1
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Pang H, Zhao Q. Antibody-Bridged DNAzyme Walker for Sensitive Detection of Small Molecules. Anal Chem 2024; 96:6366-6372. [PMID: 38598690 DOI: 10.1021/acs.analchem.4c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Sensitive detection of small molecules with biological and environmental interests is important for many applications, such as food safety, disease diagnosis, and environmental monitoring. Herein, we propose a highly selective antibody-bridged DNAzyme walker to sensitively detect small molecules. The antibody-bridged DNAzyme walker consists of a track, small-molecule-labeled DNAzyme walking strand, and antibody against small molecules. The track is built by co-modifying fluorophore-labeled substrates and small-molecule-labeled DNA linkers onto a gold nanoparticle (AuNP). In the absence of the target molecule, the antibody binds small molecule labels at the DNAzyme walking strand and the DNA linker, driving the DNAzyme walking strand on the surface of the AuNP. The attached DNAzyme walking strand moves along the track and cleaves substrates to generate high fluorescence signals to achieve signal amplification. As target molecules exist, they competitively bind with antibody to displace the small-molecule-labeled linker and DNAzyme walking strand, rendering the DNAzyme walker inactive in substrate cleavage and causing weak fluorescence. By using this antibody-bridged DNAzyme walker, we achieved sensitive detection of two biologically important small molecules, digoxin and folic acid. This work provides a new paradigm by combining the signal amplification strategy of a DNA walker and immunorecognition for sensitive and selective detection of small molecules.
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Affiliation(s)
- Han Pang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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2
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Chen T, Yang J, Tang Y, Fan X, Zhou W, Jiang B, Wang D. Label-free and highly sensitive detection of microRNA from cancer cells via target-induced cascade amplification generation of lighting-up RNA aptamers. Anal Chim Acta 2024; 1289:342187. [PMID: 38245202 DOI: 10.1016/j.aca.2023.342187] [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: 10/23/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024]
Abstract
The abnormal expression levels of miRNAs have been proven to be highly related to the generation of various diseases and are also closely associated with the stages and types of disease development. The novel RNA aptamers-based homogenous fluorescent methods were simple, with low background signal and high signal-to-noise ratio, but lacked effective signal amplification technology to achieve sensitive detection of trace miRNA markers. There is an urgent need for combining effective nucleic acid amplification technology with RNA aptamer to achieve highly sensitive and accurate detection of miRNA. For this purpose, a new DNA multi-arm nanostructure-based dual rolling circle transcription machinery for the generation of lighting-up MG RNA aptamers is constructed for label-free and highly sensitive sensing of miRNA-21. In this system, the target miRNA-21 induces a structural transformation of the DNA multi-arm nanostructure probe to recycle miRNA-21 and trigger two independent rolling circle transcription reactions to generate two long RNAs, which can partially hybridize with each other to generate large amounts of complete MG RNA aptamers. These RNA aptamers can associate with organic MG dye to produce significantly enhanced fluorescence signals to accomplish ultrasensitive miRNA-21 detection down to 0.9 fM. In addition, this method exhibits high selectivity to distinguish miRNA-21 even with single nucleotide mismatch, and also has potential application capability to monitor different expression levels of miRNA-21 from different cancer cells. The effective collaboration between MG RNA aptamer and rolling circle transcription reaction makes this fluorescent method show the significant advantages of low background signal, high signal-to-noise ratio and high detection sensitivity. It has great potential to be a promising means to achieve label-free and highly sensitive monitoring of other trace biological markers via a simple change of target sequence.
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Affiliation(s)
- Tiantian Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Jirong Yang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Yaqin Tang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Xiaocheng Fan
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Wenjiao Zhou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Ding Wang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
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3
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Abstract
CRISPR/Cas systems are powerful tools for sensitive nucleic acid molecular diagnosis due to their specific nucleic acid recognition and high trans-cleavage activity and have also allowed for quantification of non-nucleic acid targets, relying on a strategy to convert the target detection to analysis of nucleic acids. Here, we describe a CRISPR/Cas12a-powered immunosorbent assay for sensitive small-molecule detection by using the antibody coated on the microplate to recognize the target and the small molecule-labeled active DNA (acDNA) to trigger the activity of CRISPR/Cas12a. In the absence of small-molecule targets, acDNA probes are captured by the antibody on the microplate and then activate Cas12a in catalytic trans-cleavage of fluorescent DNA reporters, generating strong fluorescence. The presence of small-molecule targets displaces the acDNA probes from the antibody, causing a decrease of acDNA probes on the microplate and reduction of activated Cas12a, so the fluorescence signal decreases, and small molecules can be detected by monitoring the fluorescence change. After systematically optimizing experimental conditions (e.g., Cas12a reaction), the proposed method achieved the detection of three model small molecules, biotin, digoxin, and folic acid, with low detection limits, and a flexible detection concentration range was obtained by simply changing the amount of acDNA probes and immobilized antibodies. The assay showed high selectivity and good applicability in complex media. The integration of the CRISPR/Cas12a system improves the analytical performance of immunoassay, broadening and facilitating its applications in rapid, simple, and sensitive small molecule analysis.
