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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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Green U, Aizenshtat Z, Ruthstein S, Cohen H. Reducing the spin–spin interaction of stable carbon radicals. Phys Chem Chem Phys 2013; 15:6182-4. [DOI: 10.1039/c3cp50533b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mönig J, Goslich R, Asmus KD. Thermodynamics of S.˙.S 2σ/1σ* Three-electron Bonds and Deprotonation Kinetics of Thioether Radical Cations in Aqueous Solution. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19860900205] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sato S, Ohashi Y, Kojima M, Watanabe T, Honda Y, Watanabe T. Degradation of sulfide linkages between isoprenes by lipid peroxidation catalyzed by manganese peroxidase. CHEMOSPHERE 2009; 77:798-804. [PMID: 19740510 DOI: 10.1016/j.chemosphere.2009.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 07/31/2009] [Accepted: 08/05/2009] [Indexed: 05/28/2023]
Abstract
Scission of sulfide linkages in vulcanized rubber has been a major concern since the early 20th century, because devulcanization is a key process for recycling waste rubber products as polymer materials that pose low environmental risks. We herein demonstrate that lipid peroxidation (LPO) of linoleic acid by manganese peroxidase (MnP), a proposed lignin-degradation system in the early stage of selective white rot fungi, cleaves sulfide bond in a model rubber compound, di(2-methylpent-2-enyl) sulfide, to 2,4-dimethylthiophene and 2-methyl-2-pentenal. The major intermediate of the LPO process, 2,4-decadienal was directly oxidized by MnP to cleave the sulfur-carbon bond. We propose that electrophilic radicals from 2,4-decadienal abstract one electron from a sulfur atom of the model compound to produce the sulfur radical cation intermediate, which in turn reacts with molecular oxygen to cleave the sulfur-carbon bond. The discovery of free radical-mediated scission of sulfide bond coupled with Mn oxidation provides a novel strategy for recycling vulcanized rubber wastes.
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Affiliation(s)
- Shin Sato
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji Kyoto 611-0011, Japan
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Strzelczak G, Korzeniowska-Sobczuk A, Bobrowski K. Electron spin resonance study of radiation-induced radicals in polycrystalline aromatic carboxylic acids containing a thioether group. Radiat Phys Chem Oxf Engl 1993 2005. [DOI: 10.1016/j.radphyschem.2004.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gajewski E, Dizdaroglu M, Krutzsch HC, Simic MG. OH radical-induced crosslinks of methionine peptides. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1984; 46:47-55. [PMID: 6611320 DOI: 10.1080/09553008414551051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Reactions of radiation-generated OH radicals with methionine (Met) and its homopeptides, L-Met-L-Met and tri-L-Met, were investigated through reaction products. Samples of irradiated Met and HCl-hydrolysates of its irradiated homopeptides were trimethylsilylated and analysed by capillary gas chromatography-mass spectrometry. Mass spectra taken revealed the formation of three products, 2-amino-4-(methyldithio)butanoic acid, 4,4'-thiobis(2-aminobutanoic acid) and homocystine. G values of these products were determined to be 0.10, 0.16 and 0.30, respectively.
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