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Nuntawong P, Senoo A, Tayama Y, Caaveiro JMM, Morimoto S, Sakamoto S. An aptamer-based fluorometric method for the rapid berberine detection in Kampo medicines. Anal Chim Acta 2024; 1318:342930. [PMID: 39067935 DOI: 10.1016/j.aca.2024.342930] [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: 02/01/2024] [Revised: 06/08/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Berberine (BBR), a key component in Kampo medicine, is a cationic benzylisoquinoline alkaloid whose detection plays a critical role in the quality control of these traditional remedies. Traditional methods for detecting BBR often involve complex procedures, which can be time-consuming and costly. To address this challenge, our study focuses on developing a simpler, faster, and more efficient detection method for BBR in Kampo medicine formulations. RESULTS We successfully developed a rapid fluorometric detection method for BBR using colloidal gold nanoparticle-based systematic evolution of ligands by exponential enrichment (GOLD-SELEX). Initially, specific single-stranded DNA (ssDNA) sequences were selected for their ability to enhance BBR's fluorescence intensity. The optimal ssDNA sequence, identified as BBR38, was further truncated to produce BBR38S, a stem-loop ssDNA that improved fluorescence upon interaction with BBR. To further enhance the fluorescence, the BBR38S aptamer underwent additional modifications, including stem truncation and nucleotide mutations, resulting in the higher fluorescence variant BBR38S-3 A10C. The final product, TetBBR38S, a tetramer version of BBR38S-3 A10C, exhibited a linear detection range of 0.780-50.0 μg mL-1 and a limit of detection of 0.369 μg mL-1. The assay demonstrated sufficient selectivity and was successfully applied to analyze 128 different Kampo medicine formulations, accurately detecting BBR content with high precision. SIGNIFICANCE This study represents an advancement in Kampo medicine research, marking the first successful application of an aptamer-based approach for BBR detection in complex matrices. The developed method is not only simple and rapid (with a detection time of 5 min) but also cost-effective, which is crucial for widespread application.
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Affiliation(s)
- Poomraphie Nuntawong
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akinobu Senoo
- Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yorie Tayama
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Jose M M Caaveiro
- Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Satoshi Morimoto
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Seiichi Sakamoto
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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Dong H, Wang H, Guo Z, Huang J, Zhang P, Guo Y, Sun X. Combination of Capture-SELEX and Post-SELEX for procymidone-specific aptamer selection and broad-specificity aptamer discovery, and development of aptamer-based lateral flow assay. Anal Chim Acta 2024; 1318:342922. [PMID: 39067914 DOI: 10.1016/j.aca.2024.342922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Due to its wide application, procymidone has become one of the pesticides with high detection rates in supervision and sampling. Therefore, it is necessary to establish a rapid and efficient method for the detection of procymidone. However, an important bottleneck restricting the development of rapid detection methods of procymidone is that its specific recognition elements are rarely reported. In this work, Capture-SELEX and post-SELEX were used in aptamer screening, and the obtained aptamers were used to construct an aptamer-based lateral flow assay (LFA). RESULTS Firstly, a specific aptamer Seq15 was obtained for procymidone by Capture-SELEX, and its dissociation constant (Kd) was 24.22 nM. Secondly, post-SELEX was used to analyze and modify Seq15 to improve its performance, and the Kd of the truncated sequence Seq15-2 was 21.28 nM. In addition to this, the broad-specificity aptamer Seq17-1 was obtained via post-SELEX. Seq17-1 could broadly recognize dicarboximide fungicides (procymidone, iprodione, chlozolinate, dimethachlon and vinclozolin) and their metabolic derivative (3,5-dichloroaniline). Finally, the specific aptamer-based LFA of procymidone was constructed, and the limit of detection (LOD) was 0.79 ng/mL. Meanwhile, the LODs of dicarboximide fungicides and their metabolic derivative were 0.62, 0.64, 0.71, 0.69, 0.64 and 0.66 ng/mL, respectively. The above LFAs were highly specific and stable, and had been successfully used for the detection of vegetable samples. SIGNIFICANCE Under the combination of Capture-SELEX and Post-SELEX, this study not only provides specific recognition elements for rapid detection of procymidone, but also provides new ideas for the discovery of broad-specificity aptamers. Combining broad-specificity primary detection and single-specificity quantification, a composite aptamer-based LFA detection platform has been developed, which significantly improves detection efficiency.
