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Stephens C, Goodey NM, Gubler U. A beginners guide to SELEX and DNA aptamers. Anal Biochem 2025; 703:115890. [PMID: 40320157 DOI: 10.1016/j.ab.2025.115890] [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: 01/27/2025] [Revised: 03/25/2025] [Accepted: 05/02/2025] [Indexed: 05/09/2025]
Abstract
SELEX stands for "Systematic Evolution of Ligands by Exponential Enrichment." It is an in vitro, iterative, PCR-based, target-specific selection strategy used to generate single-stranded DNA (ssDNA) aptamers that bind a target of interest. Properly selected aptamers bind their targets with high affinity and specificity and have utility in a multitude of detection assays. They are thus similar to antibodies but have the advantage of being more stable and cheaper to produce. The SELEX process encompasses several steps, some of which are critical to the successful isolation of an aptamer. Careful analysis and optimization of the SELEX process are thus important. This review summarizes our own experience when we, as complete novices, were setting up the SELEX system in our lab. It is thus meant to give some general and practical but concise pointers for anyone interested in initiating their own SELEX experiments. As such, the review covers key elements of the SELEX process, including library design, target selection and immobilization strategies, aptamer binding conditions, partitioning techniques, and PCR optimization. We also discuss common pitfalls such as by-product formation and single-stranded DNA recovery challenges, along with practical strategies to overcome them. Emerging trends and post-SELEX considerations, such as sequencing, structure prediction, and chemical modifications, are included to guide beginners through every stage of aptamer development.
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Affiliation(s)
- Cameron Stephens
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA
| | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA.
| | - Ueli Gubler
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA.
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2
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Wei T, Liu Q, Li J, Song S, Zhang L. Functional Aptamers In Vitro Evolution for Protein-Protein Interaction Blockage. Anal Chem 2025; 97:4341-4349. [PMID: 39964138 DOI: 10.1021/acs.analchem.4c04609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2025]
Abstract
As aptamer development progresses, their applications have expanded significantly beyond high affinity to include functional capabilities. Currently, the identification of functional aptamers relies on traditional SELEX techniques, followed by functional validation and computer-assisted redesign of high-affinity aptamers. However, high affinity does not guarantee optimal functionality, making the search for functional aptamers from binding pools time-consuming and labor-intensive. Addressing this challenge, we introduce functional aptamers in vitro evolution (FAIVE), a novel screening method that links sequence functionality to fluorescence intensity. We demonstrated the effectiveness of FAIVE by obtaining modified DNA aptamers capable of disrupting the interaction between the SARS-CoV-2 spike receptor-binding domain (RBD) and hACE2, targeting protein-protein interaction inhibition. Furthermore, we investigated the criteria for validating the quality of the bead library generated for selection by modeling the emulsion PCR process, providing theoretical insights for future applications. The concept of incorporating fluorescent signal reporting of aptamer functionality into the aptamer selection process holds the potential to facilitate the identification of aptamers with diverse functionalities and is readily adaptable to various research contexts.
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Affiliation(s)
- Tongxuan Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qinguo Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Song Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Liqin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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3
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Xia B, Shaheen N, Chen H, Zhao J, Guo P, Zhao Y. RNA aptamer-mediated RNA nanotechnology for potential treatment of cardiopulmonary diseases. Pharmacol Res 2025; 213:107659. [PMID: 39978660 DOI: 10.1016/j.phrs.2025.107659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 01/14/2025] [Accepted: 02/14/2025] [Indexed: 02/22/2025]
Abstract
Ribonucleic acid (RNA) aptamers are single-stranded RNAs that bind to target proteins or other molecules with high specificity and affinity, modulating biological functions through distinct mechanisms. These aptamers can act n as antagonists to block pathological interactions, agonists to activate signaling pathways, or delivery vehicles for therapeutic cargos such as siRNAs and miRNAs. The advances in RNA nanotechnology further enhances the versatility of RNA aptamers, offering scalable platforms for engineering. In this review, we have summarized recent developments in RNA aptamer-mediated RNA nanotechnology and provide an overview of its potential in treating cardiovascular and respiratory disorders, including atherosclerosis, acute coronary syndromes, heart failure, lung cancer, pulmonary hypertension, asthma, chronic obstructive pulmonary disease (COPD), acute lung injury, viral respiratory infections, and pulmonary fibrosis. By integrating aptamer technologies with innovative delivery systems, RNA aptamers hold the potential to revolutionize the treatment landscape for cardiopulmonary diseases.
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Affiliation(s)
- Boyu Xia
- Department of Physiology and Cell Biology, College of Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Nargis Shaheen
- Department of Physiology and Cell Biology, College of Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Huilong Chen
- Department of Physiology and Cell Biology, College of Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Jing Zhao
- Department of Physiology and Cell Biology, College of Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yutong Zhao
- Department of Physiology and Cell Biology, College of Medicine, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.
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4
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Hao S, Su J. Whispering gallery mode optical resonators for biological and chemical detection: current practices, future perspectives, and challenges. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 88:016402. [PMID: 39626318 DOI: 10.1088/1361-6633/ad99e7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Accepted: 12/03/2024] [Indexed: 12/24/2024]
Abstract
Sensors are important for a wide variety of applications include medical diagnostics and environmental monitoring. Due to their long photon confinement times, whispering gallery mode (WGM) sensors are among the most sensitive sensors currently in existence. We briefly discuss what are WGM sensors, the principles of WGM sensing, and the history of the field, beginning with Mie theory. We discuss recent work in the field on using these WGM resonators as sensors, focusing particularly on biological and chemical sensing applications. We discuss how sensorgrams are acquired and fundamental measurement limits. In addition, we discuss how to interpret binding curves and extract physical parameters such as binding affinity constants. We discuss the controversy surrounding single-molecule detection and discuss hybrid WGM nanoparticle sensors. In addition, we place these sensors in context with others sensing technologies both labeled and label-free. Finally, we discuss what we believe are the most promising applications for these devices, outline remaining challenges, and provide an outlook for the future.
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Affiliation(s)
- Shuang Hao
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, United States of America
| | - Judith Su
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, United States of America
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, United States of America
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5
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Su Y, Zhou L. Review of single-molecule immunoassays: Non-chip and on-chip Assays. Anal Chim Acta 2024; 1322:342885. [PMID: 39182983 DOI: 10.1016/j.aca.2024.342885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 08/27/2024]
Abstract
Enhancing the sensitivity of immunoassays is an important requirement in the field of immunology, especially in light of rapid developments in genetic testing, making the detection of low-abundance protein biomarkers crucial. Therefore, innovations in highly sensitive immunoassays are imperative. This demand has led to the emergence of single-molecule immunoassays (SMIs), driving advancements in early diagnostic techniques, and ushering in a new era of immunoassays. This review begins by tracing the development of immunoassays and offers a detailed discussion of SMI technology across two distinct pathways: non-chip (SMI without microfluidic chips) and on-chip (SMI with microfluidic chips). Furthermore, we evaluated and compared these methods using two pathways. In addition, this review discusses the significance of SMI techniques in the diagnosis of various diseases and their current applications in laboratory and clinical settings. The progress of SMI in commercial applications and suggestions for innovative directions are also summarized. Despite the considerable potential of SMI, these technologies face challenges in practical application, particularly in developing countries and economically disadvantaged regions. The final section of this review addresses the challenges and prospects of these technologies.
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Affiliation(s)
- Yan Su
- State Key Laboratory of Biochemical Engineering, PLA Key Laboratory of Biopharmaceutical Production & Formulation Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Zhou
- State Key Laboratory of Biochemical Engineering, PLA Key Laboratory of Biopharmaceutical Production & Formulation Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Innovation Academy for Green Manufacture Institute, Chinese Academy of Sciences, Beijing, 100190, China; Biosafety Research Center Yangtze River Delta in Zhangjiagang, Suzhou, 215611, China.
