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Duan M, Ren K, Chen X, Chang Y, Lv Z, Wang Z, Wu S, Duan N. Discovery and design of an aptamer that inhibits Shiga toxin type 2 activity by blocking Stx2 B subunit-Gb3 interaction. Int J Biol Macromol 2024; 277:134365. [PMID: 39089540 DOI: 10.1016/j.ijbiomac.2024.134365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Shiga toxin (Stx) is the definitive virulence factor of Stx-producing Escherichia coli. This bacterial pathogen can contaminate food and threaten human health. Binding of the B subunit of Stx to the specific receptor globotriaosylceramide (Gb3) on the cell membrane is a key step for Stx to enter cells and exert its toxicity. In this work, we aimed to screen for aptamers targeting the Stx 2 B subunit, to interfere with the interaction of Stx2 B subunit and Gb3, thereby blocking Stx2 from entering cells. The results of molecular simulation docking, competitive ELISA, flow cytometry, and laser confocal microscopy confirmed that aptamers S4, S5, and S6 can mediate the interaction between Stx2 B subunit and Gb3. To further improve the inhibition effect, multiple aptamer sequences were tailored and were fused. The bivalent modification aptamer B2 inhibited Stx2 toxicity to Vero cells with inhibition rate of 53 %. Furthermore, the aptamer B2 reduced Stx2 damage to the mice, indicating that it has great potential to interfere with Stx2 binding to Gb3 receptors in vivo and in vitro. This work provides a theoretical and experimental basis for the application of aptamers in the inhibition of Stx2 toxicity and control of food hazards.
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Affiliation(s)
- Mengxia Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Kexin Ren
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaowan Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuting Chang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ziyu Lv
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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2
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Kosel J, Ropret P. The potential of aptamers for the analysis of ceramic bound proteins found within pottery. Sci Rep 2024; 14:19947. [PMID: 39198509 PMCID: PMC11358422 DOI: 10.1038/s41598-024-70048-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
Archaeological pottery are the most numerous objects found during excavations and reflect the culinary practices of the past. However, their functionality for cooking/storing specific foods or drinks cannot be deduced solely from comparing their shapes and sizes. Analysis of protein residues bound to ceramics can reveal the protein/animal type through their amino acid sequence, thus enabling direct identification of food types. Therefore, the aim of our experimental study was to test sixteen aptamers for the analysis of proteinaceous organic residues found within the porous structure of pottery. Traditionally prepared archaeological ceramic replicas were cooked for 5 days in various food/protein suspensions, were UV aged, buried for a year, excavated, and extensively cleaned. Their shards were analysed using immunofluorescence microscopy with aptamers. Results show that eight aptamers (Clone1 and Kirby for egg residuals; seqU5 and BLG14 for milk residuals; HA for blood residuals; Gli4 for gluten residuals; Par1 for fish residuals; and D1 for collagen residuals) produced a successful/specific immunofluorescence microscopy result when they were hybridised to shards containing target protein residuals. Interestingly, on whole egg control samples, when the egg lysozyme-targeting aptamer Kirby was used, fluorescence intensity was 3.1 times greater compared to that observed with anti-ovalbumin antibodies.
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Affiliation(s)
- Janez Kosel
- Institute for the Protection of Cultural Heritage of Slovenia, Conservation Centre, Research Institute, Ljubljana, Slovenia.
| | - Polonca Ropret
- Institute for the Protection of Cultural Heritage of Slovenia, Conservation Centre, Research Institute, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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3
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Li L, Li M, Qiu Y, Dong Y. A sensitive CRISPR/Cas12a-assisted fluorescent aptasensor for rapid detection of food allergens. Int J Biol Macromol 2024; 274:133444. [PMID: 38936584 DOI: 10.1016/j.ijbiomac.2024.133444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Food allergens elicit abnormal immune system responses among allergic individuals and sensitive detection for allergenic ingredient is greatly significant. To address this need, a novel fluorescent aptasensor, assisted by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), have been developed for food allergens. In this study, aptamer offers distinctive recognition capabilities in binding specific targets, while CRISPR-associated-12a protein (Cas12a) holds precise cis-cleavage for cutting fluorescent signal probes. Notably, the utilization of Cas12a cis-cleavage activity, rather than trans-cleavage, eliminates the necessity for additional fluorescent probes, thus reducing interference between substances and enhancing sensitivity. Throughout the process, complementary DNA (cDNA) plays a crucial dual role in target recognition conversion and signal presentation, representing a key challenge and innovative aspect of this study. To evaluate the performance of the aptasensor, lysozyme (LYS) is employed as a representative model target of food allergens. Under optimal conditions, the developed aptasensor could achieve an exceptional low limit of detection (LOD) of 6.10 pM with a dynamic detection range of 10 pM-320 pM. The aptasensor demonstrates high selectivity and great recovery rates. This strategy yields promising outcomes, holding the potential to serve as a valuable reference for various food allergens detection.
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Affiliation(s)
- Ling Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Menglei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Yinghua Qiu
- Center for Molecular Diagnostics and Precision Medicine, Drexel University College of Medicine, Philadelphia 19102, USA
| | - Yiyang Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
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4
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Toma L, Mattarozzi M, Ronda L, Marassi V, Zattoni A, Fortunati S, Giannetto M, Careri M. Are Aptamers Really Promising as Receptors for Analytical Purposes? Insights into Anti-Lysozyme DNA Aptamers through a Multitechnique Study. Anal Chem 2024; 96:2719-2726. [PMID: 38294352 DOI: 10.1021/acs.analchem.3c05883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Aptamers are recognition elements increasingly used for the development of biosensing strategies, especially in the detection of proteins or small molecule targets. Lysozyme, which is recognized as an important biomarker for various diseases and a major allergenic protein found in egg whites, is one of the main analytical targets of aptamer-based biosensors. However, since aptamer-based strategies can be prone to artifacts and data misinterpretation, rigorous strategies for multifaceted characterization of the aptamer-target interaction are needed. In this work, a multitechnique approach has been devised to get further insights into the binding performance of the anti-lysozyme DNA aptamers commonly used in the literature. To study molecular interactions between lysozyme and different anti-lysozyme DNA aptamers, measurements based on a magneto-electrochemical apta-assay, circular dichroism spectroscopy, fluorescence spectroscopy, and asymmetrical flow field-flow fractionation were performed. The reliability and versatility of the approach were proved by investigating a SELEX-selected RNA aptamer reported in the literature, that acts as a positive control. The results confirmed that an interaction in the low micromolar range is present in the investigated binding buffers, and the binding is not associated with a conformational change of either the protein or the DNA aptamer. The similar behavior of the anti-lysozyme DNA aptamers compared to that of randomized sequences and polythymine, used as negative controls, showed nonsequence-specific interactions. This study demonstrates that severe testing of aptamers resulting from SELEX selection is the unique way to push these biorecognition elements toward reliable and reproducible results in the analytical field.
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Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- CNR, Institute of Biophysics, Pisa 56124, Italy
| | - Valentina Marassi
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Andrea Zattoni
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Simone Fortunati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
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Zheng M, Ye J, Liu H, Wu Y, Shi Y, Xie Y, Wang S. FAM Tag Size Separation-Based Capture-Systematic Evolution of Ligands by Exponential Enrichment for Sterigmatocystin-Binding Aptamers with High Specificity. Anal Chem 2024; 96:710-720. [PMID: 38175632 DOI: 10.1021/acs.analchem.3c03675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sterigmatocystin (ST) is a known toxin whose aptamer has rarely been reported because ST is a water-insoluble small-molecule target with few active sites, leading to difficulty in obtaining its aptamer using traditional target fixation screening methods. To obtain aptamer for ST, we incorporated FAM tag size separation into the capture-systematic evolution of ligands by exponential enrichment and combined it with molecular activation for aptamer screening. The screening process was monitored using a quantitative polymerase chain reaction fluorescence amplification curve and recovery of negative-, counter-, and positive-selected ssDNA. The affinity and specificity of the aptamer were verified by constructing an aptamer-affinity column, and the binding sites were predicted using molecular docking simulations. The results showed that the Kd value of the H Seq02 aptamer was 25.3 nM. The aptamer-affinity column based on 2.3 nmol of H Seq02 exhibited a capacity of about 80 ng, demonstrating better specificity than commercially available antibody affinity columns. Molecular simulation docking predicted the binding sites for H Seq02 and ST, further explaining the improved specificity. In addition, circular dichroism and isothermal titration calorimetry were used to verify the interaction between the aptamer and target ST. This study lays the foundation for the development of a new ST detection method.
