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Wang S, Zhou Z, Cao M, Pan Y, Zhang Y, Fang Y, Sun Q, Lei X, Le T. A comprehensive review of aptamer screening and application for lateral flow strip: Current status and future perspectives. Talanta 2024; 275:126181. [PMID: 38692047 DOI: 10.1016/j.talanta.2024.126181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
The detection of biomarkers is of great significance for medical diagnosis, food safety, environmental monitoring, and agriculture. However, bio-detection technology at present often necessitates complex instruments, expensive reagents, specialized expertise, and prolonged procedures, making it challenging to fulfill the demand for rapid, sensitive, user-friendly, and economical testing. In contrast, lateral flow strip (LFS) technology offers simple, fast, and visually accessible detection modality, allowing real-time analysis of clinical specimens, thus finding widespread utility across various domains. Within the realm of LFS, the application of aptamers as molecular recognition probes presents distinct advantages over antibodies, including cost-effectiveness, smaller size, ease of synthesis, and chemical stability. In recent years, aptamer-based LFS has found extensive application in qualitative, semi-quantitative, and quantitative detection across food safety, environmental surveillance, clinical diagnostics, and other domains. This review provided a concise overview of different aptamer screening methodologies, selection strategies, underlying principles, and procedural, elucidating their respective advantages, limitations, and applications. Additionally, we summarized recent strategies and mechanisms for aptamer-based LFS, such as the sandwich and competitive methods. Furthermore, we classified LFSs constructed based on aptamers, considering the rapid advancements in this area, and discussed their applications in biological and chemical detection. Finally, we delved into the current challenges and future directions in the development of aptamer and aptamer-based LFS. Although this review was not thoroughly, it would serve as a valuable reference for understanding the research progress of aptamer-based LFS and aid in the development of new types of aptasensors.
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Affiliation(s)
- Sixian Wang
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China.
| | - Zhaoyang Zhou
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Mingdong Cao
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Yangwei Pan
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Yongkang Zhang
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Yu Fang
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Qi Sun
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Xianlu Lei
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China
| | - Tao Le
- College of Life Sciences, Chongqing Collaborative Innovation Center for Rapid Detection of Food Quality and Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Chongqing Normal University, Chongqing, 401331, China.
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2
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 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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Williams NB, Batool S, Zumrut HE, Patel R, Sosa G, Jamal M, Mallikaratchy P. An In Vitro Selection Platform to Identify Multiple Aptamers against Multiple Cell-Surface Markers Using Ligand-Guided Selection. Biochemistry 2022; 61:1600-1613. [PMID: 35829681 PMCID: PMC10117398 DOI: 10.1021/acs.biochem.2c00105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamer ligand discovery against multiple molecules expressed on whole cells is an essential component in molecular tool development. However, owing to their intrinsic structural characteristics, cell-surface receptors have proven to be challenging targets in ligand discovery. Several variants to systematic evolution of ligands by exponential enrichment (SELEX) have been introduced to address the ″target problem″ for aptamer screening. To this end, we introduced a variant of SELEX, termed ligand-guided selection (LIGS), to identify highly specific aptamers against complex cell-surface markers in their native state. So far, the application of LIGS has been aimed at identifying aptamers against the most dominant receptors on the cell surface. Here, we report that LIGS can be expanded to identify two receptors on the same cell surface, paving the way to generate a multiplexed ligand discovery platform based on SELEX-targeting membrane receptors in their native functional state. Using CD19 and CD20 expressed on Toledo cells as a model system, multiple aptamer families were evolved against Toledo cells. We then utilized two monoclonal antibodies (mAbs) against CD20 and CD19 to selectively partition specific aptamers against CD19 and CD20. Following biochemical characterization, we introduce two specific aptamers against CD19 and two specific aptamers against CD20 with high affinity. Multi-target LIGS, as reported here, demonstrates a successful combinatorial approach for nucleic acid library screening to generate multiple artificial nucleic acid ligands against multiple receptors expressed on a single cell.
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Affiliation(s)
- Nicole B Williams
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Sana Batool
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Hasan E Zumrut
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Rutika Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - German Sosa
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Mohammad Jamal
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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4
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Ozturk M, Nilsen-Hamilton M, Ilgu M. Aptamer Applications in Neuroscience. Pharmaceuticals (Basel) 2021; 14:1260. [PMID: 34959661 PMCID: PMC8709198 DOI: 10.3390/ph14121260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges.
