1
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Sun L, Xiang Y, Du Y, Wang Y, Ma J, Wang Y, Wang X, Wang G, Chen T. Template-independent synthesis and 3'-end labelling of 2'-modified oligonucleotides with terminal deoxynucleotidyl transferases. Nucleic Acids Res 2024; 52:10085-10101. [PMID: 39149896 PMCID: PMC11417362 DOI: 10.1093/nar/gkae691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024] Open
Abstract
Xenobiotic nucleic acids (XNAs) are artificial genetic polymers with altered structural moieties and useful features, such as enhanced biological and chemical stability. Enzymatic synthesis and efficient labelling of XNAs are crucial for their broader application. Terminal deoxynucleotidyl transferases (TdTs) have been exploited for the de novo synthesis and labelling of DNA and demonstrated the capability of recognizing various substrates. However, the activities of TdTs for the synthesis and labelling of commonly used XNAs with 2' modifications have not been systematically explored. In this work, we explored and demonstrated the varied activities of three TdTs (bovine TdT, MTdT-evo and murine TdT) for the template-independent incorporation of 2'-methoxy NTPs, 2'-fluoro NTPs and 2'-fluoroarabino NTPs into the 3' ends of single- and double-stranded DNAs and the extension of 2'-modified XNAs with (d)NTPs containing a natural or unnatural nucleobase. Taking advantages of these activities, we established a strategy for protecting single-stranded DNAs from exonuclease I degradation by TdT-synthesized 2'-modified XNA tails and methods for 3'-end labelling of 2'-modified XNAs by TdT-mediated synthesis of G-quadruplex-containing tails or incorporation of nucleotides with a functionalized nucleobase. A DNA-2'-fluoroarabino nucleic acid (FANA) chimeric hydrogel was also successfully constructed based on the extraordinary activity of MTdT-evo for template-independent FANA synthesis.
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Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yuming Xiang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yangming Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Yaxin Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Xueting Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Guangyuan Wang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
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2
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Liu Y, Chen B, He M, Hu B. Detection of terminal deoxynucleotidyl transferase activity based on self-mediated nucleic acid elongation and elemental labeling inductively coupled plasma-mass spectrometry. Talanta 2024; 274:125979. [PMID: 38537358 DOI: 10.1016/j.talanta.2024.125979] [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: 01/22/2024] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 05/04/2024]
Abstract
Terminal deoxynucleotidyl transferase (TdT), a specialized DNA polymerase, is recognized as a promising biomarker for acute leukemia. Herein, taking the advantage of the self-mediated strand elongation property of TdT, a simple and sensitive method for TdT activity assay was developed based on gold nanoparticles (AuNPs) labeling inductively coupled plasma mass spectrometry (ICP-MS). In the presence of TdT, the primer DNA on magnetic beads is elongated with an adenine-rich single stranded long chain that can label poly-thymine modified AuNPs. After acid elution, the labeled AuNPs were detected by ICP-MS, and the signal intensity of 197Au reflected the TdT activity. Under the optimal conditions, the limit of detection for TdT activity is down to 0.054 U mL-1, along with good selectivity and strong tolerance to other interfering proteins. Furthermore, it achieves a straightforward and accurate detection of TdT activity in acute lymphoblastic leukemia cells without sample pre-processing and tool enzyme addition. Therefore, the proposed method shows great promise as a valuable tool for TdT-related biological research and leukemia therapeutics.
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Affiliation(s)
- Yuwei Liu
- Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Beibei Chen
- Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Man He
- Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Bin Hu
- Department of Chemistry, Wuhan University, Wuhan, 430072, China.
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3
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Tian S, Yuan Y, Luo F, Lin C, Wang J, Qiu B, Lin Z, Wang W. Dual Self-Amplification Homogeneous Electrochemiluminescence Biosensor for Terminal Deoxynucleotidyl Transferase Activity Based on Controlling the Surface Morphology and Charge of Reporter Nanoparticles. Anal Chem 2023; 95:18603-18610. [PMID: 38048177 DOI: 10.1021/acs.analchem.3c04579] [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: 12/06/2023]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is upregulated in several types of leukemia and is considered a disease biomarker and a potential therapeutic target for leukemia. In this research, a homogeneous electrochemiluminescence (ECL) method based on the control of surface charge and morphology of tris (2,2'-bipyridine) ruthenium(II) chloride hexahydrate-doped silica nanoparticles (Ru@SiO2 NPs) has been designed for TdT activity detection. A small amount of short single-stranded DNA (ssDNA) was modified onto the surface of Ru@SiO2 NPs, and the nanoparticles with a slight positive charge experienced electrostatic attraction with the indium tin oxide (ITO) electrode with a negative charge, so relatively high ECL signals had been detected. Under the action of TdT, the ssDNA was significantly elongated, carrying numerous negative charges on its phosphate backbone, so the overall negative charge of the reporter nanoparticles was enhanced, resulting in a strong electrostatic repulsion with the ITO electrode. Simultaneously, the long ssDNA wrapped around the nanoparticles hindered the approach of the coreactant. Due to the dual effects, the ECL response of the system decreased. The constructed biosensor exhibited excellent sensitivity toward TdT over a range spanning from 1 to 100 U/L. The limit of detection is as low as 1.78 U/L. The developed approach was effectively applied to detect TdT activity in leukemic patients' leukocyte extracts.
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Affiliation(s)
- Shaohua Tian
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Yong Yuan
- Department of Translational Medicine, Zhongshan People's Hospital, Zhongshan 528400, Guangdong, China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Cuiying Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Weijia Wang
- Department of Translational Medicine, Zhongshan People's Hospital, Zhongshan 528400, Guangdong, China
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4
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Zhao QG, Zhou YJ, Cao DX, Tang AN, Kong DM. DNA-Functionalized Porphyrinic Metal-Organic Framework-Based Drug Delivery System for Targeted Bimodal Cancer Therapy. J Med Chem 2023; 66:15370-15379. [PMID: 37963839 DOI: 10.1021/acs.jmedchem.3c01479] [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: 11/16/2023]
Abstract
A DNA-functionalized porphyrinic MOF (porMOF) drug delivery system was successfully constructed. porMOF as a photosensitizer and drug delivery carrier can integrate photodynamic therapy (PDT) and chemotherapy. Via the strong coordination interaction between the zirconium cluster of porMOF and the terminal phosphate group of DNA, the stable modification of the DNA layer on the porMOF surface is achieved. Meanwhile, the introduction of C/G-rich base pairs into the DNA double-stranded structure provides more binding sites of chemotherapeutic drug doxorubicin (DOX). AS1411, an aptamer of nucleolin proteins that are overexpressed by cancer cells, is introduced in the double-stranded terminal, which can endow the nanosystem with the ability to selectively recognize cancer cells. C-rich sequences in DNA double strands form an i-motif structure under acidic conditions to promote the highly efficient release of DOX in cancer cells. In vitro and in vivo experiments demonstrate that the synergistic PDT/chemotherapy modality achieves highly efficient cancer cell killing and tumor ablation without undesirable side effects.
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Affiliation(s)
- Qiu-Ge Zhao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Yun-Jie Zhou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Dong-Xiao Cao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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5
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Zhang D, Cai X, Zhang Q, Zhang C. Target-initiated fluorescent aptasensor based on multisite strand displacement amplification for label-free detection of ochratoxin A. Chem Commun (Camb) 2023; 59:13155-13158. [PMID: 37847525 DOI: 10.1039/d3cc04746f] [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: 10/18/2023]
Abstract
We developed a fluorescent aptasensor for label-free detection of ochratoxin A (OTA) based on TdT- and DNA polymerase-assisted multisite strand displacement amplification. This aptasensor exhibits good specificity and high sensitivity with a limit of detection (LOD) of 0.18 ng mL-1, and it can be further applied for the accurate quantification of OTA in complex real samples, holding promising applications in the field of food safety.
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Affiliation(s)
- Dandan Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, Sichuan, China
| | - Xiangyue Cai
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, Sichuan, China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chunyang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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6
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Wang Q, Chen B, Zheng D, Xia J, Wu L, Xu J. Intramolecular Accelerated Assembly of Molecular Beacons: A DNA Nanoarchitecture-based Spatial Confinement Strategy toward Terminal Deoxynucleotidyl Transferase Biosensing. Anal Chem 2023; 95:13708-13715. [PMID: 37625083 DOI: 10.1021/acs.analchem.3c03103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Physiological function analysis of terminal deoxynucleotidyl transferase (TdT) in clinical medicine and hematopathology highlights its significance to be extensively utilized as a diagnostic biomarker for leukemia diagnosis. Herein, taking advantage of the spatial-confinement effect on a three-dimensional (3D) DNA nanoarchitecture, we reported a target-triggered intramolecular accelerated molecular beacon (MB) assembly for rapid and real-time analysis of TdT activity. In this strategy, the 3D DNA nanoarchitecture is first engineered via a cross-linking network hybridization chain reaction (HCR). A number of MBs, which were designed with a polythymine (poly-T) loop, were then conjugated on the scaffold DNA nanoarchitecture, allowing the obtained MB-DNA nanoarchitecture to contain lots of free 3'-hydroxyl (OH) termini inside or outside the super DNA nanostructure. Moreover, the distance between different MBs is closed, and the local concentration of MB is significantly improved owing to the confinement of MBs on this DNA nanoarchitecture. Once encountered with target TdT, the free -OH groups can be recognized by TdT immediately to catalyze the template-independent incorporation of adenine nucleotides, which results in the generation of multiple poly-A chains that rapidly react with many MBs via an intramolecular accelerated assembly process. The time-dependent substantial enhancement of the fluorescence from MBs can thus be applied for robustly analyzing TdT. Our observations suggest that the DNA nanostructure-based spatial confinement effect enables a high molecular collision frequency to accelerate the reaction kinetics, and the super DNA nanoarchitecture exhibits a better nuclease resistance to maintain signal stability. With these advantages, TdT can be rapidly detected with high sensitivity, specificity, and biostability.
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Affiliation(s)
- Qi Wang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui Hefei, 230601, P. R. China
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Baoqiang Chen
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Dan Zheng
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Juan Xia
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Lijun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui Hefei, 230601, P. R. China
| | - Jianguo Xu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing 314001, P. R. China
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, Hefei 230009, P. R. China
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7
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Fangyu Zhou, Chen H, Fan T, Guo Z, Liu F. Fluorescence turn-off strategy for sensitive detection of DNA methyltransferase activity based on DNA-templated gold nanoclusters. Heliyon 2023; 9:e17724. [PMID: 37449164 PMCID: PMC10336507 DOI: 10.1016/j.heliyon.2023.e17724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
DNA methylation results in a variety of human diseases and the DNA methylation process is mediated by DNA methyltransferases, which have therefore become potential targets for disease treatment. In this study, a turn-off nanogold biological probe system was successfully created for determining the activity of DNA methyltransferases (M.SssI MTase). A dumbbell-shaped DNA probe with a site-recognizable region of M. SssI MTase and a fluorescent signal probe based on a DNA-templated gold nanocluster (DNA-AuNC) probe combined for the quantitative detection of M. SssI MTase. This dumbbell-shaped DNA probe was methylated by M. SssI MTase, and the dumbbell-shaped DNA probe with a methyl group was recognized by an endonuclease (GlaI) and cleaved into hairpin DNA. The dGTP was added to the 3'-OH terminus of hairpin DNA fragments in the presence of terminal deoxynucleotidyl transferase (TdT), and the hairpin DNA was extended with a G-rich sequence that can be used as an inactivation probe. When the inactivation probe was combined with the signal probe, the fluorescent signal disappeared due to the photoinduced electron transfer effect. Methyltransferase activity was then detected based on the turn-off principle of the fluorescence signal from the DNA-AuNCs. The bioprobe enabled sensitive detection of M. SssI MTase with a detection limit of 0.178 U mL-1 and good specificity. The bioprobe demonstrated good detection efficiency in both human serum and cell lysates, and its unique fluorescence turn-off mechanism provided good resistance to interference, thus increasing its potential application in complex biological samples. Moreover, it is suitable for screening and assessing the inhibitory activity of M. SssI MTase inhibitors, and therefore has significant potential for disease diagnosis and drug discovery.
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Affiliation(s)
- Fangyu Zhou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Tingting Fan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Zixia Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Feng Liu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
- National & Local United Engineering Lab for Personalized Anti-Tumor Drugs, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, PR China
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8
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Xiao Y, Yi H, Zhu J, Chen S, Wang G, Liao Y, Lei Y, Chen L, Zhang X, Ye F. Evaluation of DNA adduct damage using G-quadruplex-based DNAzyme. Bioact Mater 2023; 23:45-52. [DOI: 10.1016/j.bioactmat.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/15/2022] [Accepted: 10/02/2022] [Indexed: 11/11/2022] Open
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9
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Yi M, Gong Y, Zhan Q, Dai Y, Yang T, Cheng X, Ding S, Gu B, Cheng W, Zhang D. A one-pot CRISPR-Cas12a-based toolbox enables determination of terminal deoxynucleotidyl transferase activity for acute leukemia screening. Anal Chim Acta 2023; 1254:341115. [PMID: 37005025 DOI: 10.1016/j.aca.2023.341115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
An isothermal, one-pot toolbox (called OPT-Cas) based on CRISPR-Cas12a collateral cleavage capability is proposed for highly sensitive and selective determination of terminal deoxynucleotidyl transferase (TdT) activity. Oligonucleotide primers with 3'-hydroxyl (OH) terminal were randomly introduced for TdT-induced elongation. In the presence of TdT, dTTP nucleotides polymerized at the 3' terminals of the primers to generate abundant polyT-tails, which function as triggers for the synchronous activation of Cas12a proteins. Finally, the activated Cas12a trans-cleaved FAM and BHQ1 dual-labeled single-stranded DNA (ssDNA-FQ) reporters, producing significantly amplified fluorescence signals. This one-pot assay, that is primer, crRNA, Cas12a protein and ssDNA-FQ reporter are all in one tube, allows simple but high-sensitive quantification of TdT activity with a low detection limit of 6.16 × 10-5 U μL-1 in the concentration scope from 1 × 10-4 U μL-1 to 1 × 10-1 U μL-1, and achieves extraordinary selectivity with other interfering proteins. Furthermore, the OPT-Cas was successfully used to detect TdT in complex matrices and accurate determination of TdT activity in acute lymphoblastic leukemia cells, which might be a reliable technique platform for the diagnosis of TdT-related diseases and biomedical research applications.
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10
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Checkerboard arranged G4 nanostructure-supported electrochemical platform and its application to unique bio-enzymes examination. Bioelectrochemistry 2023; 149:108282. [DOI: 10.1016/j.bioelechem.2022.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
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11
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Liu Q, Hu K, She Y, Hu Y. In-situ growth G4-nanowire-driven electrochemical biosensor for probing H2O2 in living cell and the activity of terminal deoxynucleotidyl transferase. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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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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13
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Hu Z, Ye W, Zhang Z, Xie T, Yuan W, Wu T. Sensitive detection of abasic sites in double-stranded DNA based on the selective reaction of enzymes. Anal Chim Acta 2022; 1223:340220. [DOI: 10.1016/j.aca.2022.340220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022]
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14
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Fan W, Han P, Feng Q, Sun Y, Ren W, Lawson T, Liu C. Nucleic Acid Substrate-Independent DNA Polymerization on the Exosome Membrane: A Mechanism Study and Application in Exosome Analysis. Anal Chem 2022; 94:2172-2179. [PMID: 35044159 DOI: 10.1021/acs.analchem.1c04636] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As generally acknowledged, terminal deoxynucleotidyl transferase (TdT) can only elongate DNA substrates from their 3'-OH ends. Herein, for the first time, we report that TdT-catalyzed DNA polymerization can directly proceed on the exosome membrane without the mediation of any nucleic acids. We prove that both the glycosyl and phenolic hydroxyl groups on the membrane proteins can initiate the DNA polymerization. Accordingly, we have developed powerful strategies for high-sensitive exosome profiling based on a conventional flow cytometer and an emerging CRISPR/Cas system. By using our strategy, the featured membrane protein distributions of different cancer cell-derived exosomes can be figured out, which can clearly distinguish plasma samples of breast cancer patients from those of healthy people. This work paves new ways for exosome profiling and liquid biopsy and expands the understanding of TdT, holding great significance in developing TdT-based sensing systems as well as establishing protein/nucleic acid hybrid biomaterials.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an 710119, Shaanxi Province, P. R. China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an 710119, Shaanxi Province, P. R. China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Pihua Han
- Shaanxi Provincial Cancer Hospital, Xi'an 710061, Shaanxi Province, P. R. China
| | - Qinya Feng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an 710119, Shaanxi Province, P. R. China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an 710119, Shaanxi Province, P. R. China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Yuanyuan Sun
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an 710119, Shaanxi Province, P. R. China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an 710119, Shaanxi Province, P. R. China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Thomas Lawson
- ARC Center of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an 710119, Shaanxi Province, P. R. China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an 710119, Shaanxi Province, P. R. China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
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15
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Zhang D, Wang Y, Jin X, Xiao Q, Huang S. A label-free and ultrasensitive electrochemical biosensor for oral cancer overexpressed 1 gene via exonuclease III-assisted target recycling and dual enzyme-assisted signal amplification strategies. Analyst 2022; 147:2412-2424. [DOI: 10.1039/d2an00367h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free and ultrasensitive electrochemical biosensor for ORAOV1 gene via exonuclease III-assisted target recycling and dual enzyme-assisted signal amplification strategies. The detection limit of ORAOV1 gene was as low as 0.019 fM.
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Affiliation(s)
- Dongyou Zhang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Yali Wang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Xiaoyu Jin
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, P. R. China
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Framework nucleic acid-wrapped protein-inorganic hybrid nanoflowers with three-stage amplified fluorescence polarization for terminal deoxynucleotidyl transferase activity biosensing. Biosens Bioelectron 2021; 193:113564. [PMID: 34416433 DOI: 10.1016/j.bios.2021.113564] [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: 04/28/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 11/21/2022]
Abstract
Herein, we proposed a terminal deoxynucleotidyl transferase (TdT), a potential biomarker of lymphoid tumors, responsive fluorescence polarization (FP)- sensing protocol based on framework nucleic acid (FNA)-wrapped protein-inorganic hybrid nanoflowers. To achieve this goal, a pair of poly-A-composed extension primers (EPa and EPb) was designed, and protein-inorganic hybrid nanoflowers were synthesized by a biomineralization reaction. EPa was labeled with carboxyfluorescein (FAM) fluorophore to create the preliminary FP signal. EPb was labeled with biotin to conjugate with hybrid nanoflowers. Upon introduction of TdT into the dTTP pool, both EPa and EPb can be catalyzed by TdT to incorporate numerous T bases, thereby facilitating intermolecular hybridization between 'A' and 'T' bases. The final assembled FNA-wrapped hybrid nanoflowers with greatly enhanced molecular volume and weight restrict the free rotation of attached FAMs, causing a great FP enhancement from a designated three-stage FP amplification. Under optimized conditions, the TdT can be detected with a detection limit of 0.023 U/mL and a linear detection from 0.1 U/mL to 100 U/mL within 20 min. As a proof-of-concept study, the first exploitation of FNA and protein-inorganic nanoflowers to improve the FP signal and the merit of FP without sample separation and washing opens a new avenue for biochemical study and disease diagnosis.
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17
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Jiang H, Ji P, Xu Y, Liu X, Kong D. Self-paired dumbbell DNA -assisted simple preparation of stable circular DNAzyme and its application in Pb 2+ sensor. Anal Chim Acta 2021; 1175:338733. [PMID: 34330440 DOI: 10.1016/j.aca.2021.338733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 01/20/2023]
Abstract
During its development in recent decades, DNAzyme has become a promising candidate for application in biosensor field. However, it still suffers from the problem of thermodynamic and biological instability such as nuclease digestion, which limits its applications in complex samples. Here we have presented a simple and common strategy to resolve this problem by engineering the linear DNAzyme into a circular shape DNAzyme based on the integration of substrate and enzyme parts into one single-stranded sequence. This circular DNAzyme system is indeed endowed with excellent stability due to the stable intramolecular double-stranded formation and extraordinary resistance to nuclease digestion due to the closed structure. We demonstrated that this circular DNAzyme system gained excellent stability and could active under conditions across a broader range of temperature, salt concentrations, and pH. Depending on this circular DNAzyme, combing with Terminal deoxynucleotidyl transferase (TdT)-generated G-quadruplexes, a label free colorimetric sensing platform for Pb2+ quantitation was developed, and a detection limit of 0.085 nM was achieved. Then the enzyme digestion cycle amplification was introduced to further improve the sensitivity of the sensing system, an ultralow detection limit of 0.0015 nM for this fluorescence method was achieved. Based on the two sensing platforms, ultrasensitive analysis of Pb2+ in environmental water and food samples was successfully realized. It is anticipated that this stable circular DNAzyme design will be helpful for trace detection in complex samples.
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Affiliation(s)
- Hongxin Jiang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Pingping Ji
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Yaping Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Xiaowei Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Deming Kong
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China
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18
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Fan W, Liu D, Ren W, Liu C. Trends of Bead Counting-Based Technologies Toward the Detection of Disease-Related Biomarkers. Front Chem 2021; 8:600317. [PMID: 33409266 PMCID: PMC7779676 DOI: 10.3389/fchem.2020.600317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022] Open
Abstract
Nowadays, the biomolecular assay platforms built-up based on bead counting technologies have emerged to be powerful tools for the sensitive and high-throughput detection of disease biomarkers. In this mini-review, we classified the bead counting technologies into statistical counting platforms and digital counting platforms. The design principles, the readout strategies, as well as the pros and cons of these platforms are introduced in detail. Finally, we point out that the digital bead counting technologies will lead the future trend for the absolute quantification of critical biomarkers, and the integration of new signal amplification approaches and routine optical/clinical instruments may provide new opportunities in building-up easily accessible digital assay platforms.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Xi'an, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Dou Liu
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Xi'an, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Xi'an, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Xi'an, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, China.,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, China
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19
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Wang X, Xu J, Qin P, Yan C, Liu G, Chen W. Self-assembly of a polythymine embedded activatable molecular beacon for one-step quantification of terminal deoxynucleotidyl transferase activity. Anal Chim Acta 2020; 1141:127-135. [PMID: 33248645 DOI: 10.1016/j.aca.2020.10.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 02/07/2023]
Abstract
We describe an isothermal, single-reaction, and one-step method for signal-on quantification of terminal deoxynucleotidyl transferase (TdT) activity based on the periodic elongation and assembly of polythymine embedded activatable molecular beacon (PTA-MB) into DNA nanostructures. PTA-MB is easily designed according to the rule of the conventional molecular beacon (MB) but engineered with a polyT composed loop. Upon exposure to the specific target TdT, the MB is first elongated with an adenine-rich (A-rich) long chain so that it can then act as the anchoring substrate to capture many original PTA-MBs along its strand. Their unfolding contributes to preliminary fluorescence emission. Significantly, the assembled PTA-MBs can also be elongated and hybridized with residual free PTA-MBs for the second round of signal amplification. Accordingly, multiple rounds of elongation, assembly, and activation of initial PTA-MBs can lead to the formation of DNA nanostructures and induce a dramatically enhanced fluorescence signal for qualitative and quantitative evaluation of TdT activity. The final assay indicated a limit of detection (LOD) of 0.042 U mL-1 TdT and showed excellent selectivity for TdT versus other common enzymes. Moreover, the practical applicability was validated by direct/absolute quantification of TdT in real biological specimens and accurate monitoring of the activity of TdT pretreated by low/high temperature and heavy metal ions. These findings demonstrated that this functional PTA-MB and its unique assembly behavior is most likely to promote the study of oligonucleotide probe-based DNA assembly, providing a reliable, convenient, and universal platform for precise and point-of-care monitoring of various biomolecules.
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Affiliation(s)
- Xinxin Wang
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Panzhu Qin
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chao Yan
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China; Research Center for Biomedical and Health Science, School of Life and Health, Anhui Science & Technology University, Fengyang, 233100, China
| | - Guodong Liu
- Research Center for Biomedical and Health Science, School of Life and Health, Anhui Science & Technology University, Fengyang, 233100, China
| | - Wei Chen
- Engineering Research Center of Bio-process, MOE, School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
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20
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Kim HY, Song J, Park KS, Park HG. Simple and label-free strategy for terminal transferase assay using a personal glucose meter. Chem Commun (Camb) 2020; 56:8912-8915. [PMID: 32638717 DOI: 10.1039/d0cc02869j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein developed a simple personal glucose meter (PGM)-based method for terminal transferase (TdT) activity assay by utilizing the glucose oxidase (GOx)-mimicking activity of cerium oxide nanoparticles (CeO2 NPs). Using this strategy, the TdT activity was reliably determined down to 0.7 U mL-1 with high selectivity against other non-specific enzymes.
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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21
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LIU Z, LIU T, TAO CA, CHEN X, HUANG J, WANG F, WANG J. Amplified Analysis of DNA or Proteins by TdT-generated DNAzyme. ANAL SCI 2020; 36:835-840. [DOI: 10.2116/analsci.19p387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhuoliang LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
| | - Tianxiong LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Cheng-an TAO
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Xianzhe CHEN
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jian HUANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Fang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jianfang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
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22
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Li X, Du Z, Lin S, Tian J, Tian H, Xu W. ExoIII and TdT dependent isothermal amplification (ETDA) colorimetric biosensor for ultra-sensitive detection of Hg2+. Food Chem 2020; 316:126303. [DOI: 10.1016/j.foodchem.2020.126303] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/22/2019] [Accepted: 01/26/2020] [Indexed: 01/01/2023]
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23
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Tian W, Wang G, Liu X, Ren W, Liu C, Li Z. A terminal extension-actuated isothermal exponential amplification strategy toward the ultrasensitive and versatile detection of enzyme activity in a single cell. Talanta 2020; 211:120704. [PMID: 32070604 DOI: 10.1016/j.talanta.2019.120704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 11/29/2022]
Abstract
Terminal deoxynucleotidyl transferase (TdT) plays an important role in regulating a wide range of genomic processes. The sensitive and accurate detection of cellular TdT activity, particularly at the single-cell level, is highly significant for leukemia-associated biomedical and biological studies. Nevertheless, owing to the limited sensitivity of the existing TdT assays, the quantification of TdT activity at the single-cell level remains a big challenge. Herein, a simple but ultrasensitive method for assaying TdT activity is proposed based on terminal extension actuated loop-mediated isothermal amplification (TEA-LAMP). By using the TdT-induced extension product as an actuator, TdT activity is amplified twice by terminal extension and LAMP in an exponential manner and finally converted to a remarkably amplified fluorescent signal. In this study, as low as 2 × 10-8 U/μL TdT can be clearly detectable with the elegant TEA-LAMP strategy. Such an ultrahigh sensitivity enables the direct determination of TdT activity in individual single cells. In the meantime, by employing TdT as a co-factor, this strategy can also be applied to detecting other enzymes that can catalyze the DNA terminal hydroxylation. This work not only reports the up-to-now most sensitive TdT detection strategy at a single-cell level but also opens the new gate for versatile enzyme activity detection.
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Affiliation(s)
- Weimin Tian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Gaoting Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Xiaoling Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Wei Ren
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Chenghui Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
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24
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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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25
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Wang L, Pan Y, Liu Y, Sun Z, Huang Y, Li J, Yang J, Xiang Y, Li G. Fabrication of an Aptamer-Coated Liposome Complex for the Detection and Profiling of Exosomes Based on Terminal Deoxynucleotidyl Transferase-Mediated Signal Amplification. ACS APPLIED MATERIALS & INTERFACES 2020; 12:322-329. [PMID: 31840492 DOI: 10.1021/acsami.9b18869] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The exosome is a promising biomarker carrying many kinds of membrane proteins with huge heterogeneity, so the sensitive and multiplex analysis of exosomes is very significant for disease diagnosis and exploration of their biological functions. Herein, we propose an efficient method for highly sensitive detection and heterogeneity identification of exosomes based on the design and fabrication of an aptamer-coated liposome complex coupled with terminal deoxynucleotidyl transferase (TdT)-mediated polymerization. Specifically, in the presence of target exosomes, the aptamers immobilized on the surface of 1,2-dioleoyl-3-trimethylammonium-propane liposomes prefer to bind with exosomal membrane proteins due to the high affinity. The resulting aptamer-exosome complex will be accessible to TdT to switch on the polymerization reaction for signal amplification, achieving highly sensitive detection of exosomes. Furthermore, the proposed method can be employed to profile different exosomal membrane proteins by making use of a cluster of corresponding aptamers and obtain a fingerprint map of various cancer cell-derived exosomes. Thus, our approach may provide a highly sensitive and robust strategy for the identification of exosome heterogeneity with advantages of being label-free and having no separation, potentially enabling the precise subpopulation of exosomes with practical value in clinical applications.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Yanhong Pan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Yunfei Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Zhaowei Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Yue Huang
- Department of Food Science and Engineering, College of Light Industry and Food Engineering , Nanjing Forestry University , Nanjing 210037 , China
| | - Jinlong Li
- Department of Laboratory Medicine, The Second Hospital of Nanjing , Nanjing University of Chinese Medicine , Nanjing 210003 , P. R. China
| | - Jie Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences , Nanjing University , Nanjing 210023 , P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, 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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26
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Fan W, Qi Y, Lu X, Ren W, Liu C, Li Z. An emulsion-free digital flow cytometric platform for the precise quantification of microRNA based on single molecule extension-illuminated microbeads (dFlowSeim). Chem Commun (Camb) 2020; 56:7179-7182. [PMID: 32463032 DOI: 10.1039/d0cc03059g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An emulsion-free digital flow cytometric platform is developed for precise quantification of nucleic acids based on single molecule extension-illuminated microbeads.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
| | - Yan Qi
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
| | - Xiaohui Lu
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
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27
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Lei S, Liu Z, Xu L, Zou L, Li G, Ye B. A "signal-on" electrochemical biosensor based on DNAzyme-driven bipedal DNA walkers and TdT-mediated cascade signal amplification strategy. Anal Chim Acta 2019; 1100:40-46. [PMID: 31987151 DOI: 10.1016/j.aca.2019.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022]
Abstract
In this work, a dual amplified signal enhancement approach based on coupling deoxyribozyme (DNAzyme)-driven bipedal DNA walkers (BDW) and terminal deoxynucleotidyl transferase (TdT)-mediated DNA elongation signal amplifications has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. In presence of thrombin, the BDW complex, which is comprised from the target thrombin and two DNAzyme-containing probes, can exhibit autonomous cleavage behavior on the surface of the substrate DNA (SD) modified electrode, and remove the cleaved DNA fragment from the electrode surface. Subsequently, the TdT can catalyze the elongation of the SD with free 3'-OH termini and formation of many G-quadruplex sequence replicates with the presence of 2'-deoxyaguanosine-5'-triphosphate (dGTP) and adenosine 5'-triphosphate (dATP) at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a "signal-on" and completely label-free fashion. Under optimized conditions, the response peak current was linear with the concentration of thrombin in the range from 0.5 pM to 100000 pM with detection limit of 0.31 pM. This research provides us a sustainable idea for the hyphenated multiple amplification strategies and a stable and effective method for the detection of protein biomarkers.
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Affiliation(s)
- Sheng Lei
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Zi Liu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lingling Xu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Baoxian Ye
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China.
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28
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Du YC, Wang SY, Li XY, Wang YX, Tang AN, Kong DM. Terminal deoxynucleotidyl transferase-activated nicking enzyme amplification reaction for specific and sensitive detection of DNA methyltransferase and polynucleotide kinase. Biosens Bioelectron 2019; 145:111700. [DOI: 10.1016/j.bios.2019.111700] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022]
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29
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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30
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Unique G4-nanowires-mediated switch-modulated electrochemical biosensing for sensitive detection of nickel ion and histidine. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.05.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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31
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A label-free fluorescence method based on terminal deoxynucleotidyl transferase and thioflavin T for detecting prostate-specific antigen. Anal Bioanal Chem 2019; 411:5779-5784. [DOI: 10.1007/s00216-019-01958-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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32
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Zhang Y, Tian J, Li K, Tian H, Xu W. Label-free visual biosensor based on cascade amplification for the detection of Salmonella. Anal Chim Acta 2019; 1075:144-151. [PMID: 31196420 DOI: 10.1016/j.aca.2019.05.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/29/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
Salmonella is a widely distributed, extremely harmful bacteria, the presence of which requires confirmation via an on-site visual biosensor. In this study, we constructed a label-free, cascade amplification visualization biosensor for the sensitive and rapid detection of Salmonella enterica subsp. enterica serovar typhimurium based on the RDTG principle (recombinase polymerase amplification (RPA), duplex-specific enzyme (DSN) cleavage, terminal deoxynucleotidyl transferase (TdT) extension and G-quadruplexes output). Following DNA extraction of Salmonella spp., the first step in the construction involved the recognition and amplification of nucleic acids, carried out by RPA, to achieve the first signal amplification within 10 min. This RPA product was then specifically cleaved by DSN to produce a large number of small double-stranded DNA (dsDNA) products with 3'-OH within 15 min to achieve the second signal amplification. Thereafter, TdT was employed to empower these small 3'-OH dsDNA products to extend and produce a large number of long G-rich single-stranded DNAs (ssDNAs) within 20 min, thus realizing the third signal increase. These long G-rich ssDNA products displayed a color change that could be directly observed through the naked eye by adding H2O2/3,3',5,5'-tetramethylbenzidine (TMB). The RDTG biosensor for the detection of Salmonella spp. has several advantages, including a low limit of 6 cfu/mL. It is an isothermal-free instrument, simple to operate, with a rapid detection time of less than 1.5 h. Furthermore, it can be visually characterized and quantified by a microplate reader to detect Salmonella spp., in food and environmental samples, and it has broad application prospects.
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Affiliation(s)
- Yuan Zhang
- College of Food Science and Technology Agricultural University of Hebei, 071001, Baoding, China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jingjing Tian
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kai Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hongtao Tian
- College of Food Science and Technology Agricultural University of Hebei, 071001, Baoding, China.
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China.
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Liu X, Wang H, Deng K, Kwee S, Huang H, Tang L. Single Primer Based Multisite Strand Displacement Reaction Amplification Strategy for Rapid Detection of Terminal Deoxynucleotidyl Transferase Activity. Anal Chem 2019; 91:7482-7486. [DOI: 10.1021/acs.analchem.9b01816] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xinyan Liu
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Hao Wang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Keqin Deng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Sharon Kwee
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Haowen Huang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Liang Tang
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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Batule BS, Lee CY, Park KS, Park HG. Polymerization-sensitive switch-on monomer for terminal transferase activity assay. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:256-259. [PMID: 30688096 DOI: 10.1080/21691401.2018.1552593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We herein describe a simple but efficient method for the determination of terminal transferase (TdT) activity, which relies on our finding that Fe(III)-quenched boron-dipyrromethene (BODIPY)-ATP is utilized as a switch-on monomer for polymerization and enables the facile synthesis of fluorescence oligonucleotides without additional, post-processing steps. As TdT carries out the synthesis of DNA by adding the monomers into growing chains, Fe(III) is displaced from BODIPY with the release of pyrophosphate group, which consequently leads to the generation of highly fluorescent long oligonucleotides. With this strategy, we selectively detected the TdT activity with high sensitivity. In addition, its practical applicability was successfully demonstrated by determining TdT activities in human serum.
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Affiliation(s)
- Bhagwan S Batule
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
| | - Chang Yeol Lee
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
| | - Ki Soo Park
- b Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , Republic of Korea
| | - Hyun Gyu Park
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
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Luo X, Xue B, Feng G, Zhang J, Lin B, Zeng P, Li H, Yi H, Zhang XL, Zhu H, Nie Z. Lighting up the Native Viral RNA Genome with a Fluorogenic Probe for the Live-Cell Visualization of Virus Infection. J Am Chem Soc 2019; 141:5182-5191. [PMID: 30860368 DOI: 10.1021/jacs.8b10265] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA viruses represent a major global health threat, and the visualization of their RNA genome in infected cells is essential for virological research and clinical diagnosis. Due to the lack of chemical toolkits for the live-cell imaging of viral RNA genomes, especially native viral genomes without labeling and genetic modification, studies on native virus infection at the single-live-cell level are challenging. Herein, taking hepatitis C virus (HCV) as a representative RNA virus, we propose that the innate noncanonical G-quadruplex (G4) structure of viral RNA can serve as a specific imaging target and report a new benzothiazole-based G4-targeted fluorescence light-up probe, ThT-NE, for the direct visualization of the native RNA genome of HCV in living host cells. We demonstrate the use of the ThT-NE probe for several previously intractable applications, including the sensitive detection of individual virus-infected cells by small-molecule staining, real-time monitoring of the subcellular distribution of the viral RNA genome in live cells, and continuous live-cell tracking of the infection and propagation of clinically isolated native HCV. The fluorogenic-probe-based viral RNA light-up system opens up a promising chemical strategy for cutting-edge live-cell viral analysis, providing a potentially powerful tool for viral biology, medical diagnosis, and drug development.
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Affiliation(s)
- Xingyu Luo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Binbin Xue
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , People's Republic of China
| | - Guangfu Feng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Jiaheng Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , People's Republic of China
| | - Pan Zeng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , People's Republic of China
| | - Haibo Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine , Wuhan University , Wuhan 430071 , Hubei , People's Republic of China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
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Chi BZ, Wang CL, Wang ZQ, Pi T, Zhong XL, Deng CQ, Feng YC, Li ZM. Fluorometric determination of the activity of the biomarker terminal deoxynucleotidyl transferase via the enhancement of the fluorescence of silver nanoclusters by in-situ grown DNA tails. Mikrochim Acta 2019; 186:241. [DOI: 10.1007/s00604-019-3288-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/29/2019] [Indexed: 11/28/2022]
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37
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Wang Y, Sun X, Zeng J, Deng M, Li N, Chen Q, Zhu H, Liu F, Xing X. Label-free and sensitive detection assay for terminal deoxynucleotidyl transferase via polyadenosine-coralyne fluorescence enhancement strategy. Anal Biochem 2019; 567:85-89. [PMID: 30157446 DOI: 10.1016/j.ab.2018.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is a unique template-free polymerase that randomly adds multiple deoxyribonucleoside triphosphates (dNTPs) to the 3'-OH terminus of ssDNA. This characteristic makes TdT a versatile enzymatic tool in many fields. Moreover, aberrant TdT expression is a well-recognized biomarker of several leukemic diseases and is related to carcinogenesis. In this study, we developed a facile, rapid, label-free, and convenient assay for TdT detection. TdT-generated poly A tails formed a fluorescent enhancement complex in the presence of coralyne. To achieve a better signal-to-noise ratio, we used potassium thiocyanate (KSCN), instead of other halogen anions (KCl, KBr, KI, NaI) as the quenching agent of dissociate coralyne. Our results demonstrate that this assay is extremely facile, rapid, and label-free; at levels as low as 0.025 U/mL, TdT was distinctly detected within 55 min. And the determination of TdT activity in RBL-2H3 and Reh cells lysates exhibited a good sensing performance, demonstrating its potential applications in biochemical research and clinical diagnosis.
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Affiliation(s)
- Yuanyuan Wang
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Xu Sun
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang, 050000, China
| | - Jianxiong Zeng
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Minggang Deng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nan Li
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Qiutong Chen
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hua Zhu
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, New Jersey Medical School, NJ07103, USA
| | - Fenyong Liu
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; School of Public Health, University of California, Berkeley, CA, 94720, USA.
| | - Xiwen Xing
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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Wang S, Li D, Yuan R, Xiang Y. Simple label-free and sensitive fluorescence determination of human 8-oxoG DNA glycosylase 1 activity and inhibition viaTdT-assisted sequence extension amplification. NEW J CHEM 2019. [DOI: 10.1039/c9nj01080g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Label-free and sensitive detection of hOGG1 activity and inhibitionviaTdT-assisted sequence extension signal amplification.
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Affiliation(s)
- Sujing Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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39
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Qin Y, Liao S, Huang Y, Zhao J, Zhao S. Ultrasensitive fluorescent detection of nucleic acids based on label-free enzymatic-assisted cascade signal amplification. Anal Chim Acta 2018; 1039:91-97. [DOI: 10.1016/j.aca.2018.07.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/01/2018] [Accepted: 07/17/2018] [Indexed: 01/21/2023]
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40
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Fan K, Zheng C, Zhao Y, Fu H, Qu B, Lu L. Label-free ultrasensitive determination of EcoRI activity based on terminal deoxynucleotidyl transferase generated G-quadruplexes. Microchem J 2018. [DOI: 10.1016/j.microc.2018.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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41
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Cao J, Yao Y, Fan K, Tan G, Xiang W, Xia X, Li S, Wang W, Zhang L. Harnessing a previously unidentified capability of bacterial allosteric transcription factors for sensing diverse small molecules in vitro. SCIENCE ADVANCES 2018; 4:eaau4602. [PMID: 30498782 PMCID: PMC6261655 DOI: 10.1126/sciadv.aau4602] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/30/2018] [Indexed: 05/15/2023]
Abstract
A plethora of bacterial allosteric transcription factors (aTFs) have been identified to sense a variety of small molecules. Introduction of a novel aTF-based approach to sense diverse small molecules in vitro will signify a broad series of detection applications. Here, we found that aTFs could interact with their nicked DNA binding sites. Building from this new finding, we designed and implemented a novel aTF-based nicked DNA template-assisted signal transduction system (aTF-NAST) by using the competition between aTFs and T4 DNA ligase to bind to the nicked DNA. This aTF-NAST could reliably and modularly transduce the signal of small molecules recognized by aTFs to the ligated DNA signal, thus enabling the small molecules to be measured via various mature and robust DNA detection methods. Coupling this aTF-NAST with three DNA detection methods, we demonstrated nine novel biosensors for the detection of an antiseptic 4-hydroxybenzoic acid, a disease marker uric acid and an antibiotic tetracycline. These biosensors show impressive sensitivity and robustness in real-life analysis, highlighting the great potential of our aTF-NAST for biosensing applications.
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Affiliation(s)
- Jiaqian Cao
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
| | - Gaoyi Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Xuekui Xia
- Key Laboratory for Biosensor of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, P.R. China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
- Corresponding author. (L.Z.); (W.W.); (S.L.)
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
- Corresponding author. (L.Z.); (W.W.); (S.L.)
| | - Lixin Zhang
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, P.R. China
- Corresponding author. (L.Z.); (W.W.); (S.L.)
