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Liu M, Li CC, Luo X, Ma F, Zhang CY. 5-Hydroxymethylcytosine Glucosylation-Triggered Helicase-Dependent Amplification-Based Fluorescent Biosensor for Sensitive Detection of β-Glucosyltransferase with Zero Background Signal. Anal Chem 2020; 92:16307-16313. [DOI: 10.1021/acs.analchem.0c04382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chen-chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
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Li Z, Kitov PI, Kitova EN, Mozenah F, Rodrigues E, Chapla DG, Moremen KW, Macauley MS, Klassen JS. CUPRA-ZYME: An Assay for Measuring Carbohydrate-Active Enzyme Activities, Pathways, and Substrate Specificities. Anal Chem 2020; 92:3228-3236. [PMID: 31961140 DOI: 10.1021/acs.analchem.9b05007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Carbohydrate-Active enZymes (CAZymes) are involved in the synthesis, degradation, and modification of carbohydrates. They play critical roles in diverse physiological and pathophysiological processes, have important industrial and biotechnological applications, are important drug targets, and represent promising biomarkers for the diagnosis of a variety of diseases. Measurements of their activities, catalytic pathway, and substrate specificities are essential to a comprehensive understanding of the biological functions of CAZymes and exploiting these enzymes for industrial and biomedical applications. For glycosyl hydrolases a variety of sensitive and quantitative spectrophotometric techniques are available. However, measuring the activity of glycosyltransferases is considerably more challenging. Here, we introduce CUPRA-ZYME, a versatile and quantitative electrospray ionization mass spectrometry (ESI-MS) assay for measuring the kinetic parameters of CAZymes, monitoring reaction pathways, and profiling substrate specificities. The method employs the recently developed competitive universal proxy receptor assay (CUPRA), implemented in a time-resolved manner. Measurements of the hydrolysis kinetics of CUPRA substrates containing ganglioside oligosaccharides by the glycosyl hydrolase human neuraminidase 3 served to validate the reliability of kinetic parameters measured by CUPRA-ZYME and highlight its use in establishing catalytic pathways. Applications to libraries of substrates demonstrate the potential of the assay for quantitative profiling of the substrate specificities glycosidases and glycosyltransferases. Finally, we show how the comparison of the reactivity of CUPRA substrates and glycan substrates present on glycoproteins, measured simultaneously, affords a unique opportunity to quantitatively study how the structure and protein environment of natural glycoconjugate substrates influences CAZyme activity.
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Affiliation(s)
- Zhixiong Li
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2
| | - Pavel I Kitov
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2
| | - Elena N Kitova
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2
| | - Fahima Mozenah
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2
| | - Emily Rodrigues
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2
| | - Digantkumar G Chapla
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States.,Department of Biochemistry and Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States
| | - Matthew S Macauley
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2.,Department of Medical Microbiology and Immunology , University of Alberta , Edmonton , Alberta , Canada T6G 2E1
| | - John S Klassen
- Department of Chemistry , University of Alberta , Edmonton , Alberta , Canada T6G 2G2
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Sui C, Wang T, Zhou Y, Yin H, Meng X, Zhang S, Waterhouse GI, Xu Q, Zhuge Y, Ai S. Photoelectrochemical biosensor for hydroxymethylated DNA detection and T4-β-glucosyltransferase activity assay based on WS2 nanosheets and carbon dots. Biosens Bioelectron 2019; 127:38-44. [DOI: 10.1016/j.bios.2018.11.054] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
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Raad MD, Modavi C, Sukovich DJ, Anderson JC. Observing Biosynthetic Activity Utilizing Next Generation Sequencing and the DNA Linked Enzyme Coupled Assay. ACS Chem Biol 2017; 12:191-199. [PMID: 28103681 DOI: 10.1021/acschembio.6b00652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Currently, the identification of new genes drastically outpaces current experimental methods for determining their enzymatic function. This disparity necessitates the development of high-throughput techniques that operate with the same scalability as modern gene synthesis and sequencing technologies. In this paper, we demonstrate the versatility of the recently reported DNA-Linked Enzyme-Coupled Assay (DLEnCA) and its ability to support high-throughput data acquisition through next-generation sequencing (NGS). Utilizing methyltransferases, we highlight DLEnCA's ability to rapidly profile an enzyme's substrate specificity, determine relative enzyme kinetics, detect biosynthetic formation of a target molecule, and its potential to benefit from the scales and standardization afforded by NGS. This improved methodology minimizes the effort in acquiring biosynthetic knowledge by tying biochemical techniques to the rapidly evolving abilities in sequencing and synthesizing DNA.
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Affiliation(s)
- Markus de Raad
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Cyrus Modavi
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - David J. Sukovich
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - J. Christopher Anderson
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
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Electrogenerated chemiluminescence biosensing method for the discrimination of DNA hydroxymethylation and assay of the β-glucosyltransferase activity. Biosens Bioelectron 2016; 79:92-7. [DOI: 10.1016/j.bios.2015.11.068] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/19/2022]
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