1
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Chen YN, Shen XY, Yu Y, Xue CY, Zhou YL, Zhang XX. In-source fragmentation of nucleosides in electrospray ionization towards more sensitive and accurate nucleoside analysis. Analyst 2023; 148:1500-1506. [PMID: 36883656 DOI: 10.1039/d3an00047h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Nucleosides have been found to suffer in-source fragmentation (ISF) in electrospray ionization mass spectrometry, which leads to reduced sensitivity and ambiguous identification. In this work, a combination of theoretical calculations and nuclear magnetic resonance analysis revealed the key role of protonation at N3 near the glycosidic bond during ISF. Therefore, an ultrasensitive liquid chromatography-tandem mass spectrometry system for 5-formylcytosine detection was developed with 300 fold signal enhancement. Also, we established a MS1-only platform for nucleoside profiling and successfully identified sixteen nucleosides in the total RNA of MCF-7 cells. Taking ISF into account, we can realize analysis with higher sensitivity and less ambiguity, not only for nucleosides, but for other molecules with similar protonation and fragmentation behaviors.
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Affiliation(s)
- Yu-Nan Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Xu-Yang Shen
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Yue Yu
- Institute of Biotechnology Development, Qilu Pharmaceutical, Jinan, China
| | - Chen-Yu Xue
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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2
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Bu XM, Zhao WD, Zhang MY, Wu DQ, Wu JY, Xu X, Chen D. Matrix-assisted laser desorption/ionization high-resolution mass spectrometry for high-throughput analysis of androgenic steroid adulteration in traditional Chinese medicine based on d/d-Girard's reagent P labeling. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Ultrasensitive Simultaneous Detection of Multiple Rare Modified Nucleosides as Promising Biomarkers in Low-Put Breast Cancer DNA Samples for Clinical Multi-Dimensional Diagnosis. Molecules 2022; 27:molecules27207041. [DOI: 10.3390/molecules27207041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides with a different abundance simultaneously. In this work, an ultrasensitive quantification method based on chemical labeling, coupled with LC-MS/MS analysis, was established for the simultaneous quantification of 5hmdC, 5fdC, 5hmdU and 5fdU. Additionally, the contents of 5mdC and canonical nucleosides could be obtained at the same time. Upon derivatization, the detection sensitivities of 5hmdC, 5fdC, 5hmdU and 5fdU were dramatically enhanced by several hundred times. The established method was further applied to the simultaneous detection of nine nucleosides with different abundances in about 2 μg genomic DNA of breast tissues from 20 breast cancer patients. The DNA consumption was less than other overall reported quantification methods, thereby providing an opportunity to monitor rare, modified nucleosides in precious samples and biology processes that could not be investigated before. The contents of 5hmdC, 5hmdU and 5fdU in tumor tissues and normal tissues adjacent to the tumor were significantly changed, indicating that these three modified nucleosides may play certain roles in the formation and development of tumors and be potential cancer biomarkers. While the detection rates of 5hmdC, 5hmdU and 5fdU alone as a biomarker for breast cancer samples were 95%, 75% and 85%, respectively, by detecting these three cancer biomarkers simultaneously, two of the three were 100% consistent with the overall trend. Therefore, simultaneous detection of multiple cancer biomarkers in clinical samples greatly improved the accuracy of cancer diagnosis, indicating that our method has great application potential in clinical multidimensional diagnosis.
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4
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Agongo J, Armbruster M, Arnatt C, Edwards J. Analysis of endogenous metabolites using multifunctional derivatization and capillary RPLC-MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3397-3404. [PMID: 35980164 DOI: 10.1039/d2ay01108e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Heterogeneity in metabolite structure and charge state complicates their analysis in electrospray mass spectrometry (ESI-MS). Complications such as diminished signal response and quantitation can be reduced by sequential dual-stage derivatization and capillary RP LC-ESI-MS analysis. Our sequential dual-stage chemical derivatization reacts analyte primary amine and hydroxyl groups with a linear acyl chloride head containing a tertiary amine moiety. Analyte carboxylate groups are then coupled to a linear amine tag with a tertiary amine moiety. This increase in the number of tags on analytes increases analyte proton affinity and hydrophobicity. We derivatized 250 metabolite standards which on average improved signal to noise by >44-fold, with an average limit of detection of 66 nM and R2 of 0.98. This system detected 107 metabolites from 18 BAECs, 111 metabolites from human urine, and 153 from human serum based on retention time, exact mass, and MS/MS matches from a derivatized standard library. As a proof of concept, aortic endothelial cells were treated with epinephrine and analyzed by the dual-stage derivatization. We observed changes in 32 metabolites with many increases related to energy metabolism, specifically in the TCA cycle. A decrease in lactate levels and corresponding increase in pyruvate levels suggest that epinephrine causes a movement away from glycolytic reliance on energy and a shift towards the more efficient TCA respiration for increasing energy.
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Affiliation(s)
- Julius Agongo
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St Louis, MO, 63103, USA.
| | - Michael Armbruster
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St Louis, MO, 63103, USA.
| | - Christopher Arnatt
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St Louis, MO, 63103, USA.
| | - James Edwards
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St Louis, MO, 63103, USA.