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6
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Serafin B, Kamen A, de Crescenzo G, Henry O. Antibody-independent surface plasmon resonance assays for influenza vaccine quality control. Appl Microbiol Biotechnol 2024; 108:307. [PMID: 38656587 PMCID: PMC11043112 DOI: 10.1007/s00253-024-13145-y] [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: 01/17/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Surface plasmon resonance (SPR)-based biosensors have emerged as a powerful platform for bioprocess monitoring due to their ability to detect biointeractions in real time, without the need for labeling. Paramount for the development of a robust detection platform is the immobilization of a ligand with high specificity and affinity for the in-solution species of interest. Following the 2009 H1N1 pandemic, much effort has been made toward the development of quality control platforms for influenza A vaccine productions, many of which have employed SPR for detection. Due to the rapid antigenic drift of influenza's principal surface protein, hemagglutinin, antibodies used for immunoassays need to be produced seasonally. The production of these antibodies represents a 6-8-week delay in immunoassay and, thus, vaccine availability. This review focuses on SPR-based assays that do not rely on anti-HA antibodies for the detection, characterization, and quantification of influenza A in bioproductions and biological samples. KEY POINTS: • The single radial immunodiffusion assay (SRID) has been the gold standard for the quantification of influenza vaccines since 1979. Due to antigenic drift of influenza's hemagglutinin protein, new antibody reagents for the SRID assay must be produced each year, requiring 6-8 weeks. The resulting delay in immunoassay availability is a major bottleneck in the influenza vaccine pipeline. This review highlights ligand options for the detection and quantification of influenza viruses using surface plasmon resonance biosensors.
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Affiliation(s)
- Benjamin Serafin
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Amine Kamen
- Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Gregory de Crescenzo
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Olivier Henry
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, QC, Canada.
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7
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Brown A, Brill J, Amini R, Nurmi C, Li Y. Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications. Angew Chem Int Ed Engl 2024; 63:e202318665. [PMID: 38253971 DOI: 10.1002/anie.202318665] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.
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Affiliation(s)
- Alex Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Jake Brill
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
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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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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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10
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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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11
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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Singhal C, Bruno JG, Kaushal A, Sharma TK. Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections. ACS APPLIED BIO MATERIALS 2021; 4:3962-3984. [PMID: 35006817 DOI: 10.1021/acsabm.0c01358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.
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Affiliation(s)
- Chaitali Singhal
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | - John G Bruno
- Nanohmics, Inc., Austin, Texas 78741, United States
| | - Ankur Kaushal
- Centre of Nanotechnology, Amity University, Manesar, Gurugram, Haryana 122413, India
| | - Tarun K Sharma
- Aptamer Technology and Diagnostic Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
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14
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Minakshi P, Ghosh M, Kumar R, Brar B, Lambe UP, Banerjee S, Ranjan K, Kumar B, Goel P, Malik YS, Prasad G. An Insight into Nanomedicinal Approaches to Combat Viral Zoonoses. Curr Top Med Chem 2021; 20:915-962. [PMID: 32209041 DOI: 10.2174/1568026620666200325114400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Emerging viral zoonotic diseases are one of the major obstacles to secure the "One Health" concept under the current scenario. Current prophylactic, diagnostic and therapeutic approaches often associated with certain limitations and thus proved to be insufficient for customizing rapid and efficient combating strategy against the highly transmissible pathogenic infectious agents leading to the disastrous socio-economic outcome. Moreover, most of the viral zoonoses originate from the wildlife and poor knowledge about the global virome database renders it difficult to predict future outbreaks. Thus, alternative management strategy in terms of improved prophylactic vaccines and their delivery systems; rapid and efficient diagnostics and effective targeted therapeutics are the need of the hour. METHODS Structured literature search has been performed with specific keywords in bibliographic databases for the accumulation of information regarding current nanomedicine interventions along with standard books for basic virology inputs. RESULTS Multi-arrayed applications of nanomedicine have proved to be an effective alternative in all the aspects regarding the prevention, diagnosis, and control of zoonotic viral diseases. The current review is focused to outline the applications of nanomaterials as anti-viral vaccines or vaccine/drug delivery systems, diagnostics and directly acting therapeutic agents in combating the important zoonotic viral diseases in the recent scenario along with their potential benefits, challenges and prospects to design successful control strategies. CONCLUSION This review provides significant introspection towards the multi-arrayed applications of nanomedicine to combat several important zoonotic viral diseases.
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Affiliation(s)
- Prasad Minakshi
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Mirzapur (UP) - 231001, India
| | - Rajesh Kumar
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Basanti Brar
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Upendra P Lambe
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Somesh Banerjee
- Department of Veterinary Microbiology, Immunology Section, LUVAS, Hisar-125004, India
| | - Koushlesh Ranjan
- Department of Veterinary Physiology and Biochemistry, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110, India
| | | | - Parveen Goel
- Department of Veterinary Medicine, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, 125004, India
| | - Yashpal S Malik
- Division of Standardisation, Indian Veterinary Research Institute Izatnagar - Bareilly (UP) - 243122, India
| | - Gaya Prasad
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, UP, 250110, India
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15
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Zhang H, Li X, Huang A, Yan Z, Chen Y, Bie Z. PEI-assisted boronate affinity magnetic nanoparticle-based SELEX for efficient in vitro evolution of saponin-binding aptamers. RSC Adv 2021; 11:8775-8781. [PMID: 35423405 PMCID: PMC8695300 DOI: 10.1039/d1ra00889g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Branched polyethyleneimine assisted boronate affinity magnetic nanoparticle-based aptamer evolution platform.
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Affiliation(s)
- Hui Zhang
- Department of Chemistry
- Bengbu Medical University
- Bengbu 233000
- China
| | - Xue Li
- School of Pharmacy
- Bengbu Medical University
- Bengbu 233000
- China
| | - Ailan Huang
- Department of Chemistry
- Bengbu Medical University
- Bengbu 233000
- China
| | - Zhifeng Yan
- Department of Chemistry
- Bengbu Medical University
- Bengbu 233000
- China
| | - Yang Chen
- Department of Chemistry
- Bengbu Medical University
- Bengbu 233000
- China
- School of Pharmacy
| | - Zijun Bie
- Department of Chemistry
- Bengbu Medical University
- Bengbu 233000
- China
- School of Pharmacy
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16
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Mutreja R, Baba SA, Navani NK. Nucleic Acid Aptamers as Emerging Tools for Diagnostics and Theranostics. Methods Mol Biol 2020; 2054:201-221. [PMID: 31482458 DOI: 10.1007/978-1-4939-9769-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers are ssDNA or RNA sequences (20-80 nucleotides) generated in vitro by SELEX (Systematic Evolution of Ligands using EXponential enrichment) against diverse range of targets from small molecules to bacteria, viruses, and even eukaryotic cells. Aptamers, also known as chemical bodies, bind to their respective targets with tunable affinity and specificity, making aptamers as potent probes for diagnostics and excellent ligands for drug delivery in therapeutics. In this chapter, we have described the methods for generating DNA aptamers against proteins and their use in theranostics.
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Affiliation(s)
- Ruchi Mutreja
- Chemical Biology Lab, Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India
| | - Shahnawaz Ahmad Baba
- Chemical Biology Lab, Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India
| | - Naveen Kumar Navani
- Chemical Biology Lab, Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India.
