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Luo X, Zhao Y, Cai Y, Chen J, Zhao L, Lan T, Chen Y, Ruan XZ. Dual-monomer solvatochromic probe system (DSPS) for effectively differentiating lipid raft cholesterol and active membrane cholesterol in the inner-leaflet plasma membrane. J Mater Chem B 2024; 12:2547-2558. [PMID: 38358131 DOI: 10.1039/d3tb02857g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Monitoring active membrane cholesterol and lipid raft cholesterol in the inner leaflet of the plasma membrane is significant for understanding the membrane function and cellular physiopathological processes. Limited by existing methods, it is difficult to differentiate active membrane cholesterol and lipid raft cholesterol. A novel dual-monomer solvatochromic probe system (DSPS) that targets two types of cholesterol was developed. Acrylodan-BG/SNAP-D4 composed of SNAP-D4 cholesterol-recognizing monomers and solvatochromic acrylodan-BG-sensing monomers exhibits excellent cholesterol detecting properties in terms of selectivity, accuracy, convenience and economic benefits. Cell imaging revealed that lipid raft cholesterol emitted blue fluorescence, whereas active membrane cholesterol (which partially bobbed in aqueous cytosol) displayed green fluorescence; both the fluorescence emissions increased or decreased in a cholesterol-dependent manner. This system provides a new technology for the determination of two types of cholesterol, which is beneficial for the further study of membrane function, intracellular cholesterol trafficking, and cell signaling.
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Affiliation(s)
- Xuan Luo
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, 400016, Chongqing, China.
| | - Yunfei Zhao
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, College of Pharmacy, Chongqing Medical University, 400016, Chongqing, China
| | - Yang Cai
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, College of Pharmacy, Chongqing Medical University, 400016, Chongqing, China
| | - Jun Chen
- Department of Pediatrics, Women and Children' Hospital of Chongging Medical University, 400016, Chongqing, China
| | - Lulu Zhao
- Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, College of Pharmacy, Chongqing Medical University, 400016, Chongqing, China
| | - Tianlan Lan
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, 400016, Chongqing, China.
| | - Yaxi Chen
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, 400016, Chongqing, China.
| | - Xiong Z Ruan
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, 400016, Chongqing, China.
- John Moorhead Research Laboratory, Centre for Nephrology, University College London Medical School, Royal Free Campus, University College London, London NW3 2PF, UK
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Taka N, Asami S, Sakamoto M, Matsui T, Yoshida W. Quantification of Global DNA Hydroxymethylation Level Using UHRF2 SRA-Luciferase Based on Bioluminescence Resonance Energy Transfer. Anal Chem 2022; 94:8618-8624. [DOI: 10.1021/acs.analchem.1c05619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natsumi Taka
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
| | - Shoya Asami
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
| | - Mikiya Sakamoto
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
| | - Toru Matsui
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo 192-0982, Japan
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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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Abstract
Summary Irys Extract is a software tool for generating genomic information from data collected by the BioNano Genomics Irys platform. The tool allows the user easy access to the raw data in the form of cropped images and genetically aligned intensity profiles. The latter are also made compatible with the BED format for using with popular genomic browsers such as the UCSC Genome Browser. Availability and implementation Irys Extract has been developed in Matlab R2015a, it was tested to work with IrysView 2.4.0.15879 and AutoDetect 2.1.4.9159, and it currently runs under Microsoft Windows operating systems (7-10). Irys Extract can be downloaded alongside its manual and a demo dataset at http://www.nanobiophotonix.com and https://sites.google.com/site/raniarielly/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rani Arielly
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yuval Ebenstein
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
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Shahal T, Koren O, Shefer G, Stern N, Ebenstein Y. Hypersensitive quantification of global 5-hydroxymethylcytosine by chemoenzymatic tagging. Anal Chim Acta 2018; 1038:87-96. [PMID: 30278911 DOI: 10.1016/j.aca.2018.08.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 02/07/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is an epigenetic DNA modification. Tissue-specific reduction in global 5hmC levels has been associated with various types of cancer. One of the challenges associated with detecting 5hmC levels is its extremely low content, especially in blood. The gold-standard for reliable global 5hmC quantitation is liquid chromatography-tandem mass spectroscopy (LC-MS/MS) operating in a multiple reaction monitoring (MRM) mode. Difficulties associated with 5hmC detection by LC-MS/MS include its low abundance, low ionization efficiency and possible ion suppression from co-eluted compounds. Hence, detecting 5hmC levels in blood samples for diagnosis of leukemia and other blood malignancies presents a unique challenge. To overcome these difficulties we introduce a simple chemoenzymatic method for specifically tagging 5hmC, resulting in an eight-fold increase in detection sensitivity. We demonstrate that we could quantitatively detect 5hmC levels in various human tissues, including blood samples from healthy individuals and leukemia patients, using the most basic quadrupole mass-analyzer instrument and only 200 ng of DNA. The limit of detection (LOD) of our technique is 0.001% 5hmC from 300 ng DNA, sufficient for future mass-spectroscopy based diagnostics of diseases associated with low 5hmC levels such as leukemia.
