101
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Weng C, Li X, Lu Q, Yang W, Wang J, Yan X, Li B, Sakran M, Hong J, Zhu W, Zhou X. A label-free electrochemical biosensor based on magnetic biocomposites with DNAzyme and hybridization chain reaction dual signal amplification for the determination of Pb2+. Mikrochim Acta 2020; 187:575. [DOI: 10.1007/s00604-020-04548-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/02/2020] [Indexed: 01/20/2023]
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102
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Shoara AA, Churcher ZR, Steele TWJ, Johnson PE. Analysis of the role played by ligand-induced folding of the cocaine-binding aptamer in the photochrome aptamer switch assay. Talanta 2020; 217:121022. [PMID: 32498850 DOI: 10.1016/j.talanta.2020.121022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
The Photochrome Aptamer Switch Assay (PHASA) relies on ligand binding by an aptamer to alter the local environment of a stilbene compound covalently attached to the 5' end of the aptamer. We used the PHASA with both structure switching and non-structure switching versions of the cocaine-binding aptamer. We show that the largest change in fluorescence intensity and the lowest concentration limit of detection (CLooD) is obtained using the structure-switching cocaine-binding aptamer. Fluorescence anisotropy measurements were used to quantify the affinity of the conjugated aptamer to cocaine. We also used thermal melt analysis and Nuclear Magnetic Resonance (NMR) spectroscopy to show that the addition of the stilbene to the aptamer increases the melt temperature of the cocaine-bound structure-switching aptamer by (6.4 ± 0.3) °C compared to the unconjugated aptamer while the free form of the structure-switching aptamer-stilbene conjugate remains unfolded.
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Affiliation(s)
- Aron A Shoara
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario, M3J 1P3, Canada
| | - Zachary R Churcher
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario, M3J 1P3, Canada
| | - Terry W J Steele
- School of Materials Science and Engineering (MSE), Division of Materials Technology, Nanyang Technological University (NTU), Singapore, 639798, Singapore
| | - Philip E Johnson
- Department of Chemistry & Centre for Research on Biomolecular Interactions, York University, 4700 Keele St., Toronto, Ontario, M3J 1P3, Canada.
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103
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Prante M, Segal E, Scheper T, Bahnemann J, Walter J. Aptasensors for Point-of-Care Detection of Small Molecules. BIOSENSORS 2020; 10:E108. [PMID: 32859075 PMCID: PMC7559136 DOI: 10.3390/bios10090108] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Aptamers, a group of nucleic acids which can specifically bind to a target molecule, have drawn extensive interest over the past few decades. For analytics, aptamers represent a viable alternative to gold-standard antibodies due to their oligonucleic nature combined with advantageous properties, including higher stability in harsh environments and longer shelf-life. Indeed, over the last decade, aptamers have been used in numerous bioanalytical assays and in various point-of-care testing (POCT) platforms. The latter allows for rapid on-site testing and can be performed outside a laboratory by unskilled labor. Aptamer technology for POCT is not limited just to medical diagnostics; it can be used for a range of applications, including environmental monitoring and quality control. In this review, we critically examine the use of aptamers in POCT with an emphasis on their advantages and limitations. We also examine the recent success of aptasensor technology and how these findings pave the way for the analysis of small molecules in POCT and other health-related applications. Finally, the current major limitations of aptamers are discussed, and possible approaches for overcoming these challenges are presented.
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Affiliation(s)
- Marc Prante
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Technion City, Haifa 3200003, Israel;
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
| | - Janina Bahnemann
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
| | - Johanna Walter
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
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104
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Churcher ZR, Garaev D, Hunter HN, Johnson PE. Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer. Biophys J 2020; 119:1147-1156. [PMID: 32882188 DOI: 10.1016/j.bpj.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/25/2022] Open
Abstract
We have used magnetization transfer NMR experiments to measure the exchange rate constant (kex) of the imino protons in the unbound, cocaine-bound, and quinine-bound forms of the cocaine-binding DNA aptamer. Both long-stem 1 (MN4) and short-stem 1 (MN19) variants were analyzed, corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions of this aptamer, respectively. The kex values were measured as a function of temperature from 5 to 45°C to determine the thermodynamics of the base pair opening for MN4. We find that the base pairs close to the ligand-binding site become stronger upon ligand binding, whereas those located away from the binding site do not strengthen. With the buffer conditions used in this study, we observe imino 1H signals in MN19 not previously seen, which leads us to conclude that in the free form, both stem 2 and parts of stem 3 are formed and that the base pairs in stem 1 become structured or more rigid upon binding. This is consistent with the kex values for MN19 decreasing in both stem 1 and at the ligand-binding site. Based on the temperature dependence of the kex values, we find that MN19 is more dynamic than MN4 in the free and both ligand-bound forms. For MN4, ligand-binding results in the reduction of dynamics that are localized to the binding site. These results demonstrate that an aptamer in which the base pairs are preformed also experiences a reduction in dynamics with ligand binding.
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Affiliation(s)
- Zachary R Churcher
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Devid Garaev
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Howard N Hunter
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada.
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105
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He Y, Zhou L, Deng L, Feng Z, Cao Z, Yin Y. An electrochemical impedimetric sensing platform based on a peptide aptamer identified by high-throughput molecular docking for sensitive l-arginine detection. Bioelectrochemistry 2020; 137:107634. [PMID: 32882443 DOI: 10.1016/j.bioelechem.2020.107634] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
As a primary building block for protein synthesis, l-arginine (l-Arg) is also a precursor for the synthesis of important metabolites, and is involved in various physiological and pathophysiological processes. l-Arg is a potential biomarker in clinical diagnosis and nutritional status assessment, making it valuable to quantify and monitor this biomolecule. In this study, peptide aptamers that specifically interact with l-Arg were identified by high-throughput molecular docking, and the binding capacities between the synthesized peptide aptamers and l-Arg were then measured by isothermal titration calorimetry. We hypothesized that the peptide aptamer with the greatest binding capacity could be used as the recognition element in a biosensor. A chemosynthetic peptide aptamer modified with mercaptan and spacer units (thioctic acid-GGGG-FGHIHEGY) was thus used to construct label-free electrochemical impedimetric biosensors for l-Arg based on gold electrodes. The optimum biosensor showed good sensitivity to l-Arg with a linear range of 0.1 pM-0.1 mM, and the calculated limit of detection (three times the signal-to-noise ratio) was 0.01 pM. Interference studies and assays of diluted serum samples were also carried out, and satisfactory results obtained. In conclusion, a potential method of peptide aptamer screening and biosensor fabrication for detecting small biological molecules was demonstrated.
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Affiliation(s)
- Yumin He
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Scientific Observational and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan 410125, PR China; Animal Nutrition and Human Health Laboratory, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, PR China
| | - Li Zhou
- Collaborative Innovation Center of Micro/Nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, PR China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410075, PR China
| | - Zemeng Feng
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Scientific Observational and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan 410125, PR China.
| | - Zhong Cao
- Collaborative Innovation Center of Micro/Nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, PR China
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Scientific Observational and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan 410125, PR China; Animal Nutrition and Human Health Laboratory, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, PR China
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106
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Chen Y, Xiang J, Liu B, Chen Z, Zuo X. Gold nanoparticle-engineered electrochemical aptamer biosensor for ultrasensitive detection of thrombin. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3729-3733. [PMID: 32729857 DOI: 10.1039/d0ay01163k] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In order to obtain a lower detection limit in electrochemical detection, the choice of signal amplification strategy is of great importance. In this work, we describe an electrochemical sandwich aptasensor based on a signal amplification system involving two thrombin (TB) aptamers (TBA1 and TBA2), gold nanoparticles (AuNPs) as aptamer carriers, and [Ru(NH3)6]3+ for signal conversion. In the presence of the target thrombin, TBA1 and TBA2 specifically bind to TB, and the TBA1-TB-TBA2 complexes cause the formation of a sandwich structure, meaning more [Ru(NH3)6]3+ can be adsorbed on the negatively charged phosphate backbone of the aptamers, resulting in an increase in the differential pulse voltammetry (DPV) current. Under optimal conditions, the aptasensor exhibited a linear range of 1 fM to 6 pM and a limit of detection of 0.1429 fM (S/N = 3) for TB. The proposed aptasensor displayed an excellent selectivity and reproducibility. Importantly, the aptasensor was capable of detecting TB in serum samples successfully.