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Affiliation(s)
- Mengyao Zheng
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Jin Ye
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hongmei Liu
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Yu Wu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yakun Shi
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Yanli Xie
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
| | - Songxue Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China
- Academy of National Food and Strategic Reserves Administration, Beijing 102600, China
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Shi L, Jin Y, Liu J. Electrostatic-Mediated Binding of DNA to Lysozymes: Evaluation of Aptamer-Based Assays for Highly Positively Charged Targets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:14774-14781. [PMID: 37782842 DOI: 10.1021/acs.langmuir.3c02208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Lysozymes are a highly popular protein target for the development of aptamer-based biosensors. Because a lysozyme is a polycation and DNA is a polyanion, it is essential to separate the contribution of nonspecific electrostatic interactions from specific aptamer binding. In this study, various factors affecting the binding of DNA and lysozymes, including the DNA sequence, DNA length, pH, and salt concentration, were explored using fluorescence polarization. We concluded that direct fluorescence polarization and fluorescence intensity changes are unlikely to be directly applicable for aptamer-based biosensors to detect lysozymes because all of the tested DNA sequences showed binding. These fundamental studies confirm the dominant role of electrostatic binding. We further evaluated three other methods, including label-free fluorescent detection using a DNA staining dye, label-free colorimetric detection using gold nanoparticles, and a fluorescent sensor based on the strand displacement reaction. In each case, we focused on a random DNA sequence that is not expected to bind to the lysozyme as an aptamer. Of all the methods, only the strand displacement strategy can be potentially used to evaluate aptamer binding, as the other methods all responded to nonaptamer sequences. This study provides valuable insights for assaying aptamer binding to cationic proteins that can exhibit a nonspecific attraction to DNA.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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7
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Chopra A, Swami A, Sharma R, Devi N, Mittal S, Sharma RK, Wangoo N. Femtomolar detection of staphylococcal enterotoxin 'B' using a fluorescent quantum dot based hybrid Apta-immunosensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 287:122036. [PMID: 36327805 DOI: 10.1016/j.saa.2022.122036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Food poisoning is a gastrointestinal illness caused by food-borne enterotoxin produced by the bacterium Staphylococcus aureus. The effective dose of Staphylococcal enterotoxin 'B' (SEB) is estimated to be 0.4 ng/kg of body weight, whereas the 50 % lethal dose is found to be 20 ng/kg of body weight for humans exposed by the inhalation route. The present report highlights the development of a fluorescence resonance energy transfer (FRET) based assay for the detection of Staphylococcal enterotoxin. Highly fluorescent, aqueous quantum dots were synthesized and conjugated with Staphylococcal enterotoxin 'B' specific bioreceptors. SEB specific aptamer and SEB antibody were labeled with fluorescent quantum dots for recognizing and binding two separate epitopes in the SEB. A combination of two probes against different epitopic regions in a homogeneous sandwich assay format enhanced the sensitivity and specificity of SEB detection. In the presence of the enterotoxin, both the aptamer and antibody came in close proximity with each other and FRET was observed. A linear decrease in the fluorescence at 562 nm and a corresponding increase in the signal at 644 nm was observed with increasing concentrations of SEB, when excited at the absorption maximum of quantum dots. The limit of detection for the developed assay obtained was less than 1 ng/ml. The method was employed in apple juice and quantitated using Enzyme-linked Immunosorbent Assay (ELISA). The designed assay was rapid and robust and can be extrapolated as a platform for the detection of various disease-causing agents of biomedical significance.
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Affiliation(s)
- Adity Chopra
- Department of Immunology, Rikshopitalet, Oslo University Hospital, Oslo, Norway
| | - Anuradha Swami
- Department of Applied Sciences, University Institute of Engineering & Technology (U.I.E.T.), Panjab University, Sector-25, Chandigarh 160014, India; Centre for Nanoscience & Nanotechnology, Panjab University, Sector 25, Chandigarh 160014, India
| | - Rohit Sharma
- Centre for Stem Cell and Tissue Engineering, Panjab University, Sector 14, Chandigarh 160014, India
| | - Neha Devi
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160014, India
| | - Sherry Mittal
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160014, India
| | - Rohit K Sharma
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160014, India
| | - Nishima Wangoo
- Department of Applied Sciences, University Institute of Engineering & Technology (U.I.E.T.), Panjab University, Sector-25, Chandigarh 160014, India.
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Rasetti-Escargueil C, Avril A. Medical Countermeasures against Ricin Intoxication. Toxins (Basel) 2023; 15:toxins15020100. [PMID: 36828415 PMCID: PMC9966136 DOI: 10.3390/toxins15020100] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Ricin toxin is a disulfide-linked glycoprotein (AB toxin) comprising one enzymatic A chain (RTA) and one cell-binding B chain (RTB) contained in the castor bean, a Ricinus species. Ricin inhibits peptide chain elongation via disruption of the binding between elongation factors and ribosomes, resulting in apoptosis, inflammation, oxidative stress, and DNA damage, in addition to the classically known rRNA damage. Ricin has been used in traditional medicine throughout the world since prehistoric times. Because ricin toxin is highly toxic and can be readily extracted from beans, it could be used as a bioweapon (CDC B-list). Due to its extreme lethality and potential use as a biological weapon, ricin toxin remains a global public health concern requiring specific countermeasures. Currently, no specific treatment for ricin intoxication is available. This review focuses on the drugs under development. In particular, some examples are reviewed to demonstrate the proof of concept of antibody-based therapy. Chemical inhibitors, small proteins, and vaccines can serve as alternatives to antibodies or may be used in combination with antibodies.
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Affiliation(s)
- Christine Rasetti-Escargueil
- Unité des Bactéries Anaérobies et Toxines, Institut Pasteur, 25 Avenue du Docteur Roux, 75015 Paris, France
- Correspondence:
| | - Arnaud Avril
- Unité Immunopathologies, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
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Ma L, Wei Y, Mao Y, Liu Y, Li G, Deng Y. An accurate method for antigen β-conglycinin detection in soybean meal. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Calabria D, Zangheri M, Pour SRS, Trozzi I, Pace A, Lazzarini E, Calabretta MM, Mirasoli M, Guardigli M. Luminescent Aptamer-Based Bioassays for Sensitive Detection of Food Allergens. BIOSENSORS 2022; 12:644. [PMID: 36005040 PMCID: PMC9405952 DOI: 10.3390/bios12080644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/06/2023]
Abstract
The presence of hidden allergens in food products, often due to unintended contamination along the food supply chain (production, transformation, processing, and transport), has raised the urgent need for rapid and reliable analytical methods for detecting trace levels of such species in food products. Indeed, food allergens represent a high-risk factor for allergic subjects due to potentially life-threatening adverse reactions. Portable biosensors based on immunoassays have already been developed as rapid, sensitive, selective, and low-cost analytical platforms that can replace analyses with traditional bench-top instrumentation. Recently, aptamers have attracted great interest as alternative biorecognition molecules for bioassays, since they can bind a variety of targets with high specificity and selectivity, and they enable the development of assays exploiting a variety of transduction and detection technologies. In particular, aptasensors based on luminescence detection have been proposed, taking advantage of the development of ultrasensitive tracers and enhancers. This review aims to summarize and discuss recent efforts in the field of food allergen analysis using aptamer-based bioassays with luminescence detection.
