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Ryu JJ, Jang CH. Label-free, liquid crystal-based aptasensor for detecting carbendazim at picomolar levels. Food Chem 2024; 445:138789. [PMID: 38394911 DOI: 10.1016/j.foodchem.2024.138789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024]
Abstract
We describe a simple and sensitive liquid-crystal (LC)-based method for quantifying carbendazim (CBZ) by exploiting aptamer-specific recognition at the aqueous-LC interface. The method relies on the interfacial interaction between an aptamer and cetyltrimethylammonium bromide (CTAB); this interaction varies depending on the amount of CBZ. In the absence of CBZ, the aptamer disrupts the CTAB monolayer through electrostatic attraction, leading to a transition from homeotropic to tilted ordering of the LCs. As CBZ concentrations rise, the formation of aptamer-CBZ complexes increases, preserving the vertical alignment of the LCs by reducing collapse of the CTAB layer caused by electrostatic interactions. Using these methods, we achieved a CBZ detection limit of 3.12 pM (0.000597 μg/L) over a linear range of 0.05-5 nM. Moreover, we quantified CBZ levels in peach, soil, and tap water samples. Our LC-based detection method has significant research potential, offering sensitive, and straightforward detection of CBZ.
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Affiliation(s)
- Je-Jin Ryu
- Department of Chemistry, Gachon University, Seongnam-daero 1342, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Republic of Korea
| | - Chang-Hyun Jang
- Department of Chemistry, Gachon University, Seongnam-daero 1342, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Republic of Korea.
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2
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Asmare MM, Krishnaraj C, Radhakrishnan S, Kim BS, Yoon JS, Yun SI. In silico modelling of ciprofloxacin specific aptamer for the development of high-performance biosensor. J Mol Graph Model 2024; 130:108787. [PMID: 38749234 DOI: 10.1016/j.jmgm.2024.108787] [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: 02/08/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Ciprofloxacin (CFX), a widely used fluoroquinolone antibiotic, is critical in healthcare settings for treating patients. However, improper treatment of wastewater from these facilities can lead to environmental contamination with CFX. This underscores the need for an efficient, straightforward method for early detection. In this study, a DNA aptamer was selected through a hierarchical docking workflow, and the stability and interactions were assessed by Molecular Dynamics (MD) simulation. The aptamer-CFX complex that showed the most promise had a docking score of -8.596 kcal/mol and was further analyzed using MD simulation and MM/PBSA. Based on the overall results, the identified ssDNA sequence length of 60 nt (CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG) was immobilized over a gold transducer surface through the self-assembled monolayer (SAM; Au-S-ssDNA) method. The ssDNA-modified surface has demonstrated a high affinity towards CFX, which is confirmed by cyclic voltammogram (CV) and electrochemical impedance spectroscopy measurements (EIS). The DNA-aptamer modified electrode demonstrated a good linear range (10 × 10-9 - 200 × 10-9 M), detection limit (1.0 × 10-9 M), selectivity, reproducibility, and stability. The optimized DNA-aptamer-based CFX sensor was further utilized for the accurate determination of CFX with good recoveries in real samples.
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Affiliation(s)
- Misgana Mengistu Asmare
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Chandran Krishnaraj
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea; Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Sivaprakasam Radhakrishnan
- Department of Organic Materials & Fiber Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - Byoung-Sukh Kim
- Department of Organic Materials & Fiber Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea
| | - June-Sun Yoon
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea.
| | - Soon-Il Yun
- Department of Agricultural Convergence Technology, College of Agriculture and Life Science, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea; Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54896, Republic of Korea.
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3
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Chowdhury R, Eslami S, Pham CV, Rai A, Lin J, Hou Y, Greening DW, Duan W. Role of aptamer technology in extracellular vesicle biology and therapeutic applications. NANOSCALE 2024. [PMID: 38856692 DOI: 10.1039/d4nr00207e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Extracellular vesicles (EVs) are cell-derived nanosized membrane-bound vesicles that are important intercellular signalling regulators in local cell-to-cell and distant cell-to-tissue communication. Their inherent capacity to transverse cell membranes and transfer complex bioactive cargo reflective of their cell source, as well as their ability to be modified through various engineering and modification strategies, have attracted significant therapeutic interest. Molecular bioengineering strategies are providing a new frontier for EV-based therapy, including novel mRNA vaccines, antigen cross-presentation and immunotherapy, organ delivery and repair, and cancer immune surveillance and targeted therapeutics. The revolution of EVs, their diversity as biocarriers and their potential to contribute to intercellular communication, is well understood and appreciated but is ultimately dependent on the development of methods and techniques for their isolation, characterization and enhanced targeting. As single-stranded oligonucleotides, aptamers, also known as chemical antibodies, offer significant biological, chemical, economic, and therapeutic advantages in terms of their size, selectivity, versatility, and multifunctional programming. Their integration into the field of EVs has been contributing to the development of isolation, detection, and analysis pipelines associated with bioengineering strategies for nano-meets-molecular biology, thus translating their use for therapeutic and diagnostic utility.
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Affiliation(s)
- Rocky Chowdhury
- School of Medicine, Deakin University, and IMPACT Strategic Research Centre, Waurn Ponds, VIC, 3216, Australia.
| | - Sadegh Eslami
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
| | - Cuong Viet Pham
- Molecular Imaging and Theranostics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Alin Rai
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Cardiovascular Research, Translation and Implementation, and La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Jia Lin
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yingchu Hou
- Laboratory of Tumor Molecular and Cellular Biology College of Life Sciences, Shaanxi Normal University 620 West Chang'an Avenue, Xi'an, Shaanxi, 710119, China
| | - David W Greening
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Cardiovascular Research, Translation and Implementation, and La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Wei Duan
- School of Medicine, Deakin University, and IMPACT Strategic Research Centre, Waurn Ponds, VIC, 3216, Australia.
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4
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Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
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Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
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5
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Gao L, Zhang Y, Chen L, Zhou Q, Zhou N, Xia X. Study of dual binding specificity of aptamer to ochratoxin A and norfloxacin and the development of fluorescent aptasensor in milk detection. Talanta 2024; 273:125935. [PMID: 38503123 DOI: 10.1016/j.talanta.2024.125935] [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: 07/06/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Target specificity, one of aptamer characteristics that determine recognition efficiency of biosensors, is generally considered to be an intrinsic property of aptamer. However, a high-affinity aptamer may have additional target binding specificity, little is known about the specificity of aptamer binding to multiple targets, which may result in false-positive results that hinder the accuracy of detection. Herein, an aptamer OBA3 with dual target ochratoxin A (OTA) and norfloxacin (NOR) was used as an example to explore the binding specificity mechanism and developed rapid fluorescent aptasensing methods. The nucleotide 15th T of aptamer OBA3 was demonstrated to be critical for specificity and affinity binding of target OTA via site-saturation mutagenesis. Substituting the 15th T base for C base could directly improve recognition specificity of aptamer for NOR and remove the binding affinity for OTA. The combination of π-π stacking interactions, salt bridges and hydrogen bonds between loop pocket of aptamer and quinolone skeleton, piperazinyl group may contributes to the fluoroquinolone antibiotics (NOR and difloxacin)-aptamer recognition interaction. Based on this understanding, a dual-aptamer fluorescent biosensor was fabricated for simultaneous detection of OTA and NOR, which has a linear detection range of 50-6000 nM with a detection limit of 31 nM for OTA and NOR. Combined with T15C biosensor for eliminating interference of OTA, the assay was applied to milk samples with satisfactory recovery (94.06-100.93%), which can achieve detection of OTA and NOR individually within 40 min.
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Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yue Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Lu Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Nandi Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
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Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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7
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Oliveira R, Pinho E, Barros MM, Azevedo NF, Almeida C. In vitro selection of DNA aptamers against staphylococcal enterotoxin A. Sci Rep 2024; 14:11345. [PMID: 38762575 PMCID: PMC11102521 DOI: 10.1038/s41598-024-61094-3] [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: 12/29/2022] [Accepted: 04/30/2024] [Indexed: 05/20/2024] Open
Abstract
Staphylococcal enterotoxin A (SEA) is the most frequently reported in staphylococcal food poisoning (SFP) outbreaks. Aptamers are single-stranded nucleic acids that are seen as promising alternatives to antibodies in several areas, including diagnostics. In this work, systematic evolution of ligands by exponential enrichment (SELEX) was used to select DNA aptamers against SEA. The SELEX protocol employed magnetic beads as an immobilization matrix for the target molecule and real-time quantitative PCR (qPCR) for monitoring and optimizing sequence enrichment. After 10 selection cycles, the ssDNA pool with the highest affinity was sequenced by next generation sequencing (NGS). Approximately 3 million aptamer candidates were identified, and the most representative cluster sequences were selected for further characterization. The aptamer with the highest affinity showed an experimental dissociation constant (KD) of 13.36 ± 18.62 nM. Increased temperature negatively affected the affinity of the aptamer for the target. Application of the selected aptamers in a lateral flow assay demonstrated their functionality in detecting samples containing 100 ng SEA, the minimum amount capable of causing food poisoning. Overall, the applicability of DNA aptamers in SEA recognition was demonstrated and characterized under different conditions, paving the way for the development of diagnostic tools.