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Affiliation(s)
- Haowei Dong
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Zhen Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China
| | - Jingcheng Huang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China
| | - Pengwei Zhang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China.
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong 255049, China.
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3
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Zhou X, Cao Y, Huang X, Qiu S, Xiang X, Niu H, Chen L, Wang S, Lin Z, Zhang S. Screening and Application of DNA Aptamers for Heparin-Binding Protein. Molecules 2024; 29:1717. [PMID: 38675537 PMCID: PMC11051826 DOI: 10.3390/molecules29081717] [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: 03/07/2024] [Revised: 04/01/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Rapid detection of heparin-binding protein (HBP) is essential for timely intervention in sepsis cases. Current detection techniques are usually antibody-based immunological methods, which have certain problems, such as complexity and slow detection, and fall short in meeting the urgency of clinical needs. The application of an aptamer can address these concerns well. In this study, HBP-specific DNA aptamers were screened first. Among which, Apt-01, Apt-02, and Apt-13 had a high affinity for HBP, exhibiting impressive KD values of 3.42, 1.44, and 1.04 nmol/L, respectively. Then, the aptamer of HBP and its partially complementary primer probe were combined to form double-stranded DNA (dsDNA) and synthesize a circular DNA template. The template is complementary to the primer probe, but due to the presence of dsDNA, ExoIII cleaves C2-13 as an RCA primer probe, rendering the template unable to recognize the primer probe and preventing the RCA reaction from proceeding. When the target is present, it competes with the adapter for recognition and releases C2-13, exposing its 3' end. After initiating the RCA at room temperature and reacting with SYBR GreenII at 37 °C for 20 min, fluorescence changes can be observed and quantitatively analyzed at a 530 nm wavelength, achieving quantitative biological analysis. Apt-01 was used to develop a fluorescent biosensor for HBP detection, which exhibited a good linear range (0.01 nmol/L to 10 nmol/L) and detection limit (0.0056 nmol/L). This advancement holds the potential to lay a solid groundwork for pioneering sensitive and specific methods for HBP detection and to significantly enhance the diagnostic processes for sepsis.
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Affiliation(s)
- Xi Zhou
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Yingying Cao
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Xiaocui Huang
- Department of Science Research and Training, Fujian Institute of Education, Fuzhou 350001, China;
| | - Shuqian Qiu
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Xinran Xiang
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Huimin Niu
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Li Chen
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Shuiliang Wang
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
| | - Zhenyu Lin
- MOE Key Laboratory of Analysis and Detection for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Shenghang Zhang
- Fujian Key Laboratory of Aptamers Technology, Fuzhou General Teaching Hospital (the 900th Hospital), Fujian University of Traditional Chinese Medicine, Fuzhou 350025, China; (X.Z.); (Y.C.); (S.Q.); (X.X.); (H.N.); (L.C.); (S.W.)
- Department of Clinical Laboratory Medicine, Fuzhou General Clinical Medical School, Fujian Medical University, Fuzhou 350025, China
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Manea I, Casian M, Hosu-Stancioiu O, de-Los-Santos-Álvarez N, Lobo-Castañón MJ, Cristea C. A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules. Anal Chim Acta 2024; 1297:342325. [PMID: 38438246 DOI: 10.1016/j.aca.2024.342325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/06/2024]
Abstract
This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.