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Affiliation(s)
- Donato Calabria
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
| | - Martina Zangheri
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Agrofood Research (CIRI AGRO), Alma Mater Studiorum, University of Bologna, Via Quinto Bucci 336, I-47521 Cesena, Italy
- Interdepartmental Centre for Industrial Research in Advanced Mechanical Engineering Applications and Materials Technology (CIRI MAM), Alma Mater Studiorum, University of Bologna, Viale Risorgimento 2, I-40136 Bologna, Italy
| | - Seyedeh Rojin Shariati Pour
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Ilaria Trozzi
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Andrea Pace
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Elisa Lazzarini
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Maria Maddalena Calabretta
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Mara Mirasoli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
| | - Massimo Guardigli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
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Murugesan R, Sureshkumar R, Radhakrishnan A, Jupudi S, Chennu M. Multiwalled Carbon Nanotubes as Nanomaterial Tool in the Management of Prostate Cancer: A Possible Nanoformulation Approach. Adv Pharm Bull 2022; 12:509-514. [PMID: 35935048 PMCID: PMC9348525 DOI: 10.34172/apb.2022.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/10/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
Prostate cancer (PCa) is one of the leading diseases in men all over the world caused due to over-expression of prostate-specific membrane antigen (PSMA). Currently, the detection and targeting of PCa is one of the major challenges in the prostate gland. Therefore, Bruton tyrosine kinase inhibitor molecules like ibrutinib (Ibr) loaded with nanomaterials like multi-walled carbon nanotubes (MWCNTs), which has good physico-chemical properties may be the best regimen to treat PCa. In this strategy, the chemically modified MWCNTs have excellent 'Biosensing' properties makes it easy for detecting PCa without fluorescent agent and thus targets particular site of PCa. In the present study, Ibr/MWCNTs conjugated with T30 oligonucleotide may selectively target and inhibit PSMA thereby reduce the over-expression in PCa. Hence, the proposed formulation design can extensively reduce the dosage regimen without any toxic effect. Additionally, the present hypothesis also revealed the binding mode of Ibr in the catalytic pocket of PSMA by in silico method. Therefore, we presume that if this hypothesis proves correct, it becomes an additional novel tool and one of the conceivable therapeutic options in treating PCa.
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Affiliation(s)
- Raja Murugesan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, India
| | - Raman Sureshkumar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, India
| | - Arun Radhakrishnan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, India
| | - Manisha Chennu
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, India
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Miller AA, Rao AS, Nelakanti SR, Kujalowicz C, Shi T, Rodriguez T, Ellington AD, Stovall GM. Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations. Anal Chem 2022; 94:7731-7737. [PMID: 35420426 PMCID: PMC9179646 DOI: 10.1021/acs.analchem.1c04407] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aptamers have been the subject of more than 144 000 papers to date. However, there has been a growing concern that discrepancies in the reporting of aptamer research limit the reliability of these reagents for research and other applications. These observations noting inconsistencies in the use of our RNA antilysozyme aptamer served as an impetus for our systematic review of the reporting of aptamer sequences in the literature. Our detailed examination of the literature citing the RNA antilysozyme aptamer revealed that 93% of the 61 publications reviewed reported unexplained altered sequences with 96% of those using DNA variants. The 10 most cited aptamers were examined using a standardized methodology in order to categorize the extent to which the sequences themselves and altered sequences were adequately described in the literature. Our review of 780 aptamer publications spanned decades, multiple journals, and research groups and revealed that 41% of the papers reported unexplained sequence alterations or omitted sequences. We identified 10 common categories of sequence alterations including deletions, substitutions, and additions, among others. Overall, our findings can be used as a starting point for building better practices in author submissions and publication standards, elevating the rigor and reproducibility of aptamer research.
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Affiliation(s)
- Alexandra A Miller
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Abhijit S Rao
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sujana R Nelakanti
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher Kujalowicz
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ted Shi
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ted Rodriguez
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D Ellington
- Institute for Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Gwendolyn M Stovall
- Texas Institute for Discovery Education in Science Freshman Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States.,Texas Institute for Discovery Education in Science High School Research Initiative, The University of Texas at Austin, Austin, Texas 78712, United States
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13
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Marassi V, Mattarozzi M, Toma L, Giordani S, Ronda L, Roda B, Zattoni A, Reschiglian P, Careri M. FFF-based high-throughput sequence shortlisting to support the development of aptamer-based analytical strategies. Anal Bioanal Chem 2022; 414:5519-5527. [PMID: 35182166 PMCID: PMC9242963 DOI: 10.1007/s00216-022-03971-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 01/13/2023]
Abstract
Aptamers are biomimetic receptors that are increasingly exploited for the development of optical and electrochemical aptasensors. They are selected in vitro by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure, but although they are promising recognition elements, for their reliable applicability for analytical purposes, one cannot ignore sample components that cause matrix effects. This particularly applies when different SELEX-selected aptamers and related truncated sequences are available for a certain target, and the choice of the aptamer should be driven by the specific downstream application. In this context, the present work aimed at investigating the potentialities of asymmetrical flow field-flow fractionation (AF4) with UV detection for the development of a screening method of a large number of anti-lysozyme aptamers towards lysozyme, including randomized sequences and an interfering agent (serum albumin). The possibility to work in native conditions and selectively monitor the evolution of untagged aptamer signal as a result of aptamer-protein binding makes the devised method effective as a strategy for shortlisting the most promising aptamers both in terms of affinity and in terms of selectivity, to support subsequent development of aptamer-based analytical devices.
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Affiliation(s)
- Valentina Marassi
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy. .,byFlow Srl, Bologna, Italy.
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.
| | - Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
| | - Stefano Giordani
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parco Area delle Scienze, 23/A, 43124, Parma, Italy.,Institute of Biophysics, CNR, 56124, Pisa, Italy
| | - Barbara Roda
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy.,byFlow Srl, Bologna, Italy
| | - Andrea Zattoni
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy.,byFlow Srl, Bologna, Italy
| | - Pierluigi Reschiglian
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna, Italy.,byFlow Srl, Bologna, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
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14
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Kilgour M, Liu T, Walker BD, Ren P, Simine L. E2EDNA: Simulation Protocol for DNA Aptamers with Ligands. J Chem Inf Model 2021; 61:4139-4144. [PMID: 34435773 PMCID: PMC9536994 DOI: 10.1021/acs.jcim.1c00696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present E2EDNA, a simulation protocol and accompanying code for the molecular biophysics and materials science communities. This protocol is both easy to use and sufficiently efficient to simulate single-stranded (ss)DNA and small analyte systems that are important to cellular processes and nanotechnologies such as DNA aptamer-based sensors. Existing computational tools used for aptamer design focus on cost-effective secondary structure prediction and motif analysis in the large data sets produced by SELEX experiments. As a rule, they do not offer flexibility with respect to the choice of the theoretical engine or direct access to the simulation platform. Practical aptamer optimization often requires higher accuracy predictions for only a small subset of sequences suggested, e.g., by SELEX experiments, but in the absence of a streamlined procedure, this task is extremely time and expertise intensive. We address this gap by introducing E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy. As a case study, we simulate a DNA-UTP (uridine triphosphate) complex in water using the state-of-the-art AMOEBA polarizable force field. The code is available at https://github.com/InfluenceFunctional/E2EDNA.