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Affiliation(s)
- Meric Ozturk
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Marit Nilsen-Hamilton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
| | - Muslum Ilgu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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Liu Y, Wang N, Chan CW, Lu A, Yu Y, Zhang G, Ren K. The Application of Microfluidic Technologies in Aptamer Selection. Front Cell Dev Biol 2021; 9:730035. [PMID: 34604229 PMCID: PMC8484746 DOI: 10.3389/fcell.2021.730035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
Aptamers are sequences of single-strand oligonucleotides (DNA or RNA) with potential binding capability to specific target molecules, which are increasingly used as agents for analysis, diagnosis, and medical treatment. Aptamers are generated by a selection method named systematic evolution of ligands by exponential enrichment (SELEX). Numerous SELEX methods have been developed for aptamer selections. However, the conventional SELEX methods still suffer from high labor intensity, low operation efficiency, and low success rate. Thus, the applications of aptamer with desired properties are limited. With their advantages of low cost, high speed, and upgraded extent of automation, microfluidic technologies have become promising tools for rapid and high throughput aptamer selection. This paper reviews current progresses of such microfluidic systems for aptamer selection. Comparisons of selection performances with discussions on principles, structure, operations, as well as advantages and limitations of various microfluidic-based aptamer selection methods are provided.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
| | - Nijia Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
| | - Chiu-Wing Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
| | - Aiping Lu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- School of Chinese Medicine, Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong, Hong Kong, SAR China
| | - Yuanyuan Yu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- School of Chinese Medicine, Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong, Hong Kong, SAR China
| | - Ge Zhang
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- School of Chinese Medicine, Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong, Hong Kong, SAR China
| | - Kangning Ren
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, Hong Kong, SAR China
- Institute of Research and Continuing Education, Hong Kong Baptist University, Shenzhen, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong, SAR China
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Roy D, Pascher A, Juratli MA, Sporn JC. The Potential of Aptamer-Mediated Liquid Biopsy for Early Detection of Cancer. Int J Mol Sci 2021; 22:ijms22115601. [PMID: 34070509 PMCID: PMC8199038 DOI: 10.3390/ijms22115601] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023] Open
Abstract
The early detection of cancer favors a greater chance of curative treatment and long-term survival. Exciting new technologies have been developed that can help to catch the disease early. Liquid biopsy is a promising non-invasive tool to detect cancer, even at an early stage, as well as to continuously monitor disease progression and treatment efficacy. Various methods have been implemented to isolate and purify bio-analytes in liquid biopsy specimens. Aptamers are short oligonucleotides consisting of either DNA or RNA that are capable of binding to target molecules with high specificity. Due to their unique properties, they are considered promising recognition ligands for the early detection of cancer by liquid biopsy. A variety of circulating targets have been isolated with high affinity and specificity by facile modification and affinity regulation of the aptamers. In this review, we discuss recent progress in aptamer-mediated liquid biopsy for cancer detection, its associated challenges, and its future potential for clinical applications.
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Affiliation(s)
- Dhruvajyoti Roy
- Helio Health, Irvine, CA 92618, USA
- Correspondence: ; Tel.: +1-949-8722383
| | - Andreas Pascher
- Department of General, Visceral and Transplant Surgery, University Hospital Münster, 48149 Münster, Germany; (A.P.); (M.A.J.); (J.C.S.)
| | - Mazen A. Juratli
- Department of General, Visceral and Transplant Surgery, University Hospital Münster, 48149 Münster, Germany; (A.P.); (M.A.J.); (J.C.S.)
| | - Judith C. Sporn
- Department of General, Visceral and Transplant Surgery, University Hospital Münster, 48149 Münster, Germany; (A.P.); (M.A.J.); (J.C.S.)
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Wu L, Wang Y, Xu X, Liu Y, Lin B, Zhang M, Zhang J, Wan S, Yang C, Tan W. Aptamer-Based Detection of Circulating Targets for Precision Medicine. Chem Rev 2021; 121:12035-12105. [PMID: 33667075 DOI: 10.1021/acs.chemrev.0c01140] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.
