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Davydova AS, Vorobyeva MA. Aptasensors Based on Non-Enzymatic Peroxidase Mimics: Current Progress and Challenges. BIOSENSORS 2023; 14:1. [PMID: 38275302 PMCID: PMC10813519 DOI: 10.3390/bios14010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Immunoassays based on antibodies as recognizing elements and enzymes as signal-generating modules are extensively used now in clinical lab diagnostics, food, and environmental analyses. However, the application of natural enzymes and antibodies has some drawbacks, such as relatively high manufacturing costs, thermal instability, and lot-to-lot variations that lower the reproducibility of results. Oligonucleotide aptamers are able to specifically bind their targets with high affinity and selectivity, so they represent a prospective alternative to protein antibodies for analyte recognition. Their main advantages include thermal stability and long shelf life, cost-efficient chemical synthesis, and negligible batch-to-batch variations. At the same time, a wide variety of non-protein peroxidase mimics are now available that show strong potential to replace protein enzymes. Here, we review and analyze non-protein biosensors that represent a nexus of these two concepts: aptamer-based sensors (aptasensors) with optical detection (colorimetric, luminescent, or fluorescent) based on different peroxidase mimics, such as DNAzymes, nanoparticles, or metal-organic frameworks.
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Affiliation(s)
- Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Akad. Lavrentiev, 8, 630090 Novosibirsk, Russia;
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Su J, Sun C, Du J, Xing X, Wang F, Dong H. RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy. Adv Healthc Mater 2023; 12:e2300367. [PMID: 37084038 DOI: 10.1002/adhm.202300367] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Indexed: 04/22/2023]
Abstract
Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.
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Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Fang Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
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Zhang W, Jiang X, Wu Y, Jiang J, Liu X, Liu Y, Wang W, Lai J, Wang X. Zeolitic imidazolate framework-8 encapsulating gold nanoclusters and carbon dots for ratiometric fluorescent detection of adenosine triphosphate and cellular imaging. Talanta 2023; 255:124226. [PMID: 36580808 DOI: 10.1016/j.talanta.2022.124226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/17/2022] [Accepted: 12/25/2022] [Indexed: 12/27/2022]
Abstract
A novel nanoprobe was prepared by encapsulating carbon dots (CDs) and gold nanoclusters (AuNCs) into zeolitic imidazolate framework-8 (ZIF-8) for sensitive detecting adenosine triphosphate (ATP). Under excitation at 360 nm, the obtained CDs/AuNCs@ZIF-8 nanoprobe exhibits dual-emissions at 469 nm and 660 nm, respectively, corresponding to the fluorescence emission of CDs and the aggregation-induced emission enhancement (AIEE) of AuNCs. The framework of ZIF-8 in this probe can be degraded by ATP due to the coordination competition of ATP and 2-Methylimidazole towards zinc ion (Zn2+), resulting in the release of CDs and AuNCs. The following dispersion of CDs would improve efficiencies of the fluorescence excitation and the consequent emission of CDs. On the contrary, the AIEE of AuNCs would be decreased spontaneously after the AuNCs originally restricted in ZIF-8 were allowed to escape. The intensity ratio of fluorescence at 469 nm to that at 660 nm (I469/I660) was conveniently employed as the response signal for representing the amount of ATP. This nanoprobe exhibits excellent sensitivity and selectivity toward ATP, with a limit of detection (LOD) of 0.061 μM. Besides, low cytotoxicity of this nanoprobe facilitates its application as a fluorescent indicator in fluorescence imaging of living cells. Encapsulating two types of fluorescent nanomaterials by a degradable ZIF-8 structure makes the ratiometric fluorescence response of the nanocomposite probe towards the target analyte that destroys the ZIF-8 structure possible, and simplifies the application of the probe.
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Affiliation(s)
- Wei Zhang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Xue Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yanhua Wu
- Division of Clinical Research, The First Hospital of Jilin University, Changchun, 130021, China
| | - Jing Jiang
- Division of Clinical Research, The First Hospital of Jilin University, Changchun, 130021, China
| | - Xin Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yibing Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Wei Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Jinyu Lai
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Xinghua Wang
- College of Chemistry, Jilin University, Changchun, 130012, China.
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Wang P, Zhang R, Wu Y, Chang Y, Liu M. An Electrochemical Aptasensor Integrating Zeolitic Imidazolate Framework for Highly Selective Detection of Bioaerosols. BIOSENSORS 2022; 12:bios12090725. [PMID: 36140110 PMCID: PMC9496278 DOI: 10.3390/bios12090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 12/01/2022]
Abstract
Bioaerosols are the biological materials in the air, which may cause a continuous threat to human health. However, there are many challenges in monitoring bioaerosols such as lack of sensitivity and selectivity. Herein, we synthesized a series of nanohybrids containing zeolitic imidazolate frameworks (ZIFs) and covalent organic frameworks (COFs) to construct an electrochemical aptasensor for detecting adenosine triphosphate (ATP), a biomarker for bioaerosols. The synthesized nanohybrids can not only improve the selectivity of aptasensor because of the original crystal and chemical features of ZIF-67, but also boost its sensitivity due to the excellent conductivity of COFs. After optimizing the nanohybrids, the novel developed sensing platform achieved highly selective detection of ATP with an excellent detection limit of 0.11 nM in a wide linear range from 0.1 nM to 100 nM. Furthermore, this assay was applied to detect bioaerosols in real air samples, and the result showed a positive correlation with that of the culturing-based method, suggesting its potential applicability.
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Wei J, Li Y, Si Q, Xiao Q, Chen Q, Jiao T, Chen Q, Chen X. Hemin/G-quadruplex based electrochemical sensor for highly sensitive detection of ATP in fish. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Zheng G, Zhao L, Yuan D, Li J, Yang G, Song D, Miao H, Shu L, Mo X, Xu X, Li L, Song X, Zhao Y. A genetically encoded fluorescent biosensor for monitoring ATP in living cells with heterobifunctional aptamers. Biosens Bioelectron 2022; 198:113827. [PMID: 34861524 DOI: 10.1016/j.bios.2021.113827] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 02/08/2023]
Abstract
Visualizing the dynamics of ATP in living cells is key to understanding cellular energy metabolism and related diseases. However, the live-cell applications of current methods are still limited due to challenges in biological compatibility and sensitivity to pH. Herein, a novel label-free fluorescent " turn-on " biosensor for monitoring ATP in living bacterias and mammalian cells was developed. This biosensor (Broc-ATP) employed heterobifunctional aptamers to detect ATP with high sensitivity in vitro. In our system, a very useful tandem method was established by combining four Broc-ATPs with 3 × F30 three-way junction scaffold to construct an intracellular biosensor that achieves sufficient fluorescence to respond to intracellular ATP. This intracellular biosensor can be used for sensitive and specific dynamic imaging of ATP in mammalian cells. Hence, this genetically encoded biosensor provides a robust and efficient tool for the detection of intracellular ATP dynamics and 3 × F30 tandem method expands the application of heterobifunctional aptamers in mammalian cells.