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Affiliation(s)
- Michael Kilgour
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, H3A 0B8, Canada
| | - Tao Liu
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, H3A 0B8, Canada
| | | | - Pengyu Ren
- Cockrell School of Engineering, University of Texas at Austin
| | - Lena Simine
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, H3A 0B8, Canada
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15
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Raicopol M, Pilan L. The Role of Aryldiazonium Chemistry in Designing Electrochemical Aptasensors for the Detection of Food Contaminants. MATERIALS 2021; 14:ma14143857. [PMID: 34300776 PMCID: PMC8303706 DOI: 10.3390/ma14143857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 01/19/2023]
Abstract
Food safety monitoring assays based on synthetic recognition structures such as aptamers are receiving considerable attention due to their remarkable advantages in terms of their ability to bind to a wide range of target analytes, strong binding affinity, facile manufacturing, and cost-effectiveness. Although aptasensors for food monitoring are still in the development stage, the use of an electrochemical detection route, combined with the wide range of materials available as transducers and the proper immobilization strategy of the aptamer at the transducer surface, can lead to powerful analytical tools. In such a context, employing aryldiazonium salts for the surface derivatization of transducer electrodes serves as a simple, versatile and robust strategy to fine-tune the interface properties and to facilitate the convenient anchoring and stability of the aptamer. By summarizing the most important results disclosed in the last years, this article provides a comprehensive review that emphasizes the contribution of aryldiazonium chemistry in developing electrochemical aptasensors for food safety monitoring.
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Affiliation(s)
- Matei Raicopol
- Costin Nenitzescu, Department of Organic Chemistry, Faculty of Applied Chemistry and Material Science, University Politehnica of Bucharest, 1-7 Gheorghe Polizu, 011061 Bucharest, Romania;
| | - Luisa Pilan
- Department of Inorganic Chemistry, Physical Chemistry and Electrochemistry, Faculty of Applied Chemistry and Material Science, University Politehnica of Bucharest, 1-7 Gheorghe Polizu, 011061 Bucharest, Romania
- Correspondence: ; Tel.: +40-21-402-3977
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16
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Niederlender S, Fontaine JJ, Karadjian G. Potential applications of aptamers in veterinary science. Vet Res 2021; 52:79. [PMID: 34078451 PMCID: PMC8172000 DOI: 10.1186/s13567-021-00948-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small nucleic acids that fold in a three-dimensional conformation allowing them to bind specifically to a target. This target can be an organic molecule, free or carried in cells or tissues, or inorganic components, such as metal ions. Analogous to monoclonal antibodies, aptamers however have certain advantages over the latter: e.g., high specificity for their target, no to low immunogenicity and easy in vitro selection. Since their discovery more than 30 years ago, aptamers have led to various applications, although mainly restricted to basic research. This work reviews the applications of aptamers in veterinary science to date. First, we present aptamers, how they are selected and their properties, then we give examples of applications in food and environmental safety, as well as in diagnosis and medical treatment in the field of veterinary medicine. Because examples of applications in veterinary medicine are scarce, we explore the potential avenues for future applications based on discoveries made in human medicine. Aptamers may offer new possibilities for veterinarians to diagnose certain diseases—particularly infectious diseases—more rapidly or “at the patient’s bedside”. All the examples highlight the growing interest in aptamers and the premises of a potential market. Aptamers may benefit animals as well as their owners, breeders and even public health in a “One Health” approach.
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Affiliation(s)
- Solène Niederlender
- École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 7 avenue du Général de Gaulle, 94700, Maisons-Alfort, France
| | - Jean-Jacques Fontaine
- UMR BIPAR 956, ANSES, INRAE, École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 7 avenue du Général de Gaulle, 94700, Maisons-Alfort, France
| | - Grégory Karadjian
- UMR BIPAR, Laboratoire de Santé Animale, ANSES, INRAE, École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 94700, Maisons-Alfort, France.
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17
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Senturk H, Eksin E, Işık Ö, İlaslan Z, Mısırlı F, Erdem A. Impedimetric aptasensor for lysozyme detection based on carbon nanofibres enriched screen-printed electrodes. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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An apta-aggregation based machine learning assay for rapid quantification of lysozyme through texture parameters. PLoS One 2021; 16:e0248159. [PMID: 33684138 PMCID: PMC7939288 DOI: 10.1371/journal.pone.0248159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/20/2021] [Indexed: 11/30/2022] Open
Abstract
A novel assay technique that involves quantification of lysozyme (Lys) through machine learning is put forward here. This article reports the tendency of the well- documented Ellington group anti-Lys aptamer, to produce aggregates when exposed to Lys. This property of apta-aggregation has been exploited here to develop an assay that quantifies the Lys using texture and area parameters from a photograph of the elliptical aggregate mass through machine learning. Two assay sets were made for the experimental procedure: one with high Lys concentration between 25–100 mM and another with low concentration between 1–20 mM. The high concentration set had a sample volume of 10 μl while the low concentration set had a higher sample volume of 100 μl, in order to obtain the statistical texture values reliably from the aggregate mass. The platform exhibited an experimental limit of detection of 1 mM and a response time of less than 10 seconds. Further, two potential operating modes for the aptamer were hypothesized for this aggregation property and the more accurate mode among the two was ascertained through bioinformatics studies.
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19
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Melinte G, Selvolini G, Cristea C, Marrazza G. Aptasensors for lysozyme detection: Recent advances. Talanta 2021; 226:122169. [PMID: 33676711 DOI: 10.1016/j.talanta.2021.122169] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Lysozyme is an enzyme existing in multiple organisms where it plays various vital roles. The most important role is its antibacterial activity in the human body; in fact, it is also called "the body's own antibiotic". Despite its proven utility, lysozyme can potentially trigger allergic reactions in sensitive individuals, even in trace amounts. Therefore, lysozyme determination in foods is becoming of paramount importance. Traditional detection methods are expensive, time-consuming and they cannot be applied for fast in-situ quantification. Electrochemical and optical sensors have attracted an increasing attention due to their versatility and ability to reduce the disadvantages of traditional methods. Using an aptamer as the bioreceptor, the sensor selectivity is amplified due to the specific recognition of the analyte. This review is presenting the progresses made in lysozyme determination by means of electrochemical and optical aptasensors in the last five years. A critical overview on the methodologies employed for aptamer immobilization and on the strategies for signal amplification of the assays will be described. Different optical and electrochemical aptasensors will be discussed and compared in terms of analytical performances, versatility and real samples applications.
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Affiliation(s)
- Gheorghe Melinte
- "Ugo Schiff" Chemistry Department, University of Florence, Via della Lastruccia 3, Sesto Fiorentino (FI), 50019, Italy; Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy, Strada Louis Pasteur 4, Cluj-Napoca, 400349, Romania
| | - Giulia Selvolini
- "Ugo Schiff" Chemistry Department, University of Florence, Via della Lastruccia 3, Sesto Fiorentino (FI), 50019, Italy
| | - Cecilia Cristea
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy, Strada Louis Pasteur 4, Cluj-Napoca, 400349, Romania.
| | - Giovanna Marrazza
- "Ugo Schiff" Chemistry Department, University of Florence, Via della Lastruccia 3, Sesto Fiorentino (FI), 50019, Italy; Istituto Nazionale Biostrutture e Biosistemi (INBB), Unit of Florence, Viale Delle Medaglie D'Oro 305, 00136 Roma, Italy.
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20
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Construction of an Enzymatically-Conjugated DNA Aptamer–Protein Hybrid Molecule for Use as a BRET-Based Biosensor. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10217646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA-protein conjugates are useful molecules for construction of biosensors. Herein, we report the development of an enzymatically-conjugated DNA aptamer–protein hybrid molecule for use as a bioluminescence resonance energy transfer (BRET)-based biosensor. DNA aptamers were enzymatically conjugated to a fusion protein via the catalytic domain of porcine circovirus type 2 replication initiation protein (PCV2 Rep) comprising residues 14–109 (tpRep), which was truncated from the full catalytic domain of PCV2 Rep comprising residues 1–116 by removing the flexible regions at the N- and C-terminals. For development of a BRET-based biosensor, we constructed a fusion protein in which tpRep was positioned between NanoLuc luciferase and a fluorescent protein and conjugated to single-stranded DNA aptamers that specifically bind to either thrombin or lysozyme. We demonstrated that the BRET ratios depended on the concentration of the target molecules.