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Simon L, Bognár Z, Gyurcsányi RE. Finding the Optimal Surface Density of Aptamer Monolayers by SPR Imaging Detection‐based Aptamer Microarrays. ELECTROANAL 2020. [DOI: 10.1002/elan.201900736] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- László Simon
- BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical ChemistryBudapest University of Technology and Economics, Szent Gellért tér 4 H-1111 Budapest Hungary
| | - Zsófia Bognár
- BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical ChemistryBudapest University of Technology and Economics, Szent Gellért tér 4 H-1111 Budapest Hungary
| | - Róbert E. Gyurcsányi
- BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical ChemistryBudapest University of Technology and Economics, Szent Gellért tér 4 H-1111 Budapest Hungary
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18
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Liu Q, Zhang W, Chen S, Zhuang Z, Zhang Y, Jiang L, LIN JS. SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding. J Biol Eng 2020; 14:1. [PMID: 31956340 PMCID: PMC6956507 DOI: 10.1186/s13036-019-0223-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aptamers, single-stranded DNAs or RNAs, can be selected from a library containing random sequences using a method called Systematic Evolution of Ligands by EXponential Enrichment (SELEX). In SELEX, monitoring the enriching statuses of aptamer candidates during the process is a key step until today. Conformational change of an aptamer caused by target-binding in gel can be used to indicate its statuses of binding. RESULTS In this study, an easy-to-implement gel-based diffusion method (GBDM) was developed to monitor the interaction between enriched aptamer candidates and their targets. In order to prove the concept, characterization of aptamers targeting their targets including protein (thrombin) and non-protein molecules (acetamiprid, ATP, atrazine, profenofos and roxithromycin), respectively, were performed using mini gels. Our method has advantages over the common methods including easy performed with labor- and time- saving in experimental operation. The concept has been proven by monitoring enrichment of dynamic aptamer candidate libraries targeting a small molecule 2,2-bis(4-chlorophenyl) acetic acid (DDA) during SELEX process. A mini gel cassette was designed and fabricated by our laboratory to make mini agarose gels for diffusion with different directions. CONCLUSIONS These results indicate that GBDM, in particular, chasing diffusion is suitable for monitoring the interaction between enriched aptamer candidates and their targets. These pioneering efforts are helpful for novel aptamer selection by breaking through the technical bottleneck of aptamer development and helpful for development of novel aptasensors.
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Affiliation(s)
- Qingxiu Liu
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Wei Zhang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Siying Chen
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Zhenjing Zhuang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Yi Zhang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Lingli Jiang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Jun Sheng LIN
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
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19
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Bhardwaj T, Rathore AS, Jha SK. The selection of highly specific and selective aptamers using modified SELEX and their use in process analytical techniques for Lucentis bioproduction. RSC Adv 2020; 10:28906-28917. [PMID: 35520059 PMCID: PMC9055848 DOI: 10.1039/d0ra03542d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/19/2020] [Indexed: 11/21/2022] Open
Abstract
Aptamers for Lucentis were selected using 10 rounds of a modified and highly stringent SELEX process. Affinity column chromatography was used for the binding, partitioning, and elution steps, and the regeneration of ssDNA was performed via asymmetric PCR in the SELEX process. The interaction of aptamers with Lucentis was studied by means of the HADDOCK web server docking program. In addition, the secondary structures of aptamers were interrogated using the mfold web server to check common regions responsible for better affinity towards Lucentis. The two best aptamers for Lucentis (aptamers 1 and 25) were found to have dissociation constant (Kd) values between 23 and 35 nM by means of thermofluorimetric and non-faradaic impedance spectroscopy (NFIS) analysis. The low dissociation constants in the nanomolar range showed the high specificities of the aptamers for Lucentis. Selectivity tests were also performed using both aptamers with different proteins in which negligible responses were obtained from interfering proteins with respect to Lucentis. Although neither of the two aptamers showed prominent responses to the interfering proteins, slightly better selectivity was shown by aptamer 1. The same aptamers were tested for their application in the detection of Lucentis in spiked and real media broth samples. For this detection test, interdigitated (IDT) gold electrodes on a glass substrate were fabricated using standard photolithography and thermal deposition techniques. NFIS measurements were used for the label-free detection of Lucentis in samples. The linear ranges of detection for aptamers 1 and 25 were found to be 22–100 nM and 40–100 nM, respectively. The LODs for aptamers 1 and 25 were calculated to be 22 nM and 40 nM, respectively, which were significantly better than the values from a HPLC-based detection method (about 240 nM). The real sample analysis results were cross-checked via a standard HPLC method, and better correlation was found between the HPLC and aptamer 1 results than the aptamer 25 results; hence, aptamer 1 can be further analyzed and tested for use in affinity column chromatography and detection-kit/chip-based PAT for Lucentis bioproduction. Highly specific and selective aptamers for Lucentis were selected using 10 rounds of a modified and highly stringent SELEX process.![]()
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Affiliation(s)
- Tanu Bhardwaj
- Centre for Biomedical Engineering
- Indian Institute of Technology
- New Delhi-110016
- India
| | - Anurag S. Rathore
- Department of Chemical Engineering
- Indian Institute of Technology
- New Delhi-110016
- India
| | - Sandeep Kumar Jha
- Centre for Biomedical Engineering
- Indian Institute of Technology
- New Delhi-110016
- India
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20
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Zhu L, Han J, Wang Z, Yin L, Zhang W, Peng Y, Nie Z. Competitive adsorption on gold nanoparticles for human papillomavirus 16 L1 protein detection by LDI-MS. Analyst 2019; 144:6641-6646. [PMID: 31595888 DOI: 10.1039/c9an01612k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The detection of the HPV L1 protein provides information about the infection status of the virus, reflects the replication status of the HPV virus in cervical cells, and helps understand the regression and progress of cervical lesions. Herein, we report a novel laser desorption ionization mass spectrometry (LDI MS) method for the sensitive detection of the HPV 16 L1 protein, based on non-covalent competitive adsorption between the HPV 16 L1 aptamer and melamine on gold nanoparticles (AuNPs). The intensity of the MS signal corresponding to the mass tag shows a linear relationship with the HPV 16 L1 concentration in the range 2-80 ng mL-1, with a limit of detection (LOD) of 58.8 pg mL-1. Using this method, the HPV 16 L1 protein is quantitatively analyzed in both clinical and vaccine samples. The described method is simple and has high sensitivity and good reliability.
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Affiliation(s)
- Li Zhu
- State Key Laboratory of Chemical Resource Engineering, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China. and National Institutes for Food and Drug Control, Beijing 102629, China
| | - Jing Han
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhihua Wang
- State Key Laboratory of Chemical Resource Engineering, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Lihui Yin
- National Institutes for Food and Drug Control, Beijing 102629, China
| | - Wei Zhang
- National Institutes for Food and Drug Control, Beijing 102629, China
| | - You Peng
- Department of Chemistry and Environment Engineering, Jiujiang University, Jiujiang, 332005 China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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21
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Kurt H, Eyüpoğlu AE, Sütlü T, Budak H, Yüce M. Plasmonic Selection of ssDNA Aptamers against Fibroblast Growth Factor Receptor. ACS COMBINATORIAL SCIENCE 2019; 21:578-587. [PMID: 31265241 DOI: 10.1021/acscombsci.9b00059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, we describe the selection of ssDNA aptamers targeting fibroblast growth factor receptor binding protein 3 K650E, which has roles in cell division, growth, and differentiation through the kinase cascade. The selection process was based on the label-free, real-time monitoring of binding interactions by surface plasmon resonance, allowing for convenient manipulation of the selection rounds. Next generation sequencing data provided four major motif families from which nine individual sequences were selected based on their abundance levels. Electrophoretic mobility shift assays revealed binding of the selected aptamers to the target protein without significant interference from fibroblast growth factor receptor binding protein 2, indicating the selectivity of the aptamers. The dissociation constant at equilibrium for the best aptamer candidate, SU-3, was found to be (28.2 ± 19.6) × 10-9 M (n = 5) using a single-cycle kinetic analysis method. Advantages of the experimental setup and potential applications of the selected aptamers are discussed.