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5
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Zheng Y, Zhou Y, Cui X, Yan H, Cao L, Gao L, Yin H. Investigation of the effect of antibiotics on 5-formylcytosine content in mazie seedling tissues based on photoelectrochemical biosensor. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129146. [PMID: 35594676 DOI: 10.1016/j.jhazmat.2022.129146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Given the improved photoactivity of Bi2S3 by MXene, an article photoelectrochemical biosensor was designed for 5-formyl-2'-deoxycytidine (5fdCTP) detection, where Bi2S3: MXene was selected as photoactive material, polydopamine was used as solid electron donor and 5fdCTP capture reagent, calcined ZIF-8(C-ZIF-8) was chosen as the artificial enzyme. With the catalyzed by C-ZIF-8, 4-chloro-1-naphthol was allegro oxidized by H2O2 to form the insoluble benzo-4-chlorohexadienone, and then deposited on the surface of the electrode, Resulting in a decrease of the PEC response. Under the optimum conditions, the sensor has a linear range of 0.001-200 nM and a detection limit of 0.51 pM (3σ). The suitability of the developed method was appraised by investigating the effect of antibiotics on 5fdCTP content in the genomic DNA of the roots of maize seedlings. As a new detection platform, the application of this approach can be expanded to investigative the impact of other pollutants on the content of 5fdCTP in plant or animal tissues, explore the feasibility of 5fdCTP as a new indicator for the ecotoxicological effect of pollutants, and the photoelectrochemical method as a new assessment technique for the ecotoxicological effects of pollutants.
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Affiliation(s)
- Yulin Zheng
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China.
| | - Xiaoting Cui
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China
| | - Hengming Yan
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China
| | - Lulu Cao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China
| | - Lanlan Gao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018 Taian, Shandong, People's Republic of China.
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6
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Zhang K, Fu B, Zou G, Yang W, Yan S, Tian T, Zhou X. Determination of 5-formyluracil via oxime-based nucleotide-metal coordination. Chembiochem 2022; 23:e202200355. [PMID: 35849116 DOI: 10.1002/cbic.202200355] [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: 06/21/2022] [Revised: 07/18/2022] [Indexed: 11/08/2022]
Abstract
In this article, a small chemical molecule was synthesized, and its ability to regulate activities of DNA polymerase was tested. In addition, we also used isothermal amplification technology to detect the content of 5-formyluracil sites in irradiated genomic DNA, which confirmed its capability for the detection of 5-formyluracil content in general samples. This study presents the first example of the determination of 5fU based on coordination chemistry.
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Affiliation(s)
- Kaiyuan Zhang
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Boshi Fu
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Guangrong Zou
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Wei Yang
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Shen Yan
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Tian Tian
- Wuhan University, College of Chemistry and Molecular Sciences, CHINA
| | - Xiang Zhou
- Wuhan University, College of Chemistry and Molecular Sciences, Luojia Shan, 430072, Wuhan, CHINA
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7
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Xiao F, Wang Q, Zhang K, Liu C, Zou G, Zhou X. Oxime formation coordination-directed detection of genome-wide thymine oxides with nanogram-scale sample input. Chem Sci 2022; 13:9074-9078. [PMID: 36091206 PMCID: PMC9365094 DOI: 10.1039/d2sc03013f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/12/2022] [Indexed: 11/21/2022] Open
Abstract
We report a convenient strategy to quantify 5-formyluracil (5fU) and 5-hydroxymethyluracil (5hmU) in biological samples, using only 40 ng of sample input on a laboratory real-time PCR instrument.
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Affiliation(s)
- Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Kaiyuan Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Chaoxing Liu
- University of California, Riverside Department of Chemistry, USA
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China
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8
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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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9
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Progress and Challenges in Quantifying Carbonyl-Metabolomic Phenomes with LC-MS/MS. Molecules 2021; 26:molecules26206147. [PMID: 34684729 PMCID: PMC8541004 DOI: 10.3390/molecules26206147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
Carbonyl-containing metabolites widely exist in biological samples and have important physiological functions. Thus, accurate and sensitive quantitative analysis of carbonyl-containing metabolites is crucial to provide insight into metabolic pathways as well as disease mechanisms. Although reversed phase liquid chromatography electrospray ionization mass spectrometry (RPLC-ESI-MS) is widely used due to the powerful separation capability of RPLC and high specificity and sensitivity of MS, but it is often challenging to directly analyze carbonyl-containing metabolites using RPLC-ESI-MS due to the poor ionization efficiency of neutral carbonyl groups in ESI. Modification of carbonyl-containing metabolites by a chemical derivatization strategy can overcome the obstacle of sensitivity; however, it is insufficient to achieve accurate quantification due to instrument drift and matrix effects. The emergence of stable isotope-coded derivatization (ICD) provides a good solution to the problems encountered above. Thus, LC-MS methods that utilize ICD have been applied in metabolomics including quantitative targeted analysis and untargeted profiling analysis. In addition, ICD makes multiplex or multichannel submetabolome analysis possible, which not only reduces instrument running time but also avoids the variation of MS response. In this review, representative derivatization reagents and typical applications in absolute quantification and submetabolome profiling are discussed to highlight the superiority of the ICD strategy for detection of carbonyl-containing metabolites.