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21
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Ma N, Ren X, Wang H, Kuang X, Fan D, Wu D, Wei Q. Ultrasensitive Controlled Release Aptasensor Using Thymine–Hg2+–Thymine Mismatch as a Molecular Switch for Hg2+ Detection. Anal Chem 2020; 92:14069-14075. [DOI: 10.1021/acs.analchem.0c03110] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ning Ma
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xiang Ren
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Huan Wang
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xuan Kuang
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Dawei Fan
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Dan Wu
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Qin Wei
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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22
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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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23
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Soucy JR, Bindas AJ, Koppes AN, Koppes RA. Instrumented Microphysiological Systems for Real-Time Measurement and Manipulation of Cellular Electrochemical Processes. iScience 2019; 21:521-548. [PMID: 31715497 PMCID: PMC6849363 DOI: 10.1016/j.isci.2019.10.052] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022] Open
Abstract
Recent advancements in electronic materials and subsequent surface modifications have facilitated real-time measurements of cellular processes far beyond traditional passive recordings of neurons and muscle cells. Specifically, the functionalization of conductive materials with ligand-binding aptamers has permitted the utilization of traditional electronic materials for bioelectronic sensing. Further, microfabrication techniques have better allowed microfluidic devices to recapitulate the physiological and pathological conditions of complex tissues and organs in vitro or microphysiological systems (MPS). The convergence of these models with advances in biological/biomedical microelectromechanical systems (BioMEMS) instrumentation has rapidly bolstered a wide array of bioelectronic platforms for real-time cellular analytics. In this review, we provide an overview of the sensing techniques that are relevant to MPS development and highlight the different organ systems to integrate instrumentation for measurement and manipulation of cellular function. Special attention is given to how instrumented MPS can disrupt the drug development and fundamental mechanistic discovery processes.
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Affiliation(s)
- Jonathan R Soucy
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Adam J Bindas
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Abigail N Koppes
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA; Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Ryan A Koppes
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA.
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24
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A sensitive electrochemical aptasensor based on MB-anchored GO for the rapid detection of Cronobacter sakazakii. J Solid State Electrochem 2019. [DOI: 10.1007/s10008-019-04426-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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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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26
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A review on native and denaturing purification methods for non-coding RNA (ncRNA). J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1120:71-79. [PMID: 31071581 DOI: 10.1016/j.jchromb.2019.04.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/20/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022]
Abstract
Recently, non-coding RNA (ncRNA) became the centerpiece of human genome research. Modern ncRNA-based research has revolutionized disease diagnosis and therapeutics. However, decoding structural/functional information of ncRNA requires large amount of pure RNA, and hence effective RNA preparation and purification protocols. This review focuses on purification schemes of synthetic oligonucleotides, particularly liquid chromatographic (LC) techniques as improved alternatives to urea-polyacrylamide gel electrophoresis (urea-PAGE) purification. Moreover, the review summarizes the shortcomings of urea-PAGE purification method and details the chromatographic purification such as affinity, ion-exchange (IE) or size-exclusion (SE) chromatography. Specifically, we discuss denaturing and native RNA purification schemes with newest developments. In short, the review evaluates nucleic acid purification schemes required for various structural analyses.
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27
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Bednarek S, Madan V, Sikorski PJ, Bartenschlager R, Kowalska J, Jemielity J. mRNAs biotinylated within the 5' cap and protected against decapping: new tools to capture RNA-protein complexes. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0167. [PMID: 30397103 DOI: 10.1098/rstb.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
The 5'-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5'-5' triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2. The utility of such cap-biotinylated RNAs as molecular tool was demonstrated by ultraviolet-cross-linking and affinity capture of protein-RNA complexes. In conclusion, RNAs labelled with biotin via the 5' cap structure can be applied to a variety of biological experiments based on biotin-avidin interaction or by means of biotin-specific antibodies, including protein affinity purification, pull-down assays, in vivo visualization, cellular delivery and many others.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Sylwia Bednarek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Vanesa Madan
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Ralf Bartenschlager
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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28
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Li CM, Zhan L, Zheng LL, Li YF, Huang CZ. A magnetic nanoparticle-based aptasensor for selective and sensitive determination of lysozyme with strongly scattering silver nanoparticles. Analyst 2018; 141:3020-6. [PMID: 27055576 DOI: 10.1039/c6an00489j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Qualitative and quantitative determination of lysozyme concentrations in urine and serum with high selectivity and sensitivity is important for diagnosing the progression of several diseases. In this report, we devised an improved method for specifically detecting lysozyme by combining magnetic nanoparticles (for separation and enrichment), an aptamer (for selective binding of lysozyme) and strongly scattering silver nanoparticles (AgNPs, for detection by light scattering, but also providing another level of selectivity due to their electrostatic binding with lysozyme). In this system, 0.4-30 nM lysozyme could be simply detected owing to the decreased light scattering of AgNPs in solution after magnetic separation, with a detection limit of 100 pM. In addition, lysozyme was also able to be semi-quantified by using the dark-field light scattering images of AgNPs after enrichment by the MNP-apt-lysozyme complex. Moreover, this design shows great promise for the robust and reliable detection of lysozyme in real samples, with a recovery rate ranging from 98.6% to 101.3% in human serum samples. Therefore, this assay provided robust measurements with good specificity, sensitivity, and tolerance of changes in the sample matrix. We expect that this MNP-based aptasensor may find utility in the accurate diagnosis of lysozyme-related diseases.
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Affiliation(s)
- Chun Mei Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
| | - Lei Zhan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
| | - Lin Ling Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
| | - Yuan Fang Li
- Chongqing Key Laboratory of Biomedical Analysis (Southwest University), Chongqing Science & Technology Commission, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China. and Chongqing Key Laboratory of Biomedical Analysis (Southwest University), Chongqing Science & Technology Commission, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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29
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Zhou Z, Liu M, Jiang J. The potential of aptamers for cancer research. Anal Biochem 2018; 549:91-95. [PMID: 29548926 DOI: 10.1016/j.ab.2018.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 02/09/2023]
Abstract
Aptamers are promising alternatives to antibodies and can be used as high affinity agents for the cancer detection and the targeted drug transportation. In this manuscript, we highlight the advantages of aptamers, such as high affinities, specificity and excellent chemical stabilities, which are likely to benefit for the diagnosis of cancer in its early stages and then achieve molecular-level treatment. Also, we discuss the challenges and problems in the current application of aptamers.
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Affiliation(s)
- Zhizhi Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, China.
| | - Mingying Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, China
| | - Jiahuan Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, China.