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Affiliation(s)
- Guoliang Zheng
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Liang Zhao
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Deyu Yuan
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Jia Li
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Gang Yang
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Danxia Song
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Hui Miao
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Linjuan Shu
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Ling Li
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China.
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China.
| | - Yongyun Zhao
- Center for Functional Genomics and Bioinformatics, College of Life Science, Sichuan University, Chengdu, Sichuan, 610064, PR China.
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Sianglam P, Ngamdee K, Ngeontae W. Simultaneous preconcentration and fluorescence detection of ATP by a hybrid nanocomposite of magnetic nanoparticles incorporated in mixed metal hydroxide. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:188-198. [PMID: 34935797 DOI: 10.1039/d1ay01593a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new approach for increasing the sensitivity of adenosine triphosphate (ATP) detection was demonstrated. The assay was based on the synergetic function of a hybrid nanocomposite (MNPs@MMH) composed of magnetic nanoparticles (MNPs) incorporated in a mixed metal hydroxide (MMH). MNPs@MMH can be utilized as an efficient green extractant and peroxidase catalyst. The trace level of ATP in the sample solution was first extracted by the MNPs@MMH hybrid nanocomposite through the ion exchange properties of MMH and adsorbed on the surface of the MNPs@MMH. The concentration of ATP was related to the fluorescence intensity of 2,3-diaminophenazine (DAP) generated from peroxidase-like activity of the MNPs in the presence of H2O2 and o-phenylenediamine (OPD). In the presence of ATP, the active surface of the MNPs was diminished, and the amount of DAP generated was reduced. Thus, the concentration of ATP was related to the degree of fluorescence decrease compared to the fluorescence intensity of the system without ATP. Based on the proposed strategy, a highly sensitive assay for ATP was achieved. This assay exhibited good selectivity for detection of ATP over derivatives and other common anions. The proposed assay allowed the detection of ATP in a concentration range of 2.5-20 μM with a detection limit of 0.41 μM.
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Affiliation(s)
- Pradthana Sianglam
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Kessarin Ngamdee
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wittaya Ngeontae
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
- Research Center for Environmental and Hazardous Substance Management (EHSM), Khon Kaen University, Khon Kaen 40002, Thailand
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Gu Y, Liu L, Guo J, Xiao S, Fang F, Yu X, Gopinath SCB, Wu J, Liu X. Biomolecular assembly on interdigitated electrode nanosensor for selective detection of insulin-like growth factor-1. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:30-37. [PMID: 33467925 DOI: 10.1080/21691401.2020.1865992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This research is focussed to quantify IGF1 by electroanalytical analysis on InterDigitated electrode surface and characterized by the microscopic observations. For the detection, antibody and aptamer were used to analyze the level of IGF1. The sandwich pattern (aptamer-IGF1-antibody) was designed on the chemically modified IDE surface and reached the limit of detection to 10 fM with 100 folds enhancement in the sensitivity. Different control experiments (absence of IGF1, binding with IGF2 and with non-complementary aptamer) were failed to show the current changes, discriminated the specific detection. A good detection strategy is to complement the currently following imaging systems for AAA.
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Affiliation(s)
- Yan Gu
- Department of Vascular Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Lijie Liu
- Department of Pharmacy, The Affiliated Hospital of Qingdao University, Qingdao City, China
| | - Jian Guo
- Department of Imaging, The Affiliated Hospital of Qingdao University, Qingdao City, China
| | - Shun Xiao
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao City, China
| | - Fang Fang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao City, China
| | - Xiaoyun Yu
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao City, China
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia.,Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - Jianlie Wu
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao City, China
| | - Xunqiang Liu
- Department of Vascular surgery, Yan'an Hospital Affiliated to Kunming Medical University, Kunming City, Yunnan Province, China
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Li Y, Liu J. Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds. Analyst 2021; 145:6753-6768. [PMID: 32909556 DOI: 10.1039/d0an00886a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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Qiu Z, Shen Q, Jiang C, Yao L, Sun X, Li J, Duan C, Li R, Li X, Gopinath SCB, Anbu P, Lakshmipriya T, Li X. Alzheimer's Disease Determination by a Dual Probe on Gold Nanourchins and Nanohorn Hybrids. Int J Nanomedicine 2021; 16:2311-2322. [PMID: 33776435 PMCID: PMC7989959 DOI: 10.2147/ijn.s302396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/01/2021] [Indexed: 12/16/2022] Open
Abstract
Background Alzheimer’s disease (AD) is a neurodegenerative chronic disorder that causes dementia and problems in thinking, cognitive impairment and behavioral changes. Amyloid-beta (Aβ) is a peptide involved in AD progression, and a high level of Aβ is highly correlated with severe AD. Identifying and quantifying Aβ levels helps in the early treatment of AD and reduces the factors associated with AD. Materials and Methods This research introduced a dual probe detection system involving aptamers and antibodies to identify Aβ. Aptamers and antibodies were attached to the gold (Au) urchin and hybrid on the carbon nanohorn-modified surface. The nanohorn was immobilized on the sensor surface by using an amine linker, and then a Au urchin dual probe was immobilized. Results This dual probe-modified surface enhanced the current flow during Aβ detection compared with the surface with antibody as the probe. This dual probe interacted with higher numbers of Aβ peptides and reached the detection limit at 10 fM with R2=0.992. Furthermore, control experiments with nonimmune antibodies, complementary aptamer sequences and control proteins did not display the current responses, indicating the specific detection of Aβ. Conclusion Aβ-spiked artificial cerebrospinal fluid showed a similar response to current changes, confirming the selective identification of Aβ.