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Affiliation(s)
- Ioana Manea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania
| | - Magdolna Casian
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania; Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain
| | - Oana Hosu-Stancioiu
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
| | - Noemí de-Los-Santos-Álvarez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - Cecilia Cristea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
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Liu S, Zhao F, Xu K, Cao M, Sohail M, Li B, Zhang X. Harnessing aptamers for the biosensing of cell surface glycans - A review. Anal Chim Acta 2024; 1288:342044. [PMID: 38220315 DOI: 10.1016/j.aca.2023.342044] [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: 09/15/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/16/2024]
Abstract
Cell surface glycans (CSGs) are essential for cell recognition, adhesion, and invasion, and they also serve as disease biomarkers. Traditional CSG recognition using lectins has limitations such as limited specificity, low stability, high cytotoxicity, and multivalent binding. Aptamers, known for their specific binding capacity to target molecules, are increasingly being employed in the biosensing of CSGs. Aptamers offer the advantage of high flexibility, small size, straightforward modification, and monovalent recognition, enabling their integration into the profiling of CSGs on living cells. In this review, we summarize representative examples of aptamer-based CSG biosensing and identify two strategies for harnessing aptamers in CSG detection: direct recognition based on aptamer-CSG binding and indirect recognition through protein localization. These strategies enable the generation of diverse signals including fluorescence, electrochemical, photoacoustic, and electrochemiluminescence signals for CSG detection. The advantages, challenges, and future perspectives of using aptamers for CSG biosensing are also discussed.
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Affiliation(s)
- Sirui Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Ke Xu
- Department of Cardiology, Nanjing Yuhua Hospital, Nanjing, 210012, China
| | - Min Cao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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Gupta A, Mathew R, Anand A, Bhardwaj T, Singh A, Singh K, Kumar A, Mishra PR, Sharma TK. A DNA aptamer-based assay for the detection of soluble ST2, a prognostic biomarker for monitoring heart failure. Int J Biol Macromol 2024; 256:128295. [PMID: 37992929 DOI: 10.1016/j.ijbiomac.2023.128295] [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: 06/30/2023] [Revised: 11/18/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
Heart failure (HF) is emerging as a leading cause of death worldwide. Estimation of BNP levels is a routine diagnosis in these patients. However, in patients having high body-mass index (BMI), renal disease or in geriatric patients, BNP level is reported to be noisy and leads to incongruous conclusion. Thus, for better risk stratification among heart failure patients, it is imperative to look for a superior biomarker. In recent times, sST2 has shown promise as a biomarker. Identifying such biomarkers in peripheral blood of HF patients, need an affine and selective molecular recognition element. Thus, in the current study an aptamer (sS9_P) against sST2 was identified from an aptamer library. Systematic Evolution of Ligands through Exponential enrichment (SELEX) derived aptamer evinced role of its primer binding domains in maintaining its selectivity. This aptamer candidate demonstrated dissociation constant (Kd) in low nanomolar range, and the Limit of Detection (LOD) was ~4 ng. Circular dichroism confirms the formation of complex stem-loop like structure. The well characterized sS9_P aptamer was used in an Aptamer Linked Immobilized Sorbent Assay (ALISA) to detect sST2 level in patients' serum (n = 99). Aptamer sS9_P has shown significant discrimination to differentiate HF patients and healthy volunteers with a reasonable specificity (~83 %) with a modest sensitivity of ~64 %. While sST-2 antibody has shown poor specificity of ~44% but good sensitivity (~87%). The insight obtained from this study indicates that a combination of aptamer and antibody-based assay can be used to design a point-of-care assay for the rapid detection of HF patients in emergency settings.
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Affiliation(s)
- Ankit Gupta
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Roshan Mathew
- All India Institute of Medical Sciences (AIIMS), New Delhi, Delhi 110029, India
| | - Anjali Anand
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Tanu Bhardwaj
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India; Department of Medical Biotechnology, Gujarat Biotechnology University, GIFT-City, Gandhinagar, Gujarat 382355, India
| | - Aakriti Singh
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | - Krishna Singh
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Madhya Pradesh 453552, India
| | | | - Tarun Kumar Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India; Department of Medical Biotechnology, Gujarat Biotechnology University, GIFT-City, Gandhinagar, Gujarat 382355, India.
