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Chatterjee O, Kaur GA, Shukla N, Balayan S, Singh PK, Chatterjee S, Tiwari A. Multifaceted arsenal in SELEX nanomedicine. Adv Colloid Interface Sci 2025; 342:103540. [PMID: 40344950 DOI: 10.1016/j.cis.2025.103540] [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: 02/06/2025] [Revised: 04/25/2025] [Accepted: 04/28/2025] [Indexed: 05/11/2025]
Abstract
Aptamers, short oligonucleotide sequences that bind specifically to cellular proteins and receptors, are emerging as versatile tools in molecular nanomedicine. Unlike passive tumor targeting via the enhanced permeability and retention (EPR) effect, aptamers enable precise drug delivery, enhancing therapeutic efficacy while minimizing side effects. Developed through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, aptamers offer compact size, robust structure, chemical versatility, and cost-effective synthesis. They serve as effective delivery vehicles for therapeutic molecules, including miRNA, siRNA, and small-molecule drugs, and function as antibody-like ligands for applications in cancer, diabetes, and autoimmune disorders. Since the approval of Macugen, the first aptamer targeting VEGF, aptamers have also shown promise as diagnostic sensors and theranostic agents. This review explores SELEX-derived aptamers in nanomedicine, focusing on their therapeutic and diagnostic roles, particularly in precision cancer therapies. It also addresses challenges such as degradation and clinical translation alongside prospects in vaccines, tissue engineering, and regenerative medicine.
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Affiliation(s)
- Oishika Chatterjee
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, Ulrika 590 53, Sweden; Department of Biological Sciences, Bose Institute Unified Academic Campus EN 80, Sector 5, Bidhan Nagar (Salt Lake City) Kolkata 700 091, WB, India
| | - Gun Anit Kaur
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, Ulrika 590 53, Sweden
| | - Nutan Shukla
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, Ulrika 590 53, Sweden
| | - Sapna Balayan
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, Ulrika 590 53, Sweden
| | - Pravin Kumar Singh
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, Ulrika 590 53, Sweden
| | - Subhrangsu Chatterjee
- Department of Biological Sciences, Bose Institute Unified Academic Campus EN 80, Sector 5, Bidhan Nagar (Salt Lake City) Kolkata 700 091, WB, India.
| | - Ashutosh Tiwari
- Institute of Advanced Materials, IAAM, Gammalkilsvägen 18, Ulrika 590 53, Sweden.
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Abianeh HS, Kesharwani P, Sahebkar A. The use of aptamers as therapeutic inhibitors and biosensors of TNF-alpha. Int J Biol Macromol 2025; 306:141202. [PMID: 39971069 DOI: 10.1016/j.ijbiomac.2025.141202] [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: 10/21/2024] [Revised: 01/13/2025] [Accepted: 02/15/2025] [Indexed: 02/21/2025]
Abstract
Tumor necrosis factor-alpha (TNF-α) is a pivotal cytokine in the pathogenesis of numerous inflammatory and autoimmune diseases. Precise and sensitive detection of TNF-α is essential for both clinical applications and research endeavors. In the realm of cytokine detection, particularly TNF-α, the development of highly sensitive and specific biosensors has become a focal point. The biosensing landscape encompasses a variety of biorecognition elements, each with its unique set of characteristics. TNF inhibitors come with a significant price tag and, notably, do not yield positive responses in all patients. Despite the availability of numerous FDA-approved biologic agents (e.g., infliximab, adalimumab, certolizumab pegol, etc.) and monoclonal antibodies (e.g., adalimumab) targeting TNF-α, aptamers tailored for blocking TNF-α activities have yet to receive approval. Aptamers have rapidly gained recognition as readily available, versatile, and highly effective molecular tools for both therapeutic and diagnostic purposes in the context of TNF-alpha. In this manuscript, we explore the potential of short single-stranded DNA or RNA sequences known as aptamers as biorecognition elements in biosensors designed for the detection of TNF-α. We delve into the progress made in the development of aptamer-based TNF-α inhibitors and shed light on successful studies in this burgeoning field.
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Affiliation(s)
- Hossein Samiei Abianeh
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India.
| | - Amirhossein Sahebkar
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Guérin M, Vandevenne M, Matagne A, Aucher W, Verdon J, Paoli E, Ducrotoy J, Octave S, Avalle B, Maffucci I, Padiolleau-Lefèvre S. Selection and characterization of DNA aptamers targeting the surface Borrelia protein CspZ with high-throughput cross-over SELEX. Commun Biol 2025; 8:632. [PMID: 40251423 PMCID: PMC12008269 DOI: 10.1038/s42003-025-08034-7] [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: 01/13/2025] [Accepted: 04/02/2025] [Indexed: 04/20/2025] Open
Abstract
Lyme borreliosis (LB) is the most prevalent tick-borne illness, with an estimated 700 000 cases annually in the United States and Europe. The LB diagnosis based on a two-tiered serology remains controversial due to its indirect nature and low sensitivity during the early stage of the disease. Aptamers are single-stranded DNA or RNA oligonucleotides that exhibit high selectivity and specificity for their target due to their unique three-dimensional structure. By applying cross-over-SELEX process, an enrichment of DNA oligonucleotide sequences against a surface protein of Borrelia, named CspZ, has been performed and monitored using absorbance at 260 nm, melting curves and NGS analyses. Beyond sequence enrichment, oligonucleotides binding to CspZ were observed during the selection rounds by Dot Blot and beads assays. Thirteen unique and highly redundant oligonucleotide sequences were further characterized using multiple approaches such as Dot Blot, BioLayer Interferometry and Surface Plasmon Resonance. The selected aptamers showed KD values from tens of nanomolar to the micromolar range by BLI and SPR. Two aptamers, Apta9 and Apta10, characterized by flow cytometry and epifluorescence microscopy, were able to specifically recognize Borrelia burgdorferi sensu stricto. This strategy holds promise for the development of an improved diagnostic assay.
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Affiliation(s)
- Mickaël Guérin
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Marylène Vandevenne
- Robotein®, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - André Matagne
- Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
- Laboratory of Enzymology and Protein Folding, InBioS Research Unit, University of Liège, Building B6, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Willy Aucher
- Laboratoire Ecologie & Biologie des Interactions (EBI), CNRS UMR 7267, Université de Poitiers, 86073, Poitiers, France
| | - Julien Verdon
- Laboratoire Ecologie & Biologie des Interactions (EBI), CNRS UMR 7267, Université de Poitiers, 86073, Poitiers, France
| | - Emmeline Paoli
- Laboratoire Ecologie & Biologie des Interactions (EBI), CNRS UMR 7267, Université de Poitiers, 86073, Poitiers, France
| | - Jules Ducrotoy
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Stéphane Octave
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Bérangère Avalle
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Irene Maffucci
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France
| | - Séverine Padiolleau-Lefèvre
- Unité de Génie Enzymatique et Cellulaire (GEC), CNRS UMR 7025, Université de Technologie de Compiègne, 60203, Compiègne, France.