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Affiliation(s)
- Ying Chen
- Department of Chemistry, Capital Normal University, Beijing, 100048, China.
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107
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Wang C, Zhao Q. A reagentless electrochemical sensor for aflatoxin B1 with sensitive signal-on responses using aptamer with methylene blue label at specific internal thymine. Biosens Bioelectron 2020; 167:112478. [PMID: 32810704 DOI: 10.1016/j.bios.2020.112478] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/21/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022]
Abstract
Aptamer electrochemical sensors using immobilized aptamers with redox tag rely on the target binding-induced changes of current signal on electrode, offering advantages in operation convenience, no separation, rapidity, and sensitivity. Usually, the redox tag is placed on aptamer terminal, however, sometimes the terminal label may be insensitive to target-binding and fail to generate sensitive responses. The redox tag methylene blue (MB) labeled on different sites of aptamer may experience distinct changes in local environment, distance to electrode, or interactions with aptamer bases during affinity binding, which affect the current signal. Thus, it is possible to construct aptamer electrochemical sensors with sensitive and significant responses to targets by screening a series of sites (e.g., internal thymine T) of the aptamer and placing MB tag on a specific site of the aptamer. With this strategy, we successfully fabricated an electrochemical sensor on gold electrode for rapid, reagentless, and sensitive detection of aflatoxin B1 (AFB1), an important mycotoxin causing great health risks, by using a 26-mer DNA aptamer with MB on an internal T site (e.g., 18th T) and a thiol moiety at 5' terminal. This sensor generated remarkable signal-on responses to AFB1, allowed a detection limit of 6 pM, and enabled detection of AFB1 in wine, milk and corn flour samples. This sensor can be well regenerated by rinsing with deionized water and reused, and shows good stability. This sensor and the demonstrated strategy are promising in wide applications.
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Affiliation(s)
- Chao Wang
- 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 310000, China.
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108
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Sanli S, Moulahoum H, Ghorbanizamani F, Celik EG, Timur S. Ultrasensitive covalently-linked Aptasensor for cocaine detection based on electrolytes-induced repulsion/attraction of colloids. Biomed Microdevices 2020; 22:51. [PMID: 32748213 DOI: 10.1007/s10544-020-00507-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quick and easy colorimetric sensor based on gold nanoparticles (GNPs) and aptamers for the detection of cocaine was developed. The sensor was named as 'GAPTA' and showed extremely interesting results regarding cocaine detection with a sensitivity to doses of 0.2 nM. The experimental approach consisted of creating a conjugate between GNPs (10 nm size) and aptamers as a sensing base with the addition of an electrolyte (NaCl) that plays the role of aggregation inducer. In the absence of the aptamer, the electrolyte was able to induce aggregation of the GNPs turning the color of the solution from red to blue while the presence of the aptamer is able to hinder the charges attraction and protects the GNPs from aggregating. The optimization of the aptamer and electrolyte concentration was determined to be 118 nM and 55 mM, respectively, and the resultant GAPTA sensor had a detection limit of 0.97 nM. Furthermore, the selectivity of the platform was tested in the presence of different interferents and showed a specific response towards cocaine while interference ranged between 20 and 40%. The applicability of the GAPTA biosensor was tested on synthetic saliva and demonstrated a sensitivity range between 0.2 and 25 nM. These results suggest the potential of the current colorimetric sensor in abuse drugs screening and creates a stable base for new routine platforms for biomedical and toxicology applications. Graphical abstract.
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Affiliation(s)
- Serdar Sanli
- Department of Biochemistry, Faculty of Science, Ege University, 35100-Bornova, Izmir, Turkey
| | - Hichem Moulahoum
- Department of Biochemistry, Faculty of Science, Ege University, 35100-Bornova, Izmir, Turkey.
| | - Faezeh Ghorbanizamani
- Department of Biochemistry, Faculty of Science, Ege University, 35100-Bornova, Izmir, Turkey
| | - Emine Guler Celik
- Department of Biochemistry, Faculty of Science, Ege University, 35100-Bornova, Izmir, Turkey
| | - Suna Timur
- Department of Biochemistry, Faculty of Science, Ege University, 35100-Bornova, Izmir, Turkey. .,Central Research Test and Analysis Laboratory Application and Research Center, Ege University, 35100-Bornova, Izmir, Turkey.
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109
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Khazaal AS, Springborg M, Fan C, Huwig K. Optimizing small conjugated molecules for solar-cell applications using an inverse-design method. J Mol Graph Model 2020; 100:107654. [PMID: 32682307 DOI: 10.1016/j.jmgm.2020.107654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 10/23/2022]
Abstract
Small organic conjugated molecules are key elements for low-cost photovoltaic devices. One example is cyanopyridone molecules. By modifying these molecules, for instance through optimally chosen functional groups attached to the backbone, their properties can be improved. However, the very large number of possible modifications makes it difficult to identify the best performing molecules. In the present work, we have used a computational inverse-design approach (PooMa) to identify the positions and types of functional groups attached to a modified cyanopyridone that lead to the best performance in solar-energy harvesting. A QSPR model based on five electronic descriptors has been used to determine the properties of solar cells. Our approach uses a genetic algorithm to search the chemical space containing 184 (104,976) substituted cyanopyridone systems and predicts out of those the best 20 molecules with optimal performance efficiencies (PCE). PooMa uses the Density-Functional Tight-Binding (DFTB) method for calculating the electronic properties. DFTB is a fast method with acceptable accuracy and, therefore, can be used on a normal desktop without expensive hard- or software. In order to get further information about our suggested systems, a DFT method and its derivative TD-DFT are applied.
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Affiliation(s)
- Abdullah S Khazaal
- Chemistry Department, College of Science, Tikrit University, 34001, Salahuddin, Iraq.
| | - Michael Springborg
- Physical and Theoretical Chemistry, University of Saarland, 66123, Saarbrücken, Germany; Materials Science, Tianjin University, 300350, Tianjin, China
| | - Chencheng Fan
- Physical and Theoretical Chemistry, University of Saarland, 66123, Saarbrücken, Germany
| | - Kai Huwig
- Physical and Theoretical Chemistry, University of Saarland, 66123, Saarbrücken, Germany
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110
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Zou R, Ma Y, Li C, Zhang F, Chen C, Cai C. A label-free resonance light scattering biosensor for nucleic acids using triple-helix molecular switch and G-quadruplex nanowires. Microchem J 2020. [DOI: 10.1016/j.microc.2020.104764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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111
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112
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Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci 2020; 21:ijms21124522. [PMID: 32630547 PMCID: PMC7350236 DOI: 10.3390/ijms21124522] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.
