PMC8776618 DOI: 10.1021/acs.jpcb.1c09068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O-)═S)). ESR investigations show that DMTP(O-)═S reacts with Cl2•- to form the σ2σ*1 adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O-)═S to produce [-P-S[Formula: see text]S-P-]-. -P-S[Formula: see text]Cl in G-P(O-)═S undergoes hole transfer to Gua, forming the cation radical (G•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O-)═S forms the thiyl radical (-P-S•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]-. Gua in G-P(O-)═S is oxidized unimolecularly by the -P-S• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.
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Affiliation(s)
- Sergey A. Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Alexander D. Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Ewa Radzikowska-Cieciura
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Michael D. Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Roman Dembinski
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA,Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
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Liu JM, Nishigori T, Maeyama T, Huang QR, Katada M, Kuo JL, Fujii A. Infrared Spectroscopy and Anharmonic Vibrational Analysis of (H 2O-Kr n) + ( n = 1-3): Hemibond Formation of the Water Radical Cation. J Phys Chem Lett 2021; 12:7997-8002. [PMID: 34433278 DOI: 10.1021/acs.jpclett.1c02164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The hemibond is a nonclassical covalent bond formed between a radical (cation) and a closed shell molecule. The hemibond formation ability of water has attracted great interest, concerning its role in ionization of water. While many computational studies on the water hemibond have been performed, clear experimental evidence has been hardly reported because the hydrogen bond formation overwhelms the hemibond formation. In the present study, infrared photodissociation spectroscopy is applied to (H2O-Krn)+ (n = 1-3) radical cation clusters. The observed spectra of (H2O-Krn)+ are well reproduced by the anharmonic vibrational simulations based on the hemibonded isomer structures. The firm evidence of the hemibond formation ability of water is revealed.
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Affiliation(s)
- Jing-Min Liu
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan
| | - Tomoki Nishigori
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
| | - Toshihiko Maeyama
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
| | - Qian-Rui Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan
| | - Marusu Katada
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba 6-3, Aoba-Ku, Sendai 980-8578, Japan
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6
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Li K, Fang Z, Zhao G, Li B, Chen C, Xia L, Wang L, Luo T, Wang X, Wang Z, Zhang Y, Jiang Y, Pan Q, Hu Z, Guo H, Tang B, Liu C, Sun Z, Xia K, Li J. Cross-Disorder Analysis of De Novo Mutations in Neuropsychiatric Disorders. J Autism Dev Disord 2021; 52:1299-1313. [PMID: 33970367 PMCID: PMC8854168 DOI: 10.1007/s10803-021-05031-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 12/02/2022]
Abstract
The clinical similarity among different neuropsychiatric disorders (NPDs) suggested a shared genetic basis. We catalogued 23,109 coding de novo mutations (DNMs) from 6511 patients with autism spectrum disorder (ASD), 4,293 undiagnosed developmental disorder (UDD), 933 epileptic encephalopathy (EE), 1022 intellectual disability (ID), 1094 schizophrenia (SCZ), and 3391 controls. We evaluated that putative functional DNMs contribute to 38.11%, 34.40%, 33.31%, 10.98% and 6.91% of patients with ID, EE, UDD, ASD and SCZ, respectively. Consistent with phenotype similarity and heterogeneity in different NPDs, they show different degree of genetic association. Cross-disorder analysis of DNMs prioritized 321 candidate genes (FDR < 0.05) and showed that genes shared in more disorders were more likely to exhibited specific expression pattern, functional pathway, genetic convergence, and genetic intolerance.
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Affiliation(s)
- Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Lin Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Yi Jiang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Qian Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,School of Basic Medical Science, Central South University, Changsha, Hunan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China.
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China. .,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Xiangya Road, Kaifu District, Changsha, 410013, Hunan, China.
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7
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Huang Q, Li J, Shi T, Liang J, Wang Z, Bai L, Deng Z, Zhao YL. Defense Mechanism of Phosphorothioated DNA under Peroxynitrite-Mediated Oxidative Stress. ACS Chem Biol 2020; 15:2558-2567. [PMID: 32816442 DOI: 10.1021/acschembio.0c00591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA phosphorothioation (PT) exists in many pathogenic bacteria; however, the mechanism of PT-DNA resistance to the immune response is unclear. In this work, we meticulously investigated the peroxynitrite (PN) tolerance using PT-bioengineered E. coli strains. The in vivo experiment confirms that the S+ strain survives better than the S- strain under moderately oxidative stress. The LCMS, IC, and GCMS experiments demonstrated that phosphorothioate partially converted to phosphate, and the byproduct included sulfate and elemental sulfur. When O,O-diethyl thiophosphate ester (DETP) was used, the reaction rate k1 was determined to be 4.3 ± 0.5 M-1 s-1 in the first-order for both phosphorothioate and peroxynitrite at 35 °C and pH of 8.0. The IC50 values of phosphorothioate dinucleotides are dramatically increased by 400-700-fold compared to DETP. The SH/OH Yin-Yang mechanism rationalizes the in situ DNA self-defense against PN-mediated oxidative stress at the extra bioenergetic cost of DNA modification.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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