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Kumar S, Kumar S, Arora A, Prasad AK, Maity J. 5‐Formyluridine and Its Synthetic Applications. ChemistrySelect 2022. [DOI: 10.1002/slct.202203432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Sandeep Kumar
- Bioorganic Laboratory Department of Chemistry University of Delhi Delhi India
| | - Sumit Kumar
- Bioorganic Laboratory Department of Chemistry University of Delhi Delhi India
| | - Aditi Arora
- Bioorganic Laboratory Department of Chemistry University of Delhi Delhi India
| | - Ashok K. Prasad
- Bioorganic Laboratory Department of Chemistry University of Delhi Delhi India
| | - Jyotirmoy Maity
- Department of Chemistry St. Stephen's College University of Delhi Delhi India
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2
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In vitro Scolicidal Efficacy of 5-Fluorouracil and Radiation Against Protoscoleces of Echinococcus granulosus Sensu Lato. Acta Parasitol 2022; 67:820-826. [PMID: 35113338 DOI: 10.1007/s11686-022-00518-4] [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: 10/08/2021] [Accepted: 01/03/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Cystic echinococcosis (CE) caused by Echinococcus granulosus sensu lato (s.l.) is a globally distributed zoonosis. CE treatment is difficult, but radiation and 5-fluorouracil (5-FU) can be effective. However, the combination of radiation and 5-FU has not been reported. This study evaluated the effect of combination of 5-FU and radiation on E. granulosus s.l. protoscoleces (PSCs). MATERIAL AND METHODS In this study, PSCs were collected from the liver of diseased sheep, and some were exposed to a single dose of 20 Gy 6-MV X-ray combined with (5 μg/mL or 10 μg/mL) 5-FU in vitro. Methylene blue staining was used to detect the viability of the PSCs. Transcription of EgHSP70 and Egp38 was measured by quantitative real-time PCR (qRT- PCR). RESULTS A single dose of radiation killed 18% of the PSCs, and 5-FU showed weak parasiticidal efficacy on the first day of treatment. After 14 d, 5 μg and 10 μg/mL of 5-FU killed 40.20% and 50.02% of the PSCs, whereas 20 Gy of radiation killed 31.44%. The combination of 5-FU (10 μg/mL) with 20 Gy of radiation showed 77.55% killing efficacy. qRT-PCR showed that 5-FU inhibited Egp38 expression, whereas radiation increased its expression. EgHSP70 was highly expressed 14 days after radiation treatment. The data indicate that 5-FU has parasiticidal efficacy against the PSCs of E. granulosus s.l. CONCLUSION The lethal efficacy of PSCs caused by a single dose of radiation exposure is related to the upregulated expression level of Egp38 and EgHSP70. The killing effect of 5-FU (10 μg/mL) with 20Gy of radiation was significantly better than that of single treatment group. This study provided a basis for the potential role of 5-FU combined with radiation in the treatment of CE.
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3
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Qualitative and quantitative detection of aldehydes in DNA with 2-amino benzamidoxime derivative. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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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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5
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Runtsch LS, Stadlmeier M, Schön A, Müller M, Carell T. Comparative Nucleosomal Reactivity of 5-Formyl-Uridine and 5-Formyl-Cytidine. Chemistry 2021; 27:12747-12752. [PMID: 34152627 PMCID: PMC8518870 DOI: 10.1002/chem.202102159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 11/21/2022]
Abstract
5‐Formyl‐deoxyuridine (fdU) and 5‐formyl‐deoxycytidine (fdC) are formyl‐containing nucleosides that are created by oxidative stress in differentiated cells. While fdU is almost exclusively an oxidative stress lesion formed from deoxythymidine (T), the situation for fdC is more complex. Next to formation as an oxidative lesion, it is particularly abundant in stem cells, where it is more frequently formed in an epigenetically important oxidation reaction performed by α‐ketoglutarate dependent TET enzymes from 5‐methyl‐deoxycytidine (mdC). Recently, it was shown that genomic fdC and fdU can react with the ϵ‐aminogroups of nucleosomal lysines to give Schiff base adducts that covalently link nucleosomes to genomic DNA. Here, we show that fdU features a significantly higher reactivity towards lysine side chains compared with fdC. This result shows that depending on the amounts of fdC and fdU, oxidative stress may have a bigger impact on nucleosome binding than epigenetics.