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113
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Sett A, Zara L, Dausse E, Toulmé JJ. Engineering Light-Up Aptamers for the Detection of RNA Hairpins through Kissing Interaction. Anal Chem 2020; 92:9113-9117. [PMID: 32498509 DOI: 10.1021/acs.analchem.0c01378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aptasensors are biosensors that include aptamers for detecting a target of interest. We engineered signaling aptasensors for the detection of RNA hairpins from the previously described malachite green (MG) RNA aptamer. The top part of this imperfect hairpin aptamer was modified in such a way that it can engage loop-loop (so-called kissing) interactions with RNA hairpins displaying partly complementary apical loops. These newly derived oligonucleotides named malaswitches bind their cognate fluorogenic ligand (MG) exclusively when RNA-RNA kissing complexes are formed, whereas MG does not bind to malaswitches alone. Consequently, the formation of the ternary target RNA-malaswitch RNA-MG complex results in fluorescence emission, and malaswitches constitute sensors for detecting RNA hairpins. Malaswitches were designed that specifically detect precursors of microRNAs let7b and miR-206.
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Affiliation(s)
- Arghya Sett
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France
| | - Lorena Zara
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France.,Novaptech, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France
| | - Jean-Jacques Toulmé
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France.,Novaptech, 146 rue Léo Saignat, 33076 Bordeaux, France
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114
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Campuzano S, Pedrero M, Gamella M, Serafín V, Yáñez-Sedeño P, Pingarrón JM. Beyond Sensitive and Selective Electrochemical Biosensors: Towards Continuous, Real-Time, Antibiofouling and Calibration-Free Devices. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3376. [PMID: 32560028 PMCID: PMC7348748 DOI: 10.3390/s20123376] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022]
Abstract
Nowadays, electrochemical biosensors are reliable analytical tools to determine a broad range of molecular analytes because of their simplicity, affordable cost, and compatibility with multiplexed and point-of-care strategies. There is an increasing demand to improve their sensitivity and selectivity, but also to provide electrochemical biosensors with important attributes such as near real-time and continuous monitoring in complex or denaturing media, or in vivo with minimal intervention to make them even more attractive and suitable for getting into the real world. Modification of biosensors surfaces with antibiofouling reagents, smart coupling with nanomaterials, and the advances experienced by folded-based biosensors have endowed bioelectroanalytical platforms with one or more of such attributes. With this background in mind, this review aims to give an updated and general overview of these technologies as well as to discuss the remarkable achievements arising from the development of electrochemical biosensors free of reagents, washing, or calibration steps, and/or with antifouling properties and the ability to perform continuous, real-time, and even in vivo operation in nearly autonomous way. The challenges to be faced and the next features that these devices may offer to continue impacting in fields closely related with essential aspects of people's safety and health are also commented upon.
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Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain; (M.P.); (M.G.); (V.S.); (P.Y.-S.)
| | | | | | | | | | - José Manuel Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain; (M.P.); (M.G.); (V.S.); (P.Y.-S.)
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115
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Label-free liquid crystal-based biosensor for detection of dopamine using DNA aptamer as a recognition probe. Anal Biochem 2020; 605:113807. [PMID: 32526198 DOI: 10.1016/j.ab.2020.113807] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
We present a label-free liquid crystal-based biosensor for the detection of dopamine (DA) in aqueous solutions using dopamine-binding aptamers (DBA) as recognition elements. In this system, the dimethyloctadecyl [3-(trimethoxysilyl) propyl] ammonium chloride (DMOAP) self-assembled monolayers immobilized on glass slides support the long alkyl chains that keep the liquid crystal (LC) molecules in a homeotropic orientation. Glutaraldehyde (GA) is used as a cross-linker to immobilize DBA onto the surface of glass slides. The specific binding of DA and DBA disrupts the homeotropic orientation of LCs, thereby inducing a change in the orientation from homeotropic to a random alignment. This orientation change can be converted and visualized simply as a transition from a dark optical LC image to a brighter image under a polarized optical microscope (POM), enabling the detection of DA. The developed LC-based aptasensor shows a good linear optical response towards DA in the very wide range of 1 pM-10 μM (0.19 pg/mL to 1.9 μg/mL) and has a very low detection limit of 10 pM (∼1.9 pg/mL). The biosensor also exhibited satisfactory selectivity and could be successfully applied to detect DA in human urine. The proposed LC-based aptamer sensing method offers a simple, rapid, highly sensitive and selective, and a label-free method for the analysis of DA in real clinical samples.
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116
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He J, Hu X, Gao X, Meng C, Li Y, Li X, Fan L, Yu HZ. A versatile fluorometric in situ hybridization method for the quantitation of hairpin conformations in DNA self-assembled monolayers. Analyst 2020; 145:4522-4531. [PMID: 32418997 DOI: 10.1039/d0an00657b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As the performance of hairpin DNA (hpDNA)-based biosensors is highly dependent on the yield of stem-loop (hairpin) conformations, we report herein a versatile fluorometric in situ hybridization protocol for examining hpDNA self-assembled monolayers (SAMs) on popularly used biochip substrates. Specifically, the ratio of fluorescence (FL) intensities of hpDNA SAMs (in an array format) before and after hybridization was adopted as the key parameter for performing such a determination. Upon confirming the existence of mixed and tunable DNA conformations in binary deposition solutions and efficient hybridization of the hairpin strands with the target DNA via gel electrophoresis assays, we tested the fluorometric protocol for determining the coverages of hpDNA in hpDNA/ssDNA SAMs prepared on gold; its accuracy was validated by Exonuclease I (Exo I)-assisted electrochemical quantitation. To further confirm its versatility, this FL protocol was adopted for quantifying hairpin conformations formed on glass and polycarbonate (PC) substrates. The molar ratios of surface-tethered hairpin conformations on the three different substrates were all found to be proportional to but less than those in the binary deposition solutions, and were dependent on the substrate morphology. The findings reported herein are beneficial for the construction of highly efficient DNA hairpin-based sensing surfaces, which essentially facilitates the creation of hpDNA-based biosensors with optimal detection performance.
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Affiliation(s)
- Jiale He
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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Yan J, van Smeden L, Merkx M, Zijlstra P, Prins MWJ. Continuous Small-Molecule Monitoring with a Digital Single-Particle Switch. ACS Sens 2020; 5:1168-1176. [PMID: 32189498 PMCID: PMC8177406 DOI: 10.1021/acssensors.0c00220] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
ability to continuously measure concentrations of small molecules
is important for biomedical, environmental, and industrial monitoring.
However, because of their low molecular mass, it is difficult to quantify
concentrations of such molecules, particularly at low concentrations.
Here, we describe a small-molecule sensor that is generalizable, sensitive,
specific, reversible, and suited for continuous monitoring over long
durations. The sensor consists of particles attached to a sensing
surface via a double-stranded DNA tether. The particles transiently
bind to the sensing surface via single-molecular affinity interactions,
and the transient binding is optically detected as digital binding
events via the Brownian motion of the particles. The rate of binding
events decreases with increasing analyte concentration because analyte
molecules inhibit binding of the tethered particle to the surface.
The sensor enables continuous measurements of analyte concentrations
because of the reversibility of the intermolecular bonds and digital
read-out of particle motion. We show results for the monitoring of
short single-stranded DNA sequences and creatinine, a small-molecule
biomarker (113 Da) for kidney function, demonstrating a temporal resolution
of a few minutes. The precision of the sensor is determined by the
statistics of the digital switching events, which means that the precision
is tunable by the number of particles and the measurement time.