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Affiliation(s)
- Ricardo Oliveira
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal.
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
| | - Eva Pinho
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Maria Margarida Barros
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Carina Almeida
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Mansouri S. Recent Advancements in Molecularly Imprinted Polymers Based Aptasensors: Critical Role of Nanomaterials for the Efficient Food Safety Analysis. Crit Rev Anal Chem 2024:1-16. [PMID: 38754013 DOI: 10.1080/10408347.2024.2351826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Biosensors are being studied extensively for their ability to detect and analyze molecules. There has been a growing interest in combining molecular imprinted polymers (MIPs) and aptamers to create hybrid recognition elements that offer advantages such as target binding, sensitivity, selectivity, and stability. These hybrid elements have been successfully used in identifying a wide range of analytes in food samples. However, the application of MIP-based aptasensors in different sensing approaches is still challenging due to the low conductivity of MIPs-aptamers and limited adsorption capacity of MIPs. To address these limitations, researchers have been exploring the use of nanomaterials (NMs) to design efficient multiple-recognition systems that exploit the synergies between aptamers and MIPs. These hybrid systems can enhance the sensitivity and selectivity of MIP-based aptasensors in quantifying analytical samples. This review provides a comprehensive overview of recent advancements in the field of MIP-based aptasensors. It also introduces technologies that combine MIPs and aptamers to achieve higher sensitivity and selectivity in quantifying analytical samples. The review also highlights potential future trends and practical approaches that can be employed to address the limitations of MIP-based aptasensors, including the use of new NMs, the development of new fabrication techniques, and the integration of MIP-based aptasensors with other analytical tools.
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Affiliation(s)
- Sofiene Mansouri
- Department of Biomedical Technology, College of Applied Medical Sciences, Al-Kharj, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabiain
- Laboratory of Biophysics and Medical Technologies, University of Tunis El Manar, Higher Institute of Medical Technologies of Tunis, Tunis, Tunisia
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Eigenfeld M, Lupp KFM, Schwaminger SP. Role of Natural Binding Proteins in Therapy and Diagnostics. Life (Basel) 2024; 14:630. [PMID: 38792650 PMCID: PMC11122601 DOI: 10.3390/life14050630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.
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Affiliation(s)
- Marco Eigenfeld
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kilian F. M. Lupp
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Sebastian P. Schwaminger
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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Ropii B, Bethasari M, Anshori I, Koesoema AP, Shalannanda W, Satriawan A, Setianingsih C, Akbar MR, Aditama R, Fahmi F, Sutanto E, Yazid M, Aziz M. The molecular interaction of six single-stranded DNA aptamers to cardiac troponin I revealed by docking and molecular dynamics simulation. PLoS One 2024; 19:e0302475. [PMID: 38748685 PMCID: PMC11095691 DOI: 10.1371/journal.pone.0302475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/04/2024] [Indexed: 05/19/2024] Open
Abstract
Cardiac troponin I (cTnI) is a cardiac biomarker for diagnosing ischemic heart disease and acute myocardial infarction. Current biochemical assays use antibodies (Abs) due to their high specificity and sensitivity. However, there are some limitations, such as the high-cost production of Abs due to complex instruments, reagents, and steps; the variability of Abs quality from batch to batch; the low stability at high temperatures; and the difficulty of chemical modification. Aptamer overcomes the limitations of antibodies, such as relatively lower cost, high reproducibility, high stability, and ease of being chemically modified. Aptamers are three-dimensional architectures of single-stranded RNA or DNA that bind to targets such as proteins. Six aptamers (Tro1-Tro6) with higher binding affinity than an antibody have been identified, but the molecular interaction has not been studied. In this study, six DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the similar cTnI region. The interaction between aptamer and cTnI involved hydrophobic interaction, hydrogen bonds, π-cation interactions, π-stack interactions, and salt-bridge formation. The calculated binding energy of all complexes was negative, which means that the complex formation was thermodynamically favorable. The electrostatic energy term was the main driving force of the interaction between all aptamer and cTnI. This study could be used to predict the behavior of further modified aptamer to improve aptamer performance.
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Affiliation(s)
- Bejo Ropii
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Maulidwina Bethasari
- Department of Pharmacy, Universitas Muhammadiyah Bandung, Bandung, West Java, Indonesia
| | - Isa Anshori
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
- Center for Health and Sports Technology, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Allya Paramita Koesoema
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Wervyan Shalannanda
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Ardianto Satriawan
- School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Casi Setianingsih
- Department of Computer Engineering, School of Electrical Engineering, Telkom University, Bandung Regency, West Java, Indonesia
| | - Mohammad Rizki Akbar
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Padjadjaran and Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Reza Aditama
- Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Fahmi Fahmi
- Department of Electrical Engineering, Faculty of Engineering, Universitas Sumatera Utara, Medan, North Sumatera, Indonesia
| | - Erwin Sutanto
- Department of Physics, Faculty of Science and Technology, Universitas Airlangga, Kampus C Unair Mulyorejo, Surabaya, East Java, Indonesia
| | - Muhammad Yazid
- Biomedical Engineering Department, Institut Teknologi Sepuluh Nopember, Surabaya, East Java, Indonesia
| | - Muhammad Aziz
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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Bruce-Tagoe TA, Harnish MT, Soleimani S, Ullah N, Shen T, Danquah MK. Surface plasmon resonance aptasensing and computational analysis of Staphylococcus aureus IsdA surface protein. Biotechnol Prog 2024:e3475. [PMID: 38682836 DOI: 10.1002/btpr.3475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
Staphylococcus aureus (S. aureus), a common foodborne pathogen, poses significant public health challenges due to its association with various infectious diseases. A key player in its pathogenicity, which is the IsdA protein, is an essential virulence factor in S. aureus infections. In this work, we present an integrated in-silico and experimental approach using MD simulations and surface plasmon resonance (SPR)-based aptasensing measurements to investigate S. aureus biorecognition via IsdA surface protein binding. SPR, a powerful real-time and label-free technique, was utilized to characterize interaction dynamics between the aptamer and IsdA protein, and MD simulations was used to characterize the stable and dynamic binding regions. By characterizing and optimizing pivotal parameters such as aptamer concentration and buffer conditions, we determined the aptamer's binding performance. Under optimal conditions of pH 7.4 and 150 mM NaCl concentration, the kinetic parameters were determined; ka = 3.789 × 104/Ms, kd = 1.798 × 103/s, and KD = 4.745 × 10-8 M. The simulations revealed regions of interest in the IsdA-aptamer complex. Region I, which includes interactions between amino acid residues H106 and R107 and nucleotide residues 9G, 10U, 11G and 12U of the aptamer, had the strongest interaction, based on ΔG and B-factor values, and hence contributed the most to the stability of the interaction. Region II, which covers residue 37A reflects the dynamic nature of the interaction due to frequent contacts. The approach presents a rigorous characterization of aptamer-IsdA binding behavior, supporting the potential application of the IsdA-binding aptamer system for S. aureus biosensing.
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Affiliation(s)
- Tracy Ann Bruce-Tagoe
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Michael T Harnish
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Shokoufeh Soleimani
- Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Najeeb Ullah
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Michael K Danquah
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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12
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Li X, Wang J, Yang G, Fang X, Zhao L, Luo Z, Dong Y. The Development of Aptamer-Based Gold Nanoparticle Lateral Flow Test Strips for the Detection of SARS-CoV-2 S Proteins on the Surface of Cold-Chain Food Packaging. Molecules 2024; 29:1776. [PMID: 38675595 PMCID: PMC11052266 DOI: 10.3390/molecules29081776] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic over recent years has shown a great need for the rapid, low-cost, and on-site detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, an aptamer-based colloidal gold nanoparticle lateral flow test strip was well developed to realize the visual detection of wild-type SARS-CoV-2 spike proteins (SPs) and multiple variants. Under the optimal reaction conditions, a low detection limit of SARS-CoV-2 S proteins of 0.68 nM was acquired, and the actual detection recovery was 83.3% to 108.8% for real-world samples. This suggests a potential tool for the prompt detection of SARS-CoV-2 with good sensitivity and accuracy, and a new method for the development of alternative antibody test strips for the detection of other viral targets.