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Affiliation(s)
- Leander Simon Runtsch
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Michael Stadlmeier
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Alexander Schön
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
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6
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Bai M, Cao X, Chen F, Xue J, Zhao Y, Zhao Y. Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines. Anal Chem 2021; 93:10495-10501. [PMID: 34293865 DOI: 10.1021/acs.analchem.1c01285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells. The synthesized ATP-γ-alkyne, an ATP analogue with bioorthogonal tag modified on γ-phosphate can be specifically linked to cellular 5hmU by chemoenzymatic labeling. DNA with 5-alkynephosphomethyluracil were then clicked with azide (N3)-modified 5hmU-primer. Identification of 5fU is based on selective reduction from 5fU to 5hmU, subsequent chemoenzymatic labeling of the newly generated 5hmU, and cross-linking with N3-modified 5fU-primer via click chemistry. Then, all of the 5hmU and 5fU sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. The above two kinds of barcodes can be simultaneously amplified for differentiated visualization of 5hmU and 5fU in single cells. We find these two kinds of cellular oxidative thymines are spatially organized in a cell-type-dependent style with cell-to-cell heterogeneity. We also investigate their multilevel subcellular information and explore their dynamic changes during cell cycles. Further, using DNA sequencing instead of fluorescence imaging, our proposed bioorthogonal chemical signature holds great potential to offer the sequence information of these oxidative thymines in cells and may provide a reliable chemical biology approach for studying the whole-genome oxidative thymines profiles and insights into their functional role and dynamics in biology.
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Affiliation(s)
- Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an 710049, Shaanxi, P. R. China
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7
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Ito Y, Hayashi H, Fuchi Y, Hari Y. Post-synthetic modification of oligonucleotides containing 5-mono- and 5-di-fluoromethyluridines. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Translesion DNA Synthesis Across Lesions Induced by Oxidative Products of Pyrimidines: An Insight into the Mechanism by Microscale Thermophoresis. Int J Mol Sci 2019; 20:ijms20205012. [PMID: 31658654 PMCID: PMC6829345 DOI: 10.3390/ijms20205012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/02/2023] Open
Abstract
Oxidative stress in cells can lead to the accumulation of reactive oxygen species and oxidation of DNA precursors. Oxidized nucleotides such as 2'-deoxyribo-5-hydroxyuridin (HdU) and 2'-deoxyribo-5-hydroxymethyluridin (HMdU) can be inserted into DNA during replication and repair. HdU and HMdU have attracted particular interest because they have different effects on damaged-DNA processing enzymes that control the downstream effects of the lesions. Herein, we studied the chemically simulated translesion DNA synthesis (TLS) across the lesions formed by HdU or HMdU using microscale thermophoresis (MST). The thermodynamic changes associated with replication across HdU or HMdU show that the HdU paired with the mismatched deoxyribonucleoside triphosphates disturbs DNA duplexes considerably less than thymidine (dT) or HMdU. Moreover, we also demonstrate that TLS by DNA polymerases across the lesion derived from HdU was markedly less extensive and potentially more mutagenic than that across the lesion formed by HMdU. Thus, DNA polymerization by DNA polymerase η (polη), the exonuclease-deficient Klenow fragment of DNA polymerase I (KF-), and reverse transcriptase from human immunodeficiency virus type 1 (HIV-1 RT) across these pyrimidine lesions correlated with the different stabilization effects of the HdU and HMdU in DNA duplexes revealed by MST. The equilibrium thermodynamic data obtained by MST can explain the influence of the thermodynamic alterations on the ability of DNA polymerases to bypass lesions induced by oxidative products of pyrimidines. The results also highlighted the usefulness of MST in evaluating the impact of oxidative products of pyrimidines on the processing of these lesions by damaged DNA processing enzymes.
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9
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Shahsavari S, Eriyagama DNAM, Halami B, Begoyan V, Tanasova M, Chen J, Fang S. Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection. Beilstein J Org Chem 2019; 15:1116-1128. [PMID: 31164948 PMCID: PMC6541367 DOI: 10.3762/bjoc.15.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023] Open
Abstract
Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, α-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within the ODN sequences without using any sequence- or functionality-specific conditions and procedures.