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Affiliation(s)
- Hasan Kurt
- Istanbul Medipol University, School of Engineering and Natural Sciences, Beykoz, 34810 Istanbul, Turkey
- Nanosolar Plasmonics Ltd., Gebze, 41400 Kocaeli, Turkey
| | - Alp Ertunga Eyüpoğlu
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
| | - Tolga Sütlü
- Sabanci University, SUNUM Nanotechnology Research Centre, Tuzla, 34956 Istanbul Turkey
| | - Hikmet Budak
- Montana State University, Cereal Genomics Lab, Bozeman, Montana 59717-2000, United States
| | - Meral Yüce
- Sabanci University, SUNUM Nanotechnology Research Centre, Tuzla, 34956 Istanbul Turkey
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22
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Yan J, Xiong H, Cai S, Wen N, He Q, Liu Y, Peng D, Liu Z. Advances in aptamer screening technologies. Talanta 2019; 200:124-144. [DOI: 10.1016/j.talanta.2019.03.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/20/2019] [Accepted: 03/02/2019] [Indexed: 02/07/2023]
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23
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Kim SH, Lee J, Lee BH, Song CS, Gu MB. Specific detection of avian influenza H5N2 whole virus particles on lateral flow strips using a pair of sandwich-type aptamers. Biosens Bioelectron 2019; 134:123-129. [PMID: 30986614 DOI: 10.1016/j.bios.2019.03.061] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/17/2019] [Accepted: 03/27/2019] [Indexed: 11/25/2022]
Abstract
We report a selection of a cognate pair of aptamers for whole avian influenza virus particles of H5N2 by using graphene-oxide based systemic evolution of ligands by exponential enrichment (GO-SELEX), and the application of a pair of sandwich-type binding aptamers on the lateral flow strips. The aptamers were characterized by GO-FRET assay, and Kd values of the selected aptamers were estimated to be from 6.913 × 105 to 1.27 × 106 EID50/ml (EID50/ml: 50% egg infective dose). Based on the evidence from confocal laser scanning microscope (CLSM), surface plasmon resonance (SPR), and circular dichroism (CD) spectrum analysis, the aptamers, J3APT and JH4APT, were found to be working as a cognate pair that binds to the target virus at the different sites simultaneously. This cognate pair of aptamers then was successfully applied on the lateral flow strips, clearly showing sandwich-type binding images with the presence of the certain numbers of H5N2 virus particles. On the newly developed lateral flow strips, the target virus was detectable down to 6 × 105 EID50/ml in the buffer and 1.2 × 106 EID50/ml in the duck's feces, respectively, by the naked eye. By using the ImageJ software, the LOD was found to be 1.27 × 105 EID50/ml in the buffer and 2.09 × 105 EID50/ml in the duck's feces, respectively. Interestingly, on the lateral flow strips, enhanced specificity towards the target virus (H5N2) appeared over other subtypes of H5Nx. To the best of our knowledge, this is the first report about the application of the cognate pair of aptamers for the detection of influenza virus on the lateral flow strips. This study shows the promising perspective of a cognate pair of aptamers for the on-site detection system which could be useful for rapid detection of avian influenza viruses for preventing the pandemic influenza viruses from spreading.
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Affiliation(s)
- Sang Hoon Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul, 136-701, Republic of Korea
| | - Junho Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul, 136-701, Republic of Korea
| | - Bang Hyun Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul, 136-701, Republic of Korea
| | - Chang-Seon Song
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Man Bock Gu
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul, 136-701, Republic of Korea.
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24
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Yu F, Li H, Sun W, Xu D, He F. Rapid selection of aptamers based on protein microarray. RSC Adv 2019; 9:9762-9768. [PMID: 35520705 PMCID: PMC9062193 DOI: 10.1039/c8ra09232j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/05/2019] [Indexed: 11/21/2022] Open
Abstract
We report a novel method for the efficient screening of aptamers from a complex ssDNA library based on a microarray chip, which was named Microarray-SELEX. In this method, the target protein (lactoferrin) and negative proteins (α-lactalbumin, β-lactoglobulin, bovine serum albumin, and casein) were each dotted and immobilized on a slide to form a protein microarray. Moreover, the library was added to this chip to interact with negative proteins, then with the target protein. The process of SELEX could be monitored on-line using a fluorescent microarray scanner and the whole process was performed in only six rounds. Finally, five aptamers (YFL-1, YFL-4, YFL-5, YFL-6 and YFL-7) were obtained, which showed good specificity towards lactoferrin in the presence of negative proteins. The equilibrium dissociation constants (K d) of the aptamers were in the nanomolar range. Briefly, Microarray-SELEX is a rapid, easy, sensitive and efficient method for screening aptamers.
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Affiliation(s)
- Fang Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210046 China
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210046 China
| | - Wei Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine Beijing 102206 China,
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210046 China
| | - Fuchu He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210046 China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine Beijing 102206 China,
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25
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Asha K, Kumar P, Sanicas M, Meseko CA, Khanna M, Kumar B. Advancements in Nucleic Acid Based Therapeutics against Respiratory Viral Infections. J Clin Med 2018; 8:jcm8010006. [PMID: 30577479 PMCID: PMC6351902 DOI: 10.3390/jcm8010006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
Several viruses cause pulmonary infections due to their shared tropism with cells of the respiratory tract. These respiratory problems due to viral infection become a public health concern due to rapid transmission through air/aerosols or via direct-indirect contact with infected persons. In addition, the cross-species transmission causes alterations to viral genetic makeup thereby increasing the risk of emergence of pathogens with new and more potent infectivity. With the introduction of effective nucleic acid-based technologies, post translational gene silencing (PTGS) is being increasingly used to silence viral gene targets and has shown promising approach towards management of many viral infections. Since several host factors are also utilized by these viruses during various stages of infection, silencing these host factors can also serve as promising therapeutic tool. Several nucleic acid-based technologies such as short interfering RNAs (siRNA), antisense oligonucleotides, aptamers, deoxyribozymes (DNAzymes), and ribozymes have been studied and used against management of respiratory viruses. These therapeutic nucleic acids can be efficiently delivered through the airways. Studies have also shown efficacy of gene therapy in clinical trials against respiratory syncytial virus (RSV) as well as models of respiratory diseases including severe acute respiratory syndrome (SARS), measles and influenza. In this review, we have summarized some of the recent advancements made in the area of nucleic acid based therapeutics and highlighted the emerging roles of nucleic acids in the management of some of the severe respiratory viral infections. We have also focused on the methods of their delivery and associated challenges.
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Affiliation(s)
- Kumari Asha
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.
| | - Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida 201303, India.
| | - Melvin Sanicas
- Sanofi Pasteur, Asia and JPAC Region, Singapore 257856, Singapore.
| | - Clement A Meseko
- Regional Centre for Animal Influenza, National Veterinary Research Institute, Vom 930010, Nigeria.
| | - Madhu Khanna
- Department of Respiratory Virology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110007, India.
| | - Binod Kumar
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.