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Shoaib M, Li H, Zareef M, Khan IM, Iqbal MW, Niazi S, Raza H, Yan Y, Chen Q. Recent Advances in Food Safety Detection: Split Aptamer-Based Biosensors Development and Potential Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:4397-4424. [PMID: 39943644 DOI: 10.1021/acs.jafc.4c06338] [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: 02/27/2025]
Abstract
Ensuring food safety is a shared responsibility across the entire food supply chain, encompassing manufacturers, processors, retailers, consumers, and regulatory bodies. However, traditional detection methods have several limitations, including slow processing times, high costs, limited sensitivity, and susceptibility to false positives or negatives. These shortcomings underscore the urgent need for faster, more accurate, and cost-effective detection technologies. Aptamers and aptasensors have emerged as promising alternatives. Aptamers offer advantages over traditional recognition probes due to their high affinity and specificity for diverse targets. The aptasensors enable rapid detection, cost reduction, shelf life extension, and minimal batch-to-batch variability, making them highly suitable for food safety applications. Detecting small molecules such as toxins, antibiotics, pesticides, contaminants, and heavy metals remains challenging due to steric hindrance, nonspecific binding, and reduced accuracy. Recent advancements in aptamer technology have focused on pre- and postmodifications to enhance detection performance. One of the most promising innovations is the development of split aptamers. These engineered aptamers, designed to operate in segments known as split aptamers, offer improved flexibility and binding specificity, effectively addressing the challenges of detecting small-sized targets. This review examines the evolution of aptamers and aptasensors, focusing on their application in detecting small molecules that are essential to food safety. It reported the strategies for modifying and optimizing selected aptamers, providing details on developing split aptamers as a promising approach to address the unique challenges of small-molecule detection. Additionally, recent advancements in split aptamer technology and its integration into aptasensor development are highlighted, showcasing how these innovations are revolutionizing the detection of food safety hazards by overcoming the limitations of traditional detection methods.
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Affiliation(s)
- Muhammad Shoaib
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 213013, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Huanhuan Li
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 213013, China
| | - Muhammad Zareef
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 213013, China
| | - Imran Mahmood Khan
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo 315100, China
| | - Muhammad Waheed Iqbal
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 213013, China
| | - Sobia Niazi
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Husnain Raza
- Department of Food Science, Design and Consumer Behaviour, University of Copenhagen, Rolighedsvej 26, DK-1958, Frederiksberg C, Copenhagen, Denmark
| | - Yiyong Yan
- Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen 518060, China
- Shenzhen Senlanthy Technology Co., Ltd., Shenzhen 518060, China
| | - Quansheng Chen
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
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Harkai Á, Beck YK, Tory A, Mészáros T. Selection of streptococcal glucan-binding protein C specific DNA aptamers to inhibit biofilm formation. Int J Biol Macromol 2025; 288:138579. [PMID: 39657876 DOI: 10.1016/j.ijbiomac.2024.138579] [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: 08/23/2024] [Revised: 11/13/2024] [Accepted: 12/07/2024] [Indexed: 12/12/2024]
Abstract
Streptococcus mutans is a commensal oral bacterium, yet its capacity for extensive biofilm formation is a major contributor to dental caries. This study presents a novel biofilm inhibition strategy by targeting GbpC, a cornerstone protein in S. mutans biofilm architecture, with specific DNA aptamers. Using SELEX (Systematic Evolution of Ligands by EXponential enrichment), we selectively targeted the extracellular domain of GbpC while incorporating structurally similar antigen I/II protein and a GbpC-deficient S. mutans strain as counter-targets to ensure high specificity. Aptamer selection was further refined through a panning method that combined primer-blocked asymmetric PCR with AlphaScreen technology. Detailed binding analyses via biolayer interferometry and microscale thermophoresis confirmed the interaction between top aptamer candidates and GbpC. Functional assays demonstrated that two lead aptamers evidently inhibited biofilm formation in wild-type S. mutans without affecting the GbpC-deficient strain, highlighting the aptamers' specificity. These results confirm that the selected aptamers retain specificity even in the complex bacterial culture matrix, validating the efficacy of our selection approach. Notably, these aptamers represent the first instance of using DNA aptamers to inhibit S. mutans biofilm formation by disrupting glucan binding. These aptamers hold promise as lead molecules for the development of biofilm-targeting therapies in dental care.
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Affiliation(s)
- Ákos Harkai
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Tűzoltó street 37-47., 1094 Budapest, Hungary
| | - Yoon Kee Beck
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Tűzoltó street 37-47., 1094 Budapest, Hungary
| | - Anna Tory
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Tűzoltó street 37-47., 1094 Budapest, Hungary
| | - Tamás Mészáros
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Tűzoltó street 37-47., 1094 Budapest, Hungary.
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Chinchilla-Cárdenas DJ, Cruz-Méndez JS, Petano-Duque JM, García RO, Castro LR, Lobo-Castañón MJ, Cancino-Escalante GO. Current developments of SELEX technologies and prospects in the aptamer selection with clinical applications. J Genet Eng Biotechnol 2024; 22:100400. [PMID: 39179327 PMCID: PMC11338109 DOI: 10.1016/j.jgeb.2024.100400] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
Aptamers are single-stranded oligonucleotide sequences capable of binding to specific ligands with high affinity. In this manner, they are like antibodies but have advantages such as lower manufacturing costs, lower immunogenicity, fewer batch-to-batch differences, a longer shelf life, high tolerance to different molecular milieus, and a greater number of potential targets. Due to their special features, they have been used in drug delivery, biosensor technology, therapy, and diagnostics. The methodology that allowed its production was the "Systematic Evolution of Ligands by Exponential enrichment" (SELEX). Unfortunately, the traditional protocol is time-consuming and laborious. Therefore, numerous variants with considerable optimization steps have been developed, nonetheless, there are still challenges to achieving real applications in the clinical field. Among them, are control of in vivo activities, fast renal filtration, degradation by nucleases and toxicity testing. This review focuses on current technologies based on SELEX, the critical factors for successful aptamer selection, and its upcoming biomedical and biotechnological applications.
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Affiliation(s)
- Danny Jair Chinchilla-Cárdenas
- Laboratorio de Biología Molecular y Genética Animal Mascolab, Calle 49 Sur # 45ª-300, Oficina 1202, Centro Empresarial S48 Tower, Envigado 055422, Antioquia, Colombia.
| | - Juan Sebastian Cruz-Méndez
- Laboratorio de Biología Molecular y Genética Animal Mascolab, Calle 49 Sur # 45ª-300, Oficina 1202, Centro Empresarial S48 Tower, Envigado 055422, Antioquia, Colombia.
| | - Julieth Michel Petano-Duque
- Laboratorio de Biología Molecular y Genética Animal Mascolab, Calle 49 Sur # 45ª-300, Oficina 1202, Centro Empresarial S48 Tower, Envigado 055422, Antioquia, Colombia; Group of Biosocial Studies of the Body-EBSC, Faculty of Dentistry, Universidad de Antioquia, La Candelaria, Medellín 050010, Antioquia, Colombia.
| | | | - Lyda R Castro
- Grupo de investigación Evolución, Sistemática y Ecología Molecular (GIESEMOL), Universidad del Magdalena, Santa Marta, Colombia.
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain.
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Ye Z, Chen H, Weinans H, van der Wal B, Rios JL. Novel Aptamer Strategies in Combating Bacterial Infections: From Diagnostics to Therapeutics. Pharmaceutics 2024; 16:1140. [PMID: 39339177 PMCID: PMC11435160 DOI: 10.3390/pharmaceutics16091140] [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: 07/11/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024] Open
Abstract
Bacterial infections and antimicrobial resistance are posing substantial difficulties to the worldwide healthcare system. The constraints of conventional diagnostic and therapeutic approaches in dealing with continuously changing infections highlight the necessity for innovative solutions. Aptamers, which are synthetic oligonucleotide ligands with a high degree of specificity and affinity, have demonstrated significant promise in the field of bacterial infection management. This review examines the use of aptamers in the diagnosis and therapy of bacterial infections. The scope of this study includes the utilization of aptasensors and imaging technologies, with a particular focus on their ability to detect conditions at an early stage. Aptamers have shown exceptional effectiveness in suppressing bacterial proliferation and halting the development of biofilms in therapeutic settings. In addition, they possess the capacity to regulate immune responses and serve as carriers in nanomaterial-based techniques, including radiation and photodynamic therapy. We also explore potential solutions to the challenges faced by aptamers, such as nuclease degradation and in vivo instability, to broaden the range of applications for aptamers to combat bacterial infections.