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Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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4
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Zhu F, Zhao Q. Sensitive CRISPR-Cas12a-Assisted Immunoassay for Small Molecule Detection in Homogeneous Solution. Anal Chem 2023; 95:6769-6774. [PMID: 37079720 DOI: 10.1021/acs.analchem.3c00218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Sensitive detection of small molecules is crucial for many applications, like biomedical diagnosis, food safety, and environmental analysis. Here, we describe a sensitive CRISPR-Cas12a-assisted immunoassay for small molecule detection in homogeneous solution. An active DNA (acDNA) modified with a specific small molecule serves as a competitor for antibody binding and an activator of CRISPR-Cas12a. Large-sized antibody binding with this acDNA probe inactivates the collateral cleavage activity of CRISPR-Cas12a due to a steric effect. When free small molecule target exists, it replaces the small molecule-modified acDNA from antibody, triggering catalytic cleavage of DNA reporters by CRISPR-Cas12a, and strong fluorescence is generated. With this strategy, we achieved detection of three important small molecules as models, biotin, digoxin, and folic acid, at picomolar levels by using streptavidin or antibody as recognition elements. With the progress of DNA-encoded small molecules and antibody, the proposed strategy provides a powerful toolbox for detection of small molecules in wide applications.
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Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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5
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Zhang X, Xie S, Chen X, Wang L, Li F, Liu S. An allosteric DNA switch-mediated catalytic DNA circuit for ratiometric and sensitive nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 15:124-131. [PMID: 36504112 DOI: 10.1039/d2ay01751b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Herein, a new allosteric DNA switch-mediated catalytic DNA circuit reaction strategy has been proposed for ratiometric and sensitive nucleic acid detection. The sensing system was based on two DNA hybrid probes, each of which was constructed by annealing a reconfigurable DNA hairpin with single-stranded DNA. Upon target recognition by the first DNA hybrid probe, a reconfigurable DNA switch was liberated, triggering a toehold-mediated strand displacement reaction (TSDR) with the second DNA hybrid probe, which was accompanied by the release of another reconfigurable DNA switch. This released allosteric DNA switch could further interact with the first hybrid DNA probe via the TSDR strategy to form a reciprocal strand displacement network between the two DNA hybrid probes. Theoretically, this reciprocal strand displacement reaction would continue till the complete consumption of the reaction substrates. Thus, it provides a new signal amplification method leading toward target recognition. More interestingly, it creates a ratiometric signal response mode for target recognition, which involves the fluorescence increment of one fluorophore (Cy5) and concurrent decrement of another fluorophore (Cy3) accompanied by the target-triggered reciprocal strand displacement reaction. This process could achieve a low detection limit of about 0.1 pM toward the target nucleic acid and selective discrimination toward different mismatched targets. It could also be applied for detection in a serum sample. Thus, the developed catalytic DNA circuit reaction strategy together with ratiometric signal readout provides a new avenue for programmable, reliable and sensitive detection of nucleic acids and might also pave the way for developing more advanced DNA circuits or biosensors.
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Affiliation(s)
- Xiaofan Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Shunjun Xie
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Xue Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Li Wang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China.
| | - Fang Li
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China.
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China.
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6
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Kim H, Lee S, Yoon J, Song J, Park HG. CRISPR/Cas12a collateral cleavage activity for simple and rapid detection of protein/small molecule interaction. Biosens Bioelectron 2021; 194:113587. [PMID: 34455224 DOI: 10.1016/j.bios.2021.113587] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 12/26/2022]
Abstract
To realize the full potential of the CRISPR/Cas system and expand its applicability up to the detection of molecular interactions, we herein describe a novel method to identify protein/small molecule interactions by utilizing the CRISPR/Cas12a collateral cleavage activity. This technique employs a single-stranded activator DNA modified with a specific small molecule, which would switch on the CRISPR/Cas12a collateral cleavage activity upon binding to crRNA within the CRISPR/Cas12a system. When the target protein binds to the small molecule on the activator DNA, the bound protein sterically hinders the access of the activator DNA to crRNA, thereby promoting less collateral cleavage activity of CRISPR/Cas12a. As a consequence, fewer reporter probes nearby are cleaved to produce accordingly reduced fluorescence signals in response to target protein. Based on this unique design principle, the two model protein/small molecule interactions, streptavidin/biotin and anti-digoxigenin/digoxigenin, were successfully determined down to 0.03 nM and 0.09 nM, respectively, with a fast and simple detection workflow (11 min). The practical applicability of this method was also verified by reliably detecting target streptavidin spiked in heterogeneous human serum. This work would provide great insight to construct novel strategies to identify protein/small molecule interaction by making the most of the CRISPR/Cas12a system beyond its superior capabilities in genome editing and molecular diagnostics.