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Affiliation(s)
- Zhengguo Qiu
- Department of Anesthesiology, Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, 712000, People's Republic of China
| | - Qianhe Shen
- Department of Anesthesiology, Xi'an GemFlower Changqing Hospital, Xi'an, Shaanxi, 710200, People's Republic of China
| | - Chao Jiang
- The Third Department of Neurology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710038, People's Republic of China
| | - Li Yao
- Department of Neurology, The Hospital of Xidian Group, Xi'an, Shaanxi, 710077, People's Republic of China
| | - Xiaopeng Sun
- Department of Otolaryngology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710038, People's Republic of China
| | - Jing Li
- Department of Anesthesiology, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710038, People's Republic of China
| | - Chongzhen Duan
- Department of Anesthesiology, Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, 712000, People's Republic of China
| | - Rui Li
- Department of Anesthesiology, Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, 712000, People's Republic of China
| | - Xiuli Li
- Department of Anesthesiology, Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, 712000, People's Republic of China
| | - Subash C B Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, 01000, Malaysia
| | - Periasamy Anbu
- Department of Biological Engineering, College of Engineering, Inha University, Incheon, 402-751, Republic of Korea
| | - Thangavel Lakshmipriya
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, 01000, Malaysia
| | - Xu Li
- Department of Surgery and Anesthesiology, Xi'an Hospital of Traditional Chinese Medicine, Xi'an, Shaanxi, People's Republic of China
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Ahmadi Y, Soldo R, Rathammer K, Eibler L, Barišić I. Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes. Anal Chem 2021; 93:5161-5169. [PMID: 33724777 DOI: 10.1021/acs.analchem.0c05052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Regina Soldo
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Krista Rathammer
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Laura Eibler
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
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A pH-responsive bioassay for sensitive colorimetric detection of adenosine triphosphate based on switchable DNA aptamer and metal ion-urease interactions. Anal Bioanal Chem 2021; 413:1533-1540. [PMID: 33462658 DOI: 10.1007/s00216-020-03136-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
A facile and economic colorimetric strategy was designed for ATP detection by rationally using urease, a pH-responsive molecule, and a metal-mediated switchable DNA probe. By utilizing metal ions as a modulator of urease activity, the concentration of ATP is translated into pH change, which can be readily visualized by naked eye. An unmodified single-stranded DNA probe was designed, which consists of a target binding sequence and two flanked cytosine (C)-rich sequences. This C-rich single-stranded DNA can form a hairpin structure triggered by Ag+ ions via C-Ag+-C base mismatch. Upon introduction of ATP, Ag+-coordinated hairpin DNA structure will be broken and release the included Ag+, thus inhibiting the activity of urease. Conversely, urease can hydrolyze urea and raise pH value of the solution, resulting in the color change of the sensing solution. The proposed assay allows determination of ATP as low as 1.6 nM and shows a satisfactory result in human serum. Because of simple operation and low cost of this method, we believe it has a potential in point-of-care (POC) testing in resource-limited areas. Schematic illustration of pH-responsive colorimetric sensor for ATP detection based on switchable DNA aptamer and metal ion-urease interactions.
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13
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Wang S, Su S, Yu C, Gopinath SCB, Yang Z. Immunodetection of urinary C-terminal telopeptide fragment of type II collagen: An osteoarthritis biomarker analysis. Biotechnol Appl Biochem 2020; 68:726-731. [PMID: 32621620 DOI: 10.1002/bab.1981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The urinary C-terminal telopeptide fragment of type II collagen (uCTX-II) has been reported as the efficient blood-based biomarker for osteoarthritis, which affects knees, hands, spine, and hips. This study reports a sensing strategy with antibody-conjugated gold nanoparticles (GNP) on an interdigitated electrode (IDE) to determine uCTX-II. The GNP-antibody complex was chemically immobilized on the IDE surface through the amine linker. uCTX-II was determined by monitoring the alteration in current upon interacting the GNP-complexed antibody. This strategy was improved the detection by attracting higher uCTX-II molecules, and the detection limit falls in the range of 10-100 pM with an acceptable regression value [y = 0.6254x - 0.4073, R² = 0.9787]. The sensitivity of the detection was recognized at 10 pM. Additionally, upon increasing the uCTX-II concentration, the current changes were increased in a linear fashion. Control detection with nonimmune antibody and control protein do not increase the current level, confirming the specific detection of uCTX-II. This method of detection helps in diagnosing osteoarthritis and its follow-up treatment.
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Affiliation(s)
- Shuwei Wang
- Department of Orthopedics, Shouguang Hospital of TCM, Weifang, Shandong Province, 262700, China
| | - Shanlin Su
- Department of Orthopedics, Shouguang Hospital of TCM, Weifang, Shandong Province, 262700, China
| | - Chunyun Yu
- Department of Orthopedics, Shouguang Hospital of TCM, Weifang, Shandong Province, 262700, China
| | - Subash C B Gopinath
- School of Bioprocess Engineering, Universiti Malaysia Perlis, Arau, Perlis, 02600, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar, Perlis, 01000, Malaysia
| | - Zhiquan Yang
- Department of Orthopedics, Shouguang Hospital of TCM, Weifang, Shandong Province, 262700, China
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14
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Gopinath SCB, Xuan S. DNA-RNA complementation on silicon wafer for thyroid cancer determination. Biotechnol Appl Biochem 2020; 68:554-559. [PMID: 32460382 DOI: 10.1002/bab.1961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/24/2020] [Indexed: 11/07/2022]
Abstract
One of the current issues with thyroid tumor is early diagnosis as it makes the higher possibility of curing. This research was focused to detect and quantify the level of specific target sequence complementation of miR-222 with capture DNA sequence on interdigitated electrode (IDE) sensor. The aluminum electrode with the gap and finger sizes of 10 µm was fabricated on silicon wafer, further the surface was amine-functionalized for accommodating carboxylated-DNA probe. With DNA-target RNA complementation, the detection limit was attained to be 1 fM as estimated by a linear regression analysis [y = 1.5325x - 2.1171 R² = 0.9065] and the sensitivity was at the similar level. Current responses were higher by increasing the target RNA sequence concentrations. Control experiments with mismatched/noncomplementary sequences were failed to complement the capture DNA sequence immobilized on IDE, indicating the specific target validation. This research helps diagnosing and identifying the progression with thyroid tumor and miRNA being a potential "marker" in atypia diagnosis.