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Affiliation(s)
- Zijian Ye
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Huaizhi Chen
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Harrie Weinans
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Biomechanical Engineering, Faculty of Mechanical Engineering, Delft University of Technology (TU Delft), 2628 CD Delft, The Netherlands
| | - Bart van der Wal
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jaqueline Lourdes Rios
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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Liao X, Huang L, Pu C, Li S, Feng B, Bai Y. The non-negligible non-specific adsorption of oligonucleotides in target-immobilized Mag-SELEX. Int J Biol Macromol 2024; 275:133649. [PMID: 38972649 DOI: 10.1016/j.ijbiomac.2024.133649] [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: 04/10/2024] [Revised: 06/13/2024] [Accepted: 06/30/2024] [Indexed: 07/09/2024]
Abstract
Target-immobilized magnetic beads-based Systematic Evolution of Ligands by Exponential Enrichment (target-immobilized Mag-SELEX) has emerged as a powerful tool for aptamer selection owing to its convenience, efficiency, and versatility. However, in this study we systematically investigated non-specific adsorption in target-immobilized Mag-SELEX and found that the non-specific adsorption of the oligonucleotides to target-labeled magnetic beads was comparable to that of the screening libraries, indicating a substantial portion of captured sequences likely stem from non-specific adsorption. Longer nucleic acid sequences (80 nt and above, such as polyA80 and yeast tRNA) were found to attenuate this non-specific adsorption, with more complex higher-order structures demonstrating greater efficacy, while dNTP and short sequences such as primer sequences (20 nt), polyT(59), or polyA(59), did not possess this capability. Various evidence suggested that hydrophobic interactions and other weak interactions may be the primary underlying cause of non-specific adsorption. Additionally, surface modification of magnetic beads with polar molecule polyethylene glycol (PEG) also yielded a significant reduction in non-specific adsorption. In conclusion, our research underscores the critical importance of closely monitoring non-specific adsorption in target-immobilized Mag-SELEX.
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Affiliation(s)
- Xiaoyan Liao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Guangzhou Huali Science and Technology Vocational College, Guangzhou 511325, China; Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Liujuan Huang
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Chunmin Pu
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Song Li
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Bo Feng
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yalong Bai
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
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Wang S, Zhou Z, Cao M, Pan Y, Zhang Y, Fang Y, Sun Q, Lei X, Le T. A comprehensive review of aptamer screening and application for lateral flow strip: Current status and future perspectives. Talanta 2024; 275:126181. [PMID: 38692047 DOI: 10.1016/j.talanta.2024.126181] [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: 01/23/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
The detection of biomarkers is of great significance for medical diagnosis, food safety, environmental monitoring, and agriculture. However, bio-detection technology at present often necessitates complex instruments, expensive reagents, specialized expertise, and prolonged procedures, making it challenging to fulfill the demand for rapid, sensitive, user-friendly, and economical testing. In contrast, lateral flow strip (LFS) technology offers simple, fast, and visually accessible detection modality, allowing real-time analysis of clinical specimens, thus finding widespread utility across various domains. Within the realm of LFS, the application of aptamers as molecular recognition probes presents distinct advantages over antibodies, including cost-effectiveness, smaller size, ease of synthesis, and chemical stability. In recent years, aptamer-based LFS has found extensive application in qualitative, semi-quantitative, and quantitative detection across food safety, environmental surveillance, clinical diagnostics, and other domains. This review provided a concise overview of different aptamer screening methodologies, selection strategies, underlying principles, and procedural, elucidating their respective advantages, limitations, and applications. Additionally, we summarized recent strategies and mechanisms for aptamer-based LFS, such as the sandwich and competitive methods. Furthermore, we classified LFSs constructed based on aptamers, considering the rapid advancements in this area, and discussed their applications in biological and chemical detection. Finally, we delved into the current challenges and future directions in the development of aptamer and aptamer-based LFS. Although this review was not thoroughly, it would serve as a valuable reference for understanding the research progress of aptamer-based LFS and aid in the development of new types of aptasensors.
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Affiliation(s)
- Sixian Wang
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China.
| | - Zhaoyang Zhou
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Mingdong Cao
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Yangwei Pan
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Yongkang Zhang
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Yu Fang
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Qi Sun
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Xianlu Lei
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Tao Le
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China.
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Caglayan MO, Şahin S, Üstündağ Z. An Overview of Aptamer-Based Sensor Platforms for the Detection of Bisphenol-A. Crit Rev Anal Chem 2024; 54:1320-1341. [PMID: 36001397 DOI: 10.1080/10408347.2022.2113359] [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] [Indexed: 10/15/2022]
Abstract
Endocrine disruptive compounds are natural or anthropogenic environmental micropollutants that alter the function of the endocrine system ultimately damaging the metabolism. Bisphenol A (BPA) is the most common of these pollutants and it is often used in epoxy coatings and polycarbonates as a plasticizer. Therefore, monitoring BPA levels in different environments is very important and challenging. In recent years, an increasing number of BPA detection methods have been proposed. This article presents a critical review of aptamer-based electrochemical, fluorescence-based, colorimetric, and several other BPA detection platforms published in the last decade. Furthermore, a statistical evaluation has been made using principle component analysis showing analytical performance parameters do not create very different clusters. Comparisons to other BPA detection methods are also presented so that the reader has an overall literature overview.
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Affiliation(s)
| | - Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, Bilecik, Turkey
| | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, Kütahya, Turkey
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11
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Sun J, Zhang M, Gao Q, Shao B. Screening biotoxin aptamer and their application of optical aptasensor in food stuff: a review. Front Chem 2024; 12:1425774. [PMID: 39114265 PMCID: PMC11303198 DOI: 10.3389/fchem.2024.1425774] [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: 04/30/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024] Open
Abstract
Biotoxins are ranges of toxic substances produced by animals, plants, and microorganisms, which could contaminate foods during their production, processing, transportation, or storage, thus leading to foodborne illness, even food terrorism. Therefore, proposing simple, rapid, and effective detection methods for ensuring food free from biotoxin contamination shows a highly realistic demand. Aptamers are single-stranded oligonucleotides obtained from the systematic evolution of ligands by performing exponential enrichment (SELEX). They can specifically bind to wide ranges of targets with high affinity; thus, they have become important recognizing units in safety monitoring in food control and anti-terrorism. In this paper, we reviewed the technical points and difficulties of typical aptamer screening processes for biotoxins. For promoting the understanding of food control in the food supply chain, the latest progresses in rapid optical detection of biotoxins based on aptamers were summarized. In the end, we outlined some challenges and prospects in this field. We hope this paper could stimulate widespread interest in developing advanced sensing systems for ensuring food safety.
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Affiliation(s)
- Jiefang Sun
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Meng Zhang
- School of Public Health, Capital Medical University, Beijing, China
| | - Qianlong Gao
- School of Chinese Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Bing Shao
- Beijing Center for Disease Prevention and Control, Beijing, China
- School of Public Health, Capital Medical University, Beijing, China
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12
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Zhou H, Li Y, Wu W. Aptamers: Promising Reagents in Biomedicine Application. Adv Biol (Weinh) 2024; 8:e2300584. [PMID: 38488739 DOI: 10.1002/adbi.202300584] [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: 12/05/2023] [Revised: 02/13/2024] [Indexed: 06/16/2024]
Abstract
Nucleic acid aptamers, often termed "chemical antibodies," are short, single-stranded DNA or RNA molecules, which are selected by SELEX. In addition to their high specificity and affinity comparable to traditional antibodies, aptamers have numerous unique advantages such as wider identification of targets, none or low batch-to-batch variations, versatile chemical modifications, rapid mass production, and lack of immunogenicity. These characteristics make aptamers a promising recognition probe for scientific research or even clinical application. Aptamer-functionalized nanomaterials are now emerged as a promising drug delivery system for various diseases with decreased side-effects and improved efficacy. In this review, the technological strategies for generating high-affinity and biostable aptamers are introduced. Moreover, the development of aptamers for their application in biomedicine including aptamer-based biosensors, aptamer-drug conjugates and aptamer functionalized nanomaterials is comprehensively summarized.