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Affiliation(s)
- Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yidi Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bingqian Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jialu Zhang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuang Wan
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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8
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JIANG H, LV XF, ZHAO KX. Progress of Aptamer Screening Techniques Based on Microfluidic Chips. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60015-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Eissa S, Siddiqua A, Chinnappan R, Zourob M. Electrochemical SELEX Technique for the Selection of DNA Aptamers against the Small Molecule 11-Deoxycortisol. ACS APPLIED BIO MATERIALS 2019; 2:2624-2632. [DOI: 10.1021/acsabm.9b00294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shimaa Eissa
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Ayesha Siddiqua
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh 11533, Saudi Arabia
- King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia
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Abstract
Nucleic acid aptamers have tremendous potential as molecular recognition elements in biomedical targeting, analytical arrays, and self-signaling sensors. However, practical limitations and inefficiencies in the process of selecting novel aptamers (SELEX) have hampered widespread adoption of aptamer technologies. Many factors have recently contributed to more effective aptamer screening, but no influence has done more to increase the efficiency, scale, and automation of aptamer selection than that of new microfluidic SELEX techniques. This review introduces aptamers as a powerful chemical and biological tool, briefly highlights traditional SELEX techniques and their limitations, covers in detail the recent advancements in microfluidic methods of aptamer selection and characterization, and suggests possible future directions of the field.
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Affiliation(s)
- Sean K Dembowski
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine. Int J Mol Sci 2017; 18:ijms18102142. [PMID: 29036890 PMCID: PMC5666824 DOI: 10.3390/ijms18102142] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Aptamers are short DNA/RNA oligonucleotides capable of binding to target molecules with high affinity and specificity. The process of selecting an aptamer is called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Thanks to the inherit merits, aptamers have been used in a wide range of applications, including disease diagnosis, targeted delivery agents and therapeutic uses. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, few aptamer-based products have already successfully entered into clinical and industrial use. Besides, it is still a challenge to obtain aptamers with high affinity in a more efficient way. Thus, it is important to comprehensively review the current shortage and achievement of aptamer-related technology. In this review, we first present the limitations and notable advances of aptamer selection. Then, we compare the different methods used in the kinetic characterization of aptamers. We also discuss the impetus and developments of the clinical application of aptamers.
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Gopinathan P, Hung LY, Wang CH, Chiang NJ, Wang YC, Shan YS, Lee GB. Automated selection of aptamers against cholangiocarcinoma cells on an integrated microfluidic platform. BIOMICROFLUIDICS 2017; 11:044101. [PMID: 28713479 PMCID: PMC5498186 DOI: 10.1063/1.4991005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
An integrated microfluidic system capable of automatically identifying aptamers specific to cholangiocarcinoma (CCA) cells was developed herein. The developed system was capable of performing cell-based systematic evolution of ligands via an exponential enrichment (Cell-SELEX) process on-chip, and only six rounds of Cell-SELEX were required to identify high specificity aptamers; this represents a significant improvement in speed over conventional SELEX, in which 15-20 rounds are typically required. Using the microfluidic chip developed, three aptamers specific to CCA cells (one for SNU-478 cells and two for HuCCT-1 cells) were successfully screened. This automated system could be modified to uncover aptamer probes against other cancer cells, thereby allowing for earlier diagnosis and consequently a potentially improved prognosis.
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Affiliation(s)
- Priya Gopinathan
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - Lien-Yu Hung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | | | - Yu-Chun Wang
- Institute of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
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13
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Hung LY, Wang CH, Fu CY, Gopinathan P, Lee GB. Microfluidics in the selection of affinity reagents for the detection of cancer: paving a way towards future diagnostics. LAB ON A CHIP 2016; 16:2759-74. [PMID: 27381813 DOI: 10.1039/c6lc00662k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Microfluidic technologies have miniaturized a variety of biomedical applications, and these chip-based systems have several significant advantages over their large-scale counterparts. Recently, this technology has been used for automating labor-intensive and time-consuming screening processes, whereby affinity reagents, including aptamers, peptides, antibodies, polysaccharides, glycoproteins, and a variety of small molecules, are used to probe for molecular biomarkers. When compared to conventional methods, the microfluidic approaches are faster, more compact, require considerably smaller quantities of samples and reagents, and can be automated. Furthermore, they allow for more precise control of reaction conditions (e.g., pH, temperature, and shearing forces) such that more efficient screening can be performed. A variety of affinity reagents for targeting cancer cells or cancer biomarkers are now available and will likely replace conventional antibodies. In this review article, the selection of affinity reagents for cancer cells or cancer biomarkers on microfluidic platforms is reviewed with the aim of highlighting the utility of such approaches in cancer diagnostics.
