1
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Zhao M, Guo J, Chen Z, Wang F. A disposable electrochemical magnetic immunosensor for the rapid and sensitive detection of 5-formylcytosine and 5-carboxylcytosine in DNA. Biosens Bioelectron 2024; 262:116547. [PMID: 38968775 DOI: 10.1016/j.bios.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/28/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
5-formylcytosine (5 fC) and 5-carboxylcytosine (5caC) serve as key intermediates in DNA demethylation process with significant implications for gene regulation and disease progression. In this study, we introduce a novel electrochemical sensing platform specifically designed for the sensitive and selective detection of 5 fC and 5caC in DNA. Protein A-modified magnetic beads (ProtA-MBs) coupled with specific antibodies facilitate the immunorecognition and enrichment of these modified bases. Signal amplification is achieved through several chemical reactions involving the interaction between N3-kethonaxl and guanine, copper-free click chemistry for the attachment of dibenzocyclooctyne (DBCO)-Biotin, and the subsequent recognition by streptavidin-conjugated horseradish peroxidase (SA-HRP). The assay's readout is performed on a disposable laser-induced graphene (LIG) electrode, modified with the bead-antibody-DNA complex in a magnetic field, and analyzed using differential pulse voltammetry in a system employing hydroquinone (HQ) as the redox mediator and H2O2 as the substrate. This immunosensor displayed excellent sensitivity, with detection limits of 14.8 fM for 5 fC across a 0.1-1000 pM linear range and 87.4 fM for 5caC across a 0.5-5000 pM linear range, and maintained high selectivity even in the presence of interferences from other DNA modifications. Successful application in quantifying 5 fC and 5caC in genomic DNA from cell extracts, with recovery rates between 97.7% to 102.9%, underscores its potential for clinical diagnostics. N3-kethoxal was used for the first time in an electrochemical sensor. This work not only broadens the toolkit for detecting DNA modifications but also provides a fresh impetus for the development of point-of-care testing (POCT) technologies.
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Affiliation(s)
- Mei Zhao
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Jingyi Guo
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Zilin Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
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2
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Wang W, Yang Y, Chen Z, Wang X, Zhang GL, He T, Tong L, Tang B. Simultaneous Detection of Aldehyde Metabolites by Light-Assisted Ambient Ionization Mass Spectrometry. Anal Chem 2024; 96:787-793. [PMID: 38170819 DOI: 10.1021/acs.analchem.3c04124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In the clinic, small-molecule metabolites (SMMs) in blood are highly convincing indicators for disease diagnosis, such as cancer. However, challenges still exist for detection of SMMs due to their low concentration and complicated components in blood. In this work, we report the design of a novel "selenium signature" nanoprobe (Se nanoprobe) for efficient identification of multiple aldehyde metabolites in blood. This Se nanoprobe consists of magnetic nanoparticles that can enrich aldehyde metabolites from a complex environment, functionalized with photosensitive "selenium signature" hydrazide molecules that can react with aldehyde metabolites. Upon irradiation with UV, the aldehyde derivatives can be released from the Se nanoprobe and further sprayed by mass spectrometry through ambient ionization (AIMS). By quantifying the selenium isotope distribution (MS/MS) from the derivatization product, accurate detection of several aldehyde metabolites, including valeraldehyde (Val), heptaldehyde (Hep), 2-furaldehyde (2-Fur), 10-undecenal aldehyde (10-Und), and benzaldehyde (Ben), is realized. This strategy reveals a new solution for quick and accurate cancer diagnosis in the clinic.
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Affiliation(s)
- Weiqing Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Xiaoxiao Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Guang-Lu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Tairan He
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Centre of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
- Laoshan Laboratory, Qingdao 266237, P. R. China
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3
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Zhao M, Zou G, Tang J, Guo J, Wang F, Chen Z. Probe-labeled electrochemical approach for highly selective detection of 5-carboxycytosine in DNA. Anal Chim Acta 2023; 1273:341521. [PMID: 37423653 DOI: 10.1016/j.aca.2023.341521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
5-carboxycytosine (5caC) plays a critical role as an intermediate form in DNA methylation and demethylation processes. Its distribution and quantity significantly influence the dynamic equilibrium of these processes, thereby impacting the normal physiological activities of organisms. However, the analysis of 5caC presents a significant challenge due to its low abundance in the genome, making it almost undetectable in most tissues. In response to this challenge, we propose a selective method for 5caC detection using differential pulse voltammetry (DPV) at glassy carbon electrode (GCE), hinging on probe labeling. The probe molecule Biotin LC-Hydrazide was introduced into the target base and the labeled DNA was immobilized onto the electrode surface with the help of T4 polynucleotide kinase (T4 PNK). Leveraging the precise and efficient recognition of streptavidin and biotin, streptavidin-horseradish peroxidase (SA-HRP) on the surface of the electrode catalyzed a redox reaction involving hydroquinone and hydrogen peroxide, resulting in an amplified current signal. This procedure allowed us to quantitatively detect 5caC based on variations in current signals. This method demonstrated good linearity ranging from 0.01 to 100 nM with a detection limit as low as 7.9 pM. We have successfully applied it to evaluate the 5caC levels in complex biological samples. The probe labeling contributes to a high selectivity for 5caC detection, while the sulfhydryl modification via T4 PNK efficiently circumvents the limitation of specific sequences. Encouragingly, no reports have been made about electrochemical methods for detecting 5caC in DNA, suggesting that our method offers a promising alternative for 5caC detection in clinical samples.
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Affiliation(s)
- Mei Zhao
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Tang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Jingyi Guo
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China
| | - Fang Wang
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
| | - Zilin Chen
- School of Pharmaceutical Sciences, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Wuhan University, Wuhan, 430071, China.
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4
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Liu C, Le BH, Xu W, Yang CH, Chen YH, Zhao L. Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA. Nucleic Acids Res 2023; 51:e73. [PMID: 37293974 PMCID: PMC10359467 DOI: 10.1093/nar/gkad502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.
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Affiliation(s)
- Chaoxing Liu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Brandon H Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Ching-Hsin Yang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Yu Hsuan Chen
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
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5
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Choi H, Kim H, Kim KT. Fluorescent nucleobase analogs constructed by
aldol‐type
condensation: Design, properties, and synthetic optimization for fluorogenic labeling of
5‐formyluracil. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hayeon Choi
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
| | - Hokyung Kim
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
| | - Ki Tae Kim
- Department of Chemistry Chungbuk National University Cheongju Republic of Korea
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6
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Xue L, Yu D, Wang L, Sun J, Song Y, Jia Y, Wu A, Zhang B, Mi W, Fan H, Sun H. Selective Antitumor Activity and Photocytotoxicity of Glutathione-Activated Abasic Site Trapping Agents. ACS Chem Biol 2022; 17:797-803. [PMID: 35297620 DOI: 10.1021/acschembio.2c00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abasic (AP) sites are one of the most common DNA lesions in cells. Aldehyde-reactive alkoxyamines capture AP sites and block the activity of APE1, the enzyme responsible for initiating their repair. Blocking the APE1 repair of AP sites leads to cell death, and it is an actively investigated approach for treating cancer. However, unselective AP site capture in different cells produces side effects and limits the application of alkoxyamines in chemotherapy. Herein we take advantage of the higher glutathione (GSH) concentration in cancer cells over normal cells to develop GSH-inducible agents that selectively kill cancer cells. 2,4-Dinitrobenzenesulfonamide caged coumarin-based alkoxyamines 1 and 2 are selectively revealed by GSH to release SO2 and fluorescent coumarin-based alkoxyamines 3 and 4 that trap AP sites in cells. GSH-directed AP site trapping and SO2 release result in selective cytotoxicity (defined as IC50WI38/IC50H1299) against H1299 lung cancer cells over normal WI38 lung cells, ranging from 1.8 to 2.8 for 1 and 2. The alkylating agent methylmethanesulfonate (MMS) promotes the formation of AP sites in cells and enhances the cytotoxicity of agent 1 in a dose-dependent way. Moreover, the comet assay and γH2AX assay suggest that AP adducts form a highly toxic DNA interstrand cross-link (ICL) upon photolysis, leading to further cell death. DNA flow cytometric analysis showed that 1 promoted cell apoptosis in the early stage and induced G2/M phase cell-cycle arrest. The 2,4-dinitrobenzenesulfonamide-caged alkoxyamines exhibited selective antitumor activity and photocytotoxicity in cancer cells, illuminating their potential as GSH-directed chemotherapeutic agents.
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Affiliation(s)
- Li Xue
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Dehao Yu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Lingling Wang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Jing Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Ying Song
- Institute of Biomedical Research, Yunnan University, Kunming 650500, P. R. China
| | - Yuanyuan Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Ang Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Beibei Zhang
- Institute of Biomedical Research, Yunnan University, Kunming 650500, P. R. China
| | - Wenyi Mi
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P. R. China
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Heli Fan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Huabing Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P. R. China
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7
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Qualitative and quantitative detection of aldehydes in DNA with 2-amino benzamidoxime derivative. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Ito Y, Hari Y. Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution. CHEM REC 2022; 22:e202100325. [PMID: 35119181 DOI: 10.1002/tcr.202100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
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9
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Tang J, Zou G, Chen C, Ren J, Wang F, Chen Z. Highly Selective Electrochemical Detection of 5-Formyluracil Relying on (2-Benzimidazolyl) Acetonitrile Labeling. Anal Chem 2021; 93:16439-16446. [PMID: 34813282 DOI: 10.1021/acs.analchem.1c03389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification of formylpyrimidines in DNA is crucial for a better understanding of epigenetics. Although many techniques have been explored to detect their content, more accurate methods of formylpyrimidine determination are still required due to the relatively lower sensitivity or lack of selectivity in current methods. Herein, an electrochemical method based on the covalent bonding of the azido derivative of (2-benzimidazolyl) acetonitrile (azi-BIAN) and the aldehyde group of 5-formyluracil (5fU) was proposed for the selective detection of 5fU in the presence of 5-formylcytosine (5fC) and apyrimidinic (AP) sites. Target DNA containing 5fU was first treated with azi-BIAN and then incubated with DBCO-PEG4-Biotin to introduce a biotin group by copper-free click chemistry. Next, the sulfhydryl group was attached to the 5' end of above DNA through T4 polynucleotide kinase-catalyzed reaction. Subsequently, the labeled DNA was assembled onto the AuNPs-modified glassy carbon electrode (AuNPs/GCE) through Au-S bonds, and the streptavidin-horseradish peroxidase conjugate (SA-HRP) was further immobilized onto the surface of the above electrode by specific recognition between biotin and streptavidin. Finally, HRP catalyzed hydroquinone oxidation to benzoquinone to enhance the current signal, which was related to the amount of 5fU in nucleic acids. This method demonstrated a good linear relationship with 5fU concentrations ranging from 0.1 to 10 nM. Moreover, the level of 5fU in γ-irradiated nucleic acids was also successfully detected, indicating that the combination of molecule-depended chemical recognition and electrochemical sensing is a promising method for the selective and sensitive detection of 5fU.
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Affiliation(s)
- Jing Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Hubei Province Engineering and Technology, Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing 100080, China
| | - Guangrong Zou
- Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, School of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Chen Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Hubei Province Engineering and Technology, Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jing Ren
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Hubei Province Engineering and Technology, Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Fang Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Hubei Province Engineering and Technology, Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing 100080, China
| | - Zilin Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Hubei Province Engineering and Technology, Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing 100080, China
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10
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Yang W, Han S, Zhang X, Wang Y, Zou G, Liu C, Xu M, Zhou X. Sequencing 5-Formyluracil in Genomic DNA at Single-Base Resolution. Anal Chem 2021; 93:15445-15451. [PMID: 34775754 DOI: 10.1021/acs.analchem.1c03339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Albeit with low content, 5-formyluracil has been an important modification in genomic DNA. 5-formyluracil was found to be widely distributed among living bodies. Due to the equilibrium of keto-enol form, 5-formyluracil could be base-paired with guanine, thus inducing mutations in DNA. The highly reactive aldehyde group of 5-formyluracil could also cross-link with proteins nearby, preventing gene replication and expression. In certain cancerous tissues, the content of 5-formyluracil was found to be higher than the normal tissues adjacent to the tumor, and 5-formyluracil might be an important potential epigenetic mark. Nevertheless, the lack of a higher resolution sequencing technique has hampered the studies of 5-formyluracil. We adjusted the base-pairing of 5-formyluracil during the PCR amplification by changing the pH. Hence, we adopted the Alkaline Modulated 5-formyluracil Sequencing (AMfU-Seq), a single-base resolution analysis method, to profile 5-formyluracil at the genome scale. We analyzed the distribution of 5-formyluracil in the human thyroid carcinoma cells using AMfU-Seq. This technique can be used in the future investigations of 5-formyluracil.
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Affiliation(s)
- Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Chaoxing Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Muxin Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072 Hubei, China
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11
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Wang DM, Jia J, Huang RF, Zhang X. A base-repair based electrochemiluminescent genotoxicity sensor that detects abasic sites in double-stranded DNA films. Chem Commun (Camb) 2021; 56:12558-12561. [PMID: 32940265 DOI: 10.1039/d0cc05186a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel genotoxicity sensor was developed based on the base repair process associated with the electrochemiluminescence (ECL) detection of abasic sites in a double-stranded DNA monolayer. This is the first time that an ECL sensor with the ability to identify the removed nucleobases in a DNA duplex has been studied. The successful detection of abasic sites created by DNA glycosylase indicates its further applications for examining some other specific types of DNA damage.
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Affiliation(s)
- Dong-Mei Wang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Jia Jia
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Rong-Fu Huang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
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12
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Zhou Q, Li K, Yu KK, Li N, Shi L, Chen H, Chen SY, Yu XQ. Aqueous Wittig reaction-mediated fast fluorogenic identification and single-base resolution analysis of 5-formylcytosine in DNA. Chem Commun (Camb) 2020; 56:12158-12161. [PMID: 32909575 DOI: 10.1039/d0cc04950f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A highly reactive ylide tBuA was introduced, which could react rapidly with the 5-formyl and 4-amino groups of 5-formylcytosine (5fC) under mild conditions without any co-solvent or catalyst in a manner of Wittig olefination and intramolecular nucleophilic substitution to yield a cyclized fluorescent adduct, which meets the demands of both single-base resolution sequencing and fluorescence switch-on detection of 5fC in DNA.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Kang-Kang Yu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Na Li
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Lei Shi
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Hao Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Centre, Memphis, Tennessee 38163, USA
| | - Shan-Yong Chen
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
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13
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Xie Y, Wang Y, He Z, Yang W, Fu B, Zou G, Zhang X, Huang J, Zhou X. Selective Chemical Labeling and Sequencing of 5-Carboxylcytosine in DNA at Single-Base Resolution. Anal Chem 2020; 92:12710-12715. [PMID: 32803958 DOI: 10.1021/acs.analchem.0c03201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Carboxylcytosine (5caC) plays a vital role in the dynamics of DNA demethylation, and sequencing of its sites will help us dig out more biological functions of 5caC. Herein, we present a novel chemical method to efficiently label 5caC distinguished from other bases in DNA. Combined with bisulfite sequencing, 5caC sites can be located at single-base resolution, and the efficiency of 5caC labeling is 92% based on the Sanger sequencing data. Furthermore, dot blot assays have confirmed that 5caC-containing DNA isolated from HeLa cells was successfully labeled using our method. We expect that our strategy can be further applied to selectively tagging other carboxyl-modified bases and mapping their sites in RNA.
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Affiliation(s)
- Yalun Xie
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Boshi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Jinguo Huang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, the Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, P. R. China
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Ivancová I, Leone DL, Hocek M. Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking. Curr Opin Chem Biol 2019; 52:136-144. [DOI: 10.1016/j.cbpa.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/26/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
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15
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Zhou Q, Li K, Li LL, Yu KK, Zhang H, Shi L, Chen H, Yu XQ. Combining Wittig Olefination with Photoassisted Domino Reaction To Distinguish 5-Formylcytosine from 5-Formyluracil. Anal Chem 2019; 91:9366-9370. [PMID: 31321977 DOI: 10.1021/acs.analchem.9b02499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In view of the important epigenetic functions of 5-formylcytosine (5fC), the development of quantitative detection methods for 5fC is a long-standing issue. In this regard, how to distinguish 5fC from 5-formyluracil to achieve higher accuracy is particularly difficult because the latter one is more reactive. Herein, we reported a phosphorus ylide, YC-CN, and introduced a triple domino reaction to fluorescently switch on 5fC with excellent selectivity, which also enable us to quantify 5fC mutations induced by γ-irradiation. This Wittig-initiated covalent labeling strategy provide a novel strategy for qualitative and quantitative detection of 5fC.
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Affiliation(s)
- Qian Zhou
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Kun Li
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Ling-Ling Li
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Kang-Kang Yu
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Hong Zhang
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Lei Shi
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
| | - Hao Chen
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Centre , Memphis , Tennessee 38163 , United States
| | - Xiao-Qi Yu
- Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry , Sichuan University , Chengdu 610064 , P. R. China
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16
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Chen H, Yao L, Brown C, Rizzo CJ, Turesky RJ. Quantitation of Apurinic/Apyrimidinic Sites in Isolated DNA and in Mammalian Tissue with a Reduced Level of Artifacts. Anal Chem 2019; 91:7403-7410. [PMID: 31055913 DOI: 10.1021/acs.analchem.9b01351] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The apurinic/apyrimidinic (AP) site is a common lesion of DNA damage. The levels of AP sites reported in the literature cover a wide range, which is primarily due to the artifactual generation or loss of AP sites during processing of the DNA. Herein, we have developed a method for quantitating AP sites with a largely reduced level of artifacts by derivatizing AP sites before DNA isolation. A rapid digestion of nuclear protein was performed to minimize enzymatic DNA repair, followed by direct derivatization of AP sites in the nuclear lysate with O-(pyridin-3-yl-methyl)hydroxylamine, yielding an oxime derivative that is stable through the subsequent DNA processing steps. Quantitation was done using highly selective and sensitive liquid chromatography-tandem mass spectrometry, with a limit of quantitation at 2.2 lesions per 108 nucleotides (nts, 0.9 fmol on column). The method was applied in vivo to measure AP sites in rats undergoing oxidative stress [liver, 3.31 ± 0.47/107 nts (dosed) vs 0.91 ± 0.06/107 nts (control); kidney, 1.60 ± 0.07/107 nts (dosed) vs 1.13 ± 0.12/107 nts (control)]. The basal AP level was significantly lower than literature values. The method was also used to measure AP sites induced by the chemotherapeutic nitrogen mustard in vitro.
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Affiliation(s)
- Haoqing Chen
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Lihua Yao
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Christina Brown
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Carmelo J Rizzo
- Departments of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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