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Affiliation(s)
- Hongxin Zhou
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, P. R. China
| | - Yuhuan Li
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, P. R. China
| | - Weizhong Wu
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, P. R. China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
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13
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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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14
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Manea I, Casian M, Hosu-Stancioiu O, de-Los-Santos-Álvarez N, Lobo-Castañón MJ, Cristea C. A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules. Anal Chim Acta 2024; 1297:342325. [PMID: 38438246 DOI: 10.1016/j.aca.2024.342325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/06/2024]
Abstract
This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.
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Affiliation(s)
- Ioana Manea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania
| | - Magdolna Casian
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania; Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain
| | - Oana Hosu-Stancioiu
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
| | - Noemí de-Los-Santos-Álvarez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - Cecilia Cristea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
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15
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Kissmann AK, Bolotnikov G, Li R, Müller F, Xing H, Krämer M, Gottschalk KE, Andersson J, Weil T, Rosenau F. IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution. Appl Microbiol Biotechnol 2024; 108:284. [PMID: 38573322 PMCID: PMC10995058 DOI: 10.1007/s00253-024-13085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Runliu Li
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kay-E Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210, Vienna, Austria
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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16
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 PMCID: PMC10968798 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
| | | | | | | | | | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea; (K.S.P.); (T.-I.P.); (J.E.L.); (S.-Y.H.); (A.C.)
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17
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Ferreira L, Flanagan SP, Fogel R, Limson JL. Generation of epitope-specific hCG aptamers through a novel targeted selection approach. PLoS One 2024; 19:e0295673. [PMID: 38394285 PMCID: PMC10890750 DOI: 10.1371/journal.pone.0295673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/28/2023] [Indexed: 02/25/2024] Open
Abstract
Human chorionic gonadotropin (hCG) is a glycoprotein hormone used as a biomarker for several medical conditions, including pregnancy, trophoblastic and nontrophoblastic cancers. Most commercial hCG tests rely on a combination of antibodies, one of which is usually specific to the C-terminal peptide of the β-subunit. However, cleavage of this region in many hCG degradation variants prevents rapid diagnostic tests from quantifying all hCG variants in serum and urine samples. An epitope contained within the core fragment, β1, represents an under-researched opportunity for developing immunoassays specific to most variants of hCG. In the study described here, we report on a SELEX procedure tailored towards the identification of two pools of aptamers, one specific to the β-subunit of hCG and another to the β1 epitope within it. The described SELEX procedure utilized antibody-blocked targets, which is an underutilized strategy to exert negative selection pressure and in turn direct aptamer enrichment to a specific epitope. We report on the first aptamers, designated as R4_64 and R6_5, each capable of recognising two distinct sites of the hCG molecule-the β-subunit and the (presumably) β1-epitope, respectively. This study therefore presents a new SELEX approach and the generation of novel aptamer sequences that display potential hCG-specific biorecognition.
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Affiliation(s)
- Lauren Ferreira
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Shane Patrick Flanagan
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
| | - Janice Leigh Limson
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, Eastern Cape, South Africa
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18
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Berkal MA, Nardin C. Pesticide biosensors: trends and progresses. Anal Bioanal Chem 2023; 415:5899-5924. [PMID: 37668672 DOI: 10.1007/s00216-023-04911-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/06/2023]
Abstract
Pesticides, chemical substances extensively employed in agriculture to optimize crop yields, pose potential risks to human and environmental health. Consequently, regulatory frameworks are in place to restrict pesticide residue concentrations in water intended for human consumption. These regulations are implemented to safeguard consumer safety and mitigate any adverse effects on the environment and public health. Although gas chromatography- and liquid chromatography-mass spectrometry (GC-MS and LC-MS) are highly efficient techniques for pesticide quantification, their use is not suitable for real-time monitoring due to the need for sophisticated laboratory pretreatment of samples prior to analysis. Since they would enable analyte detection with selectivity and sensitivity without sample pretreatment, biosensors appear as a promising alternative. These consist of a bioreceptor allowing for specific recognition of the target and of a detection platform, which translates the biological interaction into a measurable signal. As early detection systems remain urgently needed to promptly alert and act in case of pollution, we review here the biosensors described in the literature for pesticide detection to advance their development for use in the field.
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Affiliation(s)
| | - Corinne Nardin
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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19
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Han Y, Cao L, Li G, Zhou F, Bai L, Su J. Harnessing Nucleic Acids Nanotechnology for Bone/Cartilage Regeneration. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301996. [PMID: 37116115 DOI: 10.1002/smll.202301996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/29/2023] [Indexed: 06/19/2023]
Abstract
The effective regeneration of weight-bearing bone defects and critical-sized cartilage defects remains a significant clinical challenge. Traditional treatments such as autologous and allograft bone grafting have not been successful in achieving the desired outcomes, necessitating the need for innovative therapeutic approaches. Nucleic acids have attracted significant attention due to their ability to be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of nucleic acid nanotechnology offer numerous opportunities for in-cell and in vivo applications, and hold great promise for advancing the field of biomaterials. In this review, the current abilities of nucleic acid nanotechnology to be applied in bone and cartilage regeneration are summarized and insights into the challenges and future directions for the development of this technology are provided.
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Affiliation(s)
- Yafei Han
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Liehu Cao
- Department of Orthopedics, Shanghai Luodian Hospital, Shanghai, 201908, China
| | - Guangfeng Li
- Department of Orthopedics, Shanghai Zhongye Hospital, Shanghai, 201941, China
| | - Fengjin Zhou
- Department of Orthopaedics, Honghui Hospital, Xi'an Jiao Tong University, Xi'an, 710000, China
| | - Long Bai
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Jiacan Su
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
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20
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Ai L, Jiang X, Zhang K, Cui C, Liu B, Tan W. Tools and techniques for the discovery of therapeutic aptamers: recent advances. Expert Opin Drug Discov 2023; 18:1393-1411. [PMID: 37840268 DOI: 10.1080/17460441.2023.2264187] [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: 03/15/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers. AREAS COVERED The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility. EXPERT OPINION The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.
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Affiliation(s)
- Lili Ai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Xinyi Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Kejing Zhang
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Bo Liu
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, The People's Republic of China
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21
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Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
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Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
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22
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Hu Z, Li Y, Figueroa-Miranda G, Musal S, Li H, Martínez-Roque MA, Hu Q, Feng L, Mayer D, Offenhäusser A. Aptamer based biosensor platforms for neurotransmitters analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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23
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Tungsirisurp S, O'Reilly R, Napier R. Nucleic acid aptamers as aptasensors for plant biology. TRENDS IN PLANT SCIENCE 2023; 28:359-371. [PMID: 36357246 DOI: 10.1016/j.tplants.2022.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 09/23/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Our knowledge of cell- and tissue-specific quantification of phytohormones is heavily reliant on laborious mass spectrometry techniques. Genetically encoded biosensors have allowed spatial and some temporal quantification of phytohormones intracellularly, but there is still limited information on their intercellular distributions. Here, we review nucleic acid aptamers as an emerging biosensing platform for the detection and quantification of analytes with high affinity and specificity. Options for DNA aptamer technology are explained through selection, sequencing analysis and techniques for evaluating affinity and specificity, and we focus on previously developed DNA aptamers against various plant analytes. We suggest how these tools might be applied in planta for quantification of molecules of interest both intracellularly and intercellularly.