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Affiliation(s)
- Tamar Shahal
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Omri Koren
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gabi Shefer
- Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Naftali Stern
- Sagol Center for the Epigenetics of Metabolism and Aging, Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel.
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Gilat N, Tabachnik T, Shwartz A, Shahal T, Torchinsky D, Michaeli Y, Nifker G, Zirkin S, Ebenstein Y. Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers. Clin Epigenetics 2017; 9:70. [PMID: 28725280 PMCID: PMC5512773 DOI: 10.1186/s13148-017-0368-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/27/2017] [Indexed: 11/10/2022] Open
Abstract
Background The DNA modification 5-hydroxymethylcytosine (5hmC) is now referred to as the sixth base of DNA with evidence of tissue-specific patterns and correlation with gene regulation and expression. This epigenetic mark was recently reported as a potential biomarker for multiple types of cancer, but its application in the clinic is limited by the utility of recent 5hmC quantification assays. We use a recently developed, ultra-sensitive, fluorescence-based single-molecule method for global quantification of 5hmC in genomic DNA. The high sensitivity of the method gives access to precise quantification of extremely low 5hmC levels common in many cancers. Methods We assessed 5hmC levels in DNA extracted from a set of colon and blood cancer samples and compared 5hmC levels with healthy controls, in a single-molecule approach. Results Using our method, we observed a significantly reduced level of 5hmC in blood and colon cancers and could distinguish between colon tumor and colon tissue adjacent to the tumor based on the global levels of this molecular biomarker. Conclusions Single-molecule detection of 5hmC allows distinguishing between malignant and healthy tissue in clinically relevant and accessible tissue such as blood and colon. The presented method outperforms current commercially available quantification kits and may potentially be developed into a widely used, 5hmC quantification assay for research and clinical diagnostics. Furthermore, using this method, we confirm that 5hmC is a good molecular biomarker for diagnosing colon and various types of blood cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0368-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Noa Gilat
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tzlil Tabachnik
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amit Shwartz
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Shahal
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dmitry Torchinsky
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gil Nifker
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Zirkin
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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Qing Y, Tian Z, Bi Y, Wang Y, Long J, Song CX, Diao J. Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine. Bioessays 2017; 39. [DOI: 10.1002/bies.201700010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ying Qing
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
| | - Zhiqi Tian
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
- Center for Mitochondrial Biology and Medicine; The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology Xi'an Jiaotong University; Xi'an China
| | - Ying Bi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Yongyao Wang
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
- Center for Mitochondrial Biology and Medicine; The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology Xi'an Jiaotong University; Xi'an China
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine; The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology Xi'an Jiaotong University; Xi'an China
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine; University of Oxford; Oxford UK
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Oxford UK
| | - Jiajie Diao
- Department of Cancer Biology; University of Cincinnati College of Medicine; Cincinnati OH USA
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