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Affiliation(s)
- Subash C B Gopinath
- School of Bioprocess Engineering, Arau, Perlis, Malaysia.,Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar, Perlis, Malaysia
| | - Shijin Xuan
- Department of Mammary and Thyroid Surgery, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China
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15
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Detection mechanism and classification of design principles of peroxidase mimic based colorimetric sensors: A brief overview. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.01.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Deng S, Zhou B, Li W, Li H, Zhang F, Ming J. Label-free fluorescence DNA walker for protein analysis based on terminal protection and dual enzyme assisted cleavage induced G-quadruplex/berberine conformation. Analyst 2020; 145:46-51. [DOI: 10.1039/c9an01853k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Development of a simple, fast, cost-efficient and sensitive approach for accurate protein analysis is of high significance due to its potential application in disease diagnosis and biomedicine research.
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Affiliation(s)
- Shue Deng
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Baolong Zhou
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Wenjing Li
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Hui Li
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Fenglian Zhang
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Jingjing Ming
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
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17
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Xu L, Jiang B, Zhou W, Yuan R, Xiang Y. Coupling strand extension/excision amplification with target recycling enables highly sensitive and aptamer-based label-free sensing of ATP in human serum. Analyst 2019; 145:434-439. [PMID: 31793560 DOI: 10.1039/c9an02000d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Detection of aberrant ATP concentrations with high sensitivity and selectivity is of critical importance for monitoring many biological processes and disease stages. By coupling extension/excision amplification with target recycling, we have established an aptamer-based method for label-free fluorescence ATP detection in human serum with high sensitivity. The ATP target molecules associate with the aptamer-containing double hairpin probes and cause conformational changes of the probes to initiate the cyclic strand extension/excision processes in the presence of polymerase, endonuclease and assistance sequences for the recycling of ATP and the production of a large number of G-quadruplex sequences. The organic dye thioflavin T subsequently binds these G-quadruplex sequences to yield substantially enhanced fluorescence emission for achieving highly sensitive detection of ATP down to 2.2 nM in the range of 5 to 200 nM without using any labels. The developed aptamer sensing method also exhibits high selectivity and allows the monitoring of ATP at low concentrations in diluted real samples, which offers promising opportunities to establish effective signal magnification means for the detection of various biomolecules at trace levels.
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Affiliation(s)
- Lin Xu
- 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.
| | - Wenjiao Zhou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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18
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Sameiyan E, Bagheri E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. DNA origami-based aptasensors. Biosens Bioelectron 2019; 143:111662. [PMID: 31491726 DOI: 10.1016/j.bios.2019.111662] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/27/2022]
Abstract
Traditional analytical techniques face many limitations such as time-consuming process, complicated sample preparation, high consumption of reagents and need for expensive equipment. So, it is important that simple, rapid and sensitive detection methods are introduced. Nucleic acids-based assays, particularly aptamers, have a great impact on modern life sciences for biological analysis and target detection. Aptamer-based biosensors with unique recognition properties including high specificity and affinity, rapid response and simple fabrication have attracted much attention. It is believed that two- and three-dimensional structures, sometimes referred to as DNA origami, using DNA aptamers can show more selective binding affinity and better stability over other nucleic acids forms. In this review, we will focus on recent advances in the development and uses of electrochemical and optical DNA origami-based aptasensors to supply readers with a comprehensive understanding of their improvements. Also, the challenges and awards of these approaches are discussed.
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Affiliation(s)
- Elham Sameiyan
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Bagheri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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19
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Xiong Y, Cheng Y, Wang L, Li Y. An ''off-on'' phosphorescent aptasensor switch for the detection of ATP. Talanta 2018; 190:226-234. [PMID: 30172503 DOI: 10.1016/j.talanta.2018.07.060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 01/12/2023]
Abstract
An "off-on" phosphorescent aptasensor based on the 3-mercaptopropionic acid (MPA) capped Mn-doped ZnS quantum dots (MPA-Mn:ZnS QDs)/aptamer hybrid system was developed to detect adenosine triphosphate (ATP) in biological fluids. The phosphorescence of MPA-Mn:ZnS QDs was obviously quenched when ATP aptamer was added due to the aggregation induced effect. ATP aptamer, adsorbed on the surface of the phosphorescent MPA-Mn:ZnS QDs, has a high affinity for ATP. And then, with the addition of ATP, phosphorescence was gradually recovered because of the stronger special binding interaction between ATP and ATP aptamer than that between QDs and ATP aptamer. In this case, a high sensitivity and selectivity of phosphorescent aptasensor for the detection of ATP has constructed with a low detection limit of 0.9 nM and a wide linear range from 2 nM to 9 µM. What's more, the phosphorescent aptasensor does not require complex pretreatments and can effectively eliminate the interference from auto fluorescence and scattering light.
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Affiliation(s)
- Yan Xiong
- Key Laboratory of Inorganic-Organic Hybrid Functional Materials Chemistry (Tianjin Normal University), Tianjin Key Laboratory of Structure and Performance for Functional Molecule, College of Chemistry, Tianjin Normal University, Tianjin 300387, PR China
| | - Yue Cheng
- Key Laboratory of Inorganic-Organic Hybrid Functional Materials Chemistry (Tianjin Normal University), Tianjin Key Laboratory of Structure and Performance for Functional Molecule, College of Chemistry, Tianjin Normal University, Tianjin 300387, PR China
| | - Lu Wang
- Key Laboratory of Inorganic-Organic Hybrid Functional Materials Chemistry (Tianjin Normal University), Tianjin Key Laboratory of Structure and Performance for Functional Molecule, College of Chemistry, Tianjin Normal University, Tianjin 300387, PR China
| | - Yan Li
- Key Laboratory of Inorganic-Organic Hybrid Functional Materials Chemistry (Tianjin Normal University), Tianjin Key Laboratory of Structure and Performance for Functional Molecule, College of Chemistry, Tianjin Normal University, Tianjin 300387, PR China.
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20
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Liang Y, Su J, Huang Y, Li X, Tao Y, Lu C, Zhu J, Bai Z, Meng J, Lu X, Zhao Y. An ATP Aptasensor Based on the Peroxidase-like Activity of Hemin/Graphene Oxide Nanosheets. ANAL SCI 2018; 32:565-9. [PMID: 27169657 DOI: 10.2116/analsci.32.565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present work, a sensitive electrochemical aptasensor was designed for the detection of adenosine triphosphate (ATP) with hemin/graphene oxide nanosheets (HGNs). Firstly, the ATP aptamer was self-assembled on gold electrode surface, and then HGNs were captured to the modified electrode by π-π stacking. The captured HGNs could catalyze the disproportionation reaction of H2O2, and produced a detectable electrochemical signal by chronoamperometry. ATP was competitively bound to aptamer which led to the release of HGNs from the electrode surface after adding ATP. The decrease of the electrochemical signal, which was calculated by the difference of amperometric responses before and after incubation of ATP, provided a quantitative signal for ATP detection. A linear correlation was achieved between the difference of the amperometric responses and the logarithmic concentration of ATP ranging from 0.5 to 100 nM with a detection limit of 0.08 nM. Besides, the aptasensor also exhibited good selectivity toward ATP against other analogs.