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26
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Morris FD, Peterson EM, Heemstra JM, Harris JM. Single-Molecule Kinetic Investigation of Cocaine-Dependent Split-Aptamer Assembly. Anal Chem 2018; 90:12964-12970. [PMID: 30280568 DOI: 10.1021/acs.analchem.8b03637] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aptamers are short nucleic-acid biopolymers selected to have high affinity and specificity for protein or small-molecule target analytes. Aptamers can be engineered into split-aptamer biosensors comprising two nucleic acid strands that coassemble as they bind to a target, resulting in a large signal change from attached molecular probes (e.g., molecular beacons). The kinetics of split-aptamer assembly and their dependence on target recognition are largely unknown; knowledge of these kinetics could help in design and optimization of split-aptamer biosensors. In this work, we measure assembly kinetics of cocaine-dependent split-aptamer molecules using single-molecule fluorescence imaging. Assembly is monitored between a DNA strand tethered to a glass substrate and solutions containing the other strand tagged with a fluorescent label, with varying concentrations of the cocaine analyte. Dissociation rates are measured by tracking individual molecules and measuring their bound lifetimes. Dissociation-time distributions are biexponential, possibly indicating different folded states of the aptamer. The dissociation rate of only the longer-lived complex decreases with cocaine concentration, suggesting that cocaine stabilizes the long-lived aptamer complex. The variation in the slow dissociation rate with cocaine concentration is well described with an equilibrium-binding model, where the dissociation rate approaches a saturation limit consistent with the dissociation-equilibrium constant for cocaine-binding to the split aptamer. This single-molecule methodology provides a sensitive readout of cocaine-binding based on the dissociation kinetics of the split aptamer, allowing one to distinguish target-dependent aptamer assembly from background assembly. This methodology could be used to study other systems where target association affects the stability of aptamer duplexes.
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Affiliation(s)
- Frances D Morris
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Eric M Peterson
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Jennifer M Heemstra
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , United States
| | - Joel M Harris
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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27
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Yu F, Li H, Sun W, Zhao Y, Xu D, He F. Selection of aptamers against Lactoferrin based on silver enhanced and fluorescence-activated cell sorting. Talanta 2018; 193:110-117. [PMID: 30368278 DOI: 10.1016/j.talanta.2018.09.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023]
Abstract
We report a novel method for efficiently screening aptamers from a complex ssDNA library based on silver decahedral nanoparticles (AgNP) and fluorescence activated cell sorting (FACS). In this method, target protein (lactoferrin) and negative proteins (α-lactalbumin, β-lactoglobulin, bovine serum albumin, casein) were respectively immobilized on polystyrene microspheres (PS) to form PSLac, PSα-Lac, PSβ-Lac, PSBSA and PSCas. PSLac was firstly interacted with Cy5 labeled library (Lib), then hybridized with Cy5 modified silver decahedral nanoparticles (AgNPCy5) to form PSLac/Lib/AgNPCy5 conjugates. FACS was used to separate and collect PSLac/Lib/AgNPCy5 conjugates from complicated complex. AgNP was used to increase the fluorescence intensity in the selecting process and choose non-self-hybridization of Lib. Six aptamers (Ylac1, Ylac4, Ylac5, Ylac6, Ylac8 and Ylac9) were obtained after five-round of selection. These aptamers showed good specificity towards lactoferrin in the presence of negative proteins. The equilibrium dissociation constants (Kd) of six aptamers were calculated and all were in the nanomolar range. In a word, AgNP-FACS SELEX (AgFACS-SELEX) is a rapid, sensitive and highly efficient method for screening aptamers.
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Affiliation(s)
- Fang Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China.
| | - Wei Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yaju Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China.
| | - Fuchu He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, China; State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China.
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28
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Therapeutic aptamers in discovery, preclinical and clinical stages. Adv Drug Deliv Rev 2018; 134:51-64. [PMID: 30125605 DOI: 10.1016/j.addr.2018.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/11/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
The aptamer field witnessed steady growth during the past 28 years as evident from the exponentially increasing number of related publications. The field is "coming of age", but like other biomedical research areas facing a global push towards translational research to carry ideas from bench- to bedside, there is pressure to show impact for aptamers at the clinical end. Being easy-to-make, non-immunogenic, stable and high-affinity nano-ligands, aptamers are perfectly poised to move in this direction. They can specifically bind targets ranging from small molecules to complex multimeric structures, making them potentially useful in a limitless variety of therapeutic approaches. This review will summarize efforts made to accomplish the therapeutic promise of aptamers, with a focus on aptamers directly acting as therapeutic molecules, rather than those used in targeted delivery of other drugs. The review will showcase representative examples at various stages of development, covering different disease categories.
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29
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Diao D, Qiao N, Wu X, Li J, Lou X. An efficient method to evaluate experimental factor influence on in vitro binding of aptamers. Anal Biochem 2018; 556:7-15. [PMID: 29913134 DOI: 10.1016/j.ab.2018.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 12/11/2022]
Abstract
Nucleic acid-based aptamers are promising alternative to antibodies, however, their selection process (SELEX) is challenging. A number of simulations and few experiments have been reported offering insights into experimental factors (EFs) that govern the effectiveness of the selection process. Though useful, these previous studied were either lack of experimental confirmation, or considered limited EFs. A more efficient experimental method is highly desired. In this study, we developed a fast method that is capable to quantitatively probe the influence of multiple EFs. Based on the fact that the aptamer enrichment efficiency is highly affected by background binding, the binding ratio between the numbers of specific aptamer binders and nonspecific (unselected library) binders per bead was used to quantitatively evaluate EF effects. Taking thrombin and streptavidin as models, three previously studied EFs (surface coverage, buffer composition, and DNA concentration) and four never-studied ones (surface chemistry, heat treatment, elution methodology and pool purity) were investigated. The EFs greatly affected binding ratio (ranging from 0.03 ± 0.03 to 14.60 ± 2.30). The results were in good agreement with the literature, suggesting the good feasibility of our method. Our study provides guidance for the choice of EFs not only for aptamer selection, but also for binding evaluation of aptamers.
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Affiliation(s)
- Donglin Diao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Na Qiao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xiao Wu
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Jiyuan Li
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China.
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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Silver decahedral nanoparticles empowered SPR imaging-SELEX for high throughput screening of aptamers with real-time assessment. Biosens Bioelectron 2018; 109:206-213. [PMID: 29567565 DOI: 10.1016/j.bios.2018.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 01/16/2023]
Abstract
A highly efficient method for aptamer screening with real-time monitoring of the SELEX process was described by silver decahedra nanoparticles (Ag10-NPs) enhanced surface plasmon resonance imaging (SPRI). A microarray chip was developed by immobilization of target protein (Lactoferrin (Lac)) and control proteins (α-lactalbumin (α), β-lactoglobulin (β), casein, and bovine serum albumin (BSA)) on the biochip surface. Ag10-NPs were conjugated with an ssDNA library (lib) (Ag10-NPs-library) that consisted of a central 40 nt randomized sequence and a 20 nt fixed primer sequence. Introduction of the Ag10-NPs-library to the SPRI flow channels drastically increased the sensitivity of SPRI signal for real-time monitoring of SELEX. The work allows rapid screening of potential targets, and yields nine aptamers with high affinity (nanomolar range) for Lac after only six-rounds of selection. The aptamer Lac 13-26 was then further tested by SPRI, and the results demonstrated that the aptamer had the capacity to be ultra-sensitive for specific detection of Lac. The novel SPRI-SELEX method demonstrated here showed many advantages of real-time evaluation, high throughput, and high efficiency.
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Hassanpour S, Baradaran B, Hejazi M, Hasanzadeh M, Mokhtarzadeh A, de la Guardia M. Recent trends in rapid detection of influenza infections by bio and nanobiosensor. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2017.11.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Xu Y, Tan S, Liang Q, Ding M. One-Step Facile Synthesis of Aptamer-Modified Graphene Oxide for Highly Specific Enrichment of Human A-Thrombin in Plasma. SENSORS 2017; 17:s17091986. [PMID: 28902155 PMCID: PMC5621013 DOI: 10.3390/s17091986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/25/2023]
Abstract
The enrichment of low-abundance proteins in complex biological samples plays an important role in clinical diagnostics and biomedical research. This work reports a novel one-step method for the synthesis of aptamer-modified graphene oxide (GO/Apt) nanocomposites, without introducing the use of gold, for the rapid and specific separation and enrichment of human α-thrombin from buffer solutions with highly concentrated interferences. The obtained GO/Apt nanocomposites had remarkable aptamer immobilization, up to 44.8 nmol/mg. Furthermore, GO/Apt nanocomposites exhibited significant specific enrichment efficiency for human α-thrombin (>90%), even under the presence of 3000-fold interference proteins, which was better than the performance of other nanomaterials. Finally, the GO/Apt nanocomposites were applied in the specific capturing of human α-thrombin in highly concentrated human plasma solutions with negligible nonspecific binding of other proteins, which demonstrated their prospects in rare protein analysis and biosensing applications.