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10
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5-Formyluracil targeted biochemical reactions with proteins inhibit DNA replication, induce mutations and interference gene expression in living cells. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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12
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Dai Y, Yuan BF, Feng YQ. Quantification and mapping of DNA modifications. RSC Chem Biol 2021; 2:1096-1114. [PMID: 34458826 PMCID: PMC8341653 DOI: 10.1039/d1cb00022e] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.
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Affiliation(s)
- Yi Dai
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University Wuhan 430072 P. R. China +86-27-68755595 +86-27-68755595
- School of Health Sciences, Wuhan University Wuhan 430071 China
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13
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Wang Q, Yin H, Zhou Y, Wang J, Ai S. Investigation of the inhibited biotoxicity of heavy metals towards 5- formylcytosine in rice by hydrochar based on photoelectrochemical biosensor. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125293. [PMID: 33647617 DOI: 10.1016/j.jhazmat.2021.125293] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/30/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
A photoelectrochemical (PEC) biosensor was constructed for 5-formylcytosine (5fC) nucleotide detection based on Ag2S@WS2 photoactive material and FeVO4 catalytic signal quenching. After Ag2S@WS2 was modified onto the ITO substrate surface, 5fC recognition reagent of Au@4-amino3hydrazino5mercapto-1,2,4-triazol (Au@AHMT) was further modified through electrostatic adsorption. Afterwards, based on the specific chemical reaction between -NH2 and -CHO, 5fC can be selectively recognized and captured. Subsequently, the nanoenzyme of FeVO4 was recognized based on the specific reaction between the phosphate group of 5fC nucleotide and Fe3+. Under the catalysis of FeVO4, the 4-chloro-1-naphthol in the detection solution can be oxidized to generate a precipitate, which will be retained on the electrode surface to inhibit the PEC signal. The developed method presented a widely dynamic range from 0.1 to 400 nM. The detection limit was 0.062 nM (3σ). This method also showed good detection selectivity, reproducibility and stability. The applicability was verified by investigating 5fC content change in genomic DNA of rice tissues after incubated with heavy metals. Moreover, the inhibited influence of hydrochar towards heavy metals was also assessed.
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Affiliation(s)
- Qian Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment in Universities of Shandong, Shandong Agricultural University, Taian 271018, PR China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, PR China
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14
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Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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15
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Kataoka H. In-tube solid-phase microextraction: Current trends and future perspectives. J Chromatogr A 2020; 1636:461787. [PMID: 33359971 DOI: 10.1016/j.chroma.2020.461787] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 01/01/2023]
Abstract
In-tube solid-phase microextraction (IT-SPME) was developed about 24 years ago as an effective sample preparation technique using an open tubular capillary column as an extraction device. IT-SPME is useful for micro-concentration, automated sample cleanup, and rapid online analysis, and can be used to determine the analytes in complex matrices simple sample processing methods such as direct sample injection or filtration. IT-SPME is usually performed in combination with high-performance liquid chromatography using an online column switching technology, in which the entire process from sample preparation to separation to data analysis is automated using the autosampler. Furthermore, IT-SPME minimizes the use of harmful organic solvents and is simple and labor-saving, making it a sustainable and environmentally friendly green analytical technique. Various operating systems and new sorbent materials have been developed to improve its extraction efficiency by, for example, enhancing its sorption capacity and selectivity. In addition, IT-SPME methods have been widely applied in environmental analysis, food analysis and bioanalysis. This review describes the present state of IT-SPME technology and summarizes its current trends and future perspectives, including method development and strategies to improve extraction efficiency.
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Affiliation(s)
- Hiroyuki Kataoka
- School of Pharmacy, Shujitsu University, Nishigawara, Okayama 703-8516, Japan.
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16
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Alkanawati M, da Costa Marques R, Mailänder V, Landfester K, Thérien-Aubin H. Polysaccharide-Based pH-Responsive Nanocapsules Prepared with Bio-Orthogonal Chemistry and Their Use as Responsive Delivery Systems. Biomacromolecules 2020; 21:2764-2771. [PMID: 32530606 PMCID: PMC7467571 DOI: 10.1021/acs.biomac.0c00492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Indexed: 12/22/2022]
Abstract
Bio-orthogonal reactions have become an essential tool to prepare biomaterials; for example, in the synthesis of nanocarriers, bio-orthogonal chemistry allows circumventing common obstacles related to the encapsulation of delicate payloads or the occurrence of uncontrolled side reactions, which significantly limit the range of potential payloads to encapsulate. Here, we report a new approach to prepare pH-responsive nanocarriers using dynamic bio-orthogonal chemistry. The reaction between a poly(hydrazide) crosslinker and functionalized polysaccharides was used to form a pH-responsive hydrazone network. The network formation occurred at the interface of aqueous nanodroplets in miniemulsion and led to the production of nanocapsules that were able to encapsulate payloads of different molecular weights. The resulting nanocapsules displayed low cytotoxicity and were able to release the encapsulated payload, in a controlled manner, under mildly acidic conditions.