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Affiliation(s)
- Junhong Yan
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Laura van Smeden
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Peter Zijlstra
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
| | - Menno W. J. Prins
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven 5612 AZ, The Netherlands
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118
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KickStat: A Coin-Sized Potentiostat for High-Resolution Electrochemical Analysis. SENSORS 2020; 20:s20082407. [PMID: 32340294 PMCID: PMC7219484 DOI: 10.3390/s20082407] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
The demand for wearable and point-of-care devices has led to an increase in electrochemical sensor development to measure an ever-increasing array of biological molecules. In order to move from the benchtop to truly portable devices, the development of new biosensors requires miniaturized instrumentation capable of making highly sensitive amperometric measurements. To meet this demand, we have developed KickStat, a miniaturized potentiostat that combines the small size of the integrated Texas Instruments LMP91000 potentiostat chip (Texas Instruments, Dallas, TX, USA) with the processing power of the ARM Cortex-M0+ SAMD21 microcontroller (Microchip Technology, Chandler, AZ, USA) on a custom-designed 21.6 mm by 20.3 mm circuit board. By incorporating onboard signal processing via the SAMD21, we achieve 1 mV voltage increment resolution and an instrumental limit of detection of 4.5 nA in a coin-sized form factor. This elegant engineering solution allows for high-resolution electrochemical analysis without requiring extensive circuitry. We measured the faradaic current of an anti-cocaine aptamer using cyclic voltammetry and square wave voltammetry and demonstrated that KickStat’s response was within 0.6% of a high-end benchtop potentiostat. To further support others in electrochemical biosensors development, we have made KickStat’s design and firmware available in an online GitHub repository.
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119
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Zhang L, Zhang X, Feng P, Han Q, Liu W, Lu Y, Song C, Li F. Photodriven Regeneration of G-Quadruplex Aptasensor for Sensitively Detecting Thrombin. Anal Chem 2020; 92:7419-7424. [PMID: 32268723 DOI: 10.1021/acs.analchem.0c00380] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aptamers have been widely used as recognition elements in electrochemical sensors. However, as the most expensive consumable, the aptasensors regeneration is still a critical challenge for sustainable feasibility and attracting great interest from researchers, due to the high affinity between the aptamers and their targets (the dissociation constant Kd is low to subnanomolar or nanomolar). In this work, we propose a photochromic five-azobenzene-inserted thrombin-aptamer based aptasensor to improve the regenerativity. With ultraviolet light exposure, the trans-structure of azobenzene changes to cis-structure, and open the folded aptamer to realize the aptasensor regeneration. The limit of detection can be sensitive to 3 pM (S/N = 3). The thrombin concentrations were detected to be 2.48 ± 0.02 and 20.26 ± 0.98 nM (n = 3) in duck whole blood and blood serum, respectively. Utilizing surface plasmon resonance, we demonstrated that the certain azobenzene moieties can exactly increase Kd of aptamer-thrombin bounding. The photodriven conversion of thrombin-aptamer from G-quadruplex to loosen structure approaches a convenient regeneration for aptasensor, which will promote its popularization and sustainable feasibility.
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Affiliation(s)
- Liangliang Zhang
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoyu Zhang
- College of Chemistry and Materials Science Jinan University, Guangzhou 510632, China
| | - Pengju Feng
- College of Chemistry and Materials Science Jinan University, Guangzhou 510632, China
| | - Qi Han
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Wei Liu
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453000, China
| | - Ying Lu
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Chunxia Song
- Department of Applied Chemistry, Anhui Agricultural University, Hefei 230036, China
| | - Fengyu Li
- College of Chemistry and Materials Science Jinan University, Guangzhou 510632, China
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120
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Gao X, Qi L, Liu K, Meng C, Li Y, Yu HZ. Exonuclease I-Assisted General Strategy to Convert Aptamer-Based Electrochemical Biosensors from "Signal-Off" to "Signal-On". Anal Chem 2020; 92:6229-6234. [PMID: 32237711 DOI: 10.1021/acs.analchem.0c00005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In terms of how the signal varies in response to increased concentration of an analyte, sensors can be classified as either "signal-on" or "signal-off" format. While both types hold potentials to be sensitive, selective, and reusable, in many situations "signal-on" sensors are preferred for their low background signal and better selectivity. In this study, with the detection of lysozyme using its DNA aptamer as a trial system, for the first time we demonstrated that such an aptamer-based electrochemical biosensor can be converted from intrinsically "signal-off" to "signal-on" with the aid of a DNA exonuclease. The fact that the stepwise cleavage of antilysozyme aptamer catalyzed by Exonuclease I (Exo I) is entirely inhibited upon binding lysozyme leads to the selective removal of unbound DNA probes (thiolate anti-lysozyme DNA aptamer strands immobilized on gold electrode) upon the introduction of Exo I to the sensor. With the aid of electrostatically bound redox cations ([Ru(NH3)6]3+), we were able to quantitate the number of aptamer strands that are bound with lysozymes via conventional cyclic voltammetry (CV) measurements. We demonstrated that Exo I-assisted signal-on conversion protocol not only improves the sensing performance (10 times better limit of detection) but also promises a versatile strategy for DNA-based biosensor design, i.e., it can be readily adapted to other aptamer-protein binding systems (thrombin, as another example).
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Affiliation(s)
- Xiaoyi Gao
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Lin Qi
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kun Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Chenchen Meng
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yunchao Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hua-Zhong Yu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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121
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Abstract
It is challenging to tune the response of biosensors to a set of ligands, for example, cross-reactivity to a given target family while maintaining high specificity against interferents, due to the lack of suitable bioreceptors. We present a novel approach for controlling the cross-reactivity of biosensors by employing defined mixtures of aptamers that have differing binding properties. As a demonstration, we develop assays for the specific detection of a family of illicit designer drugs, the synthetic cathinones, with customized responses to each target ligand and interferent. We first use a colorimetric dye-displacement assay to show that the binding spectra of dual-aptamer mixtures can be tuned by altering the molar ratio of these bioreceptors. Optimized assays achieve broad detection of synthetic cathinones with minimal response toward interferents and generally demonstrate better sensing performance than assays utilizing either aptamer alone. The generality of this strategy is demonstrated with a dual-aptamer electrochemical sensor. Our approach enables customization of biosensor responsiveness to an extent that has yet to be achieved through any previously reported aptamer engineering techniques such as sequence mutation or truncation. Since multiple aptamers for the designated target family can routinely be identified via high-throughput sequencing, we believe our strategy offers a generally applicable method for generating near-ideal aptamer biosensors for various analytical applications, including medical diagnostics, environmental monitoring, and drug detection.
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Affiliation(s)
- Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Jordan Moliver
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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122
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Jiang C, Wang G, Hein R, Liu N, Luo X, Davis JJ. Antifouling Strategies for Selective In Vitro and In Vivo Sensing. Chem Rev 2020; 120:3852-3889. [DOI: 10.1021/acs.chemrev.9b00739] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Cheng Jiang
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Guixiang Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- College of Chemistry and Chemical Engineering, Taishan University, Taian 271021, China
| | - Robert Hein
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Nianzu Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jason J. Davis
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
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123
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Shaver A, Curtis SD, Arroyo-Currás N. Alkanethiol Monolayer End Groups Affect the Long-Term Operational Stability and Signaling of Electrochemical, Aptamer-Based Sensors in Biological Fluids. ACS APPLIED MATERIALS & INTERFACES 2020; 12:11214-11223. [PMID: 32040915 DOI: 10.1021/acsami.9b22385] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electrochemical aptamer-based (E-AB) sensors achieve highly precise measurements of specific molecular targets in untreated biological fluids. This unique ability, together with their measurement frequency of seconds or faster, has enabled the real-time monitoring of drug pharmacokinetics in live animals with unprecedented temporal resolution. However, one important weakness of E-AB sensors is that their bioelectronic interface degrades upon continuous electrochemical interrogation-a process typically seen as a drop in faradaic and an increase in charging currents over time. This progressive degradation limits their in vivo operational life to 12 h at best, a period that is much shorter than the elimination half-life of the vast majority of drugs in humans. Thus, there is a critical need to develop novel E-AB interfaces that resist continuous electrochemical interrogation in biological fluids for prolonged periods. In response, our group is pursuing the development of better packed, more stable self-assembled monolayers (SAMs) to improve the signaling and extend the operational life of in vivo E-AB sensors from hours to days. By invoking hydrophobicity arguments, we have created SAMs that do not desorb from the electrode surface in aqueous physiological solutions and biological fluids. These SAMs, formed from 1-hexanethiol solutions, decrease the voltammetric charging currents of E-AB sensors by 3-fold relative to standard monolayers of 6-mercapto-1-hexanol, increase the total faradaic current, and alter the electron transfer kinetics of the platform. Moreover, the stability of our new SAMs enables uninterrupted, continuous E-AB interrogation for several days in biological fluids, like undiluted serum, at a physiological temperature of 37 °C.