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Affiliation(s)
| | - Rachel O'Reilly
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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24
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Hmila I, Marnissi B, Kamali-Moghaddam M, Ghram A. Aptamer-Assisted Proximity Ligation Assay for Sensitive Detection of Infectious Bronchitis Coronavirus. Microbiol Spectr 2023; 11:e0208122. [PMID: 36651727 PMCID: PMC9927260 DOI: 10.1128/spectrum.02081-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Infectious bronchitis virus (IBV) is a coronavirus responsible for major health problems in the poultry industry. New virus strains continue to appear, causing large economic losses. To develop a rapid and accurate new quantitative assay for diagnosis of the virus without DNA extraction, we selected highly specific single-stranded DNA (ssDNA) aptamers with a high affinity to IBV, using the systematic evolution of ligands by exponential enrichment (SELEX) technology for aptamer screening, followed by high-throughput sequencing technology. Two of these aptamers, AptIBV5 and AptIBV2, were used to establish homogenous and solid-phase proximity ligation assays (PLAs). The developed assays were evaluated for their sensitivity and specificity using collected field samples and then compared to the newly developed sandwich enzyme-linked aptamer assay (ELAA) and reverse transcription-quantitative PCR (qRT-PCR), as the gold-standard method. The solid-phase PLA showed a lower limit of detection and a broader dynamic range than the two other assays. The developed technique may serve as an alternative assay for the diagnosis of IBV, with the potential to be extended to the detection of other important animal or human viruses. IMPORTANCE Infectious bronchitis virus (IBV) causes high morbidity and mortality and large economic losses in the poultry industry. The virus has the ability to genetically mutate into new IBV strains, causing devastating disease and outbreaks. To better monitor the emergence of this virus, the development of a rapid and highly sensitive diagnostic method should be implemented. For this, we generated aptamers with high affinity and specificity to the IBV in an ssDNA library. Using two high-affinity aptamers, we developed a sandwich ELAA and a very sensitive aptamer-based proximity ligation assay (PLA). The new assay showed high sensitivity and specificity and was used to detect IBV in farm samples. The PLA was compared to the newly developed sandwich ELAA and qRT-PCR, as the gold-standard technique.
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Affiliation(s)
- Issam Hmila
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Boutheina Marnissi
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur of Tunis, University of Tunis El Manar, Tunis, Tunisia
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25
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Investigating Efficacy of Three DNA-Aptamers in Targeted Plasmid Delivery to Human Prostate Cancer Cell Lines. Mol Biotechnol 2023; 65:97-107. [PMID: 35834121 DOI: 10.1007/s12033-022-00528-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/23/2022] [Indexed: 01/11/2023]
Abstract
Selection of targeted and efficient carriers to deliver drugs and genes to cells and tissues is still a major challenge and to overcome this obstacle, aptamers conjugated to nanoparticles have been broadly examined. To assess whether polycation of aptamers can improve plasmid delivery efficacy, we investigated the effect of three DNA-aptamers (AS1411, WY-5a, and Sgs-8) conjugated to branched polyethylenimine (b-PEI; MW ∼25 kDa) with different combinations of gene (plasmid) for delivery to prostate cancer cell lines (DU145 and PC3). According to transfection assessments, the dual conjugation of aptamers (AS:WY) with b-PEI produced the best results and increased the efficiency of plasmid delivery to up to three folds compared to unmodified PEI. Surprisingly, triple aptamer arrangement not only reduced transfection ability but also showed cytotoxicity. While our results demonstrated potential synergistic effects of AS1411 and WY-5a aptamers for gene delivery, it is important to note that the present evidence relies on the aptamer and cell types.
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26
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Wang K, Wang M, Ma T, Li W, Zhang H. Review on the Selection of Aptamers and Application in Paper-Based Sensors. BIOSENSORS 2022; 13:39. [PMID: 36671874 PMCID: PMC9856030 DOI: 10.3390/bios13010039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
An aptamer is a synthetic oligonucleotide, referring to a single-stranded deoxyribonucleic acid or ribonucleic acid ligand produced by synthesis from outside the body using systematic evolution of ligands by exponential enrichment (SELEX) technology. Owing to their special screening process and adjustable tertiary structures, aptamers can bind to multiple targets (small molecules, proteins, and even whole cells) with high specificity and affinity. Moreover, due to their simple preparation and stable modification, they have been widely used to construct biosensors for target detection. The paper-based sensor is a product with a low price, short detection time, simple operation, and other superior characteristics, and is widely used as a rapid detection method. This review mainly focuses on the screening methods of aptamers, paper-based devices, and applicable sensing strategies. Furthermore, the design of the aptamer-based lateral flow assay (LFA), which underlies the most promising devices for commercialization, is emphasized. In addition, the development prospects and potential applications of paper-based biosensors using aptamers as recognition molecules are also discussed.
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Affiliation(s)
- Kaifei Wang
- Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Minglu Wang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Shandong Normal University, Jinan 250014, China
| | - Teng Ma
- Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Wenyu Li
- Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Hongyan Zhang
- Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250358, China
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Shandong Normal University, Jinan 250014, China
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27
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Lam SY, Lau HL, Kwok CK. Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application. BIOSENSORS 2022; 12:1142. [PMID: 36551109 PMCID: PMC9776347 DOI: 10.3390/bios12121142] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 06/01/2023]
Abstract
Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.
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Affiliation(s)
- Sin Yu Lam
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Hill Lam Lau
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Chun Kit Kwok
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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28
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Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase from Plasmodium falciparum. Pharmaceutics 2022; 14:pharmaceutics14112515. [PMID: 36432706 PMCID: PMC9695703 DOI: 10.3390/pharmaceutics14112515] [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: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
The methyl erythritol phosphate (MEP) pathway of isoprenoid biosynthesis is essential for malaria parasites and also for several human pathogenic bacteria, thus representing an interesting target for future antimalarials and antibiotics and for diagnostic strategies. We have developed a DNA aptamer (D10) against Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), the second enzyme of this metabolic route. D10 binds in vitro to recombinant DXR from P. falciparum and Escherichia coli, showing at 10 µM a ca. 50% inhibition of the bacterial enzyme. In silico docking analysis indicates that D10 associates with DXR in solvent-exposed regions outside the active center pocket. According to fluorescence confocal microscopy data, this aptamer specifically targets in P. falciparum in vitro cultures the apicoplast organelle where the MEP pathway is localized and is, therefore, a highly specific marker of red blood cells parasitized by Plasmodium vs. naïve erythrocytes. D10 is also selective for the detection of MEP+ bacteria (e.g., E. coli and Pseudomonas aeruginosa) vs. those lacking DXR (e.g., Enterococcus faecalis). Based on these results, we discuss the potential of DNA aptamers in the development of ligands that can outcompete the performance of the well-established antibody technology for future therapeutic and diagnostic approaches.
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29
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Biomimetic functional material-based sensors for food safety analysis: a review. Food Chem 2022; 405:134974. [DOI: 10.1016/j.foodchem.2022.134974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
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30
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Chen J, Zhou J, Peng Y, Xie Y, Xiao Y. Aptamers: A prospective tool for infectious diseases diagnosis. J Clin Lab Anal 2022; 36:e24725. [PMID: 36245423 PMCID: PMC9701868 DOI: 10.1002/jcla.24725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 12/05/2022] Open
Abstract
It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.