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Affiliation(s)
| | - Richard da Costa Marques
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Dermatology, University Medical Center
of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, Mainz 55131, Germany
| | - Volker Mailänder
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
- Department
of Dermatology, University Medical Center
of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, Mainz 55131, Germany
| | - Katharina Landfester
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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17
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Li F, Wang S, Yin H, Chen Y, Zhou Y, Huang J, Ai S. Photoelectrochemical Biosensor for DNA Formylation Detection in Genomic DNA of Maize Seedlings Based on Black Tio 2-Enhanced Photoactivity of MoS 2/WS 2 Heterojunction. ACS Sens 2020; 5:1092-1101. [PMID: 32159349 DOI: 10.1021/acssensors.0c00036] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
5-Formylcytosine (5fC) is a rare base found in mammalian DNA, which is thought to be involved in the demethylation of DNA. As a stable epigenetic modification, 5fC participates in gene regulation and cell differentiation, and plays an important role in the growth and development of plants. However, the abundance of 5fC is only as low as 0.002-0.02% of cytosine. Therefore, to further understand the functions of 5fC, a rapid, highly sensitive, and efficient method is needed for detecting 5fC. Herein, a novel photoelectrochemical (PEC) biosensor was constructed for 5fC detection, where a MoS2/WS2 nanosheet heterojunction was employed as a photoactive material, amino-functionalized Fe3O4 and SMCC were used as a linker, 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole was adopted as 5fC recognition reagent, and black TiO2 (B-TiO2) was used as a signal amplification unit. Under the optimal experimental conditions, this PEC biosensor showed a wide linear range of 0.01-200 nM and a low detection limit of 2.7 pM (S/N = 3). Due to the specific covalent reaction between -NH2 and -CHO, the biosensor presented high detection sensitivity, even discriminating 5fC with 5-methylcytosine and 5-hydroxymethylcytosine. The biosensor was then applied to investigate the effect of heavy metal Cd2+ on 5fC content in the root, stem, and leaves of maize seedlings.
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Affiliation(s)
- Fei Li
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Siyu Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Yan Chen
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Jing Huang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian 271018, P. R. China
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18
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Li F, Yin H, Chen Y, Wang S, Li J, Zhang Y, Li C, Ai S. Preparation of P-g-C3N4-WS2 nanocomposite and its application in photoelectrochemical detection of 5-formylcytosine. J Colloid Interface Sci 2020; 561:348-357. [DOI: 10.1016/j.jcis.2019.10.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
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19
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Zhang Z, Yang D, Tian W, Qi Y, Ren W, Li Z, Liu C. Facile Clamp-Assisted Ligation Strategy for Direct Discrimination and Background-Free Quantification of Site-Specific 5-Formylcytosine. Anal Chem 2020; 92:3477-3482. [PMID: 31970980 DOI: 10.1021/acs.analchem.9b05715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantification of site-specific 5-formylcytosine (5fC) in DNA is highly significant to better understand its biological functions. However, it is still a big challenge to precisely discriminate 5fC from cytosine (C), 5-hydroxymethylcytosine (5hmC), 5-methylcytosine (5mC), and 5-carboxycytosine (5caC) owing to their similar structures that will interfere the quantification of 5fC. To solve this issue, a novel peptide nucleic acid (PNA) clamp-assisted ligation amplification strategy coupled with a 5fC-selective chemical conversion route is employed, through which 5fC can be precisely quantified with other interfering signals completely suppressed. As a result, as low as 200 aM of site-specific 5fC-containing DNA target can be accurately determined at single-base resolution in a background-free manner.
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Affiliation(s)
- Zhenhao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Dandan Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Weimin Tian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Yan Qi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering , Shaanxi Normal University , Xi'an , Shaanxi Province 710119 , P. R. China
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20
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Affiliation(s)
- Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry and Sauvage Center for Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
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21
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Lowenthal MS, Quittman E, Phinney KW. Absolute Quantification of RNA or DNA Using Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:14569-14576. [PMID: 31638773 DOI: 10.1021/acs.analchem.9b03625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate, traceable quantification of ribonucleotide or deoxyribonucleotide oligomers is achievable using acid hydrolysis and isotope dilution mass spectrometry (ID-MS). In this work, formic acid hydrolysis is demonstrated to generate stoichiometric release of nucleobases from intact oligonucleotides, which then can be measured by ID-MS, facilitating true and precise absolute quantification of RNA, short linearized DNA, or genomic DNA. Surrogate nucleobases are quantified with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow, using multiple reaction monitoring (MRM). Nucleobases were chromatographically resolved using a novel cation-exchange separation, incorporating a pH gradient. Trueness of this quantitative assay is estimated from agreement among the surrogate nucleobases and by comparison to concentrations provided for commercial materials or Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST). Comparable concentration estimates using NanoDrop spectrophotometry or established from droplet-digital polymerase chain reaction (ddPCR) techniques agree well with the results. Acid hydrolysis-ID-LC-MS/MS provides excellent quantitative selectivity and accuracy while enabling traceability to mass unit. Additionally, this approach can be uniquely useful for quantifying modified nucleobases or mixtures.