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Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
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Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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8
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Ding Y, Liu J. Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers. Anal Chem 2023; 95:14651-14658. [PMID: 37721984 DOI: 10.1021/acs.analchem.3c02477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Qin N, Liu J, Li F, Liu J. Recent Advances in Aptasensors for Rapid Pesticide Residues Detection. Crit Rev Anal Chem 2023:1-22. [PMID: 37708008 DOI: 10.1080/10408347.2023.2257795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Pesticides are applied widely to increase agricultural output and quality, however, this practice results in residual issues that not only harm the environment but also put people and animals' lives and health at risk. As a result, it is critical to find pesticide residues in a variety of sources, including crops, water supplies, and soil. Aptamers are more flexible in their synthesis and modification, have a high level of specificity, are inexpensive, and have good stability compared to conventional detection methods. They have therefore attracted a lot of interest in the industry. This study reviews the most recent aptasensor advancements in the detection of pesticide residues. Firstly, aptamers specifically binding to many pesticides are summarized. Secondly, the combination of aptasensors with colorimetric, fluorescent, surface enhanced Raman spectroscopy (SERS), resonance Light Scattering (RLS), chemiluminescence (CL), electrochemical, and electrochemiluminescence (ECL) technologies are systematically introduced, and their advantages and disadvantages are expounded. Importantly, the aptasensors for the detection of various pesticides (organochlorine, organophosphorus, neonicotinoids, carbamates, and pyrethroids) that have been developed so far are systematically analyzed and discussed. Finally, the furture prospects and challenges of the aptasensors are highlighted. It is expected to offer suggestions for the later creation of novel, highly effective and sensitive aptasensors for the detection of pesticide residues.
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Affiliation(s)
- Na Qin
- College of Horticulture and Landscape Architecture, Tianjin Agricultural University, Tianjin, China
| | - Jinfeng Liu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Fengyun Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jingbo Liu
- College of Horticulture and Landscape Architecture, Tianjin Agricultural University, Tianjin, China
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Lu L, Yu R, Zhang L. AFB1 colorimetric aptamer sensor for the detection of AFB1 in ten different kinds of miscellaneous beans based on gold nanoparticles and smartphone imaging. Food Chem 2023; 421:136205. [PMID: 37094407 DOI: 10.1016/j.foodchem.2023.136205] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
A simple, rapid, low-cost, sensitive, intuitive, visual, label-free, colorimetric smartphone-assisted assay was developed for the measurement of aflatoxin B1 in miscellaneous beans. Ten different kinds of miscellaneous beans were treated and measured by modified QuEChERS(Quick、Easy、Cheap、Effective、Rugged、Safe) method with aflatoxin B1 nucleic acid aptamer as a recognition element and gold nanoparticles as indicators. Several factors influencing its sensitivity were investigated, including consumes and NaCl concentrations, as well as incubation time and specificity. The results showed a good linear relationship between concentrations of 0.2-8.0 ng/g under optimal conditions. With a detection limit of 0.08 ng/g, the linear regression equation was Y = 0.024X + 0.4615 (R = 0.9989). Sensor specificity is good. The content of aflatoxin B1 in bean samples was determined successfully. The recovery of aflatoxin B1 ranged from 87.18% to 110.24%. The whole thing took 15 min. This smartphone-assisted colorimetric aptamer sensor can be used to detect aflatoxin B1 in beans.
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Affiliation(s)
- Lifeng Lu
- College of Food Science, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PR China
| | - Runzhong Yu
- College of Information and Electrical Engineering, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PR China
| | - Liyuan Zhang
- College of Food Science, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing 163319, PR China; Chinese National Engineering Research Center, Daqing 163319, PR China; Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang province, Daqing 163319, PR China.
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11
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Hu Z, Li Y, Figueroa-Miranda G, Musal S, Li H, Martínez-Roque MA, Hu Q, Feng L, Mayer D, Offenhäusser A. Aptamer based biosensor platforms for neurotransmitters analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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12
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Chauhan NK, Anand A, Sharma A, Dhiman K, Gosain TP, Singh P, Singh P, Khan E, Chattopadhyay G, Kumar A, Sharma D, Ashish, Sharma TK, Singh R. Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein. Microbiol Spectr 2023; 11:e0197322. [PMID: 36507689 PMCID: PMC9927256 DOI: 10.1128/spectrum.01973-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.