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Affiliation(s)
- Jiayi Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jiahuan Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yunchi Peng
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yafeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yongjian Xiao
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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31
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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32
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Cruz-Hernández CD, Rodríguez-Martínez G, Cortés-Ramírez SA, Morales-Pacheco M, Cruz-Burgos M, Losada-García A, Reyes-Grajeda JP, González-Ramírez I, González-Covarrubias V, Camacho-Arroyo I, Cerbón M, Rodríguez-Dorantes M. Aptamers as Theragnostic Tools in Prostate Cancer. Biomolecules 2022; 12:biom12081056. [PMID: 36008950 PMCID: PMC9406110 DOI: 10.3390/biom12081056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/07/2023] Open
Abstract
Despite of the capacity that several drugs have for specific inhibition of the androgen receptor (AR), in most cases, PCa progresses to an androgen-independent stage. In this context, the development of new targeted therapies for prostate cancer (PCa) has remained as a challenge. To overcome this issue, new tools, based on nucleic acids technology, have been developed. Aptamers are small oligonucleotides with a three-dimensional structure capable of interacting with practically any desired target, even large targets such as mammalian cells or viruses. Recently, aptamers have been studied for treatment and detection of many diseases including cancer. In PCa, numerous works have reported their use in the development of new approaches in diagnostics and treatment strategies. Aptamers have been joined with drugs or other specific molecules such as silencing RNAs (aptamer–siRNA chimeras) to specifically reduce the expression of oncogenes in PCa cells. Even though these studies have shown good results in the early stages, more research is still needed to demonstrate the clinical value of aptamers in PCa. The aim of this review was to compile the existing scientific literature regarding the use of aptamers in PCa in both diagnosis and treatment studies. Since Prostate-Specific Membrane Antigen (PSMA) aptamers are the most studied type of aptamers in this field, special emphasis was given to these aptamers.
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Affiliation(s)
- Carlos David Cruz-Hernández
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Griselda Rodríguez-Martínez
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Sergio A. Cortés-Ramírez
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Miguel Morales-Pacheco
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Marian Cruz-Burgos
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Alberto Losada-García
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
| | - Juan Pablo Reyes-Grajeda
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
| | - Imelda González-Ramírez
- Departamento de Atención a la Salud, Universidad Autónoma Metropolitana–Xochimilco, Mexico City 04960, Mexico;
| | | | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (I.C.-A.); (M.C.)
| | - Marco Cerbón
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología, Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (I.C.-A.); (M.C.)
| | - Mauricio Rodríguez-Dorantes
- Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico; (C.D.C.-H.); (G.R.-M.); (S.A.C.-R.); (M.M.-P.); (M.C.-B.); (A.L.-G.)
- Correspondence:
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33
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Sanford AA, Manuel BA, Romero-Reyes MA, Heemstra JM. Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids. Chem Sci 2022; 13:7670-7684. [PMID: 35865900 PMCID: PMC9258336 DOI: 10.1039/d2sc00117a] [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: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Brea A Manuel
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Misael A Romero-Reyes
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Chemistry, Hanover College Hanover Indiana 47243 USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta GA 30332 USA
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34
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Lee J, Ryu M, Bae D, Kim HM, Eyun SI, Bae J, Lee K. Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:659-667. [PMID: 35731347 DOI: 10.1007/s12275-022-2235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 12/17/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides capable of binding with high affinity and specificity to target molecules. Because of their durability and ease of synthesis, aptamers are used in a wide range of biomedical fields, including the diagnosis of diseases and targeted delivery of therapeutic agents. The aptamers were selected using a process called systematic evolution of ligands by exponential enrichment (SELEX), which has been improved for various research purposes since its development in 1990. In this protocol, we describe a modified SELEX method that rapidly produces high aptamer screening yields using two types of magnetic beads. Using this method, we isolated an aptamer that specifically binds to an antimicrobial peptide. We suggest that by conjugating a small therapeutic-specific aptamer to a gold nanoparticle-based delivery system, which enhances the stability and intracellular delivery of peptides, aptamers selected by our method can be used for the development of therapeutic agents utilizing small therapeutic peptides.
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Affiliation(s)
- Jaemin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minkyung Ryu
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.,NES biotechnology, Seoul, 06974, Republic of Korea
| | - Dayeong Bae
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.,NES biotechnology, Seoul, 06974, Republic of Korea
| | - Hong-Man Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.,NES biotechnology, Seoul, 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeehyeon Bae
- NES biotechnology, Seoul, 06974, Republic of Korea. .,Department of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea. .,NES biotechnology, Seoul, 06974, Republic of Korea.
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35
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Kissmann AK, Andersson J, Bozdogan A, Amann V, Krämer M, Xing H, Raber HF, Kubiczek DH, Aspermair P, Knoll W, Rosenau F. Polyclonal aptamer libraries as binding entities on a graphene FET based biosensor for the discrimination of apo- and holo-retinol binding protein 4. NANOSCALE HORIZONS 2022; 7:770-778. [PMID: 35695183 DOI: 10.1039/d1nh00605c] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Oligonucleotide DNA aptamers represent an emergently important class of binding entities towards as different analytes as small molecules or even whole cells. Without requiring the canonical isolation of individual aptamers following the SELEX process, the focused polyclonal libraries prepared by this in vitro evolution and selection can directly be used to label their dedicated targets and to serve as binding molecules on surfaces. Here we report the first instance of a sensor able to discriminate between loaded and unloaded retinol-binding protein 4 (RBP4), an important biomarker for the prediction of diabetes and kidney disease. The sensor relies on two aptamer libraries tuned such that they discriminate between the protein isoforms, requiring no further sample labelling to detect RBP4 in both states. The evolution, binding properties of the libraries and the functionalization of graphene FET sensor chips are presented as well as the functionality of the resulting biosensor.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria.
| | - Anil Bozdogan
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria.
- CEST Kompetenzzentrum für Elektrochemische Oberflächentechnologie GmbH, Viktor Kaplan Straße 2, Wiener Neustadt, Austria
| | - Valerie Amann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Heinz Fabian Raber
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Dennis H Kubiczek
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Patrik Aspermair
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria.
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria.
- Danube Private University, Steiner Landstraße 124, 3500 Krems an der Donau, Austria
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
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36
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Zon G. Recent advances in aptamer applications for analytical biochemistry. Anal Biochem 2022; 644:113894. [PMID: 32763306 PMCID: PMC7403853 DOI: 10.1016/j.ab.2020.113894] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/24/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022]
Abstract
Aptamers are typically defined as relatively short (20-60 nucleotides) single-stranded DNA or RNA molecules that bind with high affinity and specificity to various types of targets. Aptamers are frequently referred to as "synthetic antibodies" but are easier to obtain, less expensive to produce, and in several ways more versatile than antibodies. The beginnings of aptamers date back to 1990, and since then there has been a continual increase in aptamer publications. The intent of the present account was to focus on recent original research publications, i.e., those appearing in 2019 through April 2020, when this account was written. A Google Scholar search of this recent literature was performed for relevance-ranking of articles. New methods for selection of aptamers were not included. Nine categories of applications were organized and representative examples of each are given. Finally, an outlook is offered focusing on "faster, better, cheaper" application performance factors as key drivers for future innovations in aptamer applications.