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MESH Headings
- Animals
- Antibodies, Immobilized/chemistry
- Antibodies, Immobilized/metabolism
- Antibodies, Neoplasm/chemistry
- Antibodies, Neoplasm/metabolism
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cells, Cultured
- Coculture Techniques
- Humans
- Immobilized Nucleic Acids/chemistry
- Immobilized Nucleic Acids/metabolism
- Immobilized Proteins/metabolism
- Lab-On-A-Chip Devices/trends
- Leukocytes/cytology
- Leukocytes/metabolism
- Ligands
- Mice
- Neoplasms/blood
- Neoplasms/diagnosis
- Neoplasms/metabolism
- Neoplasms/pathology
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/metabolism
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Affiliation(s)
- Lien-Yu Hung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
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14
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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: 25] [Impact Index Per Article: 3.1] [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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15
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Hilton JP, Olsen T, Kim J, Zhu J, Nguyen T, Barbu M, Pei R, Stojanovic M, Lin Q. Isolation of thermally sensitive protein-binding oligonucleotides on a microchip. MICROFLUIDICS AND NANOFLUIDICS 2015; 19:795-804. [PMID: 31223297 PMCID: PMC6586242 DOI: 10.1007/s10404-015-1604-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/24/2015] [Indexed: 06/07/2023]
Abstract
This paper presents a microfluidic chip capable of isolating thermally sensitive protein-binding aptamer candidates. The chip makes use of bead-immobilized target molecules and DNA (deoxyribonucleic acid) sequences to enable a simplified chip design, in which affinity selection and PCR (polymerase chain reaction) amplification of target-binding sequences occur in temperature-controlled microchambers. Using pressure-driven flow, buffer containing single-stranded DNA molecules with randomized sequences is cycled through a series of affinity selection and PCR amplification steps on microbeads. Successive introduction of the sample to each chamber effects a process of competition whereby DNA strands with weak binding strength to target molecules are rejected in favor of strongly binding sequences. Using bead-based PCR, the amplification step was miniaturized and integrated with affinity selection, resulting in significant reductions in process time and reagent use. As a demonstration, temperature-dependent selection and amplification of single-stranded oligonucleotides that bind to human Immuno-globulin E (IgE) was performed in 4 h, a 20-fold reduction in process time as compared to conventional methods that would require approximately a week. Fluorescent binding assays then demonstrated that the desired temperature specificity was imparted to the aptamer candidates within just one round of selection, and within two rounds the aptamer candidates exhibited enhanced affinity toward IgE.
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Affiliation(s)
- John P. Hilton
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Timothy Olsen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Mihaela Barbu
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Renjun Pei
- Suzhou Institute of Nano‑Tech and Nano‑Bionics, Chinese Academy of Sciences, Suzhou 215123, Jiangsu, China
| | - Milan Stojanovic
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
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16
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Stoll H, Kiessling H, Stelzle M, Wendel HP, Schütte J, Hagmeyer B, Avci-Adali M. Microfluidic chip system for the selection and enrichment of cell binding aptamers. BIOMICROFLUIDICS 2015; 9:034111. [PMID: 26180568 PMCID: PMC4474950 DOI: 10.1063/1.4922544] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
Aptamers are promising cell targeting ligands for several applications such as for the diagnosis, therapy, and drug delivery. Especially, in the field of regenerative medicine, stem cell specific aptamers have an enormous potential. Using the combinatorial chemistry process SELEX (Systematic Evolution of Ligands by Exponential enrichment), aptamers are selected from a huge oligonucleotide library consisting of approximately 10(15) different oligonucleotides. Here, we developed a microfluidic chip system that can be used for the selection of cell specific aptamers. The major drawbacks of common cell-SELEX methods are the inefficient elimination of the unspecifically bound oligonucleotides from the cell surface and the unspecific binding/uptake of oligonucleotides by dead cells. To overcome these obstacles, a microfluidic device, which enables the simultaneous performance of dielectrophoresis and electrophoresis in the same device, was designed. Using this system, viable cells can be selectively assembled by dielectrophoresis between the electrodes and then incubated with the oligonucleotides. To reduce the rate of unspecifically bound sequences, electrophoretic fields can be applied in order to draw loosely bound oligonucleotides away from the cells. Furthermore, by increasing the flow rate in the chip during the iterative rounds of SELEX, the selection pressure can be improved and aptamers with higher affinities and specificities can be obtained. This new microfluidic device has a tremendous capability to improve the cell-SELEX procedure and to select highly specific aptamers.