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Affiliation(s)
- Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Dhananjani N A M Eriyagama
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Bhaskar Halami
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Vagarshak Begoyan
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Marina Tanasova
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Jinsen Chen
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA
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10
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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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11
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Borowski R, Dziergowska A, Sochacka E, Leszczynska G. Novel entry to the synthesis of ( S)- and ( R)-5-methoxycarbonylhydroxymethyluridines – a diastereomeric pair of wobble tRNA nucleosides. RSC Adv 2019; 9:40507-40512. [PMID: 35542686 PMCID: PMC9076229 DOI: 10.1039/c9ra08548c] [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: 10/18/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022] Open
Abstract
Two novel methods for the preparation of the virtually equimolar mixtures of (S)- and (R)-diastereomers of 5-methoxycarbonylhydroxymethyluridine (mchm5U) have been developed. The first method involved α-hydroxylation of a 5-malonate ester derivative of uridine (5) with SeO2, followed by transformation to (S)- and (R)-5-carboxymethyluridines (cm5U, 8) and, finally, into the corresponding methyl esters. In the second approach, (S)- and (R)-mchm5-uridines were obtained starting from 5-formyluridine derivative (9) by hydrolysis of the imidate salt (11) prepared in the acid catalyzed reaction of 5-cyanohydrin-containing uridine (10b) with methyl alcohol. In both methods, the (S)- and (R) diastereomers of mchm5U were effectively separated by preparative C18 RP HPLC. Two novel methods for the preparation of the virtually equimolar mixtures of (S)- and (R)-diastereomers of 5-methoxycarbonylhydroxymethyluridine (mchm5U) have been developed.![]()
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Affiliation(s)
- Robert Borowski
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | | | - Elzbieta Sochacka
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
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12
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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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13
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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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14
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Kawasaki F, Martínez Cuesta S, Beraldi D, Mahtey A, Hardisty RE, Carrington M, Balasubramanian S. Sequencing 5-Hydroxymethyluracil at Single-Base Resolution. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fumiko Kawasaki
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Sergio Martínez Cuesta
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Cancer Research UK, Cambridge Institute; Li Ka Shing Centre; Robinson Way Cambridge CB2 0RE UK
| | - Dario Beraldi
- Cancer Research UK, Cambridge Institute; Li Ka Shing Centre; Robinson Way Cambridge CB2 0RE UK
| | - Areeb Mahtey
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Robyn E. Hardisty
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Mark Carrington
- Department of Biochemistry; University of Cambridge; Hopkins Building; Tennis Court Road Cambridge CB2 1QW UK
| | - Shankar Balasubramanian
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Cancer Research UK, Cambridge Institute; Li Ka Shing Centre; Robinson Way Cambridge CB2 0RE UK
- School of Clinical Medicine; University of Cambridge; Cambridge CB2 0SP UK
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15
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Kawasaki F, Martínez Cuesta S, Beraldi D, Mahtey A, Hardisty RE, Carrington M, Balasubramanian S. Sequencing 5-Hydroxymethyluracil at Single-Base Resolution. Angew Chem Int Ed Engl 2018; 57:9694-9696. [PMID: 29882366 PMCID: PMC6100112 DOI: 10.1002/anie.201804046] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/01/2018] [Indexed: 11/06/2022]
Abstract
5-hydroxymethyluracil (5hmU) is formed through oxidation of thymine both enzymatically and non-enzymatically in various biological systems. Although 5hmU has been reported to affect biological processes such as protein-DNA interactions, the consequences of 5hmU formation in genomes have not been yet fully explored. Herein, we report a method to sequence 5hmU at single-base resolution. We employ chemical oxidation to transform 5hmU to 5-formyluracil (5fU), followed by the polymerase extension to induce T-to-C base changes owing to the inherent ability of 5fU to form 5fU:G base pairing. In combination with the Illumina next generation sequencing technology, we developed polymerase chain reaction (PCR) conditions to amplify the T-to-C base changes and demonstrate the method in three different synthetic oligonucleotide models as well as part of the genome of a 5hmU-rich eukaryotic pathogen. Our method has the potential capability to map 5hmU in genomic DNA and thus will contribute to promote the understanding of this modified base.