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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7
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Yan Y, Hu T, Xiang X, Li W, Ma C. Fluorometric Detection of Streptavidin with a Cationic Conjugated Polymer and Hairpin DNA Probe. ChemistrySelect 2021. [DOI: 10.1002/slct.202100800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ying Yan
- School of Life Sciences Central South University Changsha 410013 China
| | - Tingting Hu
- School of Life Sciences Central South University Changsha 410013 China
| | - Xinying Xiang
- School of Life Sciences Central South University Changsha 410013 China
| | - Wenkai Li
- School of Life Sciences Central South University Changsha 410013 China
| | - Changbei Ma
- School of Life Sciences Central South University Changsha 410013 China
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8
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Nieuwkerk DM, Korajkic A, Valdespino EL, Herrmann MP, Harwood VJ. Critical review of methods for isothermal amplification of nucleic acids for environmental analysis. J Microbiol Methods 2020; 179:106099. [PMID: 33159993 DOI: 10.1016/j.mimet.2020.106099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
The past 30 years have seen the emergence and proliferation of isothermal amplification methods (IAMs) for rapid, sensitive detection and quantification of nucleic acids in a variety of sample types. These methods share dependence on primers and probes with quantitative PCR, but they differ in the specific enzymes and instruments employed, and are frequently conducted in a binary, rather than quantitative format. IAMs typically rely on simpler instruments than PCR analyses due to the maintenance of a single temperature throughout the amplification reaction, which could facilitate deployment of IAMs in a variety of environmental and field settings. This review summarizes the mechanisms of the most common IAM methods and their use in studies of pathogens, harmful algae and fecal indicators in environmental waters, feces, wastewater, reclaimed water, and tissues of aquatic animals. Performance metrics of sensitivity, specificity and limit of detection are highlighted, and the potential for use in monitoring and regulatory contexts is discussed.
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Affiliation(s)
- Dana M Nieuwkerk
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asja Korajkic
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erika L Valdespino
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Michael P Herrmann
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Valerie J Harwood
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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9
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Zhang B, Jiang J, Yuan Y, Guan Y. Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification. Chem Res Chin Univ 2019. [DOI: 10.1007/s40242-019-9223-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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11
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Li H, Sørensen JV, Gothelf KV. Quantitative Detection of Digoxin in Plasma Using Small-Molecule Immunoassay in a Recyclable Gravity-Driven Microfluidic Chip. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802051. [PMID: 30937271 PMCID: PMC6425438 DOI: 10.1002/advs.201802051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/25/2018] [Indexed: 05/05/2023]
Abstract
Immunoassays are critical for clinical diagnostics and biomedical research. However, two major challenges remaining in conventional immunoassays are precise quantification and development of immunoassays for small-molecule detection. Here, a two signal-mode small-molecule immunoassay containing an internal reference that provides high stability and reproducibility compared to conventional small-molecule immunoassays is presented. A system is developed for quantitative monitoring of the digoxin concentration in plasma in the clinically relevant range (0.6-2.6 nm). Furthermore, the model system is integrated into a simple gravity-driven microfluidic chip (G-Chip) requiring only 10 µL plasma. The G-Chip allows fast detection without any complex operation and can be recycled for at least 50 times. The assay, and the G-Chip in particular, has the potential for further development of point-of-care (POC) diagnostics.