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Affiliation(s)
- Neeraj Kumar Chauhan
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Anjali Anand
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Arun Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Kanika Dhiman
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Prashant Singh
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Padam Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Eshan Khan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | - Deepak Sharma
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ashish
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
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Chauhan P, Datta I, Dhiman A, Shankar U, Kumar A, Vashist A, Sharma TK, Tyagi JS. DNA Aptamer Targets Mycobacterium tuberculosis DevR/DosR Response Regulator Function by Inhibiting Its Dimerization and DNA Binding Activity. ACS Infect Dis 2022; 8:2540-2551. [PMID: 36332135 DOI: 10.1021/acsinfecdis.2c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tuberculosis is recognized as one of the major public health threats worldwide. The DevR-DevS (DosR/DosS) two-component system is considered a novel drug target in Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, owing to its central role in bacterial adaptation and long-term persistence. An increase in DevR levels and the decreased permeability of the mycobacterial cell wall during hypoxia-associated dormancy pose formidable challenges to the development of anti-DevR compounds. Using an in vitro evolution approach of Systematic Evolution of Ligands by EXponential enrichment (SELEX), we developed a panel of single-stranded DNA aptamers that interacted with Mtb DevR protein in solid-phase binding assays. The best-performing aptamer, APT-6, forms a G-quadruplex structure and inhibits DevR-dependent transcription in Mycobacterium smegmatis. Mechanistic studies indicate that APT-6 functions by inhibiting the dimerization and DNA binding activity of DevR protein. In silico studies reveal that APT-6 interacts majorly with C-terminal domain residues that participate in DNA binding and formation of active dimer species of DevR. To the best of our knowledge, this is the first report of a DNA aptamer that inhibits the function of a cytosolic bacterial response regulator. By inhibiting the dimerization of DevR, APT-6 targets an essential step in the DevR activation mechanism, and therefore, it has the potential to universally block the expression of DevR-regulated genes for intercepting dormancy pathways in mycobacteria. These findings also pave the way for exploring aptamer-based approaches to design and develop potent inhibitors against intracellular proteins of various bacterial pathogens of global concern.
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Affiliation(s)
- Priyanka Chauhan
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Ishara Datta
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore453552, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore453552, India
| | - Atul Vashist
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi110029, India
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14
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Gholikhani T, Kumar S, Valizadeh H, Mahdinloo S, Adibkia K, Zakeri-Milani P, Barzegar-Jalali M, Jimenez B. Advances in Aptamers-Based Applications in Breast Cancer: Drug Delivery, Therapeutics, and Diagnostics. Int J Mol Sci 2022; 23:ijms232214475. [PMID: 36430951 PMCID: PMC9695968 DOI: 10.3390/ijms232214475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Aptamers are synthetic single-stranded oligonucleotides (such as RNA and DNA) evolved in vitro using Systematic Evolution of Ligands through Exponential enrichment (SELEX) techniques. Aptamers are evolved to have high affinity and specificity to targets; hence, they have a great potential for use in therapeutics as delivery agents and/or in treatment strategies. Aptamers can be chemically synthesized and modified in a cost-effective manner and are easy to hybridize to a variety of nano-particles and other agents which has paved a way for targeted therapy and diagnostics applications such as in breast tumors. In this review, we systematically explain different aptamer adoption approaches to therapeutic or diagnostic uses when addressing breast tumors. We summarize the current therapeutic techniques to address breast tumors including aptamer-base approaches. We discuss the next aptamer-based therapeutic and diagnostic approaches targeting breast tumors. Finally, we provide a perspective on the future of aptamer-based sensors for breast therapeutics and diagnostics. In this section, the therapeutic applications of aptamers will be discussed for the targeting therapy of breast cancer.