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Affiliation(s)
- Ying Liang
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University
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21
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Gopinath SCB, Perumal V, Balakrishnan S, Md Arshad MK, Lakshmipriya T, Haarindraprasad R, Hashim U. Aptamer-based determination of ATP by using a functionalized impedimetric nanosensor and mediation by a triangular junction transducer. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2485-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Jafari M, Rezaei M, Kalantari H, Tabarzad M, Daraei B. DNAzyme-aptamer or aptamer-DNAzyme paradigm: Biochemical approach for aflatoxin analysis. Biotechnol Appl Biochem 2017; 65:274-280. [PMID: 28326608 DOI: 10.1002/bab.1563] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022]
Abstract
DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.
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Affiliation(s)
- Marzieh Jafari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohsen Rezaei
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Heibatullah Kalantari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Daraei
- Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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23
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Fluorometric aptamer based determination of adenosine triphosphate based on deoxyribonuclease I-aided target recycling and signal amplification using graphene oxide as a quencher. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2194-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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24
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A fluorescent aptasensing strategy for adenosine triphosphate detection using tris(bipyridine)ruthenium(II) complex containing six cyclodextrin units. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.11.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Hu T, Na W, Yan X, Su X. Sensitive fluorescence detection of ATP based on host-guest recognition between near-infrared β-Cyclodextrin-CuInS 2 QDs and aptamer. Talanta 2016; 165:194-200. [PMID: 28153242 DOI: 10.1016/j.talanta.2016.09.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/17/2016] [Accepted: 09/27/2016] [Indexed: 10/20/2022]
Abstract
We have developed a near-infrared (NIR) fluorescent aptamer-based sensor for sensitive detection of adenosine-5'-triphosphate (ATP) by using a ATP-binding aptamer and β-Cyclodextrin-CuInS2 quantum dots (β-CD-CuInS2 QDs). The fluorescence of β-CD-CuInS2 QDs has a slight enhancement with the addition of ATP-binding aptamer due to the host-guest recognition between aptamer and β-CD. When ATP is added, it will bind to aptamer to form G-quadruplexes. Aptamer-ATP complexes can enter into the hydrophobic cavities of β-CD and result in great enhancement of the fluorescence intensity. Under the optimum conditions, the fluorescence intensity of β-CD-CuInS2 QDs is proportional to the concentration of ATP, which shows a good linear response toward ATP concentration range of 6-1200μmolL-1, the detection limit for ATP is 3μmolL-1. The present assay shows a good selectivity for ATP over other biologically important proteins, and it is applied to the determination of ATP in human serum sample with satisfactory results.
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Affiliation(s)
- Tianyu Hu
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Weidan Na
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xu Yan
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xingguang Su
- Department of Analytical Chemistry, College of Chemistry, Jilin University, Changchun 130012, China.
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26
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Integrating Deoxyribozymes into Colorimetric Sensing Platforms. SENSORS 2016; 16:s16122061. [PMID: 27918487 PMCID: PMC5191042 DOI: 10.3390/s16122061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.
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27
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Zhu C, Zhao Y, Yan M, Huang Y, Yan J, Bai W, Chen A. A sandwich dipstick assay for ATP detection based on split aptamer fragments. Anal Bioanal Chem 2016; 408:4151-8. [PMID: 27052777 DOI: 10.1007/s00216-016-9506-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/04/2016] [Accepted: 03/21/2016] [Indexed: 12/01/2022]
Abstract
Aptamer-based strip assay is an easy, highly efficient and low-cost detection method, which has been developed and easily applied to onsite detection. A new sensitive sandwich dipstick assay for adenosine triphosphate (ATP) detection was successfully developed based on specific recognition between split aptamer fragments and the target. In this method, the thiolated aptamer was first conjugated to the surface of gold nanoparticles (AuNPs), while the biotin-aptamer was immobilized on the surface of a nitrocellulose filter in the test line. In the presence of ATP, the thiol-aptamer/ATP/biotin-aptamer complexes were generated, which led to an obvious increase in optical signals at the test line. Under the optimal determination conditions, an excellent linear logarithmic response to the ATP concentration was obtained within the range of 0.5 μM to 5 mM. The limit of detection (LOD) of 0.5 μM was reached at a signal-to-noise ratio of 3. The dipstick assay showed a good average recovery of 96-108 % with the RSD of less than 20 % in urine samples. The proposed method exhibited high specificity against other nucleotides such as the uridine triphosphate (UTP), cytidine triphosphate (CTP), and guanosine triphosphate (GTP). The results indicated that the dipstick strip may be considered as an inexpensive screening tool for onsite ATP determination. Graphical Abstract A simple split aptamer fragments based sandwich-type dipstick assay was developed for ATP detection.
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Affiliation(s)
- Chao Zhu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China
| | - Yan Zhao
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China
| | - Mengmeng Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China
| | - Yafei Huang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China.,College of Food Science and Technology, Hainan University, Haikou, Hainan, 570228, China
| | - Jiao Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China.,College of Food Science and Technology, Hainan University, Haikou, Hainan, 570228, China
| | - Wenhui Bai
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing, 100081, China.
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28
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Li LJ, Tian X, Kong XJ, Chu X. A G-quadruplex-based Label-free Fluorometric Aptasensor for Adenosine Triphosphate Detection. ANAL SCI 2016; 31:469-73. [PMID: 26063007 DOI: 10.2116/analsci.31.469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A G-quadruplex-based, label-free fluorescence assay was demonstrated for the detection of adenosine triphosphate (ATP). A double-stranded DNA (dsDNA), hybridized by ATP-aptamer and its complementary sequence, was employed as a substrate for ATP binding. SYBR Green I (SG I) was a fluorescent probe and exonuclease III (Exo III) was a nuclease to digest the dsDNA. Consequently, in the absence of ATP, the dsDNA was inset with SG I and was digested by Exo III, resulting in a low background signal. In the presence of ATP, the aptamer in dsDNA folded into a G-quadruplex structure that resisted the digestion of Exo III. SG I was inserted into the structure, showing high fluorescence. Owing to a decrease of the background noise, a high signal-to-noise ratio could be obtained. This sensor can detect ATP with a concentration ranging from 50 μM to 5 mM, and possesses a capacity for the sensitive determination of other targets.