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Affiliation(s)
- Hailong Li
- Center for DNA NanotechnologyInterdisciplinary Nanoscience Center, iNANOAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryJilin UniversityChangchun130012China
| | - Jesper Vinther Sørensen
- Center for DNA NanotechnologyInterdisciplinary Nanoscience Center, iNANOAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
| | - Kurt Vesterager Gothelf
- Center for DNA NanotechnologyInterdisciplinary Nanoscience Center, iNANOAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade, 1408000Aarhus CDenmark
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12
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Lee CY, Kim HY, Kim S, Park KS, Park HG. A simple and sensitive detection of small molecule-protein interactions based on terminal protection-mediated exponential strand displacement amplification. Analyst 2019; 143:2023-2028. [PMID: 29634063 DOI: 10.1039/c8an00099a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein describe a simple and sensitive strategy to detect a small molecule-protein interaction based on terminal protection-mediated exponential strand displacement amplification (eSDA). In principle, the small molecule linked to a DNA probe protects the DNA probe against the exonuclease I-catalyzed degradation after its binding to the corresponding target protein. The protected DNA probe then serves as a template to promote eSDA. Consequently, a large number of duplexes are produced, which leads to a high fluorescence from a double-stranded DNA specific fluorescent dye, SYBR Green I. As a model system to prove this sensing strategy, the interaction between biotin and streptavidin (SA), which is known to be the strongest among the non-covalent biological interactions, was selected and its analytical performance was thoroughly investigated. As a result, SA was sensitively detected with the limit of detection of 16 pM. In addition, the practical applicability of this method was successfully demonstrated by reliably determining the SA in human serum.
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Affiliation(s)
- Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21 + program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
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13
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Li XH, Zhang XL, Wu J, Lin N, Sun WM, Chen M, Ou QS, Lin ZY. Hyperbranched rolling circle amplification (HRCA)-based fluorescence biosensor for ultrasensitive and specific detection of single-nucleotide polymorphism genotyping associated with the therapy of chronic hepatitis B virus infection. Talanta 2018; 191:277-282. [PMID: 30262063 DOI: 10.1016/j.talanta.2018.08.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/14/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Detection of specific genes related to drug action can provide scientific guidance for personalized medicine. Taking the detection of a single-nucleotide polymorphism (SNP) genotyping related to the chronic hepatitis B virus (HBV) therapy as an example, a novel biosensor with high sensitivity and selectivity was developed based on the hyperbranched rolling circle amplification (HRCA) in this work. The single-base mutant DNA (mutDNA) sequence can perfectly hybridize with the specially designed discrimination padlock probe and initiate the HRCA reaction. Subsequently, a great abundant of double-strand DNA sequences were released and a strong fluorescence signal can be detected after adding SYBR Green I. In particular, the enhanced fluorescence intensity exhibits a linear relationship with the logarithm of mutDNA concentration ranging from 0.1 nM to 40 nM with a low detection limit of 0.05 nM. However, when there was even a single base mismatch in the target DNA, the HRCA was suppressed and fluorescence response process could not occur, resulting in a high selectivity of this biosensor. Moreover, this detection strategy also performs well in human serums, demonstrating its potential application in detecting SNPs in real biological samples.
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Affiliation(s)
- Xiang-Hui Li
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou 350004, Fujian, People's Republic of China
| | - Xiao-Ling Zhang
- Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, People's Republic of China
| | - Juan Wu
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou 350004, Fujian, People's Republic of China
| | - Ni Lin
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou 350004, Fujian, People's Republic of China
| | - Wei-Ming Sun
- Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, People's Republic of China
| | - Min Chen
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou 350004, Fujian, People's Republic of China.
| | - Qi-Shui Ou
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou 350004, Fujian, People's Republic of China; Department of Laboratory Medicine, The 1st Affiliated Hospital of Fujian Medical University, 20 Chazhong Road, Fuzhou 350004, Fujian, People's Republic of China.
| | - Zhen-Yu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350108, People's Republic of China
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14
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Zhou X, Cui Z, Liu L, Sun Z, Lin M, Hu Q, Wang H, Xiao X. Small molecule-protein interactions in branch migration thermodynamics: modelling and application in the homogeneous detection of proteins and small molecules. Analyst 2018; 143:2755-2759. [PMID: 29850719 DOI: 10.1039/c8an00555a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have disclosed the unique inhibition effect of small molecule-protein interactions toward the DNA branch migration process and constructed a complete thermodynamic model for it. The disclosed effect was further coupled with the steric hindrance effect to establish a homogeneous assay for proteins and small molecules with ultra-high inhibition factors and sensitivity.
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Affiliation(s)
- Xing Zhou
- Centre of Reproductive Medicine/Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.
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15
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Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing. Pharmaceuticals (Basel) 2018; 11:E35. [PMID: 29690513 PMCID: PMC6027247 DOI: 10.3390/ph11020035] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.