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30
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Li K, Deng J, Jin H, Yang X, Fan X, Li L, Zhao Y, Guan Z, Wu Y, Zhang L, Yang Z. Chemical modification improves the stability of the DNA aptamer GBI-10 and its affinity towards tenascin-C. Org Biomol Chem 2018; 15:1174-1182. [PMID: 28084479 DOI: 10.1039/c6ob02577c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamers are useful tools in molecular imaging due to their numerous attractive properties, such as excellent affinity and selectivity to diverse types of target molecules and biocompatibility. We carried out structure-activity relationship studies with the tenascin-C (TN-C) binding aptamer GBI-10, which is a promising candidate in tumor imaging. To increase the tumor targeting ability and nuclease resistance under physiological conditions, systematic modifications of GBI-10 with single and multiple 2'-deoxyinosine (2'-dI) or d-/l-isonucleoside (d-/l-isoNA) were performed. Results indicated that sector 3 of the proposed secondary structure is the most important region for specific binding with TN-C. By correlating the affinity of eighty-four GBI-10 derivatives with their predicted secondary structure by Zuker Mfold, we first validated the preferred secondary structure at 37 °C. We found that d-/l-isoNA modified GBI-10 derivatives exhibited improved affinity to the target as well as plasma stability. Affinity measurement and confocal imaging analysis highlighted one potent compound: 4AL/26TL/32TL, which possessed a significantly increased targeting ability to tumor cells. These results revealed the types of modified nucleotides, and the position and number of substituents in GBI-10 that were critical to the TN-C binding ability. Stabilized TN-C-binding DNA aptamers were prepared and they could be further developed for tumor imaging. Our strategy to introduce 2'-dI and d-/l-isoNA modifications after the selection process is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding ability.
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Affiliation(s)
- Kunfeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Jiali Deng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Liyu Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
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Khan NI, Maddaus AG, Song E. A Low-Cost Inkjet-Printed Aptamer-Based Electrochemical Biosensor for the Selective Detection of Lysozyme. BIOSENSORS 2018; 8:E7. [PMID: 29342960 PMCID: PMC5872055 DOI: 10.3390/bios8010007] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/23/2017] [Accepted: 01/10/2018] [Indexed: 11/17/2022]
Abstract
Recently, inkjet-printing has gained increased popularity in applications such as flexible electronics and disposable sensors, as well as in wearable sensors because of its multifarious advantages. This work presents a novel, low-cost immobilization technique using inkjet-printing for the development of an aptamer-based biosensor for the detection of lysozyme, an important biomarker in various disease diagnosis. The strong affinity between the carbon nanotube (CNT) and the single-stranded DNA is exploited to immobilize the aptamers onto the working electrode by printing the ink containing the dispersion of CNT-aptamer complex. The inkjet-printing method enables aptamer density control, as well as high resolution patternability. Our developed sensor shows a detection limit of 90 ng/mL with high target selectivity against other proteins. The sensor also demonstrates a shelf-life for a reasonable period. This technology has potential for applications in developing low-cost point-of-care diagnostic testing kits for home healthcare.
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Affiliation(s)
- Niazul Islam Khan
- Department of Electrical and Computer Engineering, University of New Hampshire, Durham, NH 03824, USA.
| | - Alec G Maddaus
- Department of Chemical Engineering, University of New Hampshire, Durham, NH 03824, USA.
| | - Edward Song
- Department of Electrical and Computer Engineering, University of New Hampshire, Durham, NH 03824, USA.
- Center for Advanced Materials and Manufacturing Innovation, University of New Hampshire, Durham, NH 03824, USA.
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32
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Giuffrida MC, Cigliana G, Spoto G. Ultrasensitive detection of lysozyme in droplet-based microfluidic devices. Biosens Bioelectron 2017; 104:8-14. [PMID: 29294408 DOI: 10.1016/j.bios.2017.12.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 12/27/2022]
Abstract
Lysozyme (LYS) is a bacteriolytic enzyme, available in secretions such as saliva, tears and human milk. LYS is an important defence molecule of the innate immune system, and its overexpression can be a consequence of diseases such as leukemia, kidney disease and sarcoidosis. This paper reports on a digital microfluidic-based approach that combines the gold nanoparticle-enhanced chemiluminescence with aptamer interaction to detect human lysozyme into droplets 20 nanoliters in volume. The described method allows identifying LYS with a 44.6 femtomolar limit of detection, using sample volume as low as 1μL and detection time in the range of 10min. We used luminol to generate the chemiluminescence and demonstrated that the compartmentalization of LYS in droplets also comprising gold nanoparticles provided enhanced luminescence. We functionalized the gold nanoparticles with a thiolated aptamer to achieve the required selectivity that allowed us to detect LYS in human serum.
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Affiliation(s)
- Maria Chiara Giuffrida
- Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, Catania, Italy
| | - Giovanni Cigliana
- Clinical Pathology Unit, Regina Elena National Cancer Institute, Via Chianesi, Roma, Italy
| | - Giuseppe Spoto
- Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, Catania, Italy; Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
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33
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Zheng Y, Wang Q, Yang X, Li Z, Gao L, Zhang H, Nie W, Geng X, Wang K. Investigation of the interactions between aptamer and misfolded proteins: From monomer and oligomer to fibril by single-molecule force spectroscopy. J Mol Recognit 2017; 31. [PMID: 29143447 DOI: 10.1002/jmr.2686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/10/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability. It may be attributed to the inherent structural differences of misfolded proteins and the flexible conformation of aptamer. In addition, dynamic force spectra showed that there were similar dissociation paths in the dissociation process of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer complexes. It showed that the dissociation only passed 1 energy barrier from the binding state to the detachment. However, the dynamic parameters suggested that the oligomer- and amyloid fibril-aptamer were more stable than lysozyme monomer-aptamer. The phenomena may result from the exposure of aptamer-recognized sequences on the surface and the electrostatic interactions. This work demonstrated that single-molecule force spectroscopy could be a powerful tool to study the binding behavior of the aptamer with misfolded proteins at single-molecule level, providing abundant information for researches and comprehensive applications of aptamer probes in diagnosis of amyloid diseases.
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Affiliation(s)
- Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Zhiping Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Lei Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Hua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Wenyan Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiuhua Geng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
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34
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Singh E, Meyyappan M, Nalwa HS. Flexible Graphene-Based Wearable Gas and Chemical Sensors. ACS APPLIED MATERIALS & INTERFACES 2017; 9:34544-34586. [PMID: 28876901 DOI: 10.1021/acsami.7b07063] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wearable electronics is expected to be one of the most active research areas in the next decade; therefore, nanomaterials possessing high carrier mobility, optical transparency, mechanical robustness and flexibility, lightweight, and environmental stability will be in immense demand. Graphene is one of the nanomaterials that fulfill all these requirements, along with other inherently unique properties and convenience to fabricate into different morphological nanostructures, from atomically thin single layers to nanoribbons. Graphene-based materials have also been investigated in sensor technologies, from chemical sensing to detection of cancer biomarkers. The progress of graphene-based flexible gas and chemical sensors in terms of material preparation, sensor fabrication, and their performance are reviewed here. The article provides a brief introduction to graphene-based materials and their potential applications in flexible and stretchable wearable electronic devices. The role of graphene in fabricating flexible gas sensors for the detection of various hazardous gases, including nitrogen dioxide (NO2), ammonia (NH3), hydrogen (H2), hydrogen sulfide (H2S), carbon dioxide (CO2), sulfur dioxide (SO2), and humidity in wearable technology, is discussed. In addition, applications of graphene-based materials are also summarized in detecting toxic heavy metal ions (Cd, Hg, Pb, Cr, Fe, Ni, Co, Cu, Ag), and volatile organic compounds (VOCs) including nitrobenzene, toluene, acetone, formaldehyde, amines, phenols, bisphenol A (BPA), explosives, chemical warfare agents, and environmental pollutants. The sensitivity, selectivity and strategies for excluding interferents are also discussed for graphene-based gas and chemical sensors. The challenges for developing future generation of flexible and stretchable sensors for wearable technology that would be usable for the Internet of Things (IoT) are also highlighted.