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Affiliation(s)
- Tooba Gholikhani
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
- NanoRa Pharmaceuticals Ltd., Tabriz 5166-15731, Iran
| | - Shalen Kumar
- IQ Science Limited, Wellington 5010, New Zealand
| | - Hadi Valizadeh
- Drug Applied Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Somayeh Mahdinloo
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Khosro Adibkia
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Parvin Zakeri-Milani
- Liver and Gastrointestinal Diseases Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Mohammad Barzegar-Jalali
- Pharmaceutical Analysis Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Balam Jimenez
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Correspondence:
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15
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Sanford AA, Manuel BA, Romero-Reyes MA, Heemstra JM. Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids. Chem Sci 2022; 13:7670-7684. [PMID: 35865900 PMCID: PMC9258336 DOI: 10.1039/d2sc00117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Brea A Manuel
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Misael A Romero-Reyes
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Chemistry, Hanover College Hanover Indiana 47243 USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta GA 30332 USA
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Liu R, Zhang F, Sang Y, Liu M, Shi M, Wang X. Selection and Characterization of DNA Aptamers for Constructing Aptamer-AuNPs Colorimetric Method for Detection of AFM1. Foods 2022; 11:foods11121802. [PMID: 35742000 PMCID: PMC9222373 DOI: 10.3390/foods11121802] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Aflatoxin M1 (AFM1), one of the most toxic mycotoxins, is a feed and food contaminant of global concern. To isolate the ssDNA aptamer of AFM1, synthesized magnetic graphene oxide nanomaterials, 12 rounds of subtractive systematic evolution of ligands by exponential enrichment (SELEX) selection were carried out. As a result, 24 candidate aptamers were selected, and their sequence similarity exceeded 97%. Their binding affinity and specificity were further examined by fluorescence and biofilm interferometry (BLI) methods. One aptamer (Apt-5) against AFM1 with a high affinity and specificity was isolated and demonstrated to be the optimal aptamer, whose dissociation constant reached the nanomolar level, Kd = 8.12 ± 1.51 nM. Additionally, molecular docking studies were used to predict the possible binding sites and mechanisms of the two. Based on Apt-5, an unlabeled aptamer-AuNPs colorimetric method was established to detect AFM1 in milk with a linear range of 0.078–10 ng/mL, and the actual detection limit was 0.078 ng/mL. These results demonstrated that this detection technique could be useful for the quantitative determination of AFM1 in milk and dairy products.
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17
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Li T, Wang J, Zhu L, Li C, Chang Q, Xu W. Advanced screening and tailoring strategies of pesticide aptamer for constructing biosensor. Crit Rev Food Sci Nutr 2022; 63:10974-10994. [PMID: 35699641 DOI: 10.1080/10408398.2022.2086210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rapid development of aptamers has helped address the challenges presented by the wide existed pesticides contaminations. Screening of aptamers with excellent performance is a prerequisite for successfully constructing biosensors, while further tailoring of aptamers with enhanced activity greatly improved the assay performance. Firstly, this paper reviewed the advanced screening strategies for pesticides aptamers, including immobilization screening that preserves the native structures of targets, non-immobilized screening based on nanomaterials, capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX), virtual screening in silico, high-throughput selection, and rational secondary library generation methods, which contributed significantly to improve the success rate of screening, reduce the screening time, and ensure aptamer binding affinity. Secondly, the precise tailoring strategies for pesticides aptamers were modularly elaborated, containing deletion, splitting, elongation, and fusion, which provided various advantages like cost-efficiency, enhanced binding affinity, and new derived functional motifs. Thirdly, the developed aptamer-based biosensors (aptasensors) for pesticide detection were systematically reviewed according to the different signal output modes. Finally, the challenges and future perspectives of pesticide detection are discussed comprehensively.