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Affiliation(s)
- Yuan Xu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Siyuan Tan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Qionglin Liang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Mingyu Ding
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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Agyei D, Acquah C, Tan KX, Hii HK, Rajendran SRCK, Udenigwe CC, Danquah MK. Prospects in the use of aptamers for characterizing the structure and stability of bioactive proteins and peptides in food. Anal Bioanal Chem 2017; 410:297-306. [PMID: 28884330 DOI: 10.1007/s00216-017-0599-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/01/2017] [Accepted: 08/22/2017] [Indexed: 12/28/2022]
Abstract
Food-derived bioactive proteins and peptides have gained acceptance among researchers, food manufacturers and consumers as health-enhancing functional food components that also serve as natural alternatives for disease prevention and/or management. Bioactivity in food proteins and peptides is determined by their conformations and binding characteristics, which in turn depend on their primary and secondary structures. To maintain their bioactivities, the molecular integrity of bioactive peptides must remain intact, and this warrants the study of peptide form and structure, ideally with robust, highly specific and sensitive techniques. Short single-stranded nucleic acids (i.e. aptamers) are known to have high affinity for cognate targets such as proteins and peptides. Aptamers can be produced cost-effectively and chemically derivatized to increase their stability and shelf life. Their improved binding characteristics and minimal modification of the target molecular signature suggests their suitability for real-time detection of conformational changes in both proteins and peptides. This review discusses the developmental progress of systematic evolution of ligands by exponential enrichment (SELEX), an iterative technology for generating cost-effective aptamers with low dissociation constants (K d) for monitoring the form and structure of bioactive proteins and peptides. The review also presents case studies of this technique in monitoring the structural stability of bioactive peptide formulations to encourage applications in functional foods. The challenges and potential of aptamers in this research field are also discussed. Graphical abstract Advancing bioactive proteins and peptide functionality via aptameric ligands.
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Affiliation(s)
- Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia.,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Kei Xian Tan
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia.,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Hieng Kok Hii
- Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia
| | - Subin R C K Rajendran
- Verschuren Centre for Sustainability in Energy and the Environment, Cape Breton University, Sydney, NS, B1P 6L2, Canada
| | - Chibuike C Udenigwe
- School of Nutrition Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Michael K Danquah
- Curtin Sarawak Research Institute, Curtin University, 98009, Sarawak, Malaysia. .,Department of Chemical Engineering, Curtin University, 98009, Sarawak, Malaysia.
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An aptamer-based PCR method coupled with magnetic immunoseparation for sensitive detection of Salmonella Typhimurium in ground turkey. Anal Biochem 2017. [PMID: 28645756 DOI: 10.1016/j.ab.2017.06.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aptamers are single-stranded oligonucleotide ligands that can bind to targets with high affinity and specificity. They have been widely studied in the field of diagnostics as alternatives to antibodies due to their favorable features such as easy labeling, temperature tolerance, lower cost and recognition of a wide variety of targets. In this study, an aptamer-based PCR method coupled with magnetic immunoseparation was developed to detect S. Typhimurium from ground turkey. Firstly, biotinylated polyclonal anti-S. Typhimurium antibody was immobilized on streptavidin-coated magnetic nanobeads to capture S. Typhimurium. Secondly, the aptamers were added and bound to the surface of S. Typhimurium after blocking the magnetic nanobeads with short ssDNA. Finally, the aptamers were released by heating and amplified by PCR. After optimization, this assay was able to detect 102 CFU/mL of S. Typhimurium in pure culture, and 103 CFU/mL of S. Typhimurium in ground turkey. This study demonstrated the feasibility and application of an aptamer-based PCR method coupled with magnetic immunoseparation for sensitive detection of S. Typhimurium in ground turkey.
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Amano R, Aoki K, Miyakawa S, Nakamura Y, Kozu T, Kawai G, Sakamoto T. NMR monitoring of the SELEX process to confirm enrichment of structured RNA. Sci Rep 2017; 7:283. [PMID: 28325909 PMCID: PMC5428055 DOI: 10.1038/s41598-017-00273-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/15/2017] [Indexed: 01/20/2023] Open
Abstract
RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kazuteru Aoki
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Shin Miyakawa
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Yoshikazu Nakamura
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan.
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Abstract
Rapidly evolving viral strains leading to epidemics and pandemics necessitates quick diagnostics and treatment to halt the progressive march of the disease. Optical biosensors like surface plasmon resonance (SPR) have emerged in recent times as a most reliable diagnostic device owing to their portability, reproducibility, sensitivity and specificity. SPR analyzes the kinetics of biomolecular interactions in a label-free manner. It has surpassed the conventional virus detection methods in its utility, particularly in medical diagnostics and healthcare. However, the requirement of high-end infrastructure setup and trained manpower are some of the roadblocks in realizing the true potential of SPR. This platform needs further improvisation in terms of simplicity, affordability and portability before it could be utilized in need-based remote areas of under-developed and developing countries with limited infrastructure.
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Liu X, Li H, Jia W, Chen Z, Xu D. Selection of aptamers based on a protein microarray integrated with a microfluidic chip. LAB ON A CHIP 2016; 17:178-185. [PMID: 27924973 DOI: 10.1039/c6lc01208f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We developed an efficient and fast method based on a protein microarray integrated with a microfluidic chip for the process of SELEX (systematic evolution of ligands by exponential enrichment). Lactoferrin from bovine milk was used as a target protein, while bovine serum albumin (BSA), α-lactalbumin, β-lactoglobulin and casein were used as negative proteins. They were separately dotted and immobilized to prepare the protein microarray and the resulting microarray was further integrated into a microfluidic chip for the SELEX (PMM-SELEX) process. The interaction between aptamer candidates and targets could be monitored using a fluorescence microarray scanner and the whole PMM-SELEX process was performed through seven-round selection. As a result, five aptamers (Lac-14, Lac-6a, Lac-9, Lac-5, Lac-3a) with high specificity and affinity can be repeatedly obtained during three times of independent repeated selection. Surface plasmon resonance (SPR) was used to calculate the dissociation constants (Kd). The aptamer Lac-6a was then used for detection of lactoferrin by fluorescence polarization. A linear response was observed for lactoferrin concentrations in the range of 0.78-50 μg mL-1 and the detection limit was 0.39 μg mL-1. Thus, the innovative PMM-SELEX presented shows stability, accuracy and high efficiency for aptamer screening.
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Affiliation(s)
- Xiaohui Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Wenchao Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Zhu Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
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González VM, Martín ME, Fernández G, García-Sacristán A. Use of Aptamers as Diagnostics Tools and Antiviral Agents for Human Viruses. Pharmaceuticals (Basel) 2016; 9:78. [PMID: 27999271 PMCID: PMC5198053 DOI: 10.3390/ph9040078] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
Appropriate diagnosis is the key factor for treatment of viral diseases. Time is the most important factor in rapidly developing and epidemiologically dangerous diseases, such as influenza, Ebola and SARS. Chronic viral diseases such as HIV-1 or HCV are asymptomatic or oligosymptomatic and the therapeutic success mainly depends on early detection of the infective agent. Over the last years, aptamer technology has been used in a wide range of diagnostic and therapeutic applications and, concretely, several strategies are currently being explored using aptamers against virus proteins. From a diagnostics point of view, aptamers are being designed as a bio-recognition element in diagnostic systems to detect viral proteins either in the blood (serum or plasma) or into infected cells. Another potential use of aptamers is for therapeutics of viral infections, interfering in the interaction between the virus and the host using aptamers targeting host-cell matrix receptors, or attacking the virus intracellularly, targeting proteins implicated in the viral replication cycle. In this paper, we review how aptamers working against viral proteins are discovered, with a focus on recent advances that improve the aptamers' properties as a real tool for viral infection detection and treatment.