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Affiliation(s)
- Heidi Stoll
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen , Calwerstraße 7/1, 72076 Tuebingen, Germany
| | - Heiko Kiessling
- BioMEMS and Sensors Department, Natural and Medical Sciences Institute at the University of Tübingen , Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Martin Stelzle
- BioMEMS and Sensors Department, Natural and Medical Sciences Institute at the University of Tübingen , Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Hans Peter Wendel
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen , Calwerstraße 7/1, 72076 Tuebingen, Germany
| | - Julia Schütte
- BioMEMS and Sensors Department, Natural and Medical Sciences Institute at the University of Tübingen , Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Britta Hagmeyer
- BioMEMS and Sensors Department, Natural and Medical Sciences Institute at the University of Tübingen , Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Meltem Avci-Adali
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen , Calwerstraße 7/1, 72076 Tuebingen, Germany
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17
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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18
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Lin H, Zhang W, Jia S, Guan Z, Yang CJ, Zhu Z. Microfluidic approaches to rapid and efficient aptamer selection. BIOMICROFLUIDICS 2014; 8:041501. [PMID: 25379085 PMCID: PMC4189129 DOI: 10.1063/1.4890542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/07/2014] [Indexed: 05/04/2023]
Abstract
With their advantages as molecular recognition elements, aptamers have been extensively studied and used for bioanalytical and biomedical applications. However, the process of enrichment and screening of aptamers remains a bottleneck for aptamer development. Recently, microfluidic methods have been increasingly used for rapid and efficient aptamer selection, showing their remarkable advantages over conventional methods. This review briefly introduces aptamers and their advantages. The conventional process of generating aptamers is discussed, followed by the analysis of the key obstacles to efficient aptamer selection. Microfluidic methods for highly efficient enrichment and screening of aptamers are reviewed in detail.
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Affiliation(s)
- Hui Lin
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Weiting Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Shasha Jia
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
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19
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Wang Q, Liu W, Xing Y, Yang X, Wang K, Jiang R, Wang P, Zhao Q. Screening of DNA aptamers against myoglobin using a positive and negative selection units integrated microfluidic chip and its biosensing application. Anal Chem 2014; 86:6572-9. [PMID: 24914856 DOI: 10.1021/ac501088q] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An aptamer screening method using a positive and negative selection units integrated microfluidic chip was introduced. Here, myoglobin (Myo), one of the early markers to increase after acute myocardial infarction, was used as the model. After 7-round selection, the aptamers, which exhibited dissociation constants (K(d)) in the nanomolar range (from 4.93 to 6.38 nM), were successfully obtained using a positive and negative selection units integrated microfluidic chip. The aptamer with the highest affinity (K(d) = 4.93 nM) was then used for the fabrication of a label-free supersandwich electrochemical biosensor for Myo detection based on target-induced aptamer displacement. The detection limit of this aptamer-based electrochemical biosensor was 10 pM, which was significantly lower than that of those previous antibody-based biosensors for Myo detection. This work may not only develop a strategy for screening aptamer but also offer promising alternatives to the traditional analytical and immunological methods for Myo detection.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha, Hunan 410082, China
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20
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Ren S, Jiang Y, Yoon HR, Hong SW, Shin D, Lee S, Lee DK, Jin MM, Min IM, Kim S. Label-free Detection of the Transcription Initiation Factor Assembly and Specific Inhibition by Aptamers. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.5.1279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. Anal Bioanal Chem 2014; 406:2727-32. [PMID: 24553662 PMCID: PMC3975076 DOI: 10.1007/s00216-014-7661-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/17/2014] [Accepted: 01/23/2014] [Indexed: 01/24/2023]
Abstract