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Parashar A, Bhushan V, Mahanandia NC, Kumar S, Mohanty AK. Non-SELEX method for aptamer selection against β-casomorphin-7 peptide. J Dairy Sci 2022; 105:5545-5560. [DOI: 10.3168/jds.2021-21569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/09/2022] [Indexed: 11/19/2022]
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A system for multiplexed selection of aptamers with exquisite specificity without counterselection. Proc Natl Acad Sci U S A 2022; 119:e2119945119. [PMID: 35290115 PMCID: PMC8944265 DOI: 10.1073/pnas.2119945119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aptamers have the capacity to discriminate between structurally similar small molecules. However, generating such highly specific aptamers has proven challenging using conventional processes based on counterselection against nontarget molecules. In this work, we describe a high-throughput screening platform that can characterize the specificity of millions of aptamers toward a group of structurally related molecules in a single experiment and generate exquisitely specific aptamers without any counterselection. As exemplars, we generated aptamers with high affinity and specificity toward three structurally related kynurenine metabolites using our platform. Our platform can be readily adapted to other small-molecule targets and should therefore accelerate the development of aptamer reagents with exquisite specificity. Aptamers have proven to be valuable tools for the detection of small molecules due to their remarkable ability to specifically discriminate between structurally similar molecules. Most aptamer selection efforts have relied on counterselection to eliminate aptamers that exhibit unwanted cross-reactivity to interferents or structurally similar relatives to the target of interest. However, because the affinity and specificity characteristics of an aptamer library are fundamentally unknowable a priori, it is not possible to determine the optimal counterselection parameters. As a result, counterselection experiments require trial-and-error approaches that are inherently inefficient and may not result in aptamers with the best combination of affinity and specificity. In this work, we describe a high-throughput screening process for generating high-specificity aptamers to multiple targets in parallel while also eliminating the need for counterselection. We employ a platform based on a modified benchtop sequencer to conduct a massively parallel aptamer screening process that enables the selection of highly specific aptamers against multiple structurally similar molecules in a single experiment, without any counterselection. As a demonstration, we have selected aptamers with high affinity and exquisite specificity for three structurally similar kynurenine metabolites that differ by a single hydroxyl group in a single selection experiment. This process can easily be adapted to other small-molecule analytes and should greatly accelerate the development of aptamer reagents that achieve exquisite specificity for their target analytes.
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Liu S, Xu Y, Jiang X, Tan H, Ying B. Translation of aptamers toward clinical diagnosis and commercialization. Biosens Bioelectron 2022; 208:114168. [PMID: 35364525 DOI: 10.1016/j.bios.2022.114168] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/08/2023]
Abstract
The dominance of antibodies in diagnostics has gradually changed following the discovery of aptamers in the early 1990s. Aptamers offer inherent advantages over traditional antibodies, including higher specificity, higher affinity, smaller size, greater stability, ease of manufacture, and low immunogenicity, rendering them the best candidates for point-of-care testing (POCT). In the past 20 years, the research community and pharmaceutical companies have made great efforts to promote the development of aptamer technology. Macugen® (pegaptanib) was the first aptamer drug approved by the US Food and Drug Administration (FDA), and various aptamer-based diagnostics show great promise in preclinical research and clinical trials. In this review, we introduce recent literature, ongoing clinical trials, commercial reagents of aptamer-based diagnostics, discuss the FDA regulatory mechanisms, and highlight the prospects and challenges in translating these studies into viable clinical diagnostic tools.
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Affiliation(s)
- Shan Liu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology, Chengdu, 610072, China
| | - Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, 610041, China
| | - Xin Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, 610041, China
| | - Hong Tan
- Department of General Surgery, Chengdu Integrated TCM&Western Medicine Hospital (Chengdu First People's Hospital), Chengdu, 610041, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, 610041, China.
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Nucleic Acid Nanotechnology for Diagnostics and Therapeutics in Acute Kidney Injury. Int J Mol Sci 2022; 23:ijms23063093. [PMID: 35328515 PMCID: PMC8953740 DOI: 10.3390/ijms23063093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
Acute kidney injury (AKI) has impacted a heavy burden on global healthcare system with a high morbidity and mortality in both hospitalized and critically ill patients. However, there are still some shortcomings in clinical approaches for the disease to date, appealing for an earlier recognition and specific intervention to improve long-term outcomes. In the past decades, owing to the predictable base-pairing rule and highly modifiable characteristics, nucleic acids have already become significant biomaterials for nanostructure and nanodevice fabrication, which is known as nucleic acid nanotechnology. In particular, its excellent programmability and biocompatibility have further promoted its intersection with medical challenges. Lately, there have been an influx of research connecting nucleic acid nanotechnology with the clinical needs for renal diseases, especially AKI. In this review, we begin with the diagnostics of AKI based on nucleic acid nanotechnology with a highlight on aptamer- and probe-functionalized detection. Then, recently developed nanoscale nucleic acid therapeutics towards AKI will be fully elucidated. Furthermore, the strengths and limitations will be summarized, envisioning a wiser and wider application of nucleic acid nanotechnology in the future of AKI.
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Martínez-Roque MA, Franco-Urquijo PA, García-Velásquez VM, Choukeife M, Mayer G, Molina-Ramírez SR, Figueroa-Miranda G, Mayer D, Alvarez-Salas LM. DNA aptamer selection for SARS-CoV-2 spike glycoprotein detection. Anal Biochem 2022; 645:114633. [PMID: 35247355 PMCID: PMC8889740 DOI: 10.1016/j.ab.2022.114633] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 02/07/2023]
Abstract
The rapid spread of SARS-CoV-2 infection throughout the world led to a global public health and economic crisis triggering an urgent need for the development of low-cost vaccines, therapies and high-throughput detection assays. In this work, we used a combination of Ideal-Filter Capillary Electrophoresis SELEX (IFCE-SELEX), Next Generation Sequencing (NGS) and binding assays to isolate and validate single-stranded DNA aptamers that can specifically recognize the SARS-CoV-2 Spike glycoprotein. Two selected non-competing DNA aptamers, C7 and C9 were successfully used as sensitive and specific biological recognition elements for the development of electrochemical and fluorescent aptasensors for the SARS-CoV-2 Spike glycoprotein with detection limits of 0.07 fM and 41.87 nM, respectively.
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Affiliation(s)
- Mateo Alejandro Martínez-Roque
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., CDMX, 07360, Mexico
| | - Pablo Alberto Franco-Urquijo
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., CDMX, 07360, Mexico
| | - Víctor Miguel García-Velásquez
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., CDMX, 07360, Mexico
| | - Moujab Choukeife
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121, Bonn, Germany
| | - Günther Mayer
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121, Bonn, Germany
| | - Sergio Roberto Molina-Ramírez
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Gabriela Figueroa-Miranda
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Dirk Mayer
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Luis M Alvarez-Salas
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., CDMX, 07360, Mexico.
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Arshavsky‐Graham S, Heuer C, Jiang X, Segal E. Aptasensors versus immunosensors-Which will prevail? Eng Life Sci 2022; 22:319-333. [PMID: 35382545 PMCID: PMC8961048 DOI: 10.1002/elsc.202100148] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.
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Affiliation(s)
- Sofia Arshavsky‐Graham
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Christopher Heuer
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | - Xin Jiang
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Ester Segal
- Faculty of Biotechnology and Food EngineeringTechnion ‐ Israel Institute of TechnologyHaifaIsrael
- Russell Berrie Nanotechnology InstituteTechnion ‐ Israel Institute of TechnologyHaifaIsrael
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Dursun AD, Dogan S, Kavruk M, Busra Tasbasi B, Sudagidan M, Deniz Yilmaz M, Yilmaz B, Ozalp VC, Tuna BG. Surface plasmon resonance aptasensor for soluble ICAM-1 protein in blood samples. Analyst 2022; 147:1663-1668. [DOI: 10.1039/d1an02332b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer sequence for soluble ICAM-1 was selected by the SELEX procedure. The ICAM-1 aptamer was used to develop a magnetic separation from blood samples by silica shell nanoparticles and subsequent real-time detection by SPR biosensing.