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Affiliation(s)
- Eric Singh
- Department of Computer Science, Stanford University , Stanford, California 94305, United States
| | - M Meyyappan
- Center for Nanotechnology, NASA Ames Research Center , Moffett Field, California 94035, United States
| | - Hari Singh Nalwa
- Advanced Technology Research , 26650 The Old Road, Valencia, California 91381, United States
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35
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Gopinath SCB, Perumal V, Balakrishnan S, Md Arshad MK, Lakshmipriya T, Haarindraprasad R, Hashim U. Aptamer-based determination of ATP by using a functionalized impedimetric nanosensor and mediation by a triangular junction transducer. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2485-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Purification of single-stranded DNA by co-polymerization with acrylamide and electrophoresis. Biotechniques 2017. [PMID: 28625157 DOI: 10.2144/000114557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Single-stranded DNA (ssDNA) oligonucleotides are useful as aptamers, hybridization probes and for emerging applications in DNA nanotechnology. Current methods to purify ssDNA require both a strand-separation step and a separate size-separation step but may still leave double-stranded DNA (dsDNA) impurities in the sample. Here, we use commercially available acrydite DNA primers to immobilize one strand of a PCR product within a polyacrylamide matrix. Electrophoresis moves the non-crosslinked DNA into the gel where the single-stranded product of desired size can be recovered. Our results show this method produces high yields of pure ssDNA.
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37
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Lin X, Ivanov AP, Edel JB. Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles. Chem Sci 2017; 8:3905-3912. [PMID: 28626560 PMCID: PMC5465561 DOI: 10.1039/c7sc00415j] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/14/2017] [Indexed: 01/26/2023] Open
Abstract
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.
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Affiliation(s)
- Xiaoyan Lin
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Aleksandar P Ivanov
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
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38
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Ma C, Liu H, Zhang L, Li L, Yan M, Yu J, Song X. Microfluidic Paper-Based Analytical Device for Sensitive Detection of Peptides Based on Specific Recognition of Aptamer and Amplification Strategy of Hybridization Chain Reaction. ChemElectroChem 2017. [DOI: 10.1002/celc.201600824] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chao Ma
- School of Chemistry and Chemical Engineering; University of Jinan; Jinan 250022 P.R. China
| | - Haiyun Liu
- School of Chemistry and Chemical Engineering; University of Jinan; Jinan 250022 P.R. China
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and; Measurement of Building Materials; University of Jinan; Jinan 250022 P.R. China
| | - Li Li
- School of Chemistry and Chemical Engineering; University of Jinan; Jinan 250022 P.R. China
| | - Mei Yan
- School of Chemistry and Chemical Engineering; University of Jinan; Jinan 250022 P.R. China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering; University of Jinan; Jinan 250022 P.R. China
| | - Xianrang Song
- Shandong Provincial Key Laboratory of Radiation Oncology; Shandong Cancer Hospital and Institute; Jinan 250117 P.R. China
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39
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Zheng J, Zhao C, Tian G, He L. Rapid screening for ricin toxin on letter papers using surface enhanced Raman spectroscopy. Talanta 2017; 162:552-557. [DOI: 10.1016/j.talanta.2016.10.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/28/2022]
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40
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A novel colorimetric competitive aptamer assay for lysozyme detection based on superparamagnetic nanobeads. Talanta 2016; 165:436-441. [PMID: 28153279 DOI: 10.1016/j.talanta.2016.12.083] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/27/2016] [Accepted: 12/29/2016] [Indexed: 11/21/2022]
Abstract
Lysozyme (Lys) commonly presents in wines and are known to cause toxicological impact on human health. The need of highly sensitive and reliable detection methods are evident in such matrix. In this work, we developed a competitive aptamer based assay for detection of Lys by employing carboxylated magnetic beads as a support to immobilize the target molecule Lys. The used aptamer sequence was biotinylated which further binds with Streptavidin-Alkaline phosphatase (Stp-ALP) in the micro wells. Colorimetric tests were performed in order to optimize different experimental parameters. The Lys assay showed a good linearity in the range of 5-140nM with a limit of detection (LOD) 10nM. The mid-point value (IC50) 110nM and the analysis time (60min) validated the developed aptasensor as a promising tool for routine use. The assay displayed good recoveries of Lys in the range 99.00-99.27% and was demonstrated for the detection of Lys in wine samples.
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41
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Lee JR, Haddon DJ, Gupta N, Price JV, Credo GM, Diep VK, Kim K, Hall DA, Baechler EC, Petri M, Varma M, Utz PJ, Wang SX. High-Resolution Analysis of Antibodies to Post-Translational Modifications Using Peptide Nanosensor Microarrays. ACS NANO 2016; 10:10652-10660. [PMID: 27636738 PMCID: PMC5367622 DOI: 10.1021/acsnano.6b03786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Autoantibodies are a hallmark of autoimmune diseases such as lupus and have the potential to be used as biomarkers for diverse diseases, including immunodeficiency, infectious disease, and cancer. More precise detection of antibodies to specific targets is needed to improve diagnosis of such diseases. Here, we report the development of reusable peptide microarrays, based on giant magnetoresistive (GMR) nanosensors optimized for sensitively detecting magnetic nanoparticle labels, for the detection of antibodies with a resolution of a single post-translationally modified amino acid. We have also developed a chemical regeneration scheme to perform multiplex assays with a high level of reproducibility, resulting in greatly reduced experimental costs. In addition, we show that peptides synthesized directly on the nanosensors are approximately two times more sensitive than directly spotted peptides. Reusable peptide nanosensor microarrays enable precise detection of autoantibodies with high resolution and sensitivity and show promise for investigating antibody-mediated immune responses to autoantigens, vaccines, and pathogen-derived antigens as well as other fundamental peptide-protein interactions.
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Affiliation(s)
- Jung-Rok Lee
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - D. James Haddon
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
| | - Nidhi Gupta
- Intel Corporation, Santa Clara, California 95052, United States
| | - Jordan V. Price
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, California 94720, United States
| | - Grace M. Credo
- Intel Corporation, Santa Clara, California 95052, United States
| | - Vivian K. Diep
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
| | - Kyunglok Kim
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Drew A. Hall
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Electrical and Computer Engineering, University of California, San Diego, California 92093, United States
| | - Emily C. Baechler
- Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, United States
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Madoo Varma
- Intel Corporation, Santa Clara, California 95052, United States
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
- Corresponding Author.
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Ostatná V, Kasalová-Vargová V, Kékedy-Nagy L, Černocká H, Ferapontova EE. Chronopotentiometric sensing of specific interactions between lysozyme and the DNA aptamer. Bioelectrochemistry 2016; 114:42-47. [PMID: 28063413 DOI: 10.1016/j.bioelechem.2016.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 01/08/2023]
Abstract
Specific DNA-protein interactions are vital for cellular life maintenance processes, such as transcriptional regulation, chromosome maintenance, replication and DNA repair, and their monitoring gives valuable information on molecular-level organization of those processes. Here, we propose a new method of label-free electrochemical sensing of sequence specific binding between the lysozyme protein and a single stranded DNA aptamer specific for lysozyme (DNAapta) that exploits the constant current chronopotentiometric stripping (CPS) analysis at modified mercury electrodes. Specific lysozyme-DNAapta binding was distinguished from nonspecific lysozyme-DNA interactions at thioglycolic acid-modified mercury electrodes, but not at the dithiothreitol-modified or bare mercury electrodes. Stability of the surface-attached lysozyme-DNAapta layer depended on the stripping current (Istr) intensity, suggesting that the integrity of the layer critically depends on the time of its exposure to negative potentials. Stabilities of different lysozyme-DNA complexes at the negatively polarized electrode surface were tested, and it was shown that structural transitions of the specific lysozyme-DNAapta complexes occur in the Istr ranges different from those observed for assemblies of lysozyme with DNA sequences capable of only nonspecific lysozyme-DNA interactions. Thus, the CPS allows distinct discrimination between specific and non-specific protein-DNA binding and provides valuable information on stability of the nucleic acid-protein interactions at the polarized interfaces.