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Affiliation(s)
- Xiaotong Li
- Laboratory of Food Safety and Risk Assessment, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.L.); (J.W.); (L.Z.)
| | - Jiachen Wang
- Laboratory of Food Safety and Risk Assessment, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.L.); (J.W.); (L.Z.)
| | - Ge Yang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China;
| | - Xiaona Fang
- Department of Basic Medicine, Anhui Medical College, Hefei 230601, China;
| | - Lianhui Zhao
- Laboratory of Food Safety and Risk Assessment, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.L.); (J.W.); (L.Z.)
| | - Zhaofeng Luo
- Key Laboratory of Zhejiang Province for Aptamers and Theragnostic, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yiyang Dong
- Laboratory of Food Safety and Risk Assessment, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.L.); (J.W.); (L.Z.)
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Chen X, Chang Y, Ye M, Wang Z, Wu S, Duan N. Rational Design of a Robust G-Quadruplex Aptamer as an Inhibitor to Alleviate Listeria monocytogenes Infection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15946-15958. [PMID: 38519414 DOI: 10.1021/acsami.4c00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Listeria monocytogenes (LM) is one of the most invasive foodborne pathogens that cause listeriosis, making it imperative to explore novel inhibiting strategies for alleviating its infection. The adhesion and invasion of LM within host cells are partly orchestrated by an invasin protein internalin A (InlA), which facilitates bacterial passage by interacting with the host cell E-cadherin (E-Cad). Hence, in this work, we proposed an aptamer blocking strategy by binding to the region on InlA that directly mediated E-Cad receptor engagement, thereby alleviating LM infection. An aptamer GA8 with a robust G-quadruplex (G4) structural feature was designed through truncation and base mutation from the original aptamer A8. The molecular docking and dynamics analysis showed that the InlA/aptamer GA8 binding interface was highly overlapping with the natural InlA/E-Cad binding interface, which confirmed that GA8 can tightly and stably bind InlA and block more distinct epitopes on InlA that involved the interaction with E-Cad. On the cellular level, it was confirmed that GA8 effectively blocked LM adhesion with an inhibition rate of 78%. Overall, the robust G4 aptamer-mediated design provides a new direction for the development of inhibitors against other wide-ranging and emerging pathogens.
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Affiliation(s)
- Xiaowan Chen
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Yuting Chang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Mingyue Ye
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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14
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Gubu A, Ma Y, Yu S, Zhang H, Chen Z, Ni S, Abdullah R, Xiao H, Zhang Y, Dai H, Luo H, Yu Y, Wang L, Jiang H, Zhang N, Tian Y, Li H, Lu A, Zhang B, Zhang G. Unique quinoline orientations shape the modified aptamer to sclerostin for enhanced binding affinity and bone anabolic potential. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102146. [PMID: 38444701 PMCID: PMC10914587 DOI: 10.1016/j.omtn.2024.102146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
Osteogenesis imperfecta (OI) is a rare genetic disease characterized by bone fragility and bone formation. Sclerostin could negatively regulate bone formation by antagonizing the Wnt signal pathway, whereas it imposes severe cardiac ischemic events in clinic. Our team has screened an aptamer that could promote bone anabolic potential without cardiovascular risk. However, the affinity of the aptamer is lower and needs to be improved. In the study, hydrophobic quinoline molecule with unique orientations (seven subtypes) were incorporated into key sites of a bone anabolic aptamer against sclerostin to form a modified aptamer library. Among all the quinoline modifications, 5-quinoline modification could shape the molecular recognition of modified aptamers to sclerostin to facilitate enhancing its binding to sclerostin toward the highest affinity by interacting with newly participated binding sites in sclerostin. Further, 5-quinoline modification could facilitate the modified aptamer attenuating the suppressed effect of the transfected sclerostin on both Wnt signaling and bone formation marker expression levels in vitro, promoting bone anabolism in OI mice (Col1a2+/G610C). The proposed quinoline-oriented modification strategy could shape the molecular recognition of modified aptamers to proteins to facilitate enhancing its binding affinity and therapeutic potency.
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Affiliation(s)
- Amu Gubu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Yuan Ma
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Increasepharm & Hong Kong Baptist University Joint Centre for Nucleic Acid Drug Discovery, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Sifan Yu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, School of Chinese Medicine, The Chinese University of Hong Kong, Shen Zhen 518063, China
| | - Huarui Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Zefeng Chen
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Increasepharm & Hong Kong Baptist University Joint Centre for Nucleic Acid Drug Discovery, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Shuaijian Ni
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Razack Abdullah
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Huan Xiao
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yihao Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Hong Dai
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Hang Luo
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuanyuan Yu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Luyao Wang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Hewen Jiang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ning Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuan Tian
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Haitian Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Aiping Lu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ge Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
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15
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Yang R, Zhao L, Wang F, Chen J, Ma X, Luan Y, Kong W. High-throughput extraction and automatic purification of alternariol from edible and medicinal herbs based on aptamer-functionalized magnetic nanoparticles. J Sep Sci 2024; 47:e2300870. [PMID: 38471979 DOI: 10.1002/jssc.202300870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/24/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Mycotoxin contamination is widespread in plants and herbs, posing serious threats to the consumer and human health. Of them, alternariol (AOH) has attracted great attention as an "emerging" mycotoxin in medicinal herbs. However, a specific and high-throughput extraction method for AOH is currently lacking. Thus, developing an efficient pre-treatment technique for AOH detection is extremely vital. Here, a novel automated magnetic solid-phase extraction method was proposed for the highly efficient extraction of AOH. Combining the aptamer-functionalized magnetic nanoparticles (AMNPs) and the automatic purification instrument, AOH could be extracted in medicinal herbs in high throughput (20 samples) and a short time (30 min). The main parameters affecting extraction were optimized, and the method was finally carried out by incubation AMNPs with 3 mL of sample solution for 10 min, and then desorption in 75% methanol for liquid-phase detection. Under optimal conditions, good reproducibility, stability, and selectivity were realized with an adsorption capacity of 550.84 ng/mg. AOH extraction in three edible herbs showed good resistance to matrix interference with recovery rates from 86% to 111%. In combination with AMNPs and the automatic purification instrument, high-throughput and labor-free extraction of AOH in different complex matrices was achieved, which could be extended in other complex matrices.
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Affiliation(s)
- Ruiqi Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Liping Zhao
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fengchao Wang
- College of Sciences, Shanghai Institute of Technology, Shanghai, China
| | - Jin Chen
- College of Sciences, Shanghai Institute of Technology, Shanghai, China
| | - Xiao Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yunxia Luan
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weijun Kong
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
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16
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Qin Y, Zhang S, Qian J, Meng F, Yao J, Zhang M. Lable-free aptamer portable colorimetric smartphone for gliadin detection in food. Front Bioeng Biotechnol 2024; 12:1338408. [PMID: 38440327 PMCID: PMC10910070 DOI: 10.3389/fbioe.2024.1338408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
For individuals with celiac disease (CD), the current clinical therapy option available is a lifelong gluten-free diet. Therefore, it is essential to swiftly and efficiently detect gluten in foods. A colorimetric sensor has been developed, which operates by regulating the aggregation and dispersion state of AuNPs induced by high concentration NaCl through the specific binding of gliadin and aptamer, thereby achieving rapid detection of gliadin in flour. It is found that the sensor exhibits good linearity in the concentration range of 0.67-10 μM and the LOD (3σ/S) is 12 nM. And it can accurately distinguish various types of free-gliadin samples, with a spiked recovery rate of 85%-122.3%. To make the detection process more convenient, the colorimetric results of the biosensor were translated into RGB color-gamut parameters by a smartphone color-picking program for further analysis. Gliadin can still be accurately quantified with the established smartphone platform, and a correlation coefficient of 0.988 was found. The proposed portable smartphone aptamer colorimetric sensing device has achieved satisfactory results in the rapid detection of gliadin in food.
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Affiliation(s)
- Yadi Qin
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Sicheng Zhang
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Jie Qian
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Fanxing Meng
- College life Science and Technology, Xinjiang University, Urumqi, China
| | - Jun Yao
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
- Key Laboratory of Active Components and Drug Release Technology of Natural Medicines in Xinjiang, Xinjiang Medical University, Urumqi, China
| | - Minwei Zhang
- College life Science and Technology, Xinjiang University, Urumqi, China
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17
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Jia Y, Chen S, Wang Q, Li J. Recent progress in biosensor regeneration techniques. NANOSCALE 2024; 16:2834-2846. [PMID: 38291996 DOI: 10.1039/d3nr05456j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Biosensors are widely used in various applications, from medical diagnostics to environmental monitoring. Their widespread and continuous use necessitates regeneration methods to ensure cost-effectiveness and sustainability. In the realm of advancing human-centric bioelectronics for continuous monitoring, employing these sensors for real-time, in situ detection of biomarkers presents a considerable challenge. This mini-review examines diverse strategies utilized for the regeneration of biosensors, categorizing them based on their underlying mechanisms and discussing representative works. We explore methods ranging from surface engineering/re-functionalization, chemical treatments, allosteric regulation of bioreceptors, to manipulations of electric/magnetic fields, highlighting their working principles and exemplary studies. The advantages of each method, such as simplicity, high regeneration efficiency, and versatility, are discussed alongside their challenges, including degradation over cycles, limited applicability, and potential damage to sensors. As the demand for continuous and real-time biosensing escalates, the development of efficient and reliable regeneration strategies becomes essential. This mini-review offers an overview of the current landscape of biosensor regeneration, aiming to guide future research and innovations in this area.
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Affiliation(s)
- Yizhen Jia
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Shulin Chen
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Qi Wang
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jinghua Li
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH 43210, USA.
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18
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D'Agata R, Bellassai N, Spoto G. Exploiting the design of surface plasmon resonance interfaces for better diagnostics: A perspective review. Talanta 2024; 266:125033. [PMID: 37562226 DOI: 10.1016/j.talanta.2023.125033] [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: 04/13/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Surface Plasmon Resonance based-sensors are promising tools for precision diagnostics as they can provide tests useful for early and, whenever possible, non-invasive disease detection and monitoring. The design of novel, robust and effective interfaces enabling the sensing of a variety of molecular interactions in a highly selective and sensitive manner is a necessary step to obtain both accurate and reliable detection by SPR. This review covers the recent research efforts in this area, specifically emphasizing well-designed interfaces and applications in real-life samples. In particular, after a short introduction which identifies some of the critical challenges, the emerging strategies for the integration of the linker, the metal substrate and the recognition element on the sensing interface will be explored and discussed in three sections, as well as the opportunities for building SPR biosensors, easy to use, and with excellent sensitivities. Finally, a summary of some of the more promising and latest diagnostic applications will be provided, presenting a new window into the near-future perspectives.
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Affiliation(s)
- Roberta D'Agata
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy; INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136, Roma, Italy.
| | - Noemi Bellassai
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy; INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136, Roma, Italy
| | - Giuseppe Spoto
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy; INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136, Roma, Italy
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19
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Zhou C, Yang G, Meng P, Qin W, Li Y, Lin Z, Hui W, Zhang H, Lu F. Identification and engineering of the aprE regulatory region and relevant regulatory proteins in Bacillus licheniformis 2709. Enzyme Microb Technol 2024; 172:110310. [PMID: 37925770 DOI: 10.1016/j.enzmictec.2023.110310] [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: 05/10/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 11/07/2023]
Abstract
Bacillus licheniformis 2709 is the main industrial producer of alkaline protease (AprE), but its biosynthesis is strictly controlled by a highly sophisticated transcriptional network. In this study, the UP elements of aprE located 74-98, 98-119 and 140-340 bp upstream of the transcriptional start site (TSS) were identified, which presented obvious effects on the transcription of aprE. To further analyze the transcriptional mechanism, the specific proteins binding to the approximately 500-bp DNA sequences were subsequently captured by reverse-chromatin immunoprecipitation (reverse-ChIP) and DNA pull-down (DPD) assays, which captured the transcriptional factors CggR, FruR, and YhcZ. The study demonstrated that CggR, FruR and YhcZ had no significant effect on cell growth and aprE expression. Then, aprE expression was significantly enhanced by deleting a potential negative regulatory factor binding site in the genome. The AprE enzyme activity in shake flasks of the genomic mutant BL ∆1 was 47% higher than in the original strain, while the aprE transcription level increased 3.16 times. The protocol established in this study provides a valuable reference for the high-level production of proteins in other Bacillus species. At the same time, it will help reveal the molecular mechanism of the transcriptional regulatory network of aprE and provide important theoretical guidance for further enhancing the yield of AprE.
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Affiliation(s)
- Cuixia Zhou
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China; Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Guangcheng Yang
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China.
| | - Panpan Meng
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Weishuai Qin
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Yanyan Li
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Zhenxian Lin
- School of biology and brewing engineering, Taishan University, Taian 271018, PR China
| | - Wei Hui
- Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huitu Zhang
- Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Fuping Lu
- Key laboratory of industrial fermentation microbiology, Ministry of education, College of biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China.
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20
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Marzano M, D'Errico S, Greco F, Falanga AP, Terracciano M, Di Prisco D, Piccialli G, Borbone N, Oliviero G. Polymorphism of G-quadruplexes formed by short oligonucleotides containing a 3'-3' inversion of polarity: From G:C:G:C tetrads to π-π stacked G-wires. Int J Biol Macromol 2023; 253:127062. [PMID: 37748594 DOI: 10.1016/j.ijbiomac.2023.127062] [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: 07/13/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
G-wires are supramolecular DNA structures based on the G-quadruplex (G4) structural motif obtained by the self-assembly of interlocked slipped G-rich oligonucleotide (ON) strands, or by end-to-end stacking of G4 units. Despite the increasing interest towards G-wires due to their potential applications in DNA nanotechnologies, the self-assembly process to obtain G-wires having a predefined length and stability is still neither completely understood nor controlled. In our previous studies, we demonstrated that the d(5'CG2-3'-3'-G2C5') ON, characterized by the presence of a 3'-3'-inversion of polarity site self-assembles into a G-wire structure when annealed in the presence of K+ ions. Herein, by using CD, PAGE, HPLC size exclusion chromatography, and NMR investigations we studied the propensity of shorter analogues having sequences 5'CGn-3'-3'-GmC5' (with n = 1 and 1 ≤ m ≤ 3) to form the corresponding G-quadruplexes and stacked G-wires. The results revealed that the formation of G-wires starting from d(5'CGn-3'-3'-GmC5') ONs is possible only for the sequences having n and m > 1 in which both guanosines flanking the 5'-ending cytosines are not involved into the 3'-3' phosphodiester bond.
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Affiliation(s)
- Maria Marzano
- CESTEV, University of Naples Federico II, Via Tommaso De Amicis 95, 80131 Naples, Italy
| | - Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Daria Di Prisco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy.
| | - Giorgia Oliviero
- ISBE-IT, University of Naples Federico II, Corso Umberto I, 80138 Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
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Zheng D, Zhang J, Jiang W, Xu Y, Meng H, Poh CL, Chen CH. Graphene oxide aptasensor droplet assay for detection of metabolites secreted by single cells applied to synthetic biology. LAB ON A CHIP 2023; 24:137-147. [PMID: 38054213 DOI: 10.1039/d3lc00959a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Synthetic biology harnesses the power of natural microbes by re-engineering metabolic pathways to manufacture desired compounds. Droplet technology has emerged as a high-throughput tool to screen single cells for synthetic biology, while the challenges in sensitive flexible single-cell secretion assay for bioproduction of high-value chemicals remained. Here, a novel droplet modifiable graphene oxide (GO) aptasensor was developed, enabling sensitive flexible detection of different target compounds secreted from single cells. Fluorophore-labeled aptamers were stably anchored on GO through π-π stacking interactions to minimize the non-specific interactions for low-background detection of target compounds with high signal-to-noise ratios. The assay's versatility was exhibited by adapting aptamer sequences to measure metabolic secretions like ATP and naringenin. To show the case, engineered E. coli were constructed for the bioproduction of naringenin. The high signal-to-noise ratio assay (∼2.72) was approached to precisely measure the naringenins secreted from single E. coli in the droplets. Consequently, secretory cells (Gib) were clearly distinguished from wild-type (WT) cells, with a low overlap in cell populations (∼0%) for bioproduction.
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Affiliation(s)
- Dan Zheng
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Jingyun Zhang
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Wenxin Jiang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Haixu Meng
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
| | - Chueh Loo Poh
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, 117583, Singapore.
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen, China
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Lin B, Xiao F, Jiang J, Zhao Z, Zhou X. Engineered aptamers for molecular imaging. Chem Sci 2023; 14:14039-14061. [PMID: 38098720 PMCID: PMC10718180 DOI: 10.1039/d3sc03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.
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Affiliation(s)
- Bingqian Lin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Jinting Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Zhengjia Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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He X, Wang S, Ma C, Xu GR, Ma J, Xie H, Zhu W, Liu H, Wang L, Wang Y. Utilizing Electrochemical Biosensors as an Innovative Platform for the Rapid and On-Site Detection of Animal Viruses. Animals (Basel) 2023; 13:3141. [PMID: 37835747 PMCID: PMC10571726 DOI: 10.3390/ani13193141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/19/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Animal viruses are a significant threat to animal health and are easily spread across the globe with the rise of globalization. The limitations in diagnosing and treating animal virus infections have made the transmission of diseases and animal deaths unpredictable. Therefore, early diagnosis of animal virus infections is crucial to prevent the spread of diseases and reduce economic losses. To address the need for rapid diagnosis, electrochemical sensors have emerged as promising tools. Electrochemical methods present numerous benefits, including heightened sensitivity and selectivity, affordability, ease of use, portability, and rapid analysis, making them suitable for real-time virus detection. This paper focuses on the construction of electrochemical biosensors, as well as promising biosensor models, and expounds its advantages in virus detection, which is a promising research direction.
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Affiliation(s)
- Xun He
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Shan Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Caoyuan Ma
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Guang-Ri Xu
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Jinyou Ma
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Hongbing Xie
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Wei Zhu
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
| | - Hongyang Liu
- Shuangliao Animal Disease Control Center, Siping 136400, China;
| | - Lei Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China
| | - Yimin Wang
- Henan Institute of Science and Technology, Xinxiang 453003, China; (X.H.); (S.W.); (C.M.); (G.-R.X.); (J.M.); (H.X.); (W.Z.)
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China
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Liao Y, Zhang N, Chai D, Liu B, Li J, Fang Y, Zhang D, Liu R, Li Z. Rational design of a ratiometric fluorescent aptasensor for patulin in traditional Chinese medicine through the studies of the interaction mechanism between its DNA aptamer and the target molecule. Analyst 2023; 148:5233-5242. [PMID: 37725068 DOI: 10.1039/d3an00923h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Patulin (PAT) is a kind of mycotoxin which must be monitored for the sake of quality and safety in traditional Chinese medicine (TCM) owing to its harm to human health. On this account, a rationally designed ratiometric fluorescent aptasensor was developed based on the studies of the interaction mechanism between PAT and its aptamer (PAT-APT). First, CD spectroscopy, molecular docking, and molecular dynamic simulation were applied to investigate the details on how PAT-APT binds with its target molecule. The results indicated that the structure of PAT-APT changed to a certain extent and was stabilized after binding with PAT. C-11, C-37 and C-38 were the key sites for the recognition and interaction between PAT-APT and its target. Second, based on these results, a ratiometric aptasensor was designed using fluorescence resonance energy transfer (FRET) and synchronous fluorescence spectroscopy. A complementary sequence (cDNA) to the aptamer with an appropriate length and hybridization position was obtained through rational design and optimization. Both PAT-APT and cDNA were labeled using a pair of fluorophores, which could generate FRET when the two single-stranded oligonucleotides hybridized. The accurate detection of PAT could be realized according to the change ratio of the fluorescence intensity at the corresponding wavelengths of the two fluorophores before and after the assay. The aptasensor achieved an ultralow limit of detection of 0.16 nM, perfect selectivity, and satisfactory practicability in complex TCM samples. To our knowledge, this is the first aptasensor for PAT designed through the interaction mechanism between its aptamer and the target molecule. Moreover, the assay for PAT is cost-effective, does not need complicated pretreatment and only takes less than an hour. In summary, this study makes a contribution to the safety control of TCM and provides a thinking mode from mechanism to rational design to conquer the problem of sensitive aptasensing of one component in a complex system.
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Affiliation(s)
- Yumeng Liao
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Nan Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Danni Chai
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Boshi Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Jingrong Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Yuting Fang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Di Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Rui Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
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Chen P, Hu C, Tao X, Zhou Z, Wang L, Yang X, Che Z, Chen X, Huang Y. Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Bekkouche I, Kuznetsova MN, Rejepov DT, Vetcher AA, Shishonin AY. Recent Advances in DNA Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2449. [PMID: 37686956 PMCID: PMC10490369 DOI: 10.3390/nano13172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Maria N. Kuznetsova
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Dovlet T. Rejepov
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
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Fujiwara S, Hata M, Onohara I, Kawasaki D, Sueyoshi K, Hisamoto H, Suzuki M, Yasukawa T, Endo T. Dielectrophoretic trapping of nanosized biomolecules on plasmonic nanohole arrays for biosensor applications: simple fabrication and visible-region detection. RSC Adv 2023; 13:21118-21126. [PMID: 37449027 PMCID: PMC10337744 DOI: 10.1039/d3ra03245k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
Surface plasmon resonance is an optical phenomenon that can be applied for label-free, real-time sensing to directly measure biomolecular interactions and detect biomarkers in solutions. Previous studies using plasmonic nanohole arrays have monitored and detected various biomolecules owing to the propagating surface plasmon polaritons (SPPs). Extraordinary optical transmission (EOT) that occurs in the near-infrared (NIR) and infrared (IR) regions is usually used for detection. Although these plasmonic nanohole arrays improve the sensitivity and throughput for biomolecular detection, these arrays have the following disadvantages: (1) molecular diffusion in the solution (making the detection of biomolecules difficult), (2) the device fabrication's complexities, and (3) expensive equipments for detection in the NIR or IR regions. Therefore, there is a need to fabricate plasmonic nanohole arrays as biomolecular detection platforms using a simple and highly reproducible procedure based on other SPP modes in the visible region instead of the EOT in the NIR or IR regions while suppressing molecular diffusion in the solution. In this paper, we propose the combination of a polymer-based gold nanohole array (Au NHA) obtained through an easy process as a simple platform and dielectrophoresis (DEP) as a biomolecule manipulation method. This approach was experimentally demonstrated using SPP and LSPR modes (not EOT) in the visible region and simple, label-free, rapid, cost-effective trapping and enrichment of nanoparticles (trapping time: <50 s) and bovine serum albumin (trapping time: <1000 s) was realized. These results prove that the Au NHA-based DEP devices have great potential for real-time digital and Raman bioimaging, in addition to biomarker detection.
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Affiliation(s)
- Satoko Fujiwara
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku, Sakai Osaka 599-8531 Japan
| | - Misaki Hata
- Graduate School of Material Science, University of Hyogo 3-2-1 Kouto, Kamigori Ako Hyogo 678-1297 Japan
| | - Ikumi Onohara
- Graduate School of Material Science, University of Hyogo 3-2-1 Kouto, Kamigori Ako Hyogo 678-1297 Japan
| | - Daiki Kawasaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku, Sakai Osaka 599-8531 Japan
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku, Sakai Osaka 599-8531 Japan
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO) 5-3 Yonban-cho, Chiyoda Tokyo 102-8666 Japan
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku, Sakai Osaka 599-8531 Japan
| | - Masato Suzuki
- Graduate School of Material Science, University of Hyogo 3-2-1 Kouto, Kamigori Ako Hyogo 678-1297 Japan
- Advanced Medical Engineering Research Institute, University of Hyogo Hyogo Japan
| | - Tomoyuki Yasukawa
- Graduate School of Material Science, University of Hyogo 3-2-1 Kouto, Kamigori Ako Hyogo 678-1297 Japan
- Advanced Medical Engineering Research Institute, University of Hyogo Hyogo Japan
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University 1-1 Gakuen-cho, Naka-ku, Sakai Osaka 599-8531 Japan
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Zhang Z, Luan Y, Ru S, Teng H, Li Y, Liu M, Wang J. A novel electrochemical aptasensor for ultrasensitive detection of herbicide prometryn based on its highly specific aptamer and Ag@Au nanoflowers. Talanta 2023; 265:124838. [PMID: 37453395 DOI: 10.1016/j.talanta.2023.124838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Herbicide prometryn has become a common pollutant in aquatic environments and caused adverse impacts on ecosystems. This study developed an ultrasensitive electrochemical aptasensor for prometryn based on its highly affinitive and specific aptamer and Ag@Au nanoflowers (Ag@AuNFs) for signal amplification. Firstly, this study improved the Capture-SELEX strategy to screen aptamers and obtained aptamer P60-1, which had a high affinity (Kd: 23 nM) and could distinguish prometryn from its structural analogues. Moreover, the typical stem-loop structure in aptamer P60-1 was found to be the binding pocket for prometryn. Subsequently, an electrochemical aptasensor for prometryn was established using multiwalled carbon nanotubes and reduced graphene oxide as electrode substrate, Ag@Au NFs as signal amplification element, and aptamer P60-1 as recognition element. The aptasensor had a detection range of 0.16-500 ng/mL and a detection limit of 60 pg/mL, which was much lower than those of existing detection methods. The aptasensor had high stability and good repeatability, and could specifically detecting prometryn. Furthermore, the utility of the aptasensor was validated by measuring prometryn in environmental and biological components. Therefore, this study provides a robust and ultrasensitive aptasensor for accurate detection for prometryn pollution.
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Affiliation(s)
- Zhenzhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yunxia Luan
- Institute of Quality Standard and Testing Technology of Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Hayan Teng
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yuejiao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Minhao Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jun Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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Siavash Moakhar R, Mahimkar R, Khorrami Jahromi A, Mahshid SS, Del Real Mata C, Lu Y, Vasquez Camargo F, Dixon B, Gilleard J, J Da Silva A, Ndao M, Mahshid S. Aptamer-Based Electrochemical Microfluidic Biosensor for the Detection of Cryptosporidium parvum. ACS Sens 2023; 8:2149-2158. [PMID: 37207303 DOI: 10.1021/acssensors.2c01349] [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] [Indexed: 05/21/2023]
Abstract
Cryptosporidium parvum is a high-risk and opportunistic waterborne parasitic pathogen with highly infectious oocysts that can survive harsh environmental conditions for long periods. Current state-of-the-art methods are limited to lengthy imaging and antibody-based detection techniques that are slow, labor-intensive, and demand trained personnel. Therefore, the development of new sensing platforms for rapid and accurate identification at the point-of-care (POC) is essential to improve public health. Herein, we propose a novel electrochemical microfluidic aptasensor based on hierarchical 3D gold nano-/microislands (NMIs), functionalized with aptamers specific to C. parvum. We used aptamers as robust synthetic biorecognition elements with a remarkable ability to bind and discriminate among molecules to develop a highly selective biosensor. Also, the 3D gold NMIs feature a large active surface area that provides high sensitivity and a low limit of detection (LOD), especially when they are combined with aptamers,. The performance of the NMI aptasensor was assessed by testing the biosensor's ability to detect different concentrations of C. parvum oocysts spiked in different sample matrices, i.e., buffer, tap water, and stool, within 40 min detection time. The electrochemical measurements showed an acceptable LOD of 5 oocysts mL-1 in buffer medium, as well as 10 oocysts mL-1 in stool and tap water media, over a wide linear range of 10-100,000 oocysts mL-1. Moreover, the NMI aptasensor recognized C. parvum oocysts with high selectivity while exhibiting no significant cross-reactivity to other related coccidian parasites. The specific feasibility of the aptasensor was further demonstrated by the detection of the target C. parvum in patient stool samples. Our assay showed coherent results with microscopy and real-time quantitative polymerase chain reaction, achieving high sensitivity and specificity with a significant signal difference (p < 0.001). Therefore, the proposed microfluidic electrochemical biosensor platform could be a stepping stone for the development of rapid and accurate detection of parasites at the POC.
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Affiliation(s)
| | - Rohan Mahimkar
- Infectious Diseases and Immunity in Global Health (IDIGH), Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada
| | | | - Sahar Sadat Mahshid
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
| | | | - Yao Lu
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Fabio Vasquez Camargo
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada
| | - Brent Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, Ontario K1A 0K9, Canada
| | - John Gilleard
- Faculty of Veterinary Medicine, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1 N4, Canada
| | - Alexandre J Da Silva
- US FDA-Center for Food Safety and Applied Nutrition, College Park, Maryland 20740, United States
| | - Momar Ndao
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada
- Department of Experimental Medicine, McGill University, Montréal, Quebec H3G 2M1, Canada
| | - Sara Mahshid
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
- Department of Experimental Medicine, McGill University, Montréal, Quebec H3G 2M1, Canada
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Mulyani DE, Maksum IP. Detection of Biomarker Using Aptasensors to Determine the Type of Diabetes. Diagnostics (Basel) 2023; 13:2035. [PMID: 37370930 DOI: 10.3390/diagnostics13122035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Diabetes mellitus (DM) is a metabolic disorder characterized by elevated blood glucose levels. This disease is so serious that many experts refer to it as the "silent killer". The early detection of diabetes mellitus, whether type 1, type 2 or mitochondrial, is crucial because it can improve the success of treatment and the quality of life for patients. Aptamer-based biosensor diagnosis methods have been widely developed because they have high sensitivity and selectivity in detecting biomarkers of various diseases. Aptamers are short sequences of oligonucleotides or proteins that recognize specific ligands and bind to various target molecules, ranging from small ions to large proteins. They are promising diagnostic molecules due to their high sensitivity and selectivity, ease of modification, low toxicity, and high stability. This article aims to summarize the progress of detection methods, including detection principles, sensitivity, selectivity, and the performance of detection devices, to distinguish between types of diabetes mellitus using electrochemical aptasensors with biomarkers such as glucose, insulin, HbA1c, GHSA, and ATP.
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Affiliation(s)
- Dinda Exelsa Mulyani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia
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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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Yee BJ, Shafiqah NF, Mohd-Naim NF, Ahmed MU. A CRISPR/Cas12a-based fluorescence aptasensor for the rapid and sensitive detection of ampicillin. Int J Biol Macromol 2023:125211. [PMID: 37271263 DOI: 10.1016/j.ijbiomac.2023.125211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
This study introduces CRISPR/Cas-based aptasensor for the highly sensitive and specific detection of the antibiotic, ampicillin. Ampicillin (AMPI) is a commonly used antibiotic for treating pathogenic bacteria and is additionally added to livestock feed in agriculture. This study can enable early detection of antibiotic residues, prevent their accumulation in the environment, and ensure compliance with food safety regulations. Herein, the aptasensor was developed with the CRISPR/Cas system by utilizing three different ampicillin-specific aptamers, each conjugated with a biotin at the 5'-end. The ssDNA activator was bound to the aptamers through complementary base pairings. The attraction of the aptamers to the ampicillin target released the bound ssDNA, causing the activation of the CRISPR/Cas system. The DNA reporter probe, labelled with Cy3 and a quencher, turns on the fluorescence signal when cleaved by the activated Cas12a through trans-cleavage measured using a fluorescence spectrophotometer at 590 nm. The fluorescence signal was linearly proportional to the ampicillin target concentration with a 0.01 nM limit of detection and a read-out time of 30 min. This aptasensor showed high sensitivity towards ampicillin even in the presence of other antibiotics. The method was also successfully implemented for ampicillin detection in spiked food samples.
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Affiliation(s)
- Bong Jing Yee
- Biosensors and Nanobiotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam
| | - Nurul Faizeemah Shafiqah
- Biosensors and Nanobiotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam
| | - Noor Faizah Mohd-Naim
- PAPRSB Institute of Health Science, Univesiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Nanobiotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam.
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Liu S, Meng S, Wang M, Li W, Dong N, Liu D, Li Y, You T. In-depth interpretation of aptamer-based sensing on electrode: Dual-mode electrochemical-photoelectrochemical sensor for the ratiometric detection of patulin. Food Chem 2023; 410:135450. [PMID: 36640656 DOI: 10.1016/j.foodchem.2023.135450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/12/2022] [Accepted: 01/07/2023] [Indexed: 01/10/2023]
Abstract
Electrochemical aptasensors have been extensively used to quantify food contaminants (e.g., mycotoxin) by using high-affinity aptamer for target recognition. Yet, analytical performance of aptasensors using different aptamers can be varied for the same target. Here, four aptamers with different sequences (i.e., A22, A34, A42, and A45) of patulin (PAT) were selected to estimate sensing behaviors at electrodes with electrochemical (EC) and photoelectrochemical (PEC) assays. Synergistic effect of steric hindrance and electron transfer distance was found to significantly affect EC and PEC response for PAT at aptasensors fabricated with A22, A34, A42, or A45. Eventually, A22 emerged to be the optimal aptamer for aptasensing, despite the highest affinity of A42 to PAT. The A22-based EC-PEC dual-mode ratiometric aptasensor offered a linear range of 50 fg mL-1 - 500 ng mL-1 with a detection limit of 30 fg mL-1 for PAT, and it was applied to apple product (i.e., juice, puree) analysis.
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Affiliation(s)
- Shuda Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shuyun Meng
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Meng Wang
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Wenjia Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Na Dong
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dong Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Yuye Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Tianyan You
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Zhang HL, Lv C, Li ZH, Jiang S, Cai D, Liu SS, Wang T, Zhang KH. Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation. Front Chem 2023; 11:1144347. [PMID: 37228865 PMCID: PMC10204870 DOI: 10.3389/fchem.2023.1144347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction: Aptamers are valuable for bioassays, but aptamer-target binding is susceptible to reaction conditions. In this study, we combined thermofluorimetric analysis (TFA) and molecular dynamics (MD) simulations to optimize aptamer-target binding, explore underlying mechanisms and select preferred aptamer. Methods: Alpha-fetoprotein (AFP) aptamer AP273 (as the model) was incubated with AFP under various experimental conditions, and melting curves were measured in a real-time PCR system to select the optimal binding conditions. The intermolecular interactions of AP273-AFP were analysed by MD simulations with these conditions to reveal the underlying mechanisms. A comparative study between AP273 and control aptamer AP-L3-4 was performed to validate the value of combined TFA and MD simulation in selecting preferred aptamers. Results: The optimal aptamer concentration and buffer system were easily determined from the dF/dT peak characteristics and the melting temperature (Tm) values on the melting curves of related TFA experiments, respectively. A high Tm value was found in TFA experiments performed in buffer systems with low metal ion strength. The molecular docking and MD simulation analyses revealed the underlying mechanisms of the TFA results, i.e., the binding force and stability of AP273 to AFP were affected by the number of binding sites, frequency and distance of hydrogen bonds, and binding free energies; these factors varied in different buffer and metal ion conditions. The comparative study showed that AP273 was superior to the homologous aptamer AP-L3-4. Conclusion: Combining TFA and MD simulation is efficient for optimizing the reaction conditions, exploring underlying mechanisms, and selecting aptamers in aptamer-target bioassays.
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Affiliation(s)
| | | | | | | | | | | | - Ting Wang
- *Correspondence: Ting Wang, ; Kun-He Zhang,
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Kara N, Ayoub N, Ilgu H, Fotiadis D, Ilgu M. Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications. Molecules 2023; 28:molecules28093728. [PMID: 37175137 PMCID: PMC10180177 DOI: 10.3390/molecules28093728] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Many biological processes (physiological or pathological) are relevant to membrane proteins (MPs), which account for almost 30% of the total of human proteins. As such, MPs can serve as predictive molecular biomarkers for disease diagnosis and prognosis. Indeed, cell surface MPs are an important class of attractive targets of the currently prescribed therapeutic drugs and diagnostic molecules used in disease detection. The oligonucleotides known as aptamers can be selected against a particular target with high affinity and selectivity by iterative rounds of in vitro library evolution, known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX). As an alternative to antibodies, aptamers offer unique features like thermal stability, low-cost, reuse, ease of chemical modification, and compatibility with various detection techniques. Particularly, immobilized-aptamer sensing platforms have been under investigation for diagnostics and have demonstrated significant value compared to other analytical techniques. These "aptasensors" can be classified into several types based on their working principle, which are commonly electrochemical, optical, or mass-sensitive. In this review, we review the studies on aptamer-based MP-sensing technologies for diagnostic applications and have included new methodological variations undertaken in recent years.
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Affiliation(s)
- Nilufer Kara
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Nooraldeen Ayoub
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Huseyin Ilgu
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Muslum Ilgu
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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Zahraee H, Khoshbin Z, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. A tag-free fluorescent aptasensor for tobramycin detection using a hybridization of three aptamer strands and SYBR Green I dye. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122305. [PMID: 36603274 DOI: 10.1016/j.saa.2022.122305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/11/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
In this study, a sensitive fluorescent method is designed to detect tobramycin (TOB) drug applying a hybrid structure of three aptamer strands and SYBR Green I (SGI) fluorescent dye as the bioreceptor segment and signal indicator, respectively. The preferential binding of the aptamers to TOB resulted in the collapse of the hybridized aptamer skeleton to the single strands. So, the intercalation of SGI molecules reduced that quenched the fluorescence response. The aptasensing assay provided the superior target specificity with a detection limit (LOD) of 0.153 pM and a wide linear dynamic range over 0.5 pM-300 μM. The aptasensor could successfully quantify TOB in human serum samples. The tag-free sensor with the remarkable advantages of simplicity, easy-to-use, cost-effectiveness, and high sensitivity is superior to be applicable for clinical samples.
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Affiliation(s)
- Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Soares S, Rosado T, Barroso M, Gallardo E. Solid Phase-Based Microextraction Techniques in Therapeutic Drug Monitoring. Pharmaceutics 2023; 15:pharmaceutics15041055. [PMID: 37111541 PMCID: PMC10142207 DOI: 10.3390/pharmaceutics15041055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/18/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Therapeutic drug monitoring is an established practice for a small group of drugs, particularly those presenting narrow therapeutic windows, for which there is a direct relationship between concentration and pharmacological effects at the site of action. Drug concentrations in biological fluids are used, in addition to other clinical observation measures, to assess the patient's status, since they are the support for therapy individualization and allow assessing adherence to therapy. Monitoring these drug classes is of great importance, as it minimizes the risk of medical interactions, as well as toxic effects. In addition, the quantification of these drugs through routine toxicological tests and the development of new monitoring methodologies are extremely relevant for public health and for the well-being of the patient, and it has implications in clinical and forensic situations. In this sense, the use of new extraction procedures that employ smaller volumes of sample and organic solvents, therefore considered miniaturized and green techniques, is of great interest in this field. From these, the use of fabric-phase extractions seems appealing. Noteworthy is the fact that SPME, which was the first of these miniaturized approaches to be used in the early '90s, is still the most used solventless procedure, providing solid and sound results. The main goal of this paper is to perform a critical review of sample preparation techniques based on solid-phase microextraction for drug detection in therapeutic monitoring situations.
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Affiliation(s)
- Sofia Soares
- Centro de Investigação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), 6200-506 Covilhã, Portugal
- Laboratório de Fármaco-Toxicologia, Ubimedical, Universidade da Beira Interior, 6200-284 Covilhã, Portugal
| | - Tiago Rosado
- Centro de Investigação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), 6200-506 Covilhã, Portugal
- Laboratório de Fármaco-Toxicologia, Ubimedical, Universidade da Beira Interior, 6200-284 Covilhã, Portugal
| | - Mário Barroso
- Serviço de Química e Toxicologia Forenses, Instituto de Medicina Legal e Ciências Forenses-Delegação do Sul, 1169-201 Lisboa, Portugal
| | - Eugenia Gallardo
- Centro de Investigação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), 6200-506 Covilhã, Portugal
- Laboratório de Fármaco-Toxicologia, Ubimedical, Universidade da Beira Interior, 6200-284 Covilhã, Portugal
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40
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Hou Y, Lu X, Yang J, Tang C, Jiang H, Cai T, Chen M, Wei Z, Yu P. A label-free fluorescent aptamer sensor for testosterone based on SYBR Green I. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1546-1552. [PMID: 36883443 DOI: 10.1039/d3ay00055a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Testosterone is a steroid hormone that plays an indispensable role in the normal metabolism of organisms. However, exogenous testosterone, even as low as nmol L-1, will harm the human body due to accumulation. In this study, we developed an unlabeled fluorescent sensor for testosterone based on SYBR Green I. SYBR Green I is a fluorescent dye that can be embedded into the G-quadruplex of the testosterone aptamer T5. The fluorescence quenching effect is utilized to achieve quantitative detection, which occurs by the competition between testosterone and SYBR Green I for the T5 aptamer binding sites. In this work, we optimized the detection conditions to make the fluorescent sensor more sensitive and verify the specificity, linear range, and detection ability in the buffer and real water samples. The sensor's LOD and LOQ values were 0.27 nmol L-1 and 0.91 nmol L-1, respectively, while the detection range was linear from 0.91 nmol L-1 to 2000 nmol L-1. According to the results, the sensor shows high specificity and good performance even in real sample detection such as tap water and river water, providing an alternative method for the quantitative detection of testosterone in the environment, which is more convenient and efficient.
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Affiliation(s)
- Yucui Hou
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Hanbing Jiang
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Tongji Cai
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha 410013, Hunan Province, China.
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41
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Yuan X, Li C, Yin X, Yang Y, Ji B, Niu Y, Ren L. Epidermal Wearable Biosensors for Monitoring Biomarkers of Chronic Disease in Sweat. BIOSENSORS 2023; 13:313. [PMID: 36979525 PMCID: PMC10045998 DOI: 10.3390/bios13030313] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Biological information detection technology is mainly used for the detection of physiological and biochemical parameters closely related to human tissues and organ lesions, such as biomarkers. This technology has important value in the clinical diagnosis and treatment of chronic diseases in their early stages. Wearable biosensors can be integrated with the Internet of Things and Big Data to realize the detection, transmission, storage, and comprehensive analysis of human physiological and biochemical information. This technology has extremely wide applications and considerable market prospects in frontier fields including personal health monitoring, chronic disease diagnosis and management, and home medical care. In this review, we systematically summarized the sweat biomarkers, introduced the sweat extraction and collection methods, and discussed the application and development of epidermal wearable biosensors for monitoring biomarkers in sweat in preclinical research in recent years. In addition, the current challenges and development prospects in this field were discussed.
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Affiliation(s)
- Xichen Yuan
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi’an 710072, China
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- MOE Key Laboratory of Micro and Nano Systems for Aerospace, Northwestern Polytechnical University, Xi’an 710072, China
| | - Chen Li
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- Key Laboratory of Flexible Electronics of Zhejiang, Ningbo Institute of Northwestern Polytechnical University, Ningbo 315103, China
| | - Xu Yin
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - Yang Yang
- Ministry of Education Key Laboratory of Low-Grade Energy Utilization Technologies and Systems, Chongqing University, Chongqing 400030, China
| | - Bowen Ji
- Unmanned System Research Institute, Northwestern Polytechnical University, Xi’an 710072, China
| | - Yinbo Niu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Li Ren
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- Key Laboratory of Flexible Electronics of Zhejiang, Ningbo Institute of Northwestern Polytechnical University, Ningbo 315103, China
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In Silico Approaches for the Identification of Aptamer Binding Interactions to Leptospira spp. Cell Surface Proteins. Trop Med Infect Dis 2023; 8:tropicalmed8020125. [PMID: 36828542 PMCID: PMC9963831 DOI: 10.3390/tropicalmed8020125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. However, their functionality relies on their secondary and tertiary structures such that the combination of nucleotides determines their three-dimensional conformation. In this study, the binding mechanisms of candidate aptamers and their interactions with selected target proteins found in the cell surface of Leptospira were predicted to select high-affinity aptamers. Four aptamers were evaluated through molecular modeling and docking using available software and web-based tools, following the workflow previously designed for in silico evaluation of DNA aptamers. The most predominant and highly conserved surface-exposed proteins among pathogenic Leptospira species were used as aptamer targets. The highest number of interactions was seen in aptamers AP5 and AP1. Hydrogen bonds, along with a few hydrophobic interactions, occur in most aptamer-protein complexes. Further analysis revealed serine, threonine, glutamine, and lysine as main protein residues. H-bond interactions occur mostly with polar amino acids, as reflected in the predicted interaction profiles of aptamer-protein complexes. In silico strategies allowed the identification of key residues crucial in aptamer-target interaction during aptamer screening. Such information can be used in aptamer modification for improved binding affinity and accuracy for diagnostics application.
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Qi X, Zhang L, Wang X, Chen S, Wang X. A label-free colorimetric aptasensor based on an engineered chimeric aptamer and Au@FeP nanocomposites for the detection of kanamycin. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Liu W, Wang Y, Zhang Y, Yu T, Ge J. Analysis of Breast Cancer Biomarker HER2 Based on Single Stranded DNA Aptamer and Enzyme Signal Amplification. INT J ELECTROCHEM SC 2023. [DOI: 10.1016/j.ijoes.2023.100056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Brosseau NE, Vallée I, Mayer-Scholl A, Ndao M, Karadjian G. Aptamer-Based Technologies for Parasite Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23020562. [PMID: 36679358 PMCID: PMC9867382 DOI: 10.3390/s23020562] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 05/30/2023]
Abstract
Centuries of scientific breakthroughs have brought us closer to understanding and managing the spread of parasitic diseases. Despite ongoing technological advancements in the detection, treatment, and control of parasitic illnesses, their effects on animal and human health remain a major concern worldwide. Aptamers are single-stranded oligonucleotides whose unique three-dimensional structures enable them to interact with high specificity and affinity to a wide range of targets. In recent decades, aptamers have emerged as attractive alternatives to antibodies as therapeutic and diagnostic agents. Due to their superior stability, reusability, and modifiability, aptamers have proven to be effective bioreceptors for the detection of toxins, contaminants, biomarkers, whole cells, pathogens, and others. As such, they have been integrated into a variety of electrochemical, fluorescence, and optical biosensors to effectively detect whole parasites and their proteins. This review offers a summary of the various types of parasite-specific aptamer-based biosensors, their general mechanisms and their performance.
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Affiliation(s)
- Noah Emerson Brosseau
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
- Infectious Diseases and Immunity in Global Health (IDIGH) Program, Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Isabelle Vallée
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
| | - Anne Mayer-Scholl
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Momar Ndao
- Infectious Diseases and Immunity in Global Health (IDIGH) Program, Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Grégory Karadjian
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
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Liu X, Hu J, Ning Y, Xu H, Cai H, Yang A, Shi Z, Li Z. Aptamer Technology and Its Applications in Bone Diseases. Cell Transplant 2023; 32:9636897221144949. [PMID: 36591965 PMCID: PMC9811309 DOI: 10.1177/09636897221144949] [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] [Indexed: 01/03/2023] Open
Abstract
Aptamers are single-stranded nucleic acids (DNA, short RNA, or other artificial molecules) produced by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology, which can be tightly and specifically combined with desired targets. As a comparable alternative to antibodies, aptamers have many advantages over traditional antibodies such as a strong chemical stability and rapid bulk production. In addition, aptamers can bind targets in various ways, and are not limited like the antigen-antibody combination. Studies have shown that aptamers have tremendous potential to diagnose and treat clinical diseases. However, only a few aptamer-based drugs have been used because of limitations of the aptamers and SELEX technology. To promote the development and applications of aptamers, we present a review of the methods optimizing the SELEX technology and modifying aptamers to boost the selection success rate and improve aptamer characteristics. In addition, we review the application of aptamers to treat bone diseases.
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Affiliation(s)
- Xiangzhong Liu
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Jing Hu
- Wuhan Children’s Hospital, Tongji
Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yu Ning
- Department of Orthopaedics, Xiangyang
Hospital of Traditional Chinese Medicine Affiliated to Hubei University of Chinese
Medicine, Xiangyang, China
| | - Haijia Xu
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Hantao Cai
- Department of Orthopaedics, Wenling
First People’s Hospital, Taizhou, China
| | - Aofei Yang
- Department of Orthopaedics, Hubei
Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Zhengshuai Shi
- Department of Orthopaedics, Wuhan
Sports University, Wuhan, China
| | - Zhanghua Li
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China,Zhanghua Li, Department of Orthopaedics,
Wuhan Third Hospital, Tongren Hospital of Wuhan University, No. 216, Guanshan
Avenue, Hongshan District, Wuhan 430074, Hubei Province, China.
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Huang Z, Hu B, Wang H. Analytical methods for microplastics in the environment: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:383-401. [PMID: 36196263 PMCID: PMC9521859 DOI: 10.1007/s10311-022-01525-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/21/2022] [Indexed: 05/06/2023]
Abstract
Microplastic pollution is a recently discovered threat to ecosystems requiring the development of new analytical methods. Here, we review classical and advanced methods for microplastic analysis. Methods include visual analysis, laser diffraction particle, dynamic light scattering, scanning electron microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, thermal analysis, mass spectrometry, aptamer and in vitro selection, and flow cytometry.
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Affiliation(s)
- Zike Huang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083 China
| | - Bo Hu
- School of Engineering, The University of Edinburgh, Edinburgh, EH9 3JW UK
| | - Hui Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083 China
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Ramasanoff RR, Sokolov PA. The binding model of adenosine-specific DNA aptamer: Umbrella sampling study. J Mol Graph Model 2023; 118:108338. [PMID: 36201878 DOI: 10.1016/j.jmgm.2022.108338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]
Abstract
We report a novel model of the selective binding mechanism of adenosine-specific DNA aptamer. Our theoretical investigations of AMP (Adenosine monophosphate) dissociation from aptamer-AMP complexes reveals new details of aptamer molecular specificity and stabilisation factors. Umbrella sampling MD calculations using parmbsc1 force field shows that the disordered structure of the internal loop of the unbound aptamer hairpin has a characteristic packing of guanines, which prevents barrier-free penetration of ligands into the site cavity. Also, this disordered structure of the unbound aptamer has a network of hydrogen bonds stabilising the cavity near the target guanines within the binding sites during the whole binding process. We suggested that the first AMP molecule binds to the disordered structure of the site closest to the aptamer hairpin stem and spends some free energy on ordering of the internal loop. Then the second AMP molecule binds to the ordered site closest to the aptamer hairpin loop with a lower energy gain. As a result, the induced-fit binding model is the most applicable for this aptamer and does not contradict the modern experimental NMR and calorimetry data.
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Affiliation(s)
- Ruslan R Ramasanoff
- Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia.
| | - Petr A Sokolov
- Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia; Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034, Saint Petersburg, Russia
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Shafiei N, Mahmoodzadeh Hosseini H, Amani J, Mirhosseini SA, Jafary H. Screening and Identification of DNA Nanostructure Aptamer Using the SELEX Method for Detection of Epsilon Toxin. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2023; 22:e140505. [PMID: 38444705 PMCID: PMC10912870 DOI: 10.5812/ijpr-140505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 03/07/2024]
Abstract
Background Epsilon toxin (ETX), produced by Clostridium perfringens, is one of the most potent toxins known, with a lethal potency approaching that of botulinum neurotoxins. Epsilon toxin is responsible for enteritis. Therefore, the development of rapid and simple methods to detect ETX is imperative. Aptamers are single-stranded oligonucleotides that can bind tightly to specific target molecules with an affinity comparable to that of monoclonal antibodies (mAbs). DNA aptamers can serve as tools for the molecular identification of organisms, such as pathogen subspecies. Objectives This study aimed to isolate high-affinity single-stranded DNA (ssDNA) aptamers against ETX. Methods This study identified aptamers using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method, enzyme-linked apta-sorbent assay (ELASA), and surface plasmon resonance (SPR) to determine the affinity and specificity of the newly obtained aptamers targeting ETX. Results Several aptamers obtained through the SELEX process were studied. Among them, 2 aptamers, ETX clone 3 (ETX3; dissociation constant (Kd = 8.4 ± 2.4E-9M) and ETX11 (Kd = 6.3 ± 1.3E-9M) had favorable specificity for ETX. The limits of detection were 0.21 and 0.08 μg/mL for ETX3 and ETX11, respectively.. Conclusions The discovered aptamers can be used in various aptamer-based rapid diagnostic tests for the detection of ETX.
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Affiliation(s)
- Nafiseh Shafiei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hanieh Jafary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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50
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Sun D, Sun M, Zhang J, Lin X, Zhang Y, Lin F, Zhang P, Yang C, Song J. Computational tools for aptamer identification and optimization. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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