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Affiliation(s)
- Alexander Shaver
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
| | - Samuel D Curtis
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21202, United States
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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124
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Wijesinghe MS, Ngwa W, Chow K. Direct Electrochemical Aptamer‐Based Detection of Digoxin. ChemistrySelect 2020. [DOI: 10.1002/slct.202000286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Wilfred Ngwa
- Department of Physics and Applied Physics University of Massachusetts Lowell
- Dana-Farber Cancer Institute Brigham and Women's Hospital Harvard Medical School, Boston Massachusetts 02215 United States
| | - Kwok‐Fan Chow
- Department of Chemistry University of Massachusetts Lowell 1 University Ave., Lowell Massachusetts 01854 United States
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125
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Yu Z, Han X, Li F, Tan X, Shi W, Fu C, Yan H, Zhang G. Lengthening the aptamer to hybridize with a stem-loop DNA assistant probe for the electrochemical detection of kanamycin with improved sensitivity. Anal Bioanal Chem 2020; 412:2391-2397. [PMID: 32076786 DOI: 10.1007/s00216-020-02481-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 11/25/2022]
Abstract
By adding 6 thymines to lengthen the parent aptamer combined with the change of "on" and "off" induced by the target for an assistant stem-loop DNA probe (ASP-SLP-MB), a new folding-type electrochemical kanamycin (Kana) aptamer-engineering dual-probe-based sensor (sensor d) was developed. By purposefully reducing the background current and increasing the electron transfer efficiency of methylene blue (MB), the sensor obtained significantly enhanced detection sensitivity compared with non-aptamer-engineering one-probe-based sensor (sensor a). Such efficacy was validated by a big decrease from 530.6 to 210.2 nA for the background current signal and from 360 to 0.3 nM for the detection limit. In addition to the improved sensitivity, the sensor also exhibited good selectivity, anti-fouling detection performance, and potential quantitative analysis ability, showing a feasible potential practical analytical application in real-life complicated samples, for example, milk and serum. The released results prove that the aptamer-engineering method is effective in improving the analytical performance of folding-type sensors and provides a methodological guidance for the design and fabrication of other high-performance folding-type aptasensors. Graphical abstract.
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Affiliation(s)
- Zhigang Yu
- Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China.
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, 150040, Heilongjiang, China.
| | - Xianda Han
- Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, 150040, Heilongjiang, China
| | - Fengqin Li
- Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Xiaoping Tan
- Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Wenbing Shi
- Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Cuicui Fu
- Post-Doctoral Research Center of Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Hong Yan
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, 150040, Heilongjiang, China
| | - Guiling Zhang
- School of Materials Science and Engineering, College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin, 150040, Heilongjiang, China.
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126
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Slavkovic S, Eisen SR, Johnson PE. Designed Alteration of Binding Affinity in Structure-Switching Aptamers through the Use of Dangling Nucleotides. Biochemistry 2020; 59:663-670. [PMID: 31912723 DOI: 10.1021/acs.biochem.9b00630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to change binding affinity in a controlled fashion is a key step in the rational design of biomolecules in general and functional nucleic acids in particular. Here, we use dangling nucleotides to alter the binding affinity of structure-switching aptamers. Dangling nucleotides can stabilize or destabilize a nucleic acid structure with a known ΔG°37. When the dangling nucleotide stabilizes the structure, less free energy from ligand binding is needed to fold the molecule and hence the ligand is observed to bind tighter than in the absence of the unpaired nucleotide. For a destabilizing dangling nucleotide, the opposite occurs, and the observed binding is weaker. We demonstrate this concept using both the cocaine-binding aptamer and the ATP-binding aptamer systems. We find that for both aptamers there is a direct, but different, relationship between the predicted stabilization and the change in the observed binding free energy.
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Affiliation(s)
- Sladjana Slavkovic
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario , Canada M3J 1P3
| | - Sophie R Eisen
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario , Canada M3J 1P3
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario , Canada M3J 1P3
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127
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Wang J, Yang D, Guo X, Song Q, Tan L, Dong L. A novel RNA aptamer-modified riboswitch as chemical sensor. Anal Chim Acta 2019; 1100:240-249. [PMID: 31987147 DOI: 10.1016/j.aca.2019.11.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/20/2019] [Accepted: 11/30/2019] [Indexed: 12/19/2022]
Abstract
In this study, a novel label- and immobilization-free RNA aptamer-modified riboswitch-based biosensor was developed by using RNA aptamer modified secondary-structural scaffolds to control the identity of the ribosomal binding sequence (RBS). In the developed sensor, the duplex RNA aptamers-modified cis-repressor sequence is introduced upstream to the RBS of the indicating gene (gfp gene), leading to formatting an RNA bubble due to the none-complementary state of the RNA aptamers in the hairpin structure of the cis-repressor sequence. Without the presence of the target molecule, the ribosome cannot identify the RBS of the indicating gene as the RBS is hidden by the introduced cis-repressor, consequently, the indicating gene in the sensor would not be expressed, demonstrating the absence of the target. On the contrary, with the presence of the target molecule, the binding of aptamer with the target would induce the enlargement of the RNA bubble, leading to the separation of the cis-repressor sequence and RBS. Hence, the indicating gene would be expressed, manifesting the existence of the target. In addition, the developed sensor can quantitatively report the target concentrations by measuring the gfp gene-encoded GFP (green fluorescent protein) concentration. The approach proposed in this study can be used to construct sensors for detecting various chemicals by introducing the corresponding aptamers, therefore, this strategy can potentially provide a new set of analytical tools in the field of analytical chemistry.
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Affiliation(s)
- Jing Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China
| | - Dongmei Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China
| | - Xiaogang Guo
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, 408100, China
| | - Qitao Song
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Luxi Tan
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China.
| | - Lichun Dong
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China.
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128
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Challenges in Electrochemical Aptasensors and Current Sensing Architectures Using Flat Gold Surfaces. CHEMOSENSORS 2019. [DOI: 10.3390/chemosensors7040057] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years, reagentless aptamer biosensors, named aptasensors, have shown significant advancements. Particularly, electrochemical aptasensors could change the field of biosensors in this era, where digitalization seems to be a common goal of many fields. Biomedical devices are integrating electronic technologies for detecting pathogens, biomolecules, small molecules, and ions, and the physical-chemical properties of nucleic acid aptamers makes them very interesting for these devices. Aptamers can be easily synthesized and functionalized with functional groups for immobilization and with redox chemical groups that allow for the conversion of molecular interactions into electrical signals. Furthermore, non-labeled aptamers have also been utilized. This review presents the current challenges involved in aptasensor architectures based on gold electrodes as transducers.