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Affiliation(s)
- Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic.
| | - Veronika Kasalová-Vargová
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University, Gustav Wieds Vej 14, DK 8000 Aarhus-C, Denmark
| | - Hana Černocká
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University, Gustav Wieds Vej 14, DK 8000 Aarhus-C, Denmark
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Hwang J, Seo Y, Jo Y, Son J, Choi J. Aptamer-conjugated live human immune cell based biosensors for the accurate detection of C-reactive protein. Sci Rep 2016; 6:34778. [PMID: 27708384 PMCID: PMC5052522 DOI: 10.1038/srep34778] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/19/2016] [Indexed: 01/27/2023] Open
Abstract
C-reactive protein (CRP) is a pentameric protein that is present in the bloodstream during inflammatory events, e.g., liver failure, leukemia, and/or bacterial infection. The level of CRP indicates the progress and prognosis of certain diseases; it is therefore necessary to measure CRP levels in the blood accurately. The normal concentration of CRP is reported to be 1–3 mg/L. Inflammatory events increase the level of CRP by up to 500 times; accordingly, CRP is a biomarker of acute inflammatory disease. In this study, we demonstrated the preparation of DNA aptamer-conjugated peripheral blood mononuclear cells (Apt-PBMCs) that specifically capture human CRP. Live PBMCs functionalized with aptamers could detect different levels of human CRP by producing immune complexes with reporter antibody. The binding behavior of Apt-PBMCs toward highly concentrated CRP sites was also investigated. The immune responses of Apt-PBMCs were evaluated by measuring TNF-alpha secretion after stimulating the PBMCs with lipopolysaccharides. In summary, engineered Apt-PBMCs have potential applications as live cell based biosensors and for in vitro tracing of CRP secretion sites.
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Affiliation(s)
- Jangsun Hwang
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Youngmin Seo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yeonho Jo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jaewoo Son
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jonghoon Choi
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
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Inoue S, Seyama M, Miura T, Horiuchi T, Iwasaki Y, Takahashi JI, Hayashi K, Tamechika E. A reliable aptamer array prepared by repeating inkjet-spotting toward on-site measurement. Biosens Bioelectron 2016; 85:943-949. [PMID: 27315520 DOI: 10.1016/j.bios.2016.05.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/14/2016] [Accepted: 05/30/2016] [Indexed: 10/21/2022]
Abstract
A preparation protocol is proposed for a reliable aptamer array utilizing an ink-jet spotter. We accumulated streptavidin and biotinylated-aptamer in this order on a biotinylated-polyethylene glycol-coated gold substrate to prepare an aptamer array. The aptamer array was prepared with an alternate spotting structure where each aptamer spot was placed between reference spots formed with blocking solution thus suppressing contamination from neighboring spots during the blocking and washing processes. Four aptamer spots were prepared in a small area of 1×4.8mm(2) with five reference spots made of blocking solution. We evaluated the thrombin binding ability of the spotted aptamer array using a multi-analysis surface plasmon resonance sensor. We prepared a disposable capillary-driven flow chip designed for on-site measurement (Miura et al., 2010) with our aptamer array and detected thrombin from phosphate-buffered saline at concentrations of 50ngmL(-1) and 1μgmL(-1) (equivalent to 1.35 and 27nM, respectively). A correlation was observed between the refractive index shift and thrombin concentration. This implies that our array preparation protocol meets the requirement for the preparation of a one-time-use chip for on-site measurement.
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Affiliation(s)
- Suzuyo Inoue
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Michiko Seyama
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan.
| | - Toru Miura
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Tsutomu Horiuchi
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Yuzuru Iwasaki
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Jun-Ichi Takahashi
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Katsuyoshi Hayashi
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
| | - Emi Tamechika
- NTT Device Technology Laboratories, Nippon Telegraph and Telephone Corporation, 3-1 Morinosato Wakamiya, Atsugi-shi, Kanagawa 243-0198, Japan
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Lee DW, Park KM, Gong B, Shetty D, Khedkar JK, Baek K, Kim J, Ryu SH, Kim K. A simple modular aptasensor platform utilizing cucurbit[7]uril and a ferrocene derivative as an ultrastable supramolecular linker. Chem Commun (Camb) 2016; 51:3098-101. [PMID: 25597690 DOI: 10.1039/c4cc08027k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A simple modular aptamer-based sensor (aptasensor) platform was prepared by combining the merits of the rapid and efficient preparation of a self-assembled monolayer of cucurbit[7]uril (CB[7] SAM) and the strong and specific binding affinity of CB[7] to ferrocenemethylammonium (FA), as an ultrastable supramolecular linker, to immobilize aptamers on CB[7] SAM.
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Affiliation(s)
- Don-Wook Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 790-784, Republic of Korea
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Ma C, Liu H, Tian T, Song X, Yu J, Yan M. A simple and rapid detection assay for peptides based on the specific recognition of aptamer and signal amplification of hybridization chain reaction. Biosens Bioelectron 2016; 83:15-8. [PMID: 27093485 DOI: 10.1016/j.bios.2016.04.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 12/12/2022]
Abstract
A simple and rapid assay for the detection of peptides is designed based on the specific recognition of aptamer, the quenching effect of graphene oxide (GO) and the efficient signal amplification of hybrid chain reaction (HCR). In this assay, the hairpin structure of aptamer is opened after binding with targets, and the initiation sequence could be exposed to hairpin probe 1 (H1) to open its hairpin structure. Then the opened H1 will open the hairpin structure of hairpin probe 2 (H2), and in turn, the opened initiation sequence of H2 continues to open H1. As a result, the specific recognition of target and fluorescent signals are accumulated through the process in short 1h. Attentively, the aptamer can not only identify target peptides, but also initiate the HCR between H1 and H2. More importantly, the HCR is initiated only after the target recognition of aptamer. After HCR, the excess hairpin probes will be anchored on the GO surface, and the background is greatly reduced due to the quenching effect of GO. By using Mucin-1(MUC1) as a model peptide, the assay has a wide linear range as two orders of magnitude and the detection range is from 0.01 to 5nM with low detection limit of 3.33pM. Therefore, the simple and rapid detection of the target can be realized, and the novel assay has great potential in detecting various peptides and even cancer cells.
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Affiliation(s)
- Chao Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Haiyun Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Tian Tian
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Xianrang Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan 250117, China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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Aptamer-based 'point-of-care testing'. Biotechnol Adv 2016; 34:198-208. [PMID: 26876017 DOI: 10.1016/j.biotechadv.2016.02.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 02/06/2016] [Accepted: 02/07/2016] [Indexed: 12/13/2022]
Abstract
Aptamers are single-stranded oligonucleotides that can be artificially generated by a method called Systematic evolution of ligands by exponential enrichment (SELEX). The generated aptamers have been assessed for high-performance sensing applications due to their appealing characteristics. With either aptamers alone or complementing with antibodies, several high sensitive and portable sensors have been demonstrated for use in 'point-of-care testing'. Due to their high suitability and flexibility, aptamers are conjugated with nanostructures and utilized in field applications. Moreover, aptamers are more amenable to chemical modifications, making them capable of utilization with most developed sensors. In this overview, we discuss novel, portable, and aptamer-based sensing strategies that are suitable for 'point-of-care testing'.
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Dirkzwager RM, Kinghorn AB, Richards JS, Tanner JA. APTEC: aptamer-tethered enzyme capture as a novel rapid diagnostic test for malaria. Chem Commun (Camb) 2016; 51:4697-700. [PMID: 25692283 DOI: 10.1039/c5cc00438a] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report the rapid diagnosis of malaria by aptamer-tethered enzyme capture (APTEC) whereby an aptamer captures biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH) then activity is measured colorimetrically. The robust test was sensitive (limit of detection = 4.9 ng mL(-1)) and could reliably diagnose malaria in clinical blood samples.
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Affiliation(s)
- Roderick M Dirkzwager
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R..
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