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Affiliation(s)
- Fumiko Kawasaki
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Sergio Martínez Cuesta
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK, Cambridge InstituteLi Ka Shing CentreRobinson WayCambridgeCB2 0REUK
| | - Dario Beraldi
- Cancer Research UK, Cambridge InstituteLi Ka Shing CentreRobinson WayCambridgeCB2 0REUK
| | - Areeb Mahtey
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Robyn E. Hardisty
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Mark Carrington
- Department of BiochemistryUniversity of CambridgeHopkins BuildingTennis Court RoadCambridgeCB2 1QWUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK, Cambridge InstituteLi Ka Shing CentreRobinson WayCambridgeCB2 0REUK
- School of Clinical MedicineUniversity of CambridgeCambridgeCB2 0SPUK
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16
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17
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Liu C, Zou G, Peng S, Wang Y, Yang W, Wu F, Jiang Z, Zhang X, Zhou X. 5-Formyluracil as a Multifunctional Building Block in Biosensor Designs. Angew Chem Int Ed Engl 2018; 57:9689-9693. [DOI: 10.1002/anie.201804007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/27/2018] [Indexed: 12/12/2022]
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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Zhuoran Jiang
- 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
| | - 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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18
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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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19
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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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20
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Liu C, Wang Y, Zhang X, Wu F, Yang W, Zou G, Yao Q, Wang J, Chen Y, Wang S, Zhou X. Enrichment and fluorogenic labelling of 5-formyluracil in DNA. Chem Sci 2017; 8:4505-4510. [PMID: 28660064 PMCID: PMC5472030 DOI: 10.1039/c7sc00637c] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/02/2017] [Indexed: 12/26/2022] Open
Abstract
Recently, the detection of natural thymine modified 5-formyluracil has attracted widespread attention. Herein, we introduce a new insight into designing reagents for both the selective biotin enrichment and fluorogenic labelling of 5-formyluracil in DNA. Biotinylated o-phenylenediamine directly tethered to naphthalimide can switch on 5-formyluracil, under physiological conditions, which can then be used in cell imaging after exposure to γ-irradiation. In addition, its labelling property caused the polymerase extension to stop in the 5-formyluracil site, which gave us more information than the fluorescence did itself. The idea of detecting 5-formyluracil might be used in the synthesis of other modified diaminofluoresceins.
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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 , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Yafen Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Fan Wu
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Wei Yang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Guangrong Zou
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Qian Yao
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Jiaqi Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences , Key Laboratory of Biomedical Polymers of Ministry of Education , The Institute for Advanced Studies , Wuhan University , Hubei Province Key Laboratory of Allergy and Immunology , Wuhan , Hubei 430072 , P. R. China . ; ; Tel: +86-27-68756663
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21
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Janoušková M, Vaníková Z, Nici F, Boháčová S, Vítovská D, Šanderová H, Hocek M, Krásný L. 5-(Hydroxymethyl)uracil and -cytosine as potential epigenetic marks enhancing or inhibiting transcription with bacterial RNA polymerase. Chem Commun (Camb) 2017; 53:13253-13255. [DOI: 10.1039/c7cc08053k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
5-(Hydroxymethyl)uracil and -cytosine in DNA templates regulate transcription by bacterial RNA polymerase depending on the promoter, indicating that they may act as epigenetic marks.
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Affiliation(s)
- Martina Janoušková
- Dept. of Molecular Genetics of Bacteria
- Institute of Microbiology of the Czech Academy of Sciences
- CZ-14220 Prague 4
- Czech Republic
| | - Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
| | - Fabrizia Nici
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
| | - Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
| | - Dragana Vítovská
- Dept. of Molecular Genetics of Bacteria
- Institute of Microbiology of the Czech Academy of Sciences
- CZ-14220 Prague 4
- Czech Republic
| | - Hana Šanderová
- Dept. of Molecular Genetics of Bacteria
- Institute of Microbiology of the Czech Academy of Sciences
- CZ-14220 Prague 4
- Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 16610 Prague 6
- Czech Republic
- Dept. of Organic Chemistry
- Faculty of Science, Charles University in Prague
| | - Libor Krásný
- Dept. of Molecular Genetics of Bacteria
- Institute of Microbiology of the Czech Academy of Sciences
- CZ-14220 Prague 4
- Czech Republic
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