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Affiliation(s)
- Li Juan Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
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29
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30
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Park JW, Park Y, Kim BH. Quencher-free molecular aptamer beacons (QF-MABs) for detection of ATP. Bioorg Med Chem Lett 2015; 25:4597-600. [PMID: 26320623 DOI: 10.1016/j.bmcl.2015.08.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/11/2022]
Abstract
We have constructed a simple and efficient system-based on quencher-free molecular aptamer beacons (QF-MABs)-for probing ATP. In the absence of ATP, the fluorescence of a pyrene fluorophore on the loop position (15 nucleotides from the 5' end) of the optimal QF-MAB was quenched by the neighboring nucleobases; in its presence, fluorescence was recovered, due to a conformational change in the secondary structure of the QF-MAB.
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Affiliation(s)
- Jung Woo Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
| | - Yoojin Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Byeang Hyean Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
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31
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Wang P, Zhang T, Yang T, Jin N, Zhao Y, Fan A. A cascade amplification strategy based on rolling circle amplification and hydroxylamine amplified gold nanoparticles enables chemiluminescence detection of adenosine triphosphate. Analyst 2015; 139:3796-803. [PMID: 24899364 DOI: 10.1039/c4an00458b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A highly sensitive and selective chemiluminescent (CL) biosensor for adenosine triphosphate (ATP) was developed by taking advantage of the ATP-dependent enzymatic reaction (ATP-DER), the powerful signal amplification capability of rolling circle amplification (RCA), and hydroxylamine-amplified gold nanoparticles (Au NPs). The strategy relies on the ability of ATP, a cofactor of T4 DNA ligase, to trigger the ligation-RCA reaction. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction between the two ends of the padlock probe, producing a closed circular DNA template that initiates the RCA reaction with phi29 DNA polymerase and dNTP. Therein, many complementary copies of the circular template can be generated. The ATP-DER is eventually converted into a detectable CL signal after a series of processes, including gold probe hybridization, hydroxylamine amplification, and oxidative gold metal dissolution coupled with a simple and sensitive luminol CL reaction. The CL signal is directly proportional to the ATP level. The results showed that the detection limit of the assay is 100 pM of ATP, which compares favorably with those of other ATP detection techniques. In addition, by taking advantage of ATP-DER, the proposed CL sensing system exhibits extraordinary specificity towards ATP and could distinguish the target molecule ATP from its analogues. The proposed method provides a new and versatile platform for the design of novel DNA ligation reaction-based CL sensing systems for other cofactors. This novel ATP-DER based CL sensing system may find wide applications in clinical diagnosis as well as in environmental and biomedical fields.
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Affiliation(s)
- Ping Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China.
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32
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Zhu L, Liu Y, Yang P, Liu B. Label-free Aptasensor based on Electrodeposition of Gold Nanoparticles on Graphene and Its Application in the Quantification of Adenosine Triphosphate. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.04.100] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Stefan L, Lavergne T, Spinelli N, Defrancq E, Monchaud D. Surface-immobilized DNAzyme-type biocatalysis. NANOSCALE 2014; 6:2693-2701. [PMID: 24452273 DOI: 10.1039/c3nr05954e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The structure of the double helix of deoxyribonucleic acid (DNA, also called duplex-DNA) was elucidated sixty years ago by Watson, Crick, Wilkins and Franklin. Since then, DNA has continued to hold a fascination for researchers in diverse fields including medicine and nanobiotechnology. Nature has indeed excelled in diversifying the use of DNA: beyond its canonical role of repository of genetic information, DNA could also act as a nanofactory able to perform some complex catalytic tasks in an enzyme-mimicking manner. The catalytic capability of DNA was termed DNAzyme; in this context, a peculiar DNA structure, a quadruple helix also named quadruplex-DNA, has recently garnered considerable interest since its autonomous catalytic proficiency relies on its higher-order folding that makes it suitable to interact efficiently with hemin, a natural cofactor of many enzymes. Quadruplexes have thus been widely studied for their hemoprotein-like properties, chiefly peroxidase-like activity, i.e., their ability to perform hemin-mediated catalytic oxidation reactions. Recent literature is replete with applications of quadruplex-based peroxidase-mimicking DNAzyme systems. Herein, we take a further leap along the road to biochemical applications, assessing the actual efficiency of catalytic quadruplexes for the detection of picomolar levels of surface-bound analytes in an enzyme-linked immunosorbent (ELISA)-type assay. To this end, we exploit an innovative strategy based on the functionalization of DNA by a multitasking platform named RAFT (for regioselectivity addressable functionalized template), whose versatility enables the grafting of DNA whatever its nature (duplex-DNA, quadruplex-DNA, etc.). We demonstrate that the resulting biotinylated RAFT/quadruplex systems indeed acquire catalytic properties that allow for efficient luminescent detection of picomoles of surface-bound streptavidin. We also highlight some of the pitfalls that have to be faced during optimization, notably demonstrating that highly optimized experimental conditions can make DNA pre-catalysts catalytically competent whatever their secondary structures.
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Affiliation(s)
- Loic Stefan
- Institut de Chimie Moléculaire, Université de Bourgogne (ICMUB), CNRS UMR6302, Dijon, France.
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WANG K, TAO ZH, XU L, LIU YQ. Research and Development of Functionalized Aptamer based Biosensor. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(13)60712-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Yan X, Chen JL, Su MX, Yan F, Li B, Di B. Phosphate-containing metabolites switch on phosphorescence of ferric ion engineered carbon dots in aqueous solution. RSC Adv 2014. [DOI: 10.1039/c4ra02592j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Room temperature phosphorescence of carbon dots readily engineered by ferric ions in aqueous solution was developed for a novel “off-to-on” approach for cost-effective estimation of ATP level in human blood plasma.