We describe a versatile 96-well microplate-based device that utilizes affinity microcolumn chromatography to complement downstream plate-based processing in aptamer selections. This device is reconfigurable and is able to operate in serial and/or parallel mode with up to 96 microcolumns. We demonstrate the utility of this device by simultaneously performing characterizations of target binding using five RNA aptamers and a random library. This was accomplished through 96 total selection tests. Three sets of selections tested the effects of target concentration on aptamer binding compared to the random RNA library using aptamers to the proteins green fluorescent protein (GFP), human heat shock factor 1 (hHSF1), and negative elongation factor E (NELF-E). For all three targets, we found significant effects consistent with steric hindrance with optimum enrichments at predictable target concentrations. In a fourth selection set, we tested the partitioning efficiency and binding specificity of our three proteins’ aptamers, as well as two suspected background binding sequences, to eight targets running serially. The targets included an empty microcolumn, three affinity resins, three specific proteins, and a non-specific protein control. The aptamers showed significant enrichments only on their intended targets. Specifically, the hHSF1 and NELF-E aptamers enriched over 200-fold on their protein targets, and the GFP aptamer enriched 750-fold. By utilizing our device’s plate-based format with other complementary plate-based systems for all downstream biochemical processes and analysis, high-throughput selections, characterizations, and optimization were performed to significantly reduce the time and cost for completing large-scale aptamer selections. Schematic breakdown of a microplate-based enrichment device for the selection of aptamers (MEDUSA), which can be customized and assembled in both parallel and serial configurations. Up to 96 selections can be performed simultaneously. ![]()
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Lee S, Kang J, Ren S, Laurell T, Kim S, Jeong OC. A cross-contamination-free SELEX platform for a multi-target selection strategy. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7106-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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23
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Weng CH, Huang CJ, Lee GB. Screening of aptamers on microfluidic systems for clinical applications. SENSORS 2012; 12:9514-29. [PMID: 23012556 PMCID: PMC3444114 DOI: 10.3390/s120709514] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 12/20/2022]
Abstract
The use of microfluidic systems for screening of aptamers and their biomedical applications are reviewed in this paper. Aptamers with different nucleic acid sequences have been extensively studied and the results demonstrated a strong binding affinity to target molecules such that they can be used as promising candidate biomarkers for diagnosis and therapeutics. Recently, the aptamer screening protocol has been conducted with microfluidic-based devices. Furthermore, aptamer affinity screening by a microfluidic-based method has demonstrated remarkable advantages over competing traditional methods. In this paper, we first reviewed microfluidic systems which demonstrated efficient and rapid screening of a specific aptamer. Then, the clinical applications of screened aptamers, also performed by microfluidic systems, are further reviewed. These automated microfluidic systems can provide advantages over their conventional counterparts including more compactness, faster analysis, less sample/reagent consumption and automation. An aptamer-based compact microfluidic system for diagnosis may even lead to a point-of-care device. The use of microfluidic systems for aptamer screening and diagnosis is expected to continue growing in the near future and may make a substantial impact on biomedical applications.
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Affiliation(s)
- Chen-Hsun Weng
- Department of Microbiology and Immunology, National Cheng Kung University, Tainan 70101, Taiwan; E-Mail:
| | - Chao-Jyun Huang
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; E-Mail:
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Author to whom correspondence should be addressed; ; Tel: +886-3-571-5131 (ext. 33765); Fax: +886-3-572-2840
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Ahn JY, Lee S, Jo M, Kang J, Kim E, Jeong OC, Laurell T, Kim S. Sol-gel derived nanoporous compositions for entrapping small molecules and their outlook toward aptamer screening. Anal Chem 2012; 84:2647-53. [PMID: 22283623 DOI: 10.1021/ac202559w] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This paper reports for the first time the application of sol-gel microarrays for immobilizing nonsoluble small chemicals (Bisphenol-A; BPA). Also, known problems of sol-gel adhesion to conventional microtiter well plate substrates are circumvented by anchoring the sol-gel microspots to a porous silion surface so-called, PS-SG chips. We confirmed low molecular weight chemical immobilization inside a sol-gel network using fluorescein. BPA and the BPA specific aptamer were utilized as a model pair to verify the affinity specific interaction in the PS-SG selection system. The aptamer interacted specifically with BPA in the sol-gel spots, as shown in microarrays forming the letters "L", "U", "N", and "D". Moreover, the bound aptamer was released by heat, recovered, and verified by gel electrophoresis. The developed PS-SG chip platform will be used for screening aptamers against numerous small molecules such as toxins, metabolites, or pesticide residues.
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Affiliation(s)
- Ji-Young Ahn
- Department of Biomedical Engineering, Dongguk University, Seoul, Korea
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25
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Lee JW, Cho EJ. The Concentration-Dependent Distribution of Tris(4,7'-diphenyl-1,10'-phenanthroline) Ruthenium (II) within Sol-Gel-Derived Thin Films. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.8.2765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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