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Affiliation(s)
- Mark S Lowenthal
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Eva Quittman
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Karen W Phinney
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
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22
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Wang R, Jin X, Kong D, Chen Z, Liu J, Liu L, Cheng L. Visible‐Light Facilitated Fluorescence “Switch‐On” Labelling of 5‐Formylpyrimidine RNA. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui‐Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - De‐Long Kong
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Zhi‐Gang Chen
- BNLMS, State Key Laboratory of Polymer Physics and Chemistry, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Ji Liu
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- Key Lab of Functional Molecular Engineering of Guangdong ProvinceSouth China University of Technology Guangzhou 510640 China
- University of Chinese Academy of Sciences Beijing 100049 China
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23
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Kishikawa N, El-Maghrabey MH, Kuroda N. Chromatographic methods and sample pretreatment techniques for aldehydes determination in biological, food, and environmental samples. J Pharm Biomed Anal 2019; 175:112782. [DOI: 10.1016/j.jpba.2019.112782] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
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24
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Yu Y, Yuan F, Zhang XH, Zhao MZ, Zhou YL, Zhang XX. Ultrasensitive Determination of Rare Modified Cytosines Based on Novel Hydrazine Labeling Reagents. Anal Chem 2019; 91:13047-13053. [DOI: 10.1021/acs.analchem.9b03227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yue Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Hui Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ming-Zhe Zhao
- Capital Normal University High School, No. 33 Beiwa Road, Haidian District, Beijing, 100048, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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25
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Qi C, Ding J, Yuan B, Feng Y. Analytical methods for locating modifications in nucleic acids. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.02.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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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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27
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Zhang YF, Qi CB, Yuan BF, Feng YQ. Determination of cytidine modifications in human urine by liquid chromatography - Mass spectrometry analysis. Anal Chim Acta 2019; 1081:103-111. [PMID: 31446947 DOI: 10.1016/j.aca.2019.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
Both DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC) and RNA cytosine methylation (5-methylcytidine, m5rC) are important epigenetic marks that play regulatory roles in diverse biological processes. m5dC and m5rC can be further oxidized by the ten-eleven translocation (TET) proteins to form 5-hydroxymethyl-2'-deoxycytidine (hm5dC) and 5-hydroxymethylcytidine (hm5rC), respectively. 2'-O-methyl-5-hydroxymethylcytidine (hm5rCm) was recently also identified as a second oxidative metabolite of m5rC in RNA. Previous studies showed that the dysregulation of cytidine modifications in both DNA and RNA are closely related to a variety of human diseases. These cytidine modifications are generally excreted from cell into urine. If these cytidine modifications exhibit specific features related to certain diseases, determination of the cytidine modifications in urine could be utilized as non-invasive diagnostic of diseases. Here, we established a solid-phase extraction in combination with liquid chromatography-mass spectrometry (LC-MS/MS) analysis for simultaneous detection of these cytidine modifications in human urine samples. The developed method enabled the distinct detection of these cytidine modifications. We reported, for the first time, the presence of hm5rCm in human urine. Furthermore, we found that compared to the healthy controls, the contents of hm5dC, hm5rC, and hm5rCm showed significant increases in urine samples of cancer patients, including lymphoma patients, gastric cancer patients, and esophageal cancer patients. This study indicates that the urinary hydroxylmethylation modifications of hm5dC, hm5rC, and hm5rCm may serve as potential indicator of cancers.
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Affiliation(s)
- Yu-Fan Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Sauvage Center for Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China; Sauvage Center for Molecular Sciences, Wuhan University, Wuhan, 430072, PR China.
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
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28
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Wang Y, Zhang X, Zou G, Peng S, Liu C, Zhou X. Detection and Application of 5-Formylcytosine and 5-Formyluracil in DNA. Acc Chem Res 2019; 52:1016-1024. [PMID: 30666870 DOI: 10.1021/acs.accounts.8b00543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nucleic acids contain a variety of different base modifications, such as decoration at the fifth position of cytosine, which is one of the most important epigenetic modifications. Nucleic acid epigenetics mediate a wide variety of biological processes, including embryonic development and gene regulation, genomic imprinting, differentiation, and X-chromosome inactivation. Furthermore, the modification level can be aberrantly expressed in distinct sets of tissue that can indicate different tumor onsets and canceration. Thus, the analysis of modified nucleobases may contribute to the understanding of epigenetic modification-related biological processes and the correlation of modified nucleobase patterns with disease states for clinical diagnosis and treatment. In addition to 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine are found in organisms at a low content but are nevertheless extremely important chemical modifications, and 5-hydroxyuracil and 5-formyluracil compounds are also present. 