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Affiliation(s)
- Tianshun Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jia Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Chenwei Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qiaoying Chang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
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18
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Tan X, Yu C, Tang J, Wu W, Yang Q, Hou X. Progress in Nanomaterials-Based Enzyme and Aptamer Biosensor for the Detection of Organophosphorus Pesticides. Crit Rev Anal Chem 2022; 54:247-268. [PMID: 35549956 DOI: 10.1080/10408347.2022.2072678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the improvement of people's safety awareness, the requirement of pesticide detection is gradually increasing, and many new detection methods toward Organophosphorus pesticide (OPs) has been further developed and applied. Nanomaterials-based biosensors have played an important role in the trace detection of OPs. This article mainly introduces the detection principle of enzymes and aptamers as the identification element of biosensors. Various nanomaterials (i.e., metals and metal oxides, carbon nanotubes, graphene and graphene oxide, quantum dots, metal organic frameworks, molecular imprinted polymers, etc.) possess their unique properties and play different roles in the enzyme and aptamer-based biosensors toward OPs: (a) to produce the optical or electrochemical signal; (b) as a carrier to load the enzyme or aptamer; (c) to enhance the signal response. Besides, the intelligent portable devices provide the possibility to realize the onsite and real-time detection. The limitations of some nanomaterials and the future development are discussed. Finally, the future of enzyme and aptamer-based biosensors has prospected.
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Affiliation(s)
- Xin Tan
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Chundi Yu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Juan Tang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Xiudan Hou
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, China
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Liu R, Zhang F, Sang Y, Katouzian I, Jafari SM, Wang X, Li W, Wang J, Mohammadi Z. Screening, identification, and application of nucleic acid aptamers applied in food safety biosensing. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Parihar A, Singhal A, Kumar N, Khan R, Khan MA, Srivastava AK. Next-Generation Intelligent MXene-Based Electrochemical Aptasensors for Point-of-Care Cancer Diagnostics. NANO-MICRO LETTERS 2022; 14:100. [PMID: 35403935 PMCID: PMC8995416 DOI: 10.1007/s40820-022-00845-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/11/2022] [Indexed: 02/08/2023]
Abstract
Delayed diagnosis of cancer using conventional diagnostic modalities needs to be addressed to reduce the mortality rate of cancer. Recently, 2D nanomaterial-enabled advanced biosensors have shown potential towards the early diagnosis of cancer. The high surface area, surface functional groups availability, and excellent electrical conductivity of MXene make it the 2D material of choice for the fabrication of advanced electrochemical biosensors for disease diagnostics. MXene-enabled electrochemical aptasensors have shown great promise for the detection of cancer biomarkers with a femtomolar limit of detection. Additionally, the stability, ease of synthesis, good reproducibility, and high specificity offered by MXene-enabled aptasensors hold promise to be the mainstream diagnostic approach. In this review, the design and fabrication of MXene-based electrochemical aptasensors for the detection of cancer biomarkers have been discussed. Besides, various synthetic processes and useful properties of MXenes which can be tuned and optimized easily and efficiently to fabricate sensitive biosensors have been elucidated. Further, futuristic sensing applications along with challenges will be deliberated herein.
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Affiliation(s)
- Arpana Parihar
- grid.465028.d0000 0000 9013 9057Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026 MP India
| | - Ayushi Singhal
- grid.465028.d0000 0000 9013 9057Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026 MP India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Neeraj Kumar
- grid.465028.d0000 0000 9013 9057Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026 MP India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Raju Khan
- grid.465028.d0000 0000 9013 9057Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026 MP India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Mohd. Akram Khan
- grid.465028.d0000 0000 9013 9057Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026 MP India
| | - Avanish K. Srivastava
- grid.465028.d0000 0000 9013 9057Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal, 462026 MP India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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21
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A Novel SELEX Based on Immobilizing Libraries Enables Screening of Saxitoxin Aptamers for BLI Aptasensor Applications. Toxins (Basel) 2022; 14:toxins14030228. [PMID: 35324725 PMCID: PMC8955768 DOI: 10.3390/toxins14030228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 12/20/2022] Open
Abstract
Saxitoxin (STX) is one of the potent marine biotoxins that has high rate of lethality. However, there are no effective treatments at present, and the existing detection methods need to be further explored because of ethical problems or technical limitations. In this work, oligonucleotide aptamers toward STX were screened based on immobilizing libraries on Immobilized Metal-Chelate (IMC), such as Ni-NTA Sepharose, and the IMC-SELEX was conