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Kavruk M, Babaie Z, Kibar G, Çetin B, Yeşilkaya H, Amrani Y, Dursun AD, Özalp VC. Aptamer decorated PDA@magnetic silica microparticles for bacteria purification. Mikrochim Acta 2024; 191:285. [PMID: 38652174 PMCID: PMC11039557 DOI: 10.1007/s00604-024-06322-3] [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: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.
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Affiliation(s)
- Murat Kavruk
- Department of Medical Biology, Faculty of Medicine, İstanbul Aydın University, İstanbul, 34295, Türkiye
| | - Zahra Babaie
- Microfluidics & Lab-on-a-chip Research Group, İ.D. Bilkent University, Ankara, 06800, Türkiye
- UNAM-National Nanotech, Research Center and Institute Materials Science & Nanotech, İ.D. Bilkent University, Ankara, 06800, Türkiye
| | - Güneş Kibar
- Microfluidics & Lab-on-a-chip Research Group, İ.D. Bilkent University, Ankara, 06800, Türkiye
- UNAM-National Nanotech, Research Center and Institute Materials Science & Nanotech, İ.D. Bilkent University, Ankara, 06800, Türkiye
- Micro Nano Particles (MNP) Research Group, Materials Science and Engineering Department, Adana Alparslan Turkes Science and Technology University, Adana, 01250, Türkiye
| | - Barbaros Çetin
- Department of Medical Biology, Faculty of Medicine, İstanbul Aydın University, İstanbul, 34295, Türkiye
- Microfluidics & Lab-on-a-chip Research Group, İ.D. Bilkent University, Ankara, 06800, Türkiye
| | - Hasan Yeşilkaya
- Department Respiratory Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Yassine Amrani
- Department Respiratory Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Ali Doğan Dursun
- Department of Physiology, School of Medicine, Atilim University, Ankara, 06830, Türkiye
| | - V Cengiz Özalp
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, 06830, Türkiye.
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Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
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Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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Wang Z, Zhang C, He S, Xu D. An ultrasensitive fluorescence aptasensor for SARS-CoV-2 antigen based on hyperbranched rolling circle amplification. Talanta 2023; 255:124221. [PMID: 36608425 PMCID: PMC9792189 DOI: 10.1016/j.talanta.2022.124221] [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: 10/15/2022] [Revised: 12/11/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022]
Abstract
Sensitive and accurate diagnosis of SARS-CoV-2 infection at early stages can help to attenuate the effects of the COVID-19. Compared to RNA and antibodies detection, direct detection of viral antigens could reflect infectivity more appropriately. However, it is still a great challenge to construct a convenient, accurate and sensitive biosensor with a suitable molecular recognition element for SARS-CoV-2 antigens. Herein, we report a HRCA-based aptasensor for simple, ultrasensitive and quantitative detection of SARS-CoV-2 S1 protein and pseudovirus. The aptamer sequence used here is selected from several published aptamers by enzyme-linked oligonucleotide assay and molecular docking simulation. The sensor forms an antibody-target-aptamer sandwich complex on the surface of microplates and elicits HRCA for fluorescent detection. Without complicated operations or special instruments and reagents, the aptasensor can detect S1 protein with a LOD of 89.7 fg/mL in the linear range of 100 fg/mL to 1 μg/mL. And it can also detect SARS-CoV-2 spike pseudovirus in artificial saliva with a LOD of 51 TU/μL. Therefore, this simple and ultrasensitive aptasensor has the potential to detect SARS-CoV-2 infection at early stages. It may improve the timeliness and accuracy of SARS-CoV-2 diagnosis and demonstrate a strategy to conduct aptasensors for other targets.
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