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Shi L, Ying K, Sha L, Zhang Y, Sun L, Li G. DNA-Peptide Interaction-Modulated Charge Reversal in Biomimetic Nanochannels for Simple and Efficient Detection of Histone Deacetylases. Anal Chem 2024; 96:4817-4824. [PMID: 38482584 DOI: 10.1021/acs.analchem.3c04819] [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: 03/27/2024]
Abstract
Protein acetylation, a fundamental post-translational modification, plays a critical role in the regulation of gene expression and cellular processes. Monitoring histone deacetylases (HDACs) is important for understanding epigenetic dynamics and advancing the early diagnosis of malignancies. Here, we leverage the dynamic characteristics of DNA-peptide interactions in biomimetic nanochannels to develop a HDAC detection method. In specific, the catalysis of peptide deacetylation by HDACs triggers alterations in the charge states of the nanochannel surface to accommodate DNA molecules. Then, the interaction between DNA and peptides shifts the nanochannel surface charge from positive to negative, leading to a reversal of the ion current rectification (ICR). By calculation of the ICR ratio, quantitative detection of HDACs can be efficiently achieved using the nanochannel-based method in an enzyme-free and label-free manner. Our experimental results demonstrate that HDACs can be detected by using this method within a concentration range of 0.5-500 nM. The innate simplicity and efficiency of this strategy may render it a valuable tool for advancing both fundamental research and clinical applications in the realm of epigenetics and personalized medicine.
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Affiliation(s)
- Liu Shi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Keqin Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Lingjun Sha
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yuanyuan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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2
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Gao L, Zhou Y, Cao L, Cao Y, Zhang H, Zhang M, Yin H, Ai S. Photoelectrochemical sensor for histone deacetylase Sirt1 detection based on Z-scheme heterojunction of CuS-BiVO 4 photoactive material and the cyclic etching of MnO 2 by NADH. Talanta 2024; 268:125307. [PMID: 37866306 DOI: 10.1016/j.talanta.2023.125307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
A novel photoelectrochemical (PEC) biosensor was constructed for histone deacetylase Sirt1 detection based on the Z-Scheme heterojunction of CuS-BiVO4 and reduced nicotinamide adenine dinucleotide (NADH) induced cyclic etching of MnO2 triggered by Sirt1 enzyme catalytic histone deacetylation event. Based on the Z-Scheme heterojunction, the photoactivity of the CuS-BiVO4 was improved greatly due to the highly effective separation of the photogenerated electron-hole pairs. In the presence of MnO2 nanosheets on the CuS-BiVO4/ITO electrode surface, the photocurrent decreased due to the inhibition effect of MnO2. However, this inhibition effect was eliminated by the incubation of MnO2/CuS-BiVO4/ITO with NADH, where NADH was produced in the deacetylation process of acetylated peptide catalyzed by Sirt1 with NAD+. The formed NADH etched MnO2, resulting in an increased photocurrent. In this process, NADH was oxidized to produce NAD+, which further involved the deacetylation process. Based on this cycle, the photocurrent of the biosensor was improved greatly and the sensitive and selective detection of Sirt1 was achieved. The biosensor presented a wide linear range from 0.005 to 10 nM with the low detection limit of 3.38 pM (S/N = 3). In addition, the applicability of the developed method was evaluated by investigating the effect of sodium butyrate and perfluorohexane sulfonate on Sirt1 activity.
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Affiliation(s)
- 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, 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, 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, China
| | - Yaoyuan 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, China
| | - Haowei Zhang
- 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, China
| | - Miao Zhang
- 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, 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, China
| | - Shiyun Ai
- 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, China
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3
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Li M, Yu H, Li Y, Li X, Huang S, Liu X, Weng G, Xu L, Hou T, Guo DS, Wang Y. Rational design of supramolecular self-assembly sensor for living cell imaging of HDAC1 and its application in high-throughput screening. Biosens Bioelectron 2023; 242:115716. [PMID: 37820557 DOI: 10.1016/j.bios.2023.115716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Supramolecular chemistry offers new insights in bioimaging, but specific tracking of enzyme in living cells via supramolecular host-guest reporter pair remains challenging, largely due to the interference caused by the complex cellular environment on the binding between analytes and hosts. Here, by exploiting the principle of supramolecular tandem assay (STA) and the classic host-guest reporter pair (p-sulfonatocalix[4]arene (SC4A) and lucigenin (LCG)) and rationally designing artificial peptide library to screen sequence with high affinity of the target enzyme, we developed a "turn-on" fluorescent sensing system for intracellular imaging of histone deacetylase 1 (HDAC1), which is a potential therapeutic target for various diseases, including cancer, neurological, and cardiovascular diseases. Based on computational simulations and experimental validations, we verified that the deacetylated peptide by HDAC1 competed LCG, freeing it from the SC4A causing fluorescence increase. Enzyme kinetics experiments were further conducted to prove that this assay could detect HDAC1 specifically with high sensitivity (the LOD value is 0.015 μg/mL, ten times lower than the published method). This system was further applied for high-throughput screening of HDAC1 inhibitors over a natural compound library containing 147 compounds, resulting in the identification of a novel HDAC1 down-regulator (Ginsenoside RK3). Our results demonstrated the sensitivity and robustness of the assay system towards HDAC1. It should serve as a valuable tool for biochemical studies and drug screening.
