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Tian Y, Zhang S, Wang L, Liu S. A Modular Nanoswitch for Mix-and-Detect Protein Assay Based on Binding-Induced Cascade Dissociation of Kissing Complex. Chembiochem 2018; 19:716-722. [PMID: 29356232 DOI: 10.1002/cbic.201700649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Indexed: 01/26/2023]
Abstract
A new modular nanoswitch was described for versatile, rapid (within 1 h), homogeneous, and sensitive protein detection. The system employs two hairpins (HP1 and HP2) that can be reciprocally recognized through the apical loop-loop interaction. HP2 possesses a conformation-switching stem-loop structure, with appended single-stranded tails on each end, which can hybridize with the recognition-element-conjugated DNA strands to construct a protein-responsive HP2 scaffold. It works according to a simple mix-and-detect assay format, with the first formation of a kissing complex between HP1 and HP2 scaffolds for fluorescence quenching, and then cascade propagation from steric strain through protein binding to the dissociation of the kissing complex for fluorescence recovery. The detection universality of such a modular nanoswitch was demonstrated by using three multivalent proteins, including anti-digoxigenin (Anti-Dig) antibody, streptavidin, and thrombin, with detection limits of 0.33, 0.17, and 0.5 nm, respectively.
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Affiliation(s)
- Yishen Tian
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Shanshan Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
| | - Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Road Zhengzhou, Qingdao, Shandong, 266042, China
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Gao F, Wu J, Yao Y, Zhang Y, Liao X, Geng D, Tang D. Proximity hybridization triggered strand displacement and DNAzyme assisted strand recycling for ATP fluorescence detection in vitro and imaging in living cells. RSC Adv 2018; 8:28161-28171. [PMID: 35542748 PMCID: PMC9084323 DOI: 10.1039/c8ra05193c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 07/27/2018] [Indexed: 12/16/2022] Open
Abstract
We developed a novel strategy for ATP detection in vitro and imaging in living cells based on integrating proximity hybridization-induced strand displacement and metal ion-dependent DNAzyme recycling amplification. Four DNA oligonucleotides were used in the sensing system including two aptamer probes, enzymatic sequences and FAM-linked substrate strands. Upon the addition of ATP, the proximity binding of two aptamers to ATP led to the release of the enzymatic sequences, which hybridized with the FAM-linked substrate strand on the graphene oxide (GO) surface to form the ion-dependent DNAzyme. Subsequent catalytic cleavage of the DNAzyme by the corresponding metal ions results in recycling of the enzymatic sequences and cyclic cleavage of the substrate strand, liberating many short FAM-linked oligonuleotide fragments separated from the GO surface, which results in fluorescence enhancement due to the weak affinity of the short FAM-linked oligonuleotide fragment to GO. The amount of produced short FAM-linked oligonuleotide fragments is positively related to the concentration of ATP. This means that one target binding could result in cleaving multiplex fluorophore labelled substrate strands, which provided effective signal amplification. The vivo studies suggested that the nanoprobe was efficiently delivered into living cells and worked for specific, high-contrast imaging of target ATP. More importantly, this target-responsive nanoscissor model is an important approach for intracellular amplified detection and imaging of various analytes by selecting appropriate affinity ligands. A novel strategy for ATP imaging was developed based on proximity binding-induced strand displacement and metal ion-dependent DNAzyme recycling.![]()
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Affiliation(s)
- Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy
- School of Pharmacy
- Xuzhou Medical University
- Xuzhou
- China
| | - Jing Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy
- School of Pharmacy
- Xuzhou Medical University
- Xuzhou
- China
| | - Yao Yao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy
- School of Pharmacy
- Xuzhou Medical University
- Xuzhou
- China
| | - Yu Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy
- School of Pharmacy
- Xuzhou Medical University
- Xuzhou
- China
| | - Xianjiu Liao
- School of Pharmacy
- Youjiang Medical University for Nationalities
- Baise
- China
| | - Deqin Geng
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy
- School of Pharmacy
- Xuzhou Medical University
- Xuzhou
- China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy
- School of Pharmacy
- Xuzhou Medical University
- Xuzhou
- China
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3
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015; 54:9637-41. [PMID: 26119600 DOI: 10.1002/anie.201503182] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/28/2015] [Indexed: 12/20/2022]