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Affiliation(s)
- Ali Dogan Dursun
- Department of Physiology, School of Medicine, Atilim University, Ankara, Turkey
- Vocational School of Health Services, Atilim University, Ankara, Turkey
| | - Soner Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Murat Kavruk
- Department of Nutrition and Dietetics, School of Health Sciences, Atilim University, Ankara, Turkey
| | - B. Busra Tasbasi
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Konya, Turkey
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Konya, Turkey
| | - M. Deniz Yilmaz
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Konya, Turkey
- Department of Bioengineering, Konya Food and Agriculture University, Konya, Turkey
| | - Bayram Yilmaz
- Department of Physiology, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Veli C. Ozalp
- Department of Biology, School of Medicine, Atilim University, Ankara, Turkey
| | - Bilge G. Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul, Turkey
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Yadav ML, Parashar A, Mahanandia NC, Bhushan V, Kumar S, Mohanty AK. Aptamers based sensing of pregnancy associated glycoproteins (PAG) of bovine for early pregnancy detection. Sci Rep 2021; 11:23193. [PMID: 34853377 PMCID: PMC8636505 DOI: 10.1038/s41598-021-02551-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022] Open
Abstract
Tosyl activated magnetic beads were used for aptamer selection against PAG- 7 and 18 proteins of bovine origin. PAG proteins were immobilized on beads with further addition of biotin tagged aptamer library. The recognition of aptamers with PAG was identified by ST-HRP based approach which was colorimetric in nature. The selected aptamers were sequenced and at the same time several new aptamers were identified. Later M-fold structure and G-quadruplex score of aptamers were analyzed for their selection. Those aptamers having high G value and complex structure were chosen. In dot blot assay, aptamers recognized PAG protein in an animal after 42 days of artificial insemination which later given birth to a healthy calf. Further the cross reactivity with serum of 0th day animal (post AI) or with non pregnant animal serum was minimal. Aptamers have also shown interaction with PAG protein of buffalo origin. These selected aptamers have commercial application especially in development of biosensors for early detection of pregnancy in bovine.
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Affiliation(s)
- Munna Lal Yadav
- Translational Health Science and Technology Institute (THSTI), Faridabad, India.,Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, 132001, India
| | - Abhishek Parashar
- Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, 132001, India
| | | | - Vanya Bhushan
- Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, 132001, India
| | - Sudarshan Kumar
- Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, 132001, India
| | - Ashok Kumar Mohanty
- Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, 132001, India. .,Indian Veterinary Research Institute (IVRI), Mukteswar, 263138, India.
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Polyclonal Aptamers for Specific Fluorescence Labeling and Quantification of the Health Relevant Human Gut Bacterium Parabacteroides distasonis. Microorganisms 2021; 9:microorganisms9112284. [PMID: 34835410 PMCID: PMC8618460 DOI: 10.3390/microorganisms9112284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
Single-stranded DNA aptamers as affinity molecules for the rapid, reliable detection of intestinal bacteria are of particular interest to equip health systems with novel robust and cheap diagnostic tools for monitoring the success of supplementation strategies with selected probiotic gut bacteria in the fight against major widespread threats, such as obesity and neurodegenerative diseases. The human gut bacterium Parabacteroides distasonis (P. distasonis) is positively associated with diseases such as obesity, non-alcoholic fatty liver disease and multiple sclerosis with reduced cell counts in these diseases and is thus a promising potential probiotic bacterium for future microbial supplementation. In this paper we report on the evolution of a specific polyclonal aptamer library by the fluorescence based FluCell-SELEX directed against whole cells of P. distasonis that specifically and efficiently binds and labels P. distasonis. The aptamer library showed high binding affinity and was suited to quantitatively discriminate P. distasonis from other prominent gut bacteria also in mixtures. We believe that this library against a promising probiotic bacterium as a prototype may open new routes towards the development of novel biosensors for the easy and efficient quantitative monitoring of microbial abundance in human microbiomes in general.
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Srivastava S, Abraham PR, Mukhopadhyay S. Aptamers: An Emerging Tool for Diagnosis and Therapeutics in Tuberculosis. Front Cell Infect Microbiol 2021; 11:656421. [PMID: 34277465 PMCID: PMC8280756 DOI: 10.3389/fcimb.2021.656421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has been plaguing human civilization for centuries, and currently around one-third of the global population is affected with TB. Development of novel intervention tools for early diagnosis and therapeutics against Mycobacterium tuberculosis (M.tb) is the main thrust area in today's scenario. In this direction global efforts were made to use aptamers, the chemical antibodies as tool for TB diagnostics and therapeutics. This review describes the various aptamers introduced for targeting M.tb and highlights the need for development of novel aptamers to selectively target virulent proteins of M.tb for vaccine and anti-TB drugs. The objective of this review is to highlight the diagnostic and therapeutic application of aptamers used for tuberculosis. The discovery of aptamers, SELEX technology, different types of SELEX development processes, DNA and RNA aptamers reported for diseases and pathogenic agents as well have also been described in detail. But the emphasis of this review is on the development of aptamers which can block the function of virulent mycobacterial components for developing newer TB vaccine candidates and/or drug targets. Aptamers designed to target M.tb cell wall proteins, virulent factors, secretory proteins, or combination could orchestrate advanced diagnosis and therapeutic measures for tuberculosis.
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Affiliation(s)
- Shruti Srivastava
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Philip Raj Abraham
- Unit of OMICS, ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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Jin CR, Kim JY, Kim DH, Jeon MS, Choi YE. In Vivo Monitoring of Intracellular Metabolite in a Microalgal Cell Using an Aptamer/Graphene Oxide Nanosheet Complex. ACS APPLIED BIO MATERIALS 2021; 4:5080-5089. [PMID: 35007056 DOI: 10.1021/acsabm.1c00322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Real-time sensing and imaging of intracellular metabolites in living cells are crucial tools for the characterization of complex biological processes, including the dynamic fluctuation of metabolites. Therefore, additional efforts are required to develop in vivo detection strategies for the visualization and quantification of specific target metabolites, particularly in microalgae. In this study, we developed a strategy to monitor a specific microalgal metabolite in living cells using an aptamer/graphene oxide nanosheet (GOnS) complex. As a proof-of-concept, β-carotene, an antioxidant pigment that accumulates in most microalgal species, was chosen as a target metabolite. To achieve this, a β-carotene-specific aptamer was selected through graphene oxide-assisted systematic evolution of ligands by exponential enrichment (GO-SELEX) and characterized thereafter. The aptamer could sensitively sense the changes in the concentration of β-carotene (i.e., the target metabolite) and more specifically bind to β-carotene than to nontargets. The selected aptamer was labeled with a fluorophore (fluorescein; FAM) and allowed to form an aptamer/GOnS complex that protected the aptamer from nucleic cleavages. The aptamer/GOnS complex was delivered into the cells via electroporation, thus enabling the sensitive monitoring of β-carotene in the cell by quantifying the aptamer fluorescence intensity. The results suggest that our biocompatible strategy could be employed to visualize and semiquantify intracellular microalgae metabolites in vivo, which holds a great potential in diverse fields such as metabolite analysis and mutant screening.
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Affiliation(s)
- Cho Rok Jin
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Korea
| | - Jee Young Kim
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Korea
| | - Da Hee Kim
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Korea
| | - Min Seo Jeon
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Korea
| | - Yoon-E Choi
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Korea
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Aptamer-Modified Hydrogels. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 178:147-168. [PMID: 33796881 DOI: 10.1007/10_2021_166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Hydrogels have attracted much attention especially due to their biocompatibility and their potential for stimulus responsiveness. By combining hydrogels with aptamers, biological recognition and responsiveness can be added to hydrogels, thereby opening path to advanced applications in biosensing and biomedicine. Within this chapter aptamers will be introduced and their contributions to biological responsiveness of hydrogels will be described. Especially the aptamer-based mechanisms that result in biological responsiveness will be explained and examples for the application of these mechanisms will be given ranging from rather simple sensing approaches to advanced materials for tissue engineering and drug delivery. Since aptamers are not only highly specific bioreceptors, but represent switchable structures that can be easily manipulated using well-known DNA techniques, the combination of aptamers and hydrogels facilitates the rational design of well-programmable and target-responsive smart hydrogels.
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Li Y, Liu J. Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds. Analyst 2021; 145:6753-6768. [PMID: 32909556 DOI: 10.1039/d0an00886a] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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