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129
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Zhou Y, Yang L, Wei J, Ma K, Gong X, Shang J, Yu S, Wang F. An Autonomous Nonenzymatic Concatenated DNA Circuit for Amplified Imaging of Intracellular ATP. Anal Chem 2019; 91:15229-15234. [PMID: 31668059 DOI: 10.1021/acs.analchem.9b04126] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A robust ATP aptasensor has been successfully constructed for intracellular imaging via the autonomous nonenzymatic cascaded hybridization chain reaction (Ca-HCR) circuit. This compact aptasensor is easily assembled by integrating the sensing module and amplification module, and is furtherly introduced for selective adenosine triphosphate (ATP) assay and for the sensitive tracking of varied ATP expressions in living cells. The ATP-targeting aptamer-encoded sensing module can specifically recognize ATP and release the initiator strand for successively motivating the two-layered HCR (hybridization chain reaction) circuit via the FRET transduction mechanism. The synergistic reaction acceleration of the two HCRs contributes to the high signal gain (amplification efficiency of N2). The whole reaction process was modeled and simulated by MATLAB to deeply explore the underlying molecular reaction mechanism, implying that the cascade HCR is sufficient enough to guarantee the ATP-recognition and amplification processes. The Ca-HCR-amplified aptasensor shows high sensitivity and selectivity for in vitro ATP assay, and can monitor these varied ATP expressions in living cells via intracellular imaging technique. Furthermore, the present aptasensor can be easily extended for monitoring other low-abundance biomarkers, which is especially important for precisely understanding these related biological processes.
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Affiliation(s)
- Yangjie Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Lei Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Jinhua Shang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Shanshan Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
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130
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Li H, Li S, Dai J, Li C, Zhu M, Li H, Lou X, Xia F, Plaxco KW. High frequency, calibration-free molecular measurements in situ in the living body. Chem Sci 2019; 10:10843-10848. [PMID: 34040713 PMCID: PMC8132996 DOI: 10.1039/c9sc04434e] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abolition of the need for end-users to perform sensor calibration proved key to the widespread use of home-glucose monitors. Motivated by this observation here we have adapted electrochemical aptamer-based (E-AB) sensors, a sensing technology that is far more general than the glucose monitor, to the problem of performing calibration-free in vivo measurements of molecules other than glucose. Specifically, we first demonstrate the ability of E-AB sensors to achieve the accurate and precise measurement of cocaine, ATP and kanamycin in vitro in undiluted whole blood, achieving clinically relevant accuracy (better than ±20%) in this sample matrix without the need to calibrate individual sensors. We then demonstrate similar, calibration-free accuracy (±30%) for ATP and kanamycin measurements with sensors placed in situ in the jugular veins of live rats over multi-hour measurements runs that achieve time resolution of seconds and concentration precision of a few micromolar. Dual-reporter, electrochemical aptamer-based (E-AB) sensors achieve calibration-free measurement of multiple specific molecules in situ in the living body.![]()
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Affiliation(s)
- Hui Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Shaoguang Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan 430074 China
| | - Chengcheng Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Man Zhu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Hongxing Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara Santa Barbara California 93106 USA .,Center for Bioengineering, University of California Santa Barbara Santa Barbara California 93106 USA
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131
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Zhao Y, Li X, Yang Y, Si S, Deng C, Wu H. A simple aptasensor for Aβ 40 oligomers based on tunable mismatched base pairs of dsDNA and graphene oxide. Biosens Bioelectron 2019; 149:111840. [PMID: 31726274 DOI: 10.1016/j.bios.2019.111840] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
β-amyloid 1-40 oligomers (Aβ40O) is considered to be one of the important biomarkers for the diagnosis and treatment of Alzheimer's disease (AD). To explore a method with excellent performance is favorable for measuring the low concentration of Aβ40O in AD patients. Here, we developed a simple and fast method with a double stranded DNA (dsDNA)/graphene oxide (GO) based sensor, which was a fluorescent probe for a highly sensitive detection of Aβ40O down to 0.1 nM with a linear detectable range from 0.1 nM to 40 nM. The proposed sensor effectively reduced non-specific adsorption and improved the specificity of detection because of the covalent conjugation of a binding DNA (bDNA) containing Aβ40O-targeting aptamer (AptAβ) onto GO surface, as well as the optimization of the number of mismatch base pairs of dsDNA. Moreover, AD patients and healthy persons were distinguished by this present method. All advantages of this method are exactly what the clinical detection of AD biomarkers need. This novel aptasensor might pave a way towards the early diagnosis of AD.
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Affiliation(s)
- Yana Zhao
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Xin Li
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China
| | - Yuan Yang
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada
| | - Shihui Si
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China
| | - Chunyan Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, China.
| | - Huiyun Wu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, China.
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132
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Alkhamis O, Canoura J, Yu H, Liu Y, Xiao Y. Innovative engineering and sensing strategies for aptamer-based small-molecule detection. Trends Analyt Chem 2019; 121. [PMID: 32863483 DOI: 10.1016/j.trac.2019.115699] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aptamers are nucleic acid-based affinity reagents that have gained widespread attention as biorecognition elements for the detection of targets such as ions, small molecules, and proteins. Over the past three decades, the field of aptamer-based sensing has grown considerably. However, the advancement of aptamer-based small-molecule detection has fallen short of the high demand for such sensors in applications such as diagnostics, environmental monitoring, and forensics. This is due to two challenges: the complexity of developing generalized sensing platforms and the poor sensitivities of assays targeting small molecules. This paper will review new approaches for the streamlined development of high-performance aptamer-based sensors for small-molecule detection. We here provide historical context, explore the current state-of-the art, and offer future directions-with emphasis placed on new aptamer engineering methods, the use of cooperative binding, and label-free approaches using fully-folded, high-affinity aptamers for small-molecule sensing.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
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133
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Zejli H, Goud KY, Marty JL. An electrochemical aptasensor based on polythiophene-3-carboxylic acid assisted methylene blue for aflatoxin B1 detection. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2019.100290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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134
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Zhang X, Lazenby RA, Wu Y, White RJ. Electrochromic, Closed-Bipolar Electrodes Employing Aptamer-Based Recognition for Direct Colorimetric Sensing Visualization. Anal Chem 2019; 91:11467-11473. [PMID: 31393110 DOI: 10.1021/acs.analchem.9b03013] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this paper, we adapt the electrochemical, aptamer-based (E-AB) sensor platform to develop colorimetric aptamer-based sensors using a closed-bipolar electrode (C-BPE) system. The C-BPE E-AB sensors provide quantitative detection of target molecules based on the rate of color change of an electrochromic Prussian blue (PB) thin-film indicator electrode. The C-BPE cathode, or sensing electrode, is modified with a redox-labeled aptamer that binds to a specific target. More specifically, we employed sequences specific for adenosine triphosphate (ATP) and tobramycin as test-bed targets because these sequences are well vetted. The C-BPE anode, or indicator electrode, was coated with an electrochromic thin film comprising Prussian white (PW) that, when reduced to PB, is accompanied by a corresponding color change used for analytical detection. The rate of color change from PW to PB is facilitated by a potassium ferricyanide-catalyzed oxidation of leucomethylene blue (LB) to methylene blue (MB), the redox label conjugated to the aptamer on the sensing electrode. We demonstrate that the rate of color change is quantitatively related to the concentration of target analyte, which provides a means for naked eye determination. When combined with smartphone-based colorimetric detection, these C-BPE E-AB sensors present a user-friendly alternative to traditional E-AB sensors that rely on voltammetric analysis and a potentiostat, opening up the possibility of point-of-use applications.