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Affiliation(s)
- Víctor M González
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - M Elena Martín
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - Gerónimo Fernández
- Aptus Biotech SL, c/Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Ana García-Sacristán
- Aptus Biotech SL, c/Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
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Wang L, Wang R, Chen F, Jiang T, Wang H, Slavik M, Wei H, Li Y. QCM-based aptamer selection and detection of Salmonella typhimurium. Food Chem 2016; 221:776-782. [PMID: 27979272 DOI: 10.1016/j.foodchem.2016.11.104] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/11/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022]
Abstract
In this study, quartz crystal microbalance (QCM) was used to select aptamers against Salmonella typhimurium. To increase the success rate of Systematic Evolution of Ligands Exponential Enrichment (SELEX), the affinity of DNA pool in each round was simultaneously tracked using QCM in order to avoid the loss of high-quality aptamers. When the frequency change reached a maximum value after several rounds of selection and counter-selection, the candidate pool was cloned and sequenced. Out of three aptamer candidates, aptamer B5 showed high specificity and binding affinity with dissociation constant (Kd value) of 58.5nM, and was chosen for further studies. Subsequently, a QCM-based aptasensor was developed to detect S. typhimurium. This aptasensor was able to detect 103CFU/mL of S. typhimurium with less than 1h. This study demonstrated QCM-based selection could be more effective selection of aptamers and QCM-based aptasensor could be more sensitive in detecting S. typhimurium.
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Affiliation(s)
- Lijun Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ronghui Wang
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Fang Chen
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Tieshan Jiang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hong Wang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Michael Slavik
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hua Wei
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Yanbin Li
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA; Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA.
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Ospina-Villa JD, Zamorano-Carrillo A, Castañón-Sánchez CA, Ramírez-Moreno E, Marchat LA. Aptamers as a promising approach for the control of parasitic diseases. Braz J Infect Dis 2016; 20:610-618. [PMID: 27755981 PMCID: PMC9427573 DOI: 10.1016/j.bjid.2016.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 01/31/2023] Open
Abstract
Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction. As a result, aptamers have generated a large interest as promising tools to compete with monoclonal antibodies for detection and inhibition of specific markers of human diseases. One aptamer-based drug is currently authorized and several others are being clinically evaluated. Despite advances in the knowledge of parasite biology and host–parasite interactions from “omics” data, protozoan parasites still affect millions of people around the world and there is an urgent need for drug target discovery and novel therapeutic concepts. In this context, aptamers represent promising tools for pathogen identification and control. Recent studies have reported the identification of “aptasensors” for parasite diagnosis, and “intramers” targeting intracellular proteins. Here we discuss various strategies that have been employed for intracellular expression of aptamers and expansion of their possible application, and propose that they may be suitable for the clinical use of aptamers in parasitic infections.
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Affiliation(s)
- Juan David Ospina-Villa
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de Mexico, Mexico
| | | | - Carlos A Castañón-Sánchez
- Hospital Regional de Alta Especialidad de Oaxaca, Subdirección de Enseñanza e Investigación, Oaxaca, Mexico
| | - Esther Ramírez-Moreno
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de Mexico, Mexico
| | - Laurence A Marchat
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de Mexico, Mexico.
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42
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Li X, He Y, Ma Y, Bie Z, Liu B, Liu Z. Hybrid Approach Combining Boronate Affinity Magnetic Nanoparticles and Capillary Electrophoresis for Efficient Selection of Glycoprotein-Binding Aptamers. Anal Chem 2016; 88:9805-9812. [PMID: 27579807 DOI: 10.1021/acs.analchem.6b02907] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Capillary electrophoresis (CE) and magnetic beads have been widely used for the selection of aptamers owing to their efficient separation ability. However, these methods alone are associated with some apparent drawbacks. CE suffers from small injection volumes and thereby only a limited amount of aptamer can be collected at each round. While the magnetic beads approach is often associated with tedious procedure and nonspecific binding. Herein we present a hybrid approach that combines the above two classical aptamer selection methods to overcome the drawbacks associated with these methods alone. In this hybrid method, one single round selection by boronate affinity magnetic nanoparticles (BA-MNPs) was first performed and then followed by a CE selection of a few rounds. The BA-MNPs-based selection eliminated nonbinding sequences, enriching effective sequences in the nucleic acid library. While the CE selection, which was carried out in free solutions, eliminated steric hindrance effects in subsequent selection. Two typical glycoproteins, Ribonuclease B (RNase B) and alkaline phosphatase (ALP), were used as targets. This hybrid method allowed for efficient selection of glycoprotein-binding aptamers within 4 rounds (1 round of BA-MNPs-based selection and 3 rounds of CE selection) and the dissociation constants reached 10-8 M level. The hybrid selection approach exhibited several significant advantages, including speed, affinity, specificity, and avoiding negative selection. Using one of the selected ALP-binding aptamers as an affinity ligand, feasibility for real application of the selected aptamers was demonstrated through constructing an improved enzyme activity assay.
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Affiliation(s)
- Xinglin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Yunjie He
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University , 321 Zhongshan Road, Nanjing 210008, China
| | - Yanyan Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Zijun Bie
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Baorui Liu
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University , 321 Zhongshan Road, Nanjing 210008, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
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Kumar PKR. Monitoring Intact Viruses Using Aptamers. BIOSENSORS-BASEL 2016; 6:bios6030040. [PMID: 27527230 PMCID: PMC5039659 DOI: 10.3390/bios6030040] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022]
Abstract
Viral diagnosis and surveillance are necessary steps in containing the spread of viral diseases, and they help in the deployment of appropriate therapeutic interventions. In the past, the commonly employed viral detection methods were either cell-culture or molecule-level assays. Most of these assays are laborious and expensive, require special facilities, and provide a slow diagnosis. To circumvent these limitations, biosensor-based approaches are becoming attractive, especially after the successful commercialization of glucose and other biosensors. In the present article, I have reviewed the current progress using the biosensor approach for detecting intact viruses. At the time of writing this review, three types of bioreceptor surfaces (antibody-, glycan-, and aptamer-based) have been explored on different sensing platforms for detecting intact viruses. Among these bioreceptors, aptamer-based sensors have been increasingly explored for detecting intact viruses using surface plasmon resonance (SPR) and other platforms. Special emphasis is placed on the aptamer-based SPR platform in the present review.
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Affiliation(s)
- Penmetcha K R Kumar
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan.
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44
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Hwang C, Carothers JM. Label-free selection of RNA aptamers for metabolic engineering. Methods 2016; 106:37-41. [PMID: 27339940 DOI: 10.1016/j.ymeth.2016.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/15/2016] [Accepted: 06/19/2016] [Indexed: 01/18/2023] Open
Abstract
RNA aptamers can be assembled into genetic regulatory devices that sense and respond to levels of specific cellular metabolites and thus serve an integral part of designing dynamic control into engineered metabolic pathways. Here, we describe a practical method for generating specific and high affinity aptamers to enable the wider use of in vitro selection and a broader application of aptamers for metabolic engineering. Conventional selection methods involving either radioactive labeling of RNA or the use of label-free methods such as SPR to track aptamer enrichment require resources that are not widely accessible to research groups. We present a label-free selection method that uses small volume spectrophotometers to track RNA enrichment paired with previously characterized affinity chromatography methods. Borrowing techniques used in solid phase peptide synthesis, we present an approach for immobilizing a wide range of metabolites to an amino PEGA matrix. As an illustration, we detail laboratory techniques employed to generate aptamers that bind p-aminophenylalanine, a metabolic precursor for bio-based production of plastics and the pristinamycin family of antibiotics. We focused on the development of methods for ligand immobilization, selection via affinity chromatography, and nucleic acid quantification that can be performed with common laboratory equipment.