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Affiliation(s)
- Min Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijuan Yu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yiran Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiqing Huang
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road 487372, Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road 487372, Singapore
| | - Gaoqi Weng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Future Health Laboratory Innovation Center of Yangtze River Delta Zhejiang University, Jiaxing 314100, China.
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4
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Gao L, Zhou Y, Cao L, Cui X, Zheng Y, Yin H, Ai S. Photoelectrochemical Biosensor for Histone Deacetylase Sirt1 Detection Based on Polyaspartic Acid-Engaged and Triggered Redox Cycling Amplification and Enhanced Photoactivity of BiVO 4 by Gold Nanoparticles and SnS 2. Anal Chem 2022; 94:16936-16944. [PMID: 36416225 DOI: 10.1021/acs.analchem.2c04380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A photoelectrochemical (PEC) biosensor was established for histone deacetylase Sirt1 detection based on the polyaspartic acid (PASP)-mediated redox cycling amplification and Sirt1 catalysis deacetylation-triggered recognition of the deacetylated substrate peptide, using PASP as the recognition reagent. After BiVO4 was composited with gold nanoparticles and SnS2, the photoactivity of the composite was greatly enhanced due to the matched energy band structure. Under the catalysis of Sirt1 enzyme, the acetylated substrate peptide was deacetylated to obtain a positive peptide, which was recognized by negative PASP. In addition to the recognition function, PASP also played other triple roles. First, PASP interacted with the positive peptide to form a double-stranded structure, which led to the electrode interface changing from irregular to regular, resulting in an improved PEC response. Second, PASP was involved into redox cycle amplification due to its reduction to dehydroascorbic acid. Further, it was used for repeated preparation of ascorbic acid to provide electron donors. This process enhanced the PEC response. Third, based on the matched energy band with BiVO4, PASP effectively improved the photoactivity of BiVO4. With multiplex signal amplification, the PEC biosensor showed a wide linear range (1.83-1830 pM) and high detection sensitivity with a low detection limit of 0.732 pM (S/N = 3). The applicability of this method was evaluated by studying the effects of a known inhibitor of nicotinamide and the heavy metal ions of Cd2+ and Pb2+ on Sirt1 enzyme activity, and the results showed that this method not only provided a new platform for screening Sirt1 enzyme inhibitors but also provided new biomarkers for evaluating the ecotoxicological effects of environmental pollutants.
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Affiliation(s)
- 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, Taian, Shandong271018, 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, Taian, Shandong271018, 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, Taian, Shandong271018, 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, Taian, Shandong271018, People’s Republic of China
| | - 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, Taian, Shandong271018, 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, Taian, Shandong271018, People’s Republic of China
| | - Shiyun Ai
- 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, Taian, Shandong271018, People’s Republic of China
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5
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Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy. Toxins (Basel) 2022; 14:toxins14090622. [PMID: 36136560 PMCID: PMC9505997 DOI: 10.3390/toxins14090622] [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: 07/18/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures.
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6
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Kang W, Liu L, Yu P, Zhang T, Lei C, Nie Z. A switchable Cas12a enabling CRISPR-based direct histone deacetylase activity detection. Biosens Bioelectron 2022; 213:114468. [PMID: 35700604 DOI: 10.1016/j.bios.2022.114468] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/02/2022]
Abstract
The efficient and robust signal reporting ability of CRISPR-Cas system exhibits huge value in biosensing, but its applicability for non-nucleic acid analyte detection relies on the coupling of additional recognition modules. To address this limitation, we described a switchable Cas12a and exploited it for CRISPR-based direct analysis of histone deacetylase (HDAC) activity. Starting from the acetylation-mediated inactivation of Cas12a by anti-CRISPR protein AcrVA5, we demonstrated that the acetyl-inactivated Cas12a could be reversibly activated by HDAC-mediated deacetylation based on computational simulations (e.g., deep learning and protein-protein docking analysis) and experimental verifications. By leveraging this switchable Cas12a for both target sensing and signal amplification, we established a sensitive one-pot assay capable of detecting deacetylase sirtuin-1 with sub-nanomolar sensitivity, which is 50 times lower than the standard two-step peptide-based assay. The versability of this assay was validated by the sensitive assessment of cellular HDAC activities in different cell lines with good accuracy, making it a valuable tool for biochemical studies and clinical diagnostics.