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Affiliation(s)
- Xiao Yan
- Department of Pharmaceutical Analysis
- China Pharmaceutical University
- Nanjing 210009, China
| | - Jin-Long Chen
- Department of Pharmaceutical Analysis
- China Pharmaceutical University
- Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
- China Pharmaceutical University
| | - Meng-Xiang Su
- Department of Pharmaceutical Analysis
- China Pharmaceutical University
- Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
- China Pharmaceutical University
| | - Fang Yan
- Department of Pharmaceutical Analysis
- China Pharmaceutical University
- Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
- China Pharmaceutical University
| | - Bo Li
- Department of Pharmaceutical Analysis
- China Pharmaceutical University
- Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
- China Pharmaceutical University
| | - Bin Di
- Department of Pharmaceutical Analysis
- China Pharmaceutical University
- Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
- China Pharmaceutical University
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Bing T, Mei H, Zhang N, Qi C, Liu X, Shangguan D. Exact tailoring of an ATP controlled streptavidin binding aptamer. RSC Adv 2014. [DOI: 10.1039/c4ra00714j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Kruss S, Hilmer AJ, Zhang J, Reuel NF, Mu B, Strano MS. Carbon nanotubes as optical biomedical sensors. Adv Drug Deliv Rev 2013; 65:1933-50. [PMID: 23906934 DOI: 10.1016/j.addr.2013.07.015] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 07/16/2013] [Accepted: 07/18/2013] [Indexed: 01/11/2023]
Abstract
Biosensors are important tools in biomedical research. Moreover, they are becoming an essential part of modern healthcare. In the future, biosensor development will become even more crucial due to the demand for personalized-medicine, point-of care devices and cheaper diagnostic tools. Substantial advances in sensor technology are often fueled by the advent of new materials. Therefore, nanomaterials have motivated a large body of research and such materials have been implemented into biosensor devices. Among these new materials carbon nanotubes (CNTs) are especially promising building blocks for biosensors due to their unique electronic and optical properties. Carbon nanotubes are rolled-up cylinders of carbon monolayers (graphene). They can be chemically modified in such a way that biologically relevant molecules can be detected with high sensitivity and selectivity. In this review article we will discuss how carbon nanotubes can be used to create biosensors. We review the latest advancements of optical carbon nanotube based biosensors with a special focus on near-infrared (NIR)-fluorescence, Raman-scattering and fluorescence quenching.
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Affiliation(s)
- Sebastian Kruss
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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G-quadruplexes as sensing probes. Molecules 2013; 18:14760-79. [PMID: 24288003 PMCID: PMC6270327 DOI: 10.3390/molecules181214760] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 01/09/2023] Open
Abstract
Guanine-rich sequences of DNA are able to create tetrastranded structures known as G-quadruplexes; they are formed by the stacking of planar G-quartets composed of four guanines paired by Hoogsteen hydrogen bonding. G-quadruplexes act as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplexes form a complex with anionic porphyrin hemin and exhibit peroxidase-like activity. This review focuses on overview of sensing techniques based on G-quadruplex complexes with anionic porphyrins for detection of various analytes, including metal ions such as K+, Ca2+, Ag+, Hg2+, Cu2+, Pb2+, Sr2+, organic molecules, nucleic acids, and proteins. Principles of G-quadruplex-based detection methods involve DNA conformational change caused by the presence of analyte which leads to a decrease or an increase in peroxidase activity, fluorescence, or electrochemical signal of the used probe. The advantages of various detection techniques are also discussed.
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Xia T, Yuan J, Fang X. Conformational dynamics of an ATP-binding DNA aptamer: a single-molecule study. J Phys Chem B 2013; 117:14994-5003. [PMID: 24245799 DOI: 10.1021/jp4099667] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleic acid aptamers are single-stranded RNA or DNA molecules that bind to their targets with high specificity and affinity. Although their biomedical applications have been booming, it is still debatable whether an aptamer recognizes its target through "induced fit" or "conformational selection", a central question in molecular recognition. To address this question, an ATP-binding DNA aptamer was selected as a model system and the conformational properties of this aptamer with and without the presence of ATP were investigated by single-pair Förster resonance energy transfer (spFRET) spectroscopy. The single-molecule results indicate that the aptamer can fold into a double-stranded-like structure, similar to the ligand-bound conformation, even without the presence of ATP. The folded structure is thermally stable at high salt concentrations and becomes rather dynamic at low salt concentrations. Although in the latter condition, the aptamer prefers unfolded structures, it can occasionally migrate to the folded conformation for a short time before being unfolded again. The binding of ATP to the aptamer stabilizes the folded structure, which populates the ligand-bound state of the aptamer, thus shifting the conformational equilibrium. Collectively, our data support that the ATP-binding DNA aptamer recognizes ATP ligand through "conformational selection".
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Affiliation(s)
- Tie Xia
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and Nanotechnology, Chinese Academy of Sciences , Beijing 100190, P. R. China
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Leung KH, Lu L, Wang M, Mak TY, Chan DSH, Tang FK, Leung CH, Kwan HY, Yu Z, Ma DL. A label-free luminescent switch-on assay for ATP using a G-quadruplex-selective iridium(III) complex. PLoS One 2013; 8:e77021. [PMID: 24204723 PMCID: PMC3808368 DOI: 10.1371/journal.pone.0077021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/26/2013] [Indexed: 12/16/2022] Open
Abstract
We report herein the G-quadruplex-selective property of a luminescent cyclometallated iridium(III) complex for the detection of adenosine-5'-triphosphate (ATP) in aqueous solution. The ATP-binding aptamer was employed as the ATP recognition unit, while the iridium(III) complex was used to monitor the formation of the G-quadruplex structure induced by ATP. The sensitivity and fold enhancement of the assay were higher than those of the previously reported assay using the organic dye crystal violet as a fluorescent probe. This label-free luminescent switch-on assay exhibits high sensitivity and selectivity towards ATP with a limit of detection of 2.5 µM.