Abstract
ϕ29 DNA polymerase (ϕ29DP) is able to carry out repetitive rounds of DNA synthesis using a circular DNA template by rolling circle amplification (RCA). It also has the ability to execute 3'-5' digestion of single-stranded but not double-stranded DNA. A biosensor engineering strategy is presented that takes advantage of these two properties of ϕ29DP coupled with structure-switching DNA aptamers. The design employs a DNA assembly made of a circular DNA template, a DNA aptamer, and a pre-primer. The DNA assembly is unable to undergo RCA in the absence of cognate target owing to the formation of duplex structures. The presence of the target, however, triggers a structure-switching event that causes nucleolytic conversion of the pre-primer by ϕ29DP into a mature primer to facilitate RCA. This method relays target detection by the aptamer to the production of massive DNA amplicons, giving rise to dramatically enhanced detection sensitivity.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Qiang Zhang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - John D Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada). .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
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5
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Zhang L, Zhang K, Liu G, Liu M, Liu Y, Li J. Label-Free Nanopore Proximity Bioassay for Platelet-Derived Growth Factor Detection. Anal Chem 2015; 87:5677-82. [DOI: 10.1021/acs.analchem.5b00791] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ling Zhang
- Department of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- Department of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Guangchao Liu
- Department of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Mengjia Liu
- Department of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Yang Liu
- Department of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
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Huang Y, Liu X, Shi M, Zhao S, Hu K, Chen ZF, Liang H. Ultrasensitive fluorescence polarization aptasensors based on exonuclease signal amplification and polystyrene nanoparticle amplification. Chem Asian J 2014; 9:2755-60. [PMID: 25081952 DOI: 10.1002/asia.201402563] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Indexed: 11/08/2022]
Abstract
Here, we combine T7 exonuclease (T7 Exo) signal amplification and polystyrene nanoparticle (PS NP) amplification to develop novel fluorescence polarization (FP) aptasensors. The binding of a target/open aptamer hairpin complex or a target/single-stranded aptamer complex to dye-labeled DNA bound to PS NPs, or the self-assembly of two aptamer subunits (one of them labeled with a dye) into a target/aptamer complex on PS NPs leads to the cyclic T7 Exo-catalyzed digestion of the dye-labeled DNA or the dye-labeled aptamer subunit. This results in a substantial decrease in the FP value for the amplified sensing process. Our newly developed aptasensors exhibit a sensitivity five orders of magnitude higher than that of traditional homogeneous aptasensors and a high specificity for the target molecules. These distinct advantages of our proposed assay protocol make it a generic platform for the design of amplified aptasensors for ultrasensitive detection of various target molecules.
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Affiliation(s)
- Yong Huang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), College of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004 (China).
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Zhang H, Li F, Dever B, Wang C, Li XF, Le XC. DNA-Assemblierung mittels Affinitätsbindung für die ultraempfindliche Proteindetektion. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zhang H, Li F, Dever B, Wang C, Li XF, Le XC. Assembling DNA through affinity binding to achieve ultrasensitive protein detection. Angew Chem Int Ed Engl 2013; 52:10698-705. [PMID: 24038633 DOI: 10.1002/anie.201210022] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 03/17/2013] [Indexed: 11/06/2022]
Abstract
Recent advances in DNA assembly and affinity binding have enabled exciting developments of nanosensors and ultrasensitive assays for specific proteins. These sensors and assays share three main attractive features: 1) the detection of proteins can be accomplished by the detection of amplifiable DNA, thereby dramatically enhancing the sensitivity; 2) assembly of DNA is triggered by affinity binding of two or more probes to a single target molecule, thereby resulting in increased specificity; and 3) the assay is conducted in solution with no need for separation, thus making the assay attractive for potential point-of-care applications. We illustrate here the principle of assembling DNA through affinity binding, and we highlight novel applications to the detection of proteins.
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Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G3 (Canada) http://www.ualberta.ca/∼xcle
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