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135
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Zhao LL, Cao T, Zhou QY, Zhang XH, Zhou YL, Yang L, Zhang XX. The Exploration of a New Stable G-Triplex DNA and Its Novel Function in Electrochemical Biosensing. Anal Chem 2019; 91:10731-10737. [DOI: 10.1021/acs.analchem.9b02161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ting Cao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian-Yu Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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136
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Verdonck L, Buyst D, de Vries AM, Gheerardijn V, Madder A, Martins JC. Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization. Nucleic Acids Res 2019; 46:11671-11686. [PMID: 30418582 PMCID: PMC6294506 DOI: 10.1093/nar/gky1062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/01/2018] [Indexed: 12/15/2022] Open
Abstract
Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pKa. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pKa-motif responsible for these duplex-stabilizing and pKa-modulating properties. Here, the robustness and utility of this pKa-motif was explored by introducing multiple imidazole-tethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pKa-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pKa values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazolium-tethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the l-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.
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Affiliation(s)
- Lars Verdonck
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Dieter Buyst
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,NMR Expertise Centre, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Anne-Mare de Vries
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium.,Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
| | - José C Martins
- Department of Organic and Macromolecular Chemistry, NMR and Structure Analysis Research Group, Ghent University, Gent, Oost-Vlaanderen 9000, Belgium
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137
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Ju L, Lyu A, Hao H, Shen W, Cui H. Deep Learning-Assisted Three-Dimensional Fluorescence Difference Spectroscopy for Identification and Semiquantification of Illicit Drugs in Biofluids. Anal Chem 2019; 91:9343-9347. [DOI: 10.1021/acs.analchem.9b01315] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Li Ju
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Aihua Lyu
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Hongxia Hao
- Collaborative Innovation Center of Judicial Civilization and Key Laboratory of Evidence Science, China University of Political Science and Law, Beijing 100088, P. R. China
| | - Wen Shen
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Hua Cui
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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138
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Ma F, Qi L, Einarson O, Sen D, Yu HZ. Divergent Pair of Ultrasensitive Mechanoelectronic Nanoswitches Made out of DNA. Anal Chem 2019; 91:8244-8251. [DOI: 10.1021/acs.analchem.9b00896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fen Ma
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry (Ministry of Education), College of Chemistry and Materials Science, Northwest University, Xi′an, Shaanxi 710127, China
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139
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Poltorak L, Sudhölter EJ, de Puit M. Electrochemical cocaine (bio)sensing. From solid electrodes to soft junctions. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.02.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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140
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Wu B, Cao B, Taylor IM, Woeppel K, Cui XT. Facile Synthesis of a 3,4-Ethylene-Dioxythiophene (EDOT) Derivative for Ease of Bio-Functionalization of the Conducting Polymer PEDOT. Front Chem 2019; 7:178. [PMID: 30984745 PMCID: PMC6450363 DOI: 10.3389/fchem.2019.00178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/07/2019] [Indexed: 11/21/2022] Open
Abstract
In the pursuit of conducting polymer based bio-functional devices, a cost-effective and high yield synthesis method for a versatile monomer is desired. We report here a new synthesis strategy for a versatile monomer 2-methylene-2,3-dihydrothieno (3,4-b) (1,4) dioxine, or 3,4-ethylenedioxythiophene with a exomethylene side group (EDOT-EM). Compared to the previously reported synthesis route, the new strategy uses less steps, with faster reaction rate, and higher yield. The presence of EM group opens up endless possibility for derivatization via either hydro-alkoxy addition or thiol-ene click chemistry. EDOT-EM could be polymerized into stable and low impedance PEDOT-EM polymer using electro-polymerization method on different conducting substrates at both macro and micro scales. Facile post-functionalization of PEDOT-EM with molecules of varying size and functionality (from small molecules to DNAs and proteins) was achieved. The new synthetic route of EDOT-EM and the ease of post-functionalization of PEDOT-EM will greatly accelerate the use of conducting polymer in a broad range of organic electronics and bioelectronics applications.
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Affiliation(s)
- Bingchen Wu
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bin Cao
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ian Mitch Taylor
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kevin Woeppel
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xinyan Tracy Cui
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, United States
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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141
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Zhao Y, Xu Y, Zhang M, Xiang J, Deng C, Wu H. An electrochemical dual-signaling aptasensor for the ultrasensitive detection of insulin. Anal Biochem 2019; 573:30-36. [PMID: 30862445 DOI: 10.1016/j.ab.2019.02.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/28/2019] [Accepted: 02/28/2019] [Indexed: 01/06/2023]
Abstract
Insulin plays a central role in physiological glycolmetabolism and is associated with diabetes and related diseases. In this work, a dual-signaling electrochemical aptasensor for insulin detection with high sensitivity and specificity has been reported. Methylene blue (MB)-modified insulin-binding aptamer (IBA) as "signal-off" probe, and (DNA2)/Ferrocene (Fc) co-modified gold nanoparticles (DNA2Fc@GNPs) as the "signal-on" probe were integrated with linker mDNA to fabricate the DNA2Fc@GNPs/mDNA/MB-IBA modified Au electrode as the sensing interface, and the current responses of MB and Fc were used as signal indicators. As expected, the incubation of insulin with DNA2Fc@GNPs/mDNA/MB-IBA/Au electrode resulted in the current responses of MB and Fc decreased and increased, respectively. Based on this strategy, the detection of insulin was successfully achieved, and a linear range from 10 pM to 10 nM with the detectable lowest concentration of 0.1 pM was obtained. By measuring the insulin concentrations in serum samples, this proposed aptasensor has been proven to be of high specificity and accuracy. Moreover, the dual-signaling is useful for the more accurate and reproducible detection through their self-referencing capability. This aptasensor possesses such advantages as simplicity, rapid responses, high sensitivity, specificity and accuracy, which is significant for improving the diagnosis of insulin-related diseases.
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Affiliation(s)
- Yana Zhao
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China
| | - Youyou Xu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China
| | - Manman Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China
| | - Juan Xiang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China
| | - Chunyan Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China.
| | - Huiyun Wu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, PR China.
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142
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Idili A, Gerson J, Parolo C, Kippin T, Plaxco KW. An electrochemical aptamer-based sensor for the rapid and convenient measurement of L-tryptophan. Anal Bioanal Chem 2019; 411:4629-4635. [PMID: 30796485 DOI: 10.1007/s00216-019-01645-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/09/2019] [Accepted: 01/24/2019] [Indexed: 01/01/2023]
Abstract
The field of precision medicine-the possibility to accurately tailor pharmacological treatments to each specific patient-would be significantly advanced by the ability to rapidly, conveniently, and cost-effectively measure biomarkers directly at the point of care. Electrochemical aptamer-based (E-AB) sensors appear a promising approach to this end due to their low cost, ease of use, and good analytical performance in complex clinical samples. Thus motivated, we present here the development of an E-AB sensor for the measurement of the amino acid L-tryptophan, a diagnostic marker indicative of a number of metabolic and mental health disorders, in urine. The sensor employs a previously reported DNA aptamer able to recognize the complex formed between tryptophan and a rhodium-based receptor. We adopted the aptamer to the E-AB sensing platform by truncating it, causing it to undergo a binding-induced conformational change, modifying it with a redox-reporting methylene blue, and attaching it to an interrogating electrode. The resulting sensor is able to measure tryptophan concentrations in the micromolar range in minutes and readily discriminates between its target and other aromatic and non-aromatic amino acids. Using it, we demonstrate the measurement of clinically relevant tryptophan levels in synthetic urine in a process requiring only a single dilution step. The speed and convenience with which this is achieved suggest that the E-AB platform could significantly improve the ease and frequency with which metabolic diseases are monitored. Graphical Abstract.