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Affiliation(s)
- Lide Gu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Wanli Yan
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Le Liu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Shujun Wang
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Xu Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
- Verschuren Centre for Sustainability in Energy & the Environment, Cape Breton University, Sydney, NS B1P 6L2, Canada.
| | - Mingsheng Lyu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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16
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Wu W, Fan H, Lian X, Zhou J, Zhang T. Aligner-mediated cleavage-triggered exponential amplification for sensitive detection of nucleic acids. Talanta 2018; 185:141-145. [PMID: 29759180 DOI: 10.1016/j.talanta.2018.03.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Exponential amplification reaction (EXPAR), as a simple and high sensitive method, holds great promise in nucleic acids detection. One major challenge in EXPAR is the generation of trigger DNA with a definite 3'-end, which now relies on fingerprinting technology. However, the requirement of different endonucleases for varying target sequences and two head-to-head recognition sites in double stranded DNA, as well as the confinement of trigger DNA's 3'-end to be near/within the recognition site, usually subject EXPAR to compromised universality and/or repeated matching of reaction conditions. Herein, we report a simple and universal method for high sensitive detection of nucleic acids, termed aligner-mediated cleavage-triggered exponential amplification (AMCEA). The aligner-mediated cleavage (AMC) needs only one nicking endonuclease and can make a break at any site of choice in a programmable way. Thus, the 3'-end of target DNA can be easily redefined as required, a key step for initiating the amplification reaction. This capability endows the proposed AMCEA with excellent universality and simplicity. Moreover, it is sensitive and specific, with a detection limit at amol level, a broad dynamic range of 5~6 orders of magnitude and the ability to distinguish single nucleotide mutation. Experiments performed with human serum indicate that AMCEA is compatible with the complex biological sample, and thus has the potentials for practical applications.
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Affiliation(s)
- Wanghua Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Hongliang Fan
- Department of Environmental Medicine, Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Xiang Lian
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China.
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17
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Zhao J, Li C, Ma G, Hao W, Jia H. Colorimetric detection of protein via the terminal protection of small-molecule-linked DNA and unmodified gold nanoparticles. RSC Adv 2018; 8:38758-38764. [PMID: 35558333 PMCID: PMC9090659 DOI: 10.1039/c8ra07314g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 10/31/2018] [Indexed: 11/21/2022] Open
Abstract
A novel colorimetric strategy for protein detection was developed based on unmodified gold nanoparticles (AuNPs) and terminal protection from a target protein.
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Affiliation(s)
- Jianwei Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
| | - Cuiping Li
- College of Public Health
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Hebei University
- Baoding
- P. R. China
| | - Guimin Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
| | - Wenhui Hao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
| | - Hongxia Jia
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environment Science
- Hebei University
- Baoding
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18
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Kim H, Lee CY, Song J, Yoon J, Park KS, Park HG. Protein-induced fluorescence enhancement for a simple and universal detection of protein/small molecule interactions. RSC Adv 2018; 8:39913-39917. [PMID: 35558217 PMCID: PMC9091315 DOI: 10.1039/c8ra08515c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/19/2018] [Indexed: 12/04/2022] Open
Abstract
We herein describe a novel and efficient method for the detection of protein/small molecule (SM) interactions, which relies on the protein-induced fluorescence enhancement (PIFE). In this method, a duplex probe is designed to position Cy3 and SM at the optimal distance to maximize the effect of PIFE, which is utilized as the key component. In the presence of target proteins that bind to SM, the Cy3 is guided close to the target proteins, which significantly enhances the fluorescence signal through a process of PIFE. With this approach, we successfully analyzed a model target protein, streptavidin (STV) that interacts with biotin (BTN) in less than 10 min without any washing steps. In addition, the practical applicability of this method was demonstrated by reliably determining STV in human serum. Finally, the universal applicability of this method was demonstrated by monitoring the interaction between folate and folate receptors. We herein describe a novel and efficient method for the detection of protein/small molecule (SM) interactions, which relies on the protein-induced fluorescence enhancement (PIFE).![]()
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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19
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Sensitive immunosensing of the carcinoembryonic antigen utilizing aptamer-based in-situ formation of a redox-active heteropolyacid and rolling circle amplification. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2522-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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20
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He B. A sandwich-type electrochemical biosensor for alpha-fetoprotein based on Au nanoparticles decorating a hollow molybdenum disulfide microbox coupled with a hybridization chain reaction. NEW J CHEM 2017. [DOI: 10.1039/c7nj02431b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a sensitive sandwich-type biosensor for detecting alpha-fetoprotein (AFP) is developed by using a target-triggered hybridization chain reaction strategy.
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Affiliation(s)
- Baoshan He
- School of Food Science and Technology
- Henan University of Technology
- Zhengzhou 450001
- People's Republic of China
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