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Affiliation(s)
- Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Lin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Peihang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Tianyi Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
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7
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Xia N, Sun T, Liu L, Tian L, Sun Z. Heterogeneous sensing of post-translational modification enzymes by integrating the advantage of homogeneous analysis. Talanta 2022; 237:122949. [PMID: 34736675 DOI: 10.1016/j.talanta.2021.122949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/17/2022]
Abstract
Heterogeneous analysis has great application prospects in the detection of post-translational modification (PTM) enzymes with the advantages of signal enhancement, less sample demand, and high sensitivity and selectivity. Nevertheless, once the substrate was fixed on a solid interface, the steric hindrance might limit the approaching of catalytic center to the substrate, thus reducing the efficiency of PTM. Herein, we suggested that the avidin-modified interface could be used to develop heterogeneous sensing platforms with biotin-labeled substrates as the probes, in which the enzymatic PTM was performed in solution and the heterogeneous assay was conducted on a solid surface. The sensing strategy integrates the advantages but overcomes the defects of both homogeneous and heterogeneous assays. Protein kinase A (PKA) and histone acetyltransferase (HAT) were determined as the examples by using sequence-specific peptide substrates. The signal changes were monitored by HRP-based colorimetric assay and antibody-amplified surface plasmon resonance (SPR). The methods were used for analysis of cell lysates and evaluation of inhibition efficiency with satisfactory results. The strategy can be used for the detection of a variety of biological enzymes and provide a new idea for the design of various heterogeneous biosensors. Thus, this work should be of great significance to the popularization and practical application of biosensors.
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Affiliation(s)
- Ning Xia
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan, 455000, PR China
| | - Ting Sun
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan, 455000, PR China; School of Chemistry and Materials Science, Guizhou Education University, GaoXin Road 115, Wudang District, Guizhou, 550000, PR China
| | - Lin Liu
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan, 455000, PR China.
| | - Linxu Tian
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan, 455000, PR China
| | - Zhifang Sun
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan, 455000, PR China.
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8
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Jiang S, Ren J, Xu Q, Zou X, Li Y, Zhang CY. Simultaneous single-molecule detection of the acetyltransferase and crotonyltransferase activities of histone acetylation writer p300. Chem Commun (Camb) 2021; 57:11709-11712. [PMID: 34693944 DOI: 10.1039/d1cc05449j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate for the first time the simultaneous measurement of the acetyltransferase (HAT) and crotonyltransferase (HCT) activities of histone acetylation writer p300 by integrating antibody-based fluorescence labeling with single molecule detection. This methods exhibits good specificity and high sensitivity. Moreover, it can accurately evaluate the kinetic parameters of both the HAT and HCT activities of p300 and screen inhibitors.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Jingyi Ren
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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9
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Maurya MR, Riyaz NUSS, Reddy MSB, Yalcin HC, Ouakad HM, Bahadur I, Al-Maadeed S, Sadasivuni KK. A review of smart sensors coupled with Internet of Things and Artificial Intelligence approach for heart failure monitoring. Med Biol Eng Comput 2021; 59:2185-2203. [PMID: 34611787 DOI: 10.1007/s11517-021-02447-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
Over the last decade, there has been a huge demand for health care technologies such as sensors-based prediction using digital health. With the continuous rise in the human population, these technologies showed to be potentially effective solutions to life-threatening diseases such as heart failure (HF). Besides being a potential for early death, HF has a significantly reduced quality of life (QoL). Heart failure has no cure. However, treatment can help you live a longer and more active life with fewer symptoms. Thus, it is essential to develop technological aid solutions allowing early diagnosis and consequently, effective treatment with possibly delayed mortality. Commonly, forecasts of HF are based on the generation of vast volumes of data usually collected from an individual patient by different components of the family history, physical examination, basic laboratory results, and other medical records. Though, these data are not effectively useful for predicting this failure, nevertheless, with the aid of advanced medical technology such as interconnected multi-sensory-based devices, and based on several medical history characteristics, the broad data provided machine learning algorithms to predict risk factors for heart disease of an individual is beneficial. There will be many challenges for the next decade of advancements in HF care: exploiting an increasingly growing repertoire of interconnected internal and external sensors for the benefit of patients and processing large, multimodal datasets with new Artificial Intelligence (AI) software. Various methods for predicting heart failure and, primarily the significance of invasive and non-invasive sensors along with different strategies for machine learning to predict heart failure are presented and summarized in the present study.
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Affiliation(s)
- Muni Raj Maurya
- Center for Advanced Materials, Qatar University, P.O. Box 2713, Doha, Qatar
- Department of Mechanical and Industrial Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | | | - M Sai Bhargava Reddy
- Center for Nanoscience and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological University, Hyderabad, Telangana State, 500085, India
| | | | - Hassen M Ouakad
- Mechanical and Industrial Engineering Department, College of Engineering, Sultan Qaboos University, Al-Khoudh, 123, PO-BOX 33, Muscat, Oman.
| | - Issam Bahadur
- Mechanical and Industrial Engineering Department, College of Engineering, Sultan Qaboos University, Al-Khoudh, 123, PO-BOX 33, Muscat, Oman
| | - Somaya Al-Maadeed
- Department of Computer Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
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10
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Tao Y, Chen L, Pan M, Zhu F, Zhu D. Tailored Biosensors for Drug Screening, Efficacy Assessment, and Toxicity Evaluation. ACS Sens 2021; 6:3146-3162. [PMID: 34516080 DOI: 10.1021/acssensors.1c01600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biosensors have been flourishing in the field of drug discovery with pronounced developments in the past few years. They facilitate the screening and discovery of innovative drugs. However, there is still a lack of critical reviews that compare the merits and shortcomings of these biosensors from a pharmaceutical point of view. This contribution presents a critical and up-to-date overview on the recent progress of tailored biosensors, including surface plasmon resonance, fluorescent, photoelectrochemical, and electrochemical systems with emphasis on their mechanisms and applications in drug screening, efficacy assessment, and toxicity evaluation. Multiple functional nanomaterials have also been incorporated into the biosensors. Representative examples of each type of biosensors are discussed in terms of design strategy, response mechanism, and potential applications. In the end, we also compare the results and summarize the major insights gained from the works, demonstrating the challenges and prospects of biosensors-assisted drug discovery.
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Affiliation(s)
- Yi Tao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lin Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Meiling Pan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fei Zhu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dong Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
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11
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Han Q, Chen F, Liu S, Ge Y, Wu J, Liu D. Genetically encoded FRET fluorescent sensor designed for detecting MOF histone acetyltransferase activity in vitro and in living cells. Anal Bioanal Chem 2021; 413:5453-5461. [PMID: 34268587 DOI: 10.1007/s00216-021-03528-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/25/2022]
Abstract
Acetylation of lysine in the histone H4 N-terminal is one of the most significant epigenetic modifications in cells. Aberrant changes involving lysine acetylation modification are commonly reported in multiple types of cancers. Currently, whether it is for in vivo or in vitro, there are limited approaches for the detection of H4 lysine acetylation levels. In particular, the main problems are the high cost and the cumbersome detection process, such as for radioactive 14C isotope detection. Therefore, there is an important need to develop a simple, fast, and low-cost means of detection. In this study, we reported the development of a gene-coding protein sensor. This protein sensor was designed based on the mechanism of fluorescence resonance energy transfer (FRET). The four kinds of sensors, varying from substrate and linker length, were evaluated, with ~20% increases in response efficiency. Next, sensors with different lysine mutation sites in the substrate sequence or mutation of key amino acids in the binding domain were also analyzed to determine site specificity. We found single-site lysine mutant could not cause a significant decrease in response efficiency. Furthermore, addition of MG149, a histone acetyltransferase inhibitor, resulted in a decrease in the ratio change value. Moreover, histone deacetylase1 HDAC1 was also found to reduce the ratio change values when added to reaction system. Finally, the optimized sensor was applied to living cells and established to provide a sensitive response with overexpression and knockdown of MOF (males absent on the first). These results indicated that the sensor can be used for screening chemical drugs regulating H4 N-terminal lysine acetylation level in vitro, as well as monitoring dynamic changes of lysine acetylation levels in living cells.
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Affiliation(s)
- Qianqian Han
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Chen
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Shushan Liu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yushu Ge
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Jiang Wu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Dan Liu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230001, Anhui, China.
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12
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Hu J, Pan LY, Li Y, Zou X, Liu BJ, Jiang B, Zhang CY. Deacetylation-activated construction of single quantum dot-based nanosensor for sirtuin 1 assay. Talanta 2021; 224:121918. [PMID: 33379119 DOI: 10.1016/j.talanta.2020.121918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022]
Abstract
Sirtuin 1 (SIRT1) is an important histone deacetylase that regulates biological functions ranging from DNA repair to metabolism. The alteration of SIRT1 is associated with a variety of diseases including diabetes, inflammation, aging-related diseases, and cancers. Consequently, the detection of SIRT1 activity is of great therapeutic importance. Herein, we demonstrate for the first time the deacetylation-activated construction of single quantum dot (QD)-based nanosensor for sensitive SIRT1 assay. This nanosensor is composed of a Cy5-labeled peptide substrate and a streptavidin-coated QD. The peptide with one lysine acetyl group acts as both the Cy5 fluorophore carrier and the substrate for sensing SIRT1. In the presence of SIRT1, it removes the acetyl group in the acetylated peptide, and the resultant deacetylated peptide can react with the NHS-activated biotin reagent (sulfo-NHS-biotin) to form the biotinylated peptide. The multiple biotinylated peptides can assemble on single QD surface via biotin-streptavidin interaction, inducing efficient fluorescence resonance energy transfer (FRET) from the QD to Cy5, generating distinct Cy5 signal which can be simply quantified by total internal reflection fluorescence-based single-molecule detection. This single QD-based nanosensor can sensitively detect SIRT1 with a detection limit of as low as 3.91 pM, and it can be applied for the measurement of enzyme kinetic parameters and the screening of SIRT1 inhibitors. Moreover, this nanosensor can be used to detect the SIRT1 activity in cancer cells, providing a powerful platform for epigenetic research and SIRT1-targeted drug discovery.
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Affiliation(s)
- Juan Hu
- 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
| | - Li-Yuan Pan
- 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
| | - Yueying 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
| | - Xiaoran Zou
- 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
| | - Bing-Jie Liu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
| | - BingHua Jiang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, 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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13
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Chen Y, Zhou Y, Yin H. Recent advances in biosensor for histone acetyltransferase detection. Biosens Bioelectron 2021; 175:112880. [DOI: 10.1016/j.bios.2020.112880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022]
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14
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Araiza-Olivera D, Gutierrez-Aguilar M, Espinosa-García AM, García-García JA, Tapia-Orozco N, Sánchez-Pérez C, Palacios-Reyes C, Escárcega D, Villalón-López DN, García-Arrazola R. From bench to bedside: Biosensing strategies to evaluate endocrine disrupting compounds based on epigenetic events and their potential use in medicine. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103450. [PMID: 32622887 DOI: 10.1016/j.etap.2020.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The relationship between endocrine system disorders and health risks due to chemical environmental compounds has become a growing concern in recent years. Involuntary exposure to endocrine disruptors (EDCs) is associated with the worldwide increase of diseases such as cancer, obesity, diabetes, and neurocortical disorders. EDCs are compounds that target the nuclear hormonereceptors (NHR) leading to epigenetic changes. Consequently, the use of biosensing strategies based on epigenetic events have a great potential to provide outstanding information about the exposition of EDCs and their evaluation in human health. This review addresses the novel trends in biosensing EDCs evaluation based on DNA methylation assays associated with different human diseases.
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Affiliation(s)
- D Araiza-Olivera
- Department of Chemistry and Biomolecules, Institute of Chemistry, UNAM, Mexico.
| | | | - A M Espinosa-García
- Unidad de Medicina Genómica, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - J A García-García
- Department of Education, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - N Tapia-Orozco
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Sánchez-Pérez
- Institute of Applied Sciences and Technology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Palacios-Reyes
- Laboratory of Genetics and Molecular Diagnostics, Juarez Hospital of Mexico, Mexico City, Mexico.
| | - D Escárcega
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Ciudad de México, calle del Puente 222, Ejidos de Huipulco, Tlalpan 14380, Mexico City, Mexico.
| | - Demelza N Villalón-López
- Instituto Politénico Nacional-Escuela Nacional de Ciencias Biológicas, Departamento de Química Orgánica, Prolongación de Carpio y Plande Ayala, colonia Casco de Santo Tomás. Del, Miguel Hidalgo, 11350, Mexico.
| | - R García-Arrazola
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
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15
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Zhang Q, Hao T, Hu D, Guo Z, Wang S, Hu Y. RNA aptamer-driven ECL biosensing for tracing histone acetylation based on nano-prism substrate and cascade DNA amplification strategy. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Hallaj T, Amjadi M, Qiu X, Susumu K, Medintz IL, Hildebrandt N. Terbium-to-quantum dot Förster resonance energy transfer for homogeneous and sensitive detection of histone methyltransferase activity. NANOSCALE 2020; 12:13719-13730. [PMID: 32573632 DOI: 10.1039/d0nr03383a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The development of rapid, simple, and versatile biosensors for monitoring the activity of histone modifying enzymes (HMEs) is needed for the improvement of diagnostic assays, screening of HME inhibitors, and a better understanding of HME kinetics in different environments. Nanoparticles can play an important role in this regard by improving or complementing currently available enzyme detection technologies. Here, we present the development and application of a homogeneous methyltransferase (SET7/9) assay based on time-gated Förster resonance energy transfer (TG-FRET) between terbium complexes (Tb) and luminescent semiconductor quantum dots (QDs). Specific binding of a Tb-antibody conjugate to a SET7/9-methylated Lys4 on a histone H3(1-21) peptide substrate attached to the QD surface resulted in efficient FRET and provided the mechanism for monitoring the SET7/9 activity. Two common peptide-QD attachment strategies (biotin-streptavidin and polyhistidine-mediated self-assembly), two different QD colors (625 and 705 nm), and enzyme sensing with post- or pre-assembled QD-peptide conjugates demonstrated the broad applicability of this assay design. Limits of detection in the low picomolar concentration range, high selectivity tested against non-specific antibodies, enzymes, and co-factors, determination of the inhibition constants of the SET7/9 inhibitors SAH and (R)-PFI-2, and analysis of the co-factor (SAM) concentration-dependent enzyme kinetics of SET7/9 which followed the Michaelis-Menten model highlighted the excellent performance of this TG-FRET HME activity assay.
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Affiliation(s)
- Tooba Hallaj
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran. and Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia 5714783734, Iran
| | - Mohammad Amjadi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran.
| | - Xue Qiu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France and School of Medicine and Pharmacy, Ocean University of China. 5, Yushan Road, 266003 Qingdao, Shandong, China
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA and KeyW Corporation, Hanover, Maryland 21076, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France and nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.
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17
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Hu D, Hu Y, Zhan T, Zheng Y, Ran P, Liu X, Guo Z, Wei W, Wang S. Coenzyme A-aptamer-facilitated label-free electrochemical stripping strategy for sensitive detection of histone acetyltransferase activity. Biosens Bioelectron 2019; 150:111934. [PMID: 31818759 DOI: 10.1016/j.bios.2019.111934] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/11/2019] [Accepted: 11/26/2019] [Indexed: 02/07/2023]
Abstract
Abnormal histone acetyltransferases (HAT) activity gives rise to all kinds of cellular diseases. Herein, we first report a coenzyme A (CoA)-aptamer-facilitated label-free electrochemical stripping biosensor for sensitive detection of HAT activity via square wave voltammetry (SWV) technique. The presence of HAT can lead to the transfer of the acetyl group from acetyl coenzyme A (Ac-CoA) to lysine residues of substrate peptide, thus generating CoA molecule. Later, CoA, which acts as an initiator, can embrace its aptamer via the typical target-aptamer interaction, then arousing deoxynucleotide terminal transferase (TdT)-induced silver nanoclusters (AgNCs) as signal output. Under optimized conditions, the resultant aptasensor shows obvious electrochemical stripping signal and is employed for HAT p300 analysis in a wide concentration range from 0.01 to 100 nM with a very low detection limit of 0.0028 nM (3δ/slope). The good analytical performances of the biosensor depend on the strong interaction of CoA and its aptamer and abundant stripping resource rooted from AgNCs. Next, the proposed biosensor is used for screening HAT's inhibitors and the practical HAT detection with satisfactory results. Therefore, the new, simple and sensitive HAT biosensor presents a promising direction for HAT-targeted drug discovery and epigenetic research.
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Affiliation(s)
- Dandan Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Yufang Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China.
| | - Tianyu Zhan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Yudi Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Pingjian Ran
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Xinda Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Zhiyong Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Wenting Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Sui Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China.
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18
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Photoelectrochemical determination of the activity of histone acetyltransferase and inhibitor screening by using MoS2 nanosheets. Mikrochim Acta 2019; 186:663. [DOI: 10.1007/s00604-019-3756-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/10/2019] [Indexed: 02/07/2023]
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19
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Teixeira SR, Abreu CM, Parkes L, Davies J, Yao S, Sawhney MA, Margarit L, Gonzalez D, Pinto IM, Francis LW, Conlan RS. Direct monitoring of breast and endometrial cancer cell epigenetic response to DNA methyltransferase and histone deacetylase inhibitors. Biosens Bioelectron 2019; 141:111386. [PMID: 31220725 DOI: 10.1016/j.bios.2019.111386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/23/2019] [Accepted: 05/30/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation and histone deacetylation are key epigenetic processes involved in normal cellular function and tumorigenesis. Therapeutic strategies based on DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors are currently in use and under development for the treatment of cancers. Genome-wide DNA methylation profiling has been proposed for use in disease diagnosis, and histone modification profiling for disease stratification will follow suit. However, whether epigenome sequencing technologies will be feasible for rapid clinic diagnosis and patient treatment monitoring remains to be seen, and alternative detection technologies will almost certainly be needed. Here we used electrochemical impedance spectroscopy (EIS) employing a graphene-based screen-printed electrode system to directly measure global DNA methylation and histone H3 acetylation to compare non-cancer and breast cancer cell lines. We demonstrated that whilst global methylation was not useful as a differential marker in the cellular systems tested, histone H3 acetylation was effective at higher chromatin levels. Using breast and endometrial cancer cell models, EIS was then used to monitor cellular responses to the DNMT and HDAC inhibitors 5-Aza-2'-deoxycytidine and suberoylanilide hydroxamic acid in vitro, and proved very effective at detecting global cellular responses to either treatment, indicating that this approach could be useful in following treatment response to epigenetic drugs. Moreover, this work reports the first combined analysis of two epigenetic markers using a unified graphene-based biosensor platform, demonstrating the potential for multiplex analysis of both methylation and acetylation on the same sample.
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Affiliation(s)
- S R Teixeira
- College of Engineering, Swansea University, Bay Campus, Swansea, SA1 8QQ, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - C M Abreu
- International Iberian Nanotechnology Laboratory (INL), Portugal
| | - L Parkes
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - J Davies
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - S Yao
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - M A Sawhney
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - L Margarit
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Abertawe Bro Morganwg University Health Board, Princess of Wales Hospital Bridgend, UK
| | - D Gonzalez
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - I Mendes Pinto
- International Iberian Nanotechnology Laboratory (INL), Portugal
| | - L W Francis
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - R S Conlan
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK; Centre for NanoHealth, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
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20
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Ma G, Yu Z, Zhou W, Li Y, Fan L, Li X. Investigation of Na+ and K+ Competitively Binding with a G-Quadruplex and Discovery of a Stable K+–Na+-Quadruplex. J Phys Chem B 2019; 123:5405-5411. [DOI: 10.1021/acs.jpcb.9b02823] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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21
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Li X, Cui Y, Du Y, Tang A, Kong D. Label-Free Telomerase Detection in Single Cell Using a Five-Base Telomerase Product-Triggered Exponential Rolling Circle Amplification Strategy. ACS Sens 2019; 4:1090-1096. [PMID: 30945529 DOI: 10.1021/acssensors.9b00334] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Telomerase is a universal biomarker of malignant tumors. Sensitive and reliable analysis for telomerase activity is of vital importance for both early diagnosis and therapy of malignant tumors. Herein, a novel fluorescent strategy was proposed for sensitive and label-free detection of telomerase activity. One highlight of this strategy is that an exponential signal amplification can be triggered by a very short telomerase extension product (TEP). Without adding dATP, the designed telomerase primer can be easily controlled to extend five bases (GGGTT) to give short TEP with definite length. The resulting short TEP can then be constructed as a circular rolling circle amplification (RCA) template and thus initiate a nicking enzyme-mediated exponential RCA, producing G-rich amplification products that can be sensitively probed via specific binding between the fluorescent dye Thioflavin T (ThT) and the nucleic acid G-quadruplexes. Elevated telomerase translocation efficiency, combined with exponential signal amplification and specific probing of RCA products by ThT, endow the sensing platform with extraordinarily high detection sensitivity. The requirement for short TEP increases the possibility to analyze telomerase with low activity. The proposed sensing platform can achieve sensitive telomerase activity detection in individual cells, even with the interference of accumulated normal cells. It was also demonstrated to show excellent capability in screening for the inhibitors of telomerase. Therefore, the proposed sensing platform has great potential for not only clinical diagnosis but also anticancer drug development.
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Affiliation(s)
- XiaoYu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - YunXi Cui
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - YiChen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - AnNa Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - DeMing Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300071, P. R. China
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22
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Xu L, Zhang Q, Hu Y, Ma S, Hu D, Wang J, Rao J, Guo Z, Wang S, Wu D, Liu Q, Peng J. Ultrasensitive mushroom-like electrochemical immunosensor for probing the activity of histone acetyltransferase. Anal Chim Acta 2019; 1066:28-35. [PMID: 31027532 DOI: 10.1016/j.aca.2019.03.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/10/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
Abstract
A novel mushroom-like electrochemical immunoassay for the ultrasensitive detection of histone acetyltransferase activity (HAT p300) has been established on account of the new composite graphene oxide (GO) nanolayer. The immunoassay involves immobilization of substrate peptide onto Au electrode, acetylation in lysine of substrate peptide, and the interaction between acetyl group of lysine and acetyl-antibody (AbAc) of the GO nanolayer. The GO nanolayer comprises large amounts of methylene blue molecules (MB), giving rise to large signal amplification. Only in the presence of HAT p300, an obvious electrochemical signal appears and the peak linear current is proportion to the HAT p300 concentrations ranging from 0.01 to 150 nM with a detection limit of 0.0036 nM. The great enhancement on sensitivity of the proposed mushroom-like immunosensor derives from both the constructed Faraday cage and the extended outer Helmholtz plane (OHP). Further, the immunosensor with excellent sensitivity and selectivity can be applied for the HAT p300 activity detection in Hela cell lysates, serum and urine, hinting an improved and splendid analytical performance. Briefly, this stable, simple and ultrasensitive electrochemical immunoassay has considerable promise for further applications in the HATs-interrelated epigenetic studies and drug development.
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Affiliation(s)
- Lihua Xu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Qingqing Zhang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Yufang Hu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Shaohua Ma
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Dandan Hu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Jiao Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Jiajia Rao
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Zhiyong Guo
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| | - Sui Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Di Wu
- Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410081, PR China
| | - Qiong Liu
- Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410081, PR China
| | - Jianqiao Peng
- Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410081, PR China.
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23
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Yang S, Yang C, Huang D, Song L, Chen J, Yang Q. Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits. Chemistry 2019; 25:5389-5405. [PMID: 30328639 DOI: 10.1002/chem.201804420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Indexed: 01/06/2023]
Abstract
DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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24
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Vashistha R, Dangi AK, Kumar A, Chhabra D, Shukla P. Futuristic biosensors for cardiac health care: an artificial intelligence approach. 3 Biotech 2018; 8:358. [PMID: 30105183 PMCID: PMC6081842 DOI: 10.1007/s13205-018-1368-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/21/2018] [Indexed: 12/19/2022] Open
Abstract
Biosensor-based devices are pioneering in the modern biomedical applications and will be the future of cardiac health care. The coupling of artificial intelligence (AI) for cardiac monitoring-based biosensors for the point of care (POC) diagnostics is prominently reviewed here. This review deciphers the most significant machine-learning algorithms for the futuristic biosensors along with the internet of things, computational techniques and microchip-based essential cardiac biomarkers for real-time health monitoring and improving patient compliance. The present review also discusses the recently developed cardiac biosensors along with technical strategies involved in their mechanism of working and their applications in healthcare. Additionally, it provides a key for the ontogeny of an effective and supportive hierarchical protocol for clinical decision-making about personalized medicine through combinatory information analysis, and integrated multidisciplinary AI approaches.
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Affiliation(s)
- Rajat Vashistha
- Optimization and Mechatronics Laboratory, Department of Mechanical Engineering, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana India
| | - Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi, Dayanand University, Rohtak, Haryana 124001 India
| | - Ashwani Kumar
- Optimization and Mechatronics Laboratory, Department of Mechanical Engineering, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana India
| | - Deepak Chhabra
- Optimization and Mechatronics Laboratory, Department of Mechanical Engineering, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi, Dayanand University, Rohtak, Haryana 124001 India
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25
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Xu Y, Shi W, He X, Wu X, Li X, Ma H. Facile and Sensitive Method for Protein Kinase A Activity Assay Based on Fluorescent Off-On PolyU-peptide Assembly. Anal Chem 2017; 89:10980-10984. [PMID: 28937207 DOI: 10.1021/acs.analchem.7b02815] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phosphorylation mediated by protein kinases plays a pivotal role in metabolic and cell-signaling processes, and the dysfunction of protein kinases such as protein kinase A (PKA) may induce several human diseases. Therefore, it is of great significance to develop a facile and effective method for PKA activity assay and high-throughput screening of inhibitors. Herein, we develop a new fluorescent off-on method for PKA assay based on the assembly of anionic polyuridylic acid (polyU) and cationic fluorescent peptide. The phosphorylation of the peptide disrupts its electrostatic binding with polyU, suppresses the concentration quenching effect of polyU, and thus causes fluorescence recovery. The recovered fluorescence intensity at 585 nm is directly proportional to the PKA activity in the range of 0.1-3.2 U/mL with a detection limit of 0.05 U/mL. Using our method, the PKA activity in HeLa cell lysate is determined to be 58.2 ± 5.1 U/mg protein. The method has also been employed to evaluate the inhibitory effect of PKA inhibitors with satisfactory results and may be expected to be a promising candidate for facile and cost-effective assay of kinase activity and high-throughput inhibitor screening.
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Affiliation(s)
- Yanhui Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Wen Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinyuan He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Xiaofeng Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Xiaohua Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Huimin Ma
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
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