5-Formyluracil is found in bacteriophages, prokaryotes, and mammalian cells. The 5-formyluracil content is higher in certain cancer tissues than in the normal tissues adjacent to the tumor. The content of 5-formyluracil in different cell tissues may have cell type specificity. With the continuous use of chemical tools, new detection technologies have greatly advanced the research on natural pyrimidine modifications. These modifications dynamically regulate the gene expression in eukaryotes and prokaryotes and provide mechanistic insights into the occurrence of diseases. Natural pyrimidine modifications act not only as intermediates for DNA demethylation or oxidative damage products but also as modulators of gene expression. Therefore, the development of more effective chemical tools will help us better understand the dynamic changes of natural pyrimidine modifications in vivo. In this Account, we summarize the recent advanced techniques for the detection of 5-formylpyrimidine (5-formylcytosine and 5-formyluracil) and highlight their great potential as biomarkers in biomedical applications. Focusing on the great urgency for the detection of epigenetic modifications, our group developed a series of methods for the qualitative and quantitative analysis of 5-formylpyrimidine in the past few years, aiming at facilitating the accurate detection and mapping of these epigenetic modifications. By the construction of probes, 5-formylpyrimidine can be selectively labeled. Using mass spectrometry, the epigenetic modifications can be quantified. Upon treatment under specific conditions, 5-formylcytosine can be recognized at single-base resolution. With this Account, we anticipate providing chemical and biological researchers with some insight to unlock the complex mechanism involved in 5-formylpyrimidine-related biological processes and stimulate more collaborative research interests from the different fields of materials, biological, medicine, and chemistry to promote the translational research of epigenetics in tumor diagnosis and treatment.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Shuang Peng
- 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
| | - Chaoxing Liu
- 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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29
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Zheng J, Zheng SJ, Cai WJ, Yu L, Yuan BF, Feng YQ. Stable isotope labeling combined with liquid chromatography-tandem mass spectrometry for comprehensive analysis of short-chain fatty acids. Anal Chim Acta 2019; 1070:51-59. [PMID: 31103167 DOI: 10.1016/j.aca.2019.04.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Short-chain fatty acids (SCFAs) are one class of bacterial metabolites mainly formed by gut microbiota from undigested fibers and proteins. These molecules are able to mediate signal conduction processes of cells, acting as G protein-coupled receptors (GPR) activators and histone deacetylases (HDAC) inhibitors. It was reported that SCFAs were closely associated with various human diseases. However, it is still challenging to analyze SCFAs because of their diverse structures and broad range of concentrations. In this study, we developed a highly sensitive method for simultaneous detection of 34 SCFAs by stable isotope labeling coupled with ultra-high performance liquid chromatography-electrospray ionization-mass spectrometry (UHPLC-ESI-MS/MS) analysis. In this respect, a pair of isotope labeling reagents, N-(4-(aminomethyl)benzyl)aniline (4-AMBA) and N-(4-(aminomethyl)benzyl)aniline-d5 (4-AMBA-d5), were synthesized to label SCFAs from the feces of mice and SCFA standards, respectively. The 4-AMBA-d5 labeled SCFAs were used as internal standards to compensate the ionization variances resulting from matrix effect and thus minimize quantitation deviation in MS detection. After 4-AMBA labeling, the retention of SCFAs on the reversed-phase column increased and the separation resolution of isomers were improved. In addition, the MS responses of most SCFAs were enhanced by up to three orders of magnitude compared to unlabeled SCFAs. The limits of detection (LODs) of SCFAs were as low as 0.005 ng/mL. Moreover, good linearity for 34 SCFAs was obtained with the coefficient of determination (R2) ranging from 0.9846 to 0.9999 and the intra- and inter-day relative standard deviations (RSDs) were <17.8% and 15.4%, respectively, indicating the acceptable reproducibility of the developed method. Using the developed method, we successfully quantified 21 SCFAs from the feces of mice. Partial least squares discriminant analysis (PLS-DA) and t-test analysis showed that the contents of 9 SCFAs were significantly different between Alzheimer's disease (AD) and wide type (WT) mice fecal samples. Compared to WT mice, the contents of propionic acid, isobutyric acid, 3-hydroxybutyric acid, and 3-hydroxyisocaleric acid were decreased in AD mice, while lactic acid, 2-hydroxybutyric acid, 2-hydroxyisobutyric acid, levulinic acid, and valpronic acid were increased in AD mice. These significantly changed SCFAs in the feces of AD mice may afford to a better understanding of the pathogenesis of AD. Taken together, the developed UHPLC-ESI-MS/MS method could be applied for the sensitive and comprehensive determination of SCFAs from complex biological samples.
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Affiliation(s)
- Jie Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Shu-Jian Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Wen-Jing Cai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Lei Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China.
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30
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Xiong J, Yuan BF, Feng YQ. Mass Spectrometry for Investigating the Effects of Toxic Metals on Nucleic Acid Modifications. Chem Res Toxicol 2019; 32:808-819. [PMID: 30920205 DOI: 10.1021/acs.chemrestox.9b00042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The extensive use of toxic metals in industry and agriculture leads to their wide distribution in the environment, which raises critical concerns over their toxic effects on human health. Many toxic metals are reported to be mildly mutagenic or non-mutagenic, indicating that genetic-based mechanisms may not be primarily responsible for toxic metal-induced carcinogenesis. Increasing evidence has demonstrated that exposure to toxic metals can alter epigenetic modifications, which may lead to the dysregulation of gene expression and disease susceptibility. It is now becoming clear that a full understanding of the effects of toxic metals on cellular toxicity and carcinogenesis will need to consider both genetic- and epigenetic-based mechanisms. Uncovering the effects of toxic metals on epigenetic modifications in nucleic acids relies on the detection and quantification of these modifications. Mass spectrometry (MS)-based methods for deciphering epigenetic modifications have substantially advanced over the past decade, and they are now becoming widely used and essential tools for evaluating the effects of toxic metals on nucleic acid modifications. This Review provides an overview of MS-based methods for analysis of nucleic acid modifications. In addition, we also review recent advances in understanding the effects of exposure to toxic metals on nucleic acid modifications.