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Affiliation(s)
- Chuhern Hwang
- Departments of Chemical Engineering and Bioengineering, Molecular Engineering and Sciences Institute, and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, United States
| | - James M Carothers
- Departments of Chemical Engineering and Bioengineering, Molecular Engineering and Sciences Institute, and Center for Synthetic Biology, University of Washington, Seattle, WA 98195, United States.
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Selection of RNA Aptamers Against Botulinum Neurotoxin Type A Light Chain Through a Non-Radioactive Approach. Appl Biochem Biotechnol 2016; 180:10-25. [PMID: 27085355 DOI: 10.1007/s12010-016-2081-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/07/2016] [Indexed: 12/15/2022]
Abstract
Botulinum neurotoxin (BoNT), a category A agent, is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. Currently, antidotes are not available to reverse the flaccid paralysis caused by BoNT. In the present study, a non-radioactive-based systematic evolution of ligands by exponential enrichment (SELEX) process is developed by utilizing surface plasmon resonance to monitor the binding enrichment. Two RNA aptamers have been identified as strong binders against light chain of botulinum neurotoxin type A. These two aptamers showed strong inhibition activity on LCA, with IC50 in nanomolar range. Inhibition kinetic studies reveal mid nanomolar KI and non-competitive nature of their inhibition, suggesting that they have strong potential as antidotes that can reverse the symptom caused by BoNT/A. More importantly, we observed that the 2'-fluorine-pyrimidine-modified RNA aptamers identified here do not change their binding and biological activities. This observation could lead to a cost-effective way for SELEX, by using regular nucleotide during SELEX, and 2'-fluorine-pyrimidine-modified nucleotide for final application to enhance their RNase-resistance.
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Yüce M, Ullah N, Budak H. Trends in aptamer selection methods and applications. Analyst 2016; 140:5379-99. [PMID: 26114391 DOI: 10.1039/c5an00954e] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aptamers are target specific ssDNA, RNA or peptide sequences generated by an in vitro selection and amplification method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment), which involves repetitive cycles of binding, recovery and amplification steps. Aptamers have the ability to bind with a variety of targets such as drugs, proteins, heavy metals, and pathogens with high specificity and selectivity. Aptamers are similar to monoclonal antibodies regarding their binding affinities, but they offer a number of advantages over the existing antibody-based detection methods, which make the aptamers promising diagnostic and therapeutic tools for future biomedical and analytical applications. The aim of this review article is to provide an overview of the recent advancements in aptamer screening methods along with a concise description of the major application areas of aptamers including biomarker discovery, diagnostics, imaging and nanotechnology.
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Affiliation(s)
- Meral Yüce
- Sabanci University, Nanotechnology Research and Application Centre, 34956, Istanbul, Turkey.
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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Dausse E, Barré A, Aimé A, Groppi A, Rico A, Ainali C, Salgado G, Palau W, Daguerre E, Nikolski M, Toulmé JJ, Di Primo C. Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation. Biosens Bioelectron 2016; 80:418-425. [PMID: 26874109 DOI: 10.1016/j.bios.2016.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 01/02/2023]
Abstract
A surface plasmon resonance (SPR)-based SELEX approach has been used to raise RNA aptamers against a structured RNA, derived from XBP1 pre-mRNA, that folds as two contiguous hairpins. Thanks to the design of the internal microfluidic cartridge of the instrument, the selection was performed during the dissociation phase of the SPR analysis by recovering the aptamer candidates directly from the target immobilized onto the sensor chip surface. The evaluation of the pools was performed by SPR, simultaneously, during the association phase, each time the amplified and transcribed candidates were injected over the immobilized target. SPR coupled with SELEX from the first to the last round allowed identifying RNA aptamers that formed highly stable loop-loop complexes (KD equal to 8nM) with the hairpin located on the 5' side of the target. High throughput sequencing of two key rounds confirmed the evolution observed by SPR and also revealed the selection of hairpins displaying a loop not fully complementary to the loop of its target. These candidates were selected mainly because they bound 79 times faster to the target than those having a complementary loop. SELEX coupled with SPR is expected to speed up the selection process because selection and evaluation are performed simultaneously.
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Affiliation(s)
- Eric Dausse
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Aurélien Barré
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Ahissan Aimé
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Alexis Groppi
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Alain Rico
- Thermo Fisher Scientific, Saint Aubin F-91190, France
| | | | - Gilmar Salgado
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - William Palau
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | | | - Macha Nikolski
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Carmelo Di Primo
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
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Surface plasmon resonance: a versatile technique for biosensor applications. SENSORS 2015; 15:10481-510. [PMID: 25951336 PMCID: PMC4481982 DOI: 10.3390/s150510481] [Citation(s) in RCA: 630] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/28/2015] [Indexed: 02/07/2023]
Abstract
Surface plasmon resonance (SPR) is a label-free detection method which has emerged during the last two decades as a suitable and reliable platform in clinical analysis for biomolecular interactions. The technique makes it possible to measure interactions in real-time with high sensitivity and without the need of labels. This review article discusses a wide range of applications in optical-based sensors using either surface plasmon resonance (SPR) or surface plasmon resonance imaging (SPRI). Here we summarize the principles, provide examples, and illustrate the utility of SPR and SPRI through example applications from the biomedical, proteomics, genomics and bioengineering fields. In addition, SPR signal amplification strategies and surface functionalization are covered in the review.
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50
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Chen L, Neethirajan S. A homogenous fluorescence quenching based assay for specific and sensitive detection of influenza virus A hemagglutinin antigen. SENSORS 2015; 15:8852-65. [PMID: 25884789 PMCID: PMC4431298 DOI: 10.3390/s150408852] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/02/2015] [Accepted: 04/09/2015] [Indexed: 11/16/2022]
Abstract
Influenza pandemics cause millions of deaths worldwide. Effective surveillance is required to prevent their spread and facilitate the development of appropriate vaccines. In this study, we report the fabrication of a homogenous fluorescence-quenching-based assay for specific and sensitive detection of influenza virus surface antigen hemagglutinins (HAs). The core of the assay is composed of two nanoprobes namely the glycan-conjugated highly luminescent quantum dots (Gly-QDs), and the HA-specific antibody-modified gold nanoparticle (Ab-Au NPs). When exposed to strain-specific HA, a binding event between the HA and the two nanoprobes takes place, resulting in the formation of a sandwich complex which subsequently brings the two nanoprobes closer together. This causes a decrease in QDs fluorescence intensity due to a non-radiative energy transfer from QDs to Au NPs. A resulting correlation between the targets HA concentrations and fluorescence changes can be observed. Furthermore, by utilizing the specific interaction between HA and glycan with sialic acid residues, the assay is able to distinguish HAs originated from viral subtypes H1 (human) and H5 (avian). The detection limits in solution are found to be low nanomolar and picomolar level for sensing H1-HA and H5-HA, respectively. Slight increase in assay sensitivity was found in terms of detection limit while exposing the assay in the HA spiked in human sera solution. We believe that the developed assay could serve as a feasible and sensitive diagnostic tool for influenza virus detection and discrimination, with further improvement on the architectures.
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Affiliation(s)
- Longyan Chen
- BioNano Laboratory, School of Engineering, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Suresh Neethirajan
- BioNano Laboratory, School of Engineering, University of Guelph, Guelph, ON N1G 2W1, Canada.
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