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Affiliation(s)
- Ka-Ho Leung
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Lihua Lu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Modi Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tsun-Yin Mak
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Fung-Kit Tang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hiu-Yee Kwan
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhiling Yu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- * E-mail:
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Mi Y, Zhu W, Zhao J, Jiang J, Shen G, Yu R. A Ligation Triggered Label-Free Fluorescent Assay for Adenosine-Triphosphate Based on Nicking Endonuclease Signal Amplification and Ligand Responsive G-Quadruplex Formation. ANAL LETT 2013. [DOI: 10.1080/00032719.2012.749484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Zhu W, Zhao Z, Li Z, Li H, Jiang J, Shen G, Yu R. A label free exonuclease III-aided fluorescence assay for adenosine triphosphate based on graphene oxide and ligation reaction. NEW J CHEM 2013. [DOI: 10.1039/c2nj41055a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Bu NN, Gao A, He XW, Yin XB. Electrochemiluminescent biosensor of ATP using tetrahedron structured DNA and a functional oligonucleotide for Ru(phen)3(2+) intercalation and target identification. Biosens Bioelectron 2012; 43:200-4. [PMID: 23313611 DOI: 10.1016/j.bios.2012.11.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 09/12/2012] [Accepted: 11/26/2012] [Indexed: 02/01/2023]
Abstract
Restricted target accessibility and surface-induced perturbation of the aptamer structure are the main limitations in single-stranded DNA aptamer-based electrochemical sensors. Chemical labeling of the aptamer with a probe at the end of aptamer is inefficient and time-consuming. In this work, tetrahedron-structured DNA (ts-DNA) and a functionalized oligonucleotide (FO) were used to develop an electrochemiluminescence (ECL) aptasensor with adenosine triphosphate (ATP) as a model target. The ts-DNA was formed with three thiolated oligonucleotides and one oligonucleotide containing anti-ATP aptamer. The FO contained a complementary strand to the anti-ATP aptamer and an intermolecular duplex for Ru(phen)3(2+) intercalation. After the ts-DNA was immobilized on the electrode surface through gold-thiol interactions, hybridization between the anti-ATP aptamer and its complementary strand introduced the intercalated Ru(phen)3(2+) to the electrode. ECL emission from Ru(phen)3(2+) was observed with tripropylamine as a co-reactant. Once ATP reacted with its aptamer, the aptamer-complimentary strand duplex dissociated and the intermolecular duplex containing Ru(phen)3(2+) was released. The difference in emission before and after reaction with ATP was used to quantify ATP with a detection limit of 0.2nM. The ts-DNA increased the sensitivity compared to conventional methods, and the intercalation strategy avoided a complex chemical labeling procedure.
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Affiliation(s)
- Nan-Nan Bu
- State Key Laboratory of Medicinal Chemical Biology and Key Laboratory of Functional Polymer Material (MOE), College of Chemistry, Nankai University, Tianjin, 300071, PR China
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Li M, Zhang J, Suri S, Sooter LJ, Ma D, Wu N. Detection of adenosine triphosphate with an aptamer biosensor based on surface-enhanced Raman scattering. Anal Chem 2012; 84:2837-42. [PMID: 22380526 DOI: 10.1021/ac203325z] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A simple, ultrasensitive, highly selective, and reagent-free aptamer-based biosensor has been developed for quantitative detection of adenosine triphosphate (ATP) using surface-enhanced Raman scattering (SERS). The sensor contains a SERS probe made of gold nanostar@Raman label@SiO(2) core-shell nanoparticles in which the Raman label (malachite green isothiocyanate, MGITC) molecules are sandwiched between a gold nanostar core and a thin silica shell. Such a SERS probe brings enhanced signal and low background fluorescence, shows good water-solubility and stability, and exhibits no sign of photobleaching. The aptamer labeled with the SERS probe is designed to hybridize with the cDNA on a gold film to form a rigid duplex DNA. In the presence of ATP, the interaction between ATP and the aptamer results in the dissociation of the duplex DNA structure and thereby removal of the SERS probe from the gold film, reducing the Raman signal. The response of the SERS biosensor varies linearly with the logarithmic ATP concentration up to 2.0 nM with a limit of detection of 12.4 pM. Our work has provided an effective method for detection of small molecules with SERS.
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Affiliation(s)
- Ming Li
- Department of Mechanical and Aerospace Engineering, WVNano Initiative, West Virginia University, Morgantown, West Virginia 26506-6106, United States
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Wang RE, Zhang Y, Cai J, Cai W, Gao T. Aptamer-based fluorescent biosensors. Curr Med Chem 2012; 18:4175-84. [PMID: 21838688 DOI: 10.2174/092986711797189637] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 01/24/2023]
Abstract
Selected from random pools of DNA or RNA molecules through systematic evolution of ligands by exponential enrichment (SELEX), aptamers can bind to target molecules with high affinity and specificity, which makes them ideal recognition elements in the development of biosensors. To date, aptamer-based biosensors have used a wide variety of detection techniques, which are briefly summarized in this article. The focus of this review is on the development of aptamer-based fluorescent biosensors, with emphasis on their design as well as properties such as sensitivity and specificity. These biosensors can be broadly divided into two categories: those using fluorescently-labeled aptamers and others that employ label-free aptamers. Within each category, they can be further divided into "signal-on" and "signal-off" sensors. A number of these aptamer-based fluorescent biosensors have shown promising results in biological samples such as urine and serum, suggesting their potential applications in biomedical research and disease diagnostics.
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Affiliation(s)
- R E Wang
- Department of Chemistry, Washington University in St. Louis, MO, USA
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He HZ, Ma VPY, Leung KH, Chan DSH, Yang H, Cheng Z, Leung CH, Ma DL. A label-free G-quadruplex-based switch-on fluorescence assay for the selective detection of ATP. Analyst 2012; 137:1538-40. [PMID: 22343772 DOI: 10.1039/c2an15999f] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A G-quadruplex-based, label-free, switch-on fluorescence detection method has been developed for the selective detection of ATP in aqueous solution using crystal violet as a G-quadruplex-selective probe. The assay is highly simple and rapid, and does not require the use of fluorescent labeling.
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Affiliation(s)
- Hong-Zhang He
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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Aptamer-incorporated hydrogels for visual detection, controlled drug release, and targeted cancer therapy. Anal Bioanal Chem 2011; 402:187-94. [PMID: 22052153 DOI: 10.1007/s00216-011-5414-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/09/2011] [Accepted: 09/11/2011] [Indexed: 12/22/2022]
Abstract
Hydrogels are water-retainable materials, made from cross-linked polymers, that can be tailored to applications in bioanalysis and biomedicine. As technology advances, an increasing number of molecules have been used as the components of hydrogel systems. However, the shortcomings of these systems have prompted researchers to find new materials that can be incorporated into them. Among all of these emerging materials, aptamers have recently attracted substantial attention because of their unique properties, for example biocompatibility, selective binding, and molecular recognition, all of which make them promising candidates for target-responsive hydrogel engineering. In this work, we will review how aptamers have been incorporated into hydrogel systems to enable colorimetric detection, controlled drug release, and targeted cancer therapy.
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