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Affiliation(s)
- Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
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31
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On-line trapping/capillary hydrophilic-interaction liquid chromatography/mass spectrometry for sensitive determination of RNA modifications from human blood. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.11.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Deciphering nucleic acid modifications by chemical derivatization-mass spectrometry analysis. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.04.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Liu C, Luo X, Chen Y, Wu F, Yang W, Wang Y, Zhang X, Zou G, Zhou X. Selective Labeling Aldehydes in DNA. Anal Chem 2018; 90:14616-14621. [PMID: 30441892 DOI: 10.1021/acs.analchem.8b04822] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A naphthalimide hydroxylamine probe has been designed and synthesized to selectively label the whole natural aldehydes present in DNAs including 5-formylcytosine, 5-formyluracil, and abasic sites. The fluorescence characteristics of the generated nucleosides have been examined in detail, and the reaction activities of hydroxylamine, amine groups toward aldehydes in DNA have been discussed with others, which will be a vital reference for designing chemicals for selective labeling of DNAs.
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Affiliation(s)
- Chaoxing Liu
- 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
| | - Xiaomeng Luo
- 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
| | - Yuqi Chen
- 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
| | - Fan Wu
- 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
| | - 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
| | - 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
| | - 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
| | - 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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Huang T, Armbruster MR, Coulton JB, Edwards JL. Chemical Tagging in Mass Spectrometry for Systems Biology. Anal Chem 2018; 91:109-125. [DOI: 10.1021/acs.analchem.8b04951] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Michael R. Armbruster
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - John B. Coulton
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - James L. Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
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35
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Wang Y, Liu C, Wu F, Zhang X, Liu S, Chen Z, Zeng W, Yang W, Zhang X, Zhou Y, Weng X, Wu Z, Zhou X. Highly Selective 5-Formyluracil Labeling and Genome-wide Mapping Using (2-Benzimidazolyl)Acetonitrile Probe. iScience 2018; 9:423-432. [PMID: 30466066 PMCID: PMC6249349 DOI: 10.1016/j.isci.2018.10.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/04/2018] [Accepted: 10/23/2018] [Indexed: 02/08/2023] Open
Abstract
Chemical modifications to nucleobases have a great influence on various cellular processes, by making gene regulation more complex, thus indicating their profound impact on aspects of heredity, growth, and disease. Here, we provide the first genome-wide map of 5-formyluracil (5fU) in living tissues and evaluate the potential roles for 5fU in genomics. We show that an azido derivative of (2-benzimidazolyl)acetonitrile has high selectivity for enriching 5fU-containing genomic DNA. The results have demonstrated the feasibility of using this method to determine the genome-wide distribution of 5fU. Intriguingly, most 5fU sites were found in intergenic regions and introns. Also, distribution of 5fU in human thyroid carcinoma tissues is positively correlated with binding sites of POLR2A protein, which indicates that 5fU may distributed around POLR2A-binding sites. The derivative of (2-benzimidazolyl)acetonitrile (azi-BIAN) can selectivity label 5fU Azi-BIAN can selectively label and pull down 5fU in the genome for NGS The first genome-wide map of 5fU in mammalian genomic DNA 5fU is highly enriched at intergenic regions and introns
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Affiliation(s)
- 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
| | - Chaoxing Liu
- 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
| | - Fan Wu
- 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
| | - Sheng Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zonggui Chen
- College of Life Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Weiwu Zeng
- 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
| | - Xiaolian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Yu Zhou
- College of Life Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiaocheng Weng
- 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
| | - Zhiguo Wu
- College of Life Science, 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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36
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37
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Affiliation(s)
- Bei Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, P.R. China
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38
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Lan MD, Xiong J, You XJ, Weng XC, Zhou X, Yuan BF, Feng YQ. Existence of Diverse Modifications in Small-RNA Species Composed of 16-28 Nucleotides. Chemistry 2018; 24:9949-9956. [PMID: 29756662 DOI: 10.1002/chem.201801640] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Indexed: 11/11/2022]
Abstract
RNA contains diverse modifications that exert an important influence in a variety of cellular processes. So far, more than 150 modifications have been identified in various RNA species, mainly in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). In contrast to rRNA, tRNA, and mRNA, the known modifications in small RNA species have been primarily limited to 2'-O-ribose methylation in plants and inosine in mammals. The methylation of small RNAs in mammals is still unclear. Current methods widely used in the characterization of small RNAs are mainly based on the strategy of nucleic acid hybridization and sequencing, which cannot characterize modifications in small RNAs. Herein, we have systematically investigated modifications in small RNAs composed of 16-28 nucleotides (nt) by establishing an effective isolation and neutral enzymatic digestion of small RNAs in combination with liquid chromatography/electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This method allowed us to simultaneously detect 57 different types of nucleoside modification. By using this approach, we revealed 24 modifications in small RNAs comprising 16-28 nt from human cells. In addition, we found that the obesity-associated protein (FTO) may demethylate N6 -methyladenosine (m6 A) and N6 ,2'-O-dimethyladenosine (m6 Am) in small RNAs of 16-28 nt. Our study demonstrates the existence of diverse modifications in small RNAs composed of 16-28 nt, which may promote in-depth understanding of the regulatory roles of noncoding RNAs.
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Affiliation(s)
- Meng-Dan Lan
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
| | - Xue-Jiao You
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
| | - Xiao-Cheng Weng
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
| | - Xiang Zhou
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for, Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, P.R. China
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39
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Dietzsch J, Feineis D, Höbartner C. Chemoselective labeling and site-specific mapping of 5-formylcytosine as a cellular nucleic acid modification. FEBS Lett 2018; 592:2032-2047. [DOI: 10.1002/1873-3468.13058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Julia Dietzsch
- Institute of Organic Chemistry; University of Würzburg; Germany
| | - Doris Feineis
- Institute of Organic Chemistry; University of Würzburg; Germany
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40
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Yuan BF, Zhu QF, Guo N, Zheng SJ, Wang YL, Wang J, Xu J, Liu SJ, He K, Hu T, Zheng YW, Xu FQ, Feng YQ. Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis. Anal Chem 2018; 90:3512-3520. [PMID: 29406693 DOI: 10.1021/acs.analchem.7b05355] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gut microbiota plays important roles in the host health. The host and symbiotic gut microbiota coproduce a large number of metabolites during the metabolism of food and xenobiotics. The analysis of fecal metabolites can provide a noninvasive manner to study the outcome of the host-gut microbiota interaction. Herein, we reported the comprehensive profiling of fecal metabolome of mice by an integrated chemical isotope labeling combined with liquid chromatography-mass spectrometry (CIL-LC-MS) analysis. The metabolites are categorized into several submetabolomes based on the functional moieties (i.e., carboxyl, carbonyl, amine, and thiol) and then analysis of the individual submetabolome was performed. The combined data from the submetabolome form the metabolome with relatively high coverage. To this end, we synthesized stable isotope labeling reagents to label metabolites with different groups, including carboxyl, carbonyl, amine, and thiol groups. We detected 2302 potential metabolites, among which, 1388 could be positively or putatively identified in feces of mice. We then further confirmed 308 metabolites based on our established library of chemically labeled standards and tandem mass spectrometry analysis. With the identified metabolites in feces of mice, we established mice fecal metabolome database, which can be used to readily identify metabolites from feces of mice. Furthermore, we discovered 211 fecal metabolites exhibited significant difference between Alzheimer's disease (AD) model mice and wild type (WT) mice, which suggests the close correlation between the fecal metabolites and AD pathology and provides new potential biomarkers for the diagnosis of AD.
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Affiliation(s)
- Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Quan-Fei Zhu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Ning Guo
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Shu-Jian Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Ya-Lan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Jie Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , Wuhan Center for Magnetic Resonance (Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences) , Wuhan 430071 , P.R. China.,University of the Chinese Academy of Sciences , Beijing , 100049 , P.R. China
| | - Jing Xu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Shi-Jie Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Ke He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
| | - Ting Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , Wuhan Center for Magnetic Resonance (Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences) , Wuhan 430071 , P.R. China.,University of the Chinese Academy of Sciences , Beijing , 100049 , P.R. China
| | - Ying-Wei Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , Wuhan Center for Magnetic Resonance (Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences) , Wuhan 430071 , P.R. China.,University of the Chinese Academy of Sciences , Beijing , 100049 , P.R. China
| | - Fu-Qiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics , Wuhan Center for Magnetic Resonance (Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences) , Wuhan 430071 , P.R. China.,University of the Chinese Academy of Sciences , Beijing , 100049 , P.R. China.,Center for Excellence in Brain Science and Intelligence Technology , Chinese Academy of Sciences , Shanghai 200031 , P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry , Wuhan University , Wuhan 430072 , P.R. China
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41
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Wang Y, Liu C, Yang W, Zou G, Zhang X, Wu F, Yu S, Luo X, Zhou X. Naphthalimide derivatives as multifunctional molecules for detecting 5-formylpyrimidine by both PAGE analysis and dot-blot assays. Chem Commun (Camb) 2018; 54:1497-1500. [DOI: 10.1039/c7cc08715b] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An azide and hydrazine tethered to a naphthalimide analogue was created to selectively react with 5-formyluracil in one system and fluorogenically label 5-formylcytosine in another system.
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Affiliation(s)
- 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
- P. R. China
| | - Chaoxing Liu
- 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
- 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
- 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
- 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
- P. R. China
| | - Fan Wu
- 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
- P. R. China
| | - Shuyi Yu
- 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
- P. R. China
| | - Xiaomeng Luo
- 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
- 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
- P. R. China
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42
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Zhou Q, Li K, Liu YH, Li LL, Yu KK, Zhang H, Yu XQ. Fluorescent Wittig reagent as a novel ratiometric probe for the quantification of 5-formyluracil and its application in cell imaging. Chem Commun (Camb) 2018; 54:13722-13725. [DOI: 10.1039/c8cc07541g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For the first time a Wittig reagent was introduced into the design of a fluorescent probe for the quantification of 5-formyluracil.
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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
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University
- Chengdu 610064
- P. R. China
| | - Ling-Ling 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
| | - Hong Zhang
- 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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