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Affiliation(s)
- Andrea Idili
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Julian Gerson
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Claudio Parolo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Tod Kippin
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Department of Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA. .,Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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143
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An Z, Jang CH. Simple and Label-Free Liquid Crystal-based Optical Sensor for Highly Sensitive and Selective Endotoxin Detection by Aptamer Binding and Separation. ChemistrySelect 2019. [DOI: 10.1002/slct.201803774] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zongfu An
- Department of Bionano; Gachon University, Seongnam-daero1342, Sujeong-gu, Seongnam-si, Gyeonggi-do; 13120 Republic of Korea
| | - Chang-Hyun Jang
- Department of Chemistry; Gachon University, Seongnam-daero1342, Sujeong-gu, Seongnam-si, Gyeonggi-do; 13120 Republic of Korea
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144
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Zhang W, Yang F, Ou D, Lin G, Huang A, Liu N, Li P. Prediction, docking study and molecular simulation of 3D DNA aptamers to their targets of endocrine disrupting chemicals. J Biomol Struct Dyn 2019; 37:4274-4282. [PMID: 30477404 DOI: 10.1080/07391102.2018.1547222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Typical endocrine disrupting chemicals, including BPA (Bisphenol A), E2 (17-β-Estradiol) and PCB 72 (polychlorinated biphenyl 72), are commonly and widely present in the environment with good chemical stability that are difficult to decompose in vitro and in vivo. Most of the high-qualified antibodies are required as the key biomaterials to fabricate the immunosensor for capturing and detecting. As an ideal alternative, the short-chain oligonucleotides (aptamer) are essentially and effectively employed with the advantages of small size, chemical stability and high effectiveness for monitoring these environmental contaminants. However, the molecular interaction, acting site and mode are still not well understood. In this work, we explored the binding features of the aptamers with their targeting ligands. The molecular dynamics simulations were performed on the aptamer-ligand complex systems. The stability of each simulation system was evaluated based on its root-mean-square deviation. The affinities of these proposed ligands and the predicted binding sites are analyzed. According to the binding energy analysis, the affinities between ligands and aptamers and the stability of the systems are BPA > PCB 72 >E2. Trajectory analysis for these three complexes indicated that these three ligands were able to steadily bind with aptamers at docking site from 0 to 50 ns and contributed to alteration of conformation of aptamers.
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Affiliation(s)
- Weiwen Zhang
- The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou , P. R. China
| | - Fengxiao Yang
- The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou , P. R. China
| | - Dejin Ou
- The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou , P. R. China
| | - Ge Lin
- The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou , P. R. China
| | - Aiyun Huang
- The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou , P. R. China
| | - Nan Liu
- General Practice Center, Nanhai Hospital, Southern Medical University , Foshan , P. R. China.,School of Public Health, Guangzhou Medical University , Guangzhou , P. R. China
| | - Pinle Li
- School of Public Health, Guangzhou Medical University , Guangzhou , P. R. China
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145
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Tavakkoli N, Soltani N, Mohammadi F. A nanoporous gold-based electrochemical aptasensor for sensitive detection of cocaine. RSC Adv 2019; 9:14296-14301. [PMID: 35519350 PMCID: PMC9066177 DOI: 10.1039/c9ra01292c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022] Open
Abstract
The increasing application of aptamers in bioassays has triggered a lot of research interest for development of highly sensitive and selective sensing platforms. Herein, we report on the design of a sensitive cocaine biosensor by immobilizing the 5′-disulfide-functionalized end of an aptamer sequence on a nanoporous gold (NPG) electrode followed by the conjugation of its 3′-amino-functionalized end to 2,5-dihydroxybenzoic acid (DHBA) as the redox probe. In the presence of cocaine, the aptamer undergoes a conformational change from an open unfolded state to a closed conformation, which reduces the distance between DHBA and the electrode surface, resulting in the enhanced electron-transfer efficiency. Using square wave voltammetric method and under the optimal conditions, the cocaine aptasensor presented two linear responses in the concentration ranges between 0.05–1 and 1–35 μM, with an excellent detection limit of 21 nM. The proposed aptasensor provides a simple and low-cost method for cocaine detection with good reproducibility and accuracy. Furthermore, it could be regarded as a general model to investigate the unique function of aptamer-functionalized nanostructured electrodes to stablish highly advanced electrochemical biosensors for various target analytes of diagnostic importance. The increasing application of aptamers in bioassays has triggered a lot of research interest for development of highly sensitive and selective sensing platforms.![]()
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146
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Kanamori T, Masaki Y, Oda Y, Ohzeki H, Ohkubo A, Sekine M, Seio K. DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine. Org Biomol Chem 2019; 17:2077-2080. [DOI: 10.1039/c8ob02747a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence turn-on detection of adenosine based on microenvironmental and conformational changes of a fluorescent molecular rotor in the DNA triplex is reported.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yuki Oda
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Hiroki Ohzeki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Akihiro Ohkubo
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
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147
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A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules. Biosens Bioelectron 2018; 127:108-117. [PMID: 30594890 DOI: 10.1016/j.bios.2018.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023]
Abstract
Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photoisomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.
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148
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He Y, Chen S, Huang L, Wang Z, Wu Y, Fu F. Combination of Magnetic-Beads-Based Multiple Metal Nanoparticles Labeling with Hybridization Chain Reaction Amplification for Simultaneous Detection of Multiple Cancer Cells with Inductively Coupled Plasma Mass Spectrometry. Anal Chem 2018; 91:1171-1177. [DOI: 10.1021/acs.analchem.8b05085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ye He
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Shilong Chen
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Lin Huang
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zongwen Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongning Wu
- China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - FengFu Fu
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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149
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Gonzalez J, Martinez-Ortiz F, Torralba E, Molina A. Kinetic Influence of Surface Charge Transfer Reactions Preceded by Non-Electrochemical Processes on the Response in Cyclic Voltammetry. ChemElectroChem 2018. [DOI: 10.1002/celc.201801275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joaquin Gonzalez
- Departamento de Química Física Facultad de Química Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | - Francisco Martinez-Ortiz
- Departamento de Química Física Facultad de Química Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
| | | | - Angela Molina
- Departamento de Química Física Facultad de Química Regional Campus of International Excellence “Campus Mare Nostrum”; Universidad de Murcia; 30100 Murcia Spain
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150
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Selection of highly specific aptamers to Vibrio parahaemolyticus using cell-SELEX powered by functionalized graphene oxide and rolling circle amplification. Anal Chim Acta 2018; 1052:153-162. [PMID: 30685034 DOI: 10.1016/j.aca.2018.11.047] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/30/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023]
Abstract
Cell-SELEX is a powerful tool to screen aptamers binding to living cellular organisms such as bacteria, fungi and even oncocytes. Here, we developed an advanced cell-SELEX strategy featuring functionalized graphene oxide (GO) and isothermal rolling circle amplification (RCA) to select aptamers against a prevailing foodborne pathogen, Vibrio parahaemolyticus. Polyethyleneglycol (PEG) and chitosan (CTS) were grafted onto the sheet-like GO molecules to synthesize a PC-GO material. TEM and FT-IR characterization demonstrated that the PC-GO composites were near-nanometric scale and tethered with PEG and CTS moieties, a property that significantly improved its solubility in biological buffer solutions used in cell-SELEX process. PC-GO could bind with ssDNAs with lower affinities to target cells, therefore the selection efficiency is greatly enhanced. The cell-binding aptamer candidates (CACs) were amplified by 107 fold using complementary ring mediated (CRM-RCA), a created amplification method that generate single-stranded products, which could be directly used in the next round selection. As fueled by PC-GO and CRM-RCA, four highly specific aptamers with lowest Kd value of 10.3 ± 2.5 nM were obtained. Flow cytometry analysis showed that all the four aptamers exhibited more than 75% binding affinity to V. parahaemolyticus than to other foodborne bacteria (less than 18%). Simple procedure, high efficiency, and free from expensive thermal cycler (required by PCR amplification) will enable the established strategy to find its applications in aptamer selecting against fungi, stem and cancerous cells as well.
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