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Lu L, Su H, Liu Q, Li F. Development of a Luminescent Dinuclear Ir(III) Complex for Ultrasensitive Determination of Pesticides. Anal Chem 2018; 90:11716-11722. [PMID: 30192517 DOI: 10.1021/acs.analchem.8b03687] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To improve the G-quadruplex specificity of Ir(III) complexes, a novel dinuclear Ir(III) complex (Din Ir(III)-1) was designed and synthesized through connecting two mononuclear Ir(III) complexes via a diphenyl bridge. Din Ir(III)-1 presents 3.4-4.1-fold enhancements for G-quadruplex relative to ssDNA and 4.3-5.3-fold enhancements relative to dsDNA in luminescence intensity, respectively, demonstrating an excellent G-quadruplex selectivity. Ascribed to its superior specificity to G-quadruplex, Din Ir(III)-1 was employed to construct a highly sensitive luminescent pesticides' detection platform. The detection is based on acetylcholinesterase (AChE)-catalyzed hydrolysis product-induced DNA conformational transformation and subsequent terminal deoxynucleotidyl transferase (TdT) directed G-quadruplex formation. The assay exhibited a linear response between the emission intensity of Din Ir(III)-1 and the pesticide concentration in the range of 0.5-25 μg/L ( R2 = 0.994), and the limit of detection for the pesticide was as low as 0.37 μg/L when using aldicarb as the model pesticide. Moreover, this strategy demonstrates good applicability for the pesticide detection in real samples. It is also versatile for the detection of other organophosphate or carbamate pesticides, which have the inhibition ability toward AChE. Therefore, the proposed approach is scalable for practical application in food safety and environmental monitoring fields and will provide promising solutions for the assay of pesticide residues.
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Affiliation(s)
- Lihua Lu
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Huijuan Su
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Qingyun Liu
- College of Chemical and Environmental Engineering , Shandong University of Science and Technology , Qingdao 266510 , China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
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Zhu L, Chen D, Lu X, Qi Y, He P, Liu C, Li Z. An ultrasensitive flow cytometric immunoassay based on bead surface-initiated template-free DNA extension. Chem Sci 2018; 9:6605-6613. [PMID: 30310592 PMCID: PMC6115634 DOI: 10.1039/c8sc02752h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
An ultrasensitive flow cytometric immunoassay (TdT-FCI) is developed based on bead surface-initiated template-free DNA extension.
Proteins lack the duplication mechanism like nucleic acids, so the connection of immunoassays with effective nucleic acid amplification techniques has become a powerful way for the detection of trace protein biomarkers in biological fluids. However, such immunoassays generally suffer from rather stringent DNA sequence design and complicated operations. Herein, we propose a simple but highly sensitive flow cytometric immunoassay (FCI) by employing on-bead terminal deoxynucleotidyl transferase (TdT)-initiated template-free DNA extension as an effective signal amplification pathway (TdT-FCI), and gold nanoparticles (AuNPs) co-functionalized with both the detection antibody and a 3′-OH oligonucleotide (ODN) as the transducer to bridge the immunoassay and subsequent TdT-mediated DNA amplification. The target antigen can sandwich with the capture antibody immobilized on the magnetic beads (MBs) and the detection antibody on the AuNPs to bring a lot of ODNs onto the surface of MBs. Each ODN on the MBs can be effectively elongated by TdT in a template-free manner to produce a long poly(T) tail, which will then bind to many 6-carboxyfluorescein (FAM)-labeled poly(A)25. Since each AuNP can carry multiple ODNs and each extended ODN can ultimately capture numerous FAM-poly(A)25, efficiently amplified fluorophore accumulation on the MBs can be achieved. The fluorescent MBs can be individually interrogated with a flow cytometer and thus quantitative analysis of the target antigen can be realized. Coupled with the powerful flow cytometry analysis, the simple but efficient TdT-based signal amplification mechanism has pushed the detection limit of prostate specific antigen (PSA) down to a low level of 0.5 pg mL–1. Furthermore, based on an elegant bead size-encoding principle, we have further advanced the TdT-FCI for multiplexed antigen detection in a single reaction. Sharing the unique merits of simple design and operation, efficient signal amplification, powerful signal readout and the capability for multiplexed analysis, this TdT-FCI provides a versatile tool for detecting trace antigen biomarkers towards clinical diagnosis as well as prognosis.
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Affiliation(s)
- Liping Zhu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
| | - Desheng Chen
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
| | - Xiaohui Lu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
| | - Yan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
| | - Pan He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
| | - Chenghui Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , P. R. China .
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44
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Du YC, Cui YX, Li XY, Sun GY, Zhang YP, Tang AN, Kim K, Kong DM. Terminal Deoxynucleotidyl Transferase and T7 Exonuclease-Aided Amplification Strategy for Ultrasensitive Detection of Uracil-DNA Glycosylase. Anal Chem 2018; 90:8629-8634. [PMID: 29911858 DOI: 10.1021/acs.analchem.8b01928] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As one of the key initiators of the base excision repair process, uracil-DNA glycosylase (UDG) plays an important role in maintaining genomic integrity. It has been found that aberrant expression of UDG is associated with a variety of diseases. Thus, accurate and sensitive detection of UDG activity is of critical significance for biomedical research and early clinical diagnosis. Here, we developed a novel fluorescent sensing platform for UDG activity detection based on a terminal deoxynucleotidyl transferase (TdT) and T7 exonuclease (T7 Exo)-aided recycling amplification strategy. In this strategy, only two DNA oligonucleotides (DNA substrate containing one uracil base and Poly dT probe labeled with a fluorophore/quencher pair) are used. UDG catalyzes the removal of uracil base from the enclosed dumbbell-shape DNA substrate to give an apyrimidinic site, at which the substrate oligonucleotide is cleaved by endonuclease IV. The released 3'-end can be elongated by TdT to form a long deoxyadenine-rich (Poly dA) tail, which may be used as a recyclable template to initiate T7 Exo-mediated hybridization-digestion cycles of the Poly dT probe, giving a significantly enhanced fluorescence output. The proposed UDG-sensing strategy showed excellent selectivity and high sensitivity with a detection limit of 1.5 × 10-4 U/mL. The sensing platform was also demonstrated to work well for UDG inhibitor screening and inhibitory activity evaluation, thus holding great potential in UDG-related disease diagnosis and drug discovery. The proposed strategy can be easily used for the detection of other DNA repair-related enzymes by simply changing the recognition site in DNA substrate and might also be extended to the analysis of some DNA/RNA-processing enzymes, including restriction endonuclease, DNA methyltransferase, polynucleotide kinase, and so on.
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Affiliation(s)
- Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre 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
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin , 300071 , P R China
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin , 300071 , P R China
| | - Guo-Ying Sun
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin , 300071 , P R China
| | - Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin , 300071 , P R China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin , 300071 , P R China
| | - Kwangil Kim
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P R China.,Institute of Analysis , Kim Chaek University of Technology , Pyongyang , 999093 , Democratic People's Republic of Korea
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre 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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45
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Luminescence determination of microRNAs based on the use of terbium(III) sensitized with an enzyme-activated guanine-rich nucleotide. Mikrochim Acta 2018; 185:280. [PMID: 29725866 DOI: 10.1007/s00604-018-2819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/24/2018] [Indexed: 02/05/2023]
Abstract
A method is reported for the fluorometric quantitation of microRNA. It is making use of a luminescent probe deribed from terbium(III) ion whose fluorescence is sensitized with a guanine-rich (G-rich) nucleotide. The probe has a large Stokes' shift and strong and sharp emission bands. The assay relies on the wide substrate specificity of terminal deoxynucleotidyl transferase (TdTase), which catalyzes the formation of long G-rich nucleotides when using microRNA primer as a trigger to start the polymerization. The addition of Tb(III) induces the formation of a G-quadruplex from the G-rich nucleotide, and this strongly enhances the green fluorescence of Tb(III) (peaking at 545 nm upon photoexcitation at 290 nm). Specifically, microRNA-21 was chosen as the analyte. The fluorescence intensity of Tb(III) increases linearly in the 1 pM to 1 nM microRNA concentration range, and the detection limit is as low as 0.11 pM. The method can distinguish between family members of microRNA and performs excellently even when applied to extracts of cancer cells. Graphical abstract A fluorometric technique is reported for the determination of microRNA. It is based on signal enhancement based on the sensitization of terbium(III) via a guanine-rich nucleotide sequence. Klenow Fragment exo- (KFexo-) generates DNA sequence at the 3'-OH of microRNA, and terminal deoxynucleotidyl transferase (TdTase) catalyzes the formation of long G-rich nucleotides.
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46
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Fan W, Qi Y, Qiu L, He P, Liu C, Li Z. Click Chemical Ligation-Initiated On-Bead DNA Polymerization for the Sensitive Flow Cytometric Detection of 3'-Terminal 2'-O-Methylated Plant MicroRNA. Anal Chem 2018; 90:5390-5397. [PMID: 29600844 DOI: 10.1021/acs.analchem.8b00589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes, respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N3, can not only simplify the operation, but also achieve a much higher ligation efficiency. More importantly, the undesirable nonspecific ligation between the Aza-DBCO- and N3-modified ssDNA, can be effectively eliminated by adding Tween-20, which allows the use of cycling CNAL (CCNAL) in a background-free manner. So each plant miRNA can template many rounds of CNAL reaction to produce numerous ligation products, forming efficient signal amplification. The ligated ssDNA can be anchored on the magnetic beads (MBs) with the 3'-OH termini exposed outside. Then terminal deoxynucleotidyl transferase (TdT), a sequence-independent and template-free polymerase, would specifically catalyze the DNA polymerization along these 3'-OH termini on the MBs, forming poly(T) tails up to thousands of nucleotides long. Each poly(T) tail allows specific binding of numerous 6-carboxyfluorescein (FAM)-labeled poly(A)25 oligonucleotides to accumulate a lot of fluorophores on the MBs, leading to the second step of signal amplification. By integrating the advantages of CCNAL-TEP for highly efficient signal amplification and robust MBs signal readout with powerful flow cytometer, high sensitivity is achieved and the detection limit of plant miRNA has been pushed down to a low level of 5 fM with high specificity to well discriminate even single-base difference between miRNA targets.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Yan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Liying Qiu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Pan He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Chenghui Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
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47
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Shi T, Wang M, Li H, Wang M, Luo X, Huang Y, Wang HH, Nie Z, Yao S. Simultaneous Monitoring of Cell-surface Receptor and Tumor-targeted Photodynamic Therapy via TdT-initiated Poly-G-Quadruplexes. Sci Rep 2018; 8:5551. [PMID: 29615769 PMCID: PMC5882647 DOI: 10.1038/s41598-018-23902-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/21/2018] [Indexed: 01/03/2023] Open
Abstract
Cancer cells contain a unique set of cell surface receptors that provide potential targets for tumor theranostics. Here, we propose an efficient approach to construct G-quadruplex-based aptamers that specifically recognize cell-surface receptors and monitor them in an amplified manner. This designed aptamer combined particular sequence for the c-Met on the cell surface and poly-G-quadruplexes structures that allow a rapid and amplified fluorescent readout upon the binding of thioflavin T (ThT). The poly-G-quadruplexes also function as a carrier for photosensitizers such as TMPyP4 in that, the aptamer further trigger the production of reactive oxygen species (ROS) to commit cells to death. This unique c-Met targeting aptamer enabled simultaneous monitoring of c-Met on the cell surface with ThT and photodynamic killing of these lung cancer cells with TMPyP4. This strategy is expected to enhance the development of tumor-targeted diagnosis and drug delivery.
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Affiliation(s)
- Tianhui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Menglin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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48
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Guo J, Yuan C, Yan Q, Duan Q, Li X, Yi G. An electrochemical biosensor for microRNA-196a detection based on cyclic enzymatic signal amplification and template-free DNA extension reaction with the adsorption of methylene blue. Biosens Bioelectron 2018; 105:103-108. [PMID: 29367007 DOI: 10.1016/j.bios.2018.01.036] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/06/2018] [Accepted: 01/17/2018] [Indexed: 01/06/2023]
Abstract
A simple and sensitive electrochemical biosensor was developed for microRNA-196a detection, which is of important diagnostic significance for pancreatic cancer. It was based on cyclic enzymatic signal amplification (CESA) and template-free DNA extension reaction. In the presence of microRNA-196a, duplex-specific nuclease (DSN) catalyzed the digestion of the 3'-PO4 terminated capture probe (CP), resulting in the target recycling amplification. Meanwhile, the 3'-OH terminal of CP was exposed. Then, template-free DNA extension reaction was triggered by terminal deoxynucleotidyl transferase (TdT), producing amounts of single-stranded DNA (ssDNA). After ssDNA absorbed numerous methylene blue (MB), an ultrasensitive electrochemical readout was obtained. Based on this dual amplification mechanism, the proposed biosensor exhibited a high sensitivity for detection of microRNA-196a down to 15 aM with a linear range from 0.05 fM to 50 pM. This biosensor displayed high specificity, which could discriminate target microRNAs from one base mismatched microRNAs. It also showed good reproducibility and stability. Furthermore, it was successfully applied to the determination of microRNA-196a in plasma samples. In conclusion, with the excellent analytical performance, this biosensor might have the potential for application in clinical diagnostics of pancreatic cancer.
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Affiliation(s)
- Jing Guo
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Changjing Yuan
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Qi Yan
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Qiuyue Duan
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xiaolu Li
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Gang Yi
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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49
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Zhu R, Luo X, Deng L, Lei C, Huang Y, Nie Z, Yao S. An enzymatic polymerization-activated silver nanocluster probe for in situ apoptosis assay. Analyst 2018; 143:2908-2914. [DOI: 10.1039/c8an00535d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A DNA/AgNC probe was developed for in situ apoptosis assay based on an enzyme-polymerized poly-dA DNA chain and strand displacement.
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Affiliation(s)
- Rong Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Lu Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
- P. R. China
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50
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Ma F, Li CC, Zhang CY. Development of quantum dot-based biosensors: principles and applications. J Mater Chem B 2018; 6:6173-6190. [DOI: 10.1039/c8tb01869c] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We review the recent advances in quantum dot-based biosensors and focus on quantum dot-based fluorescent, bioluminescent, chemiluminescent, and photoelectrochemical biosensors.
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Affiliation(s)
- 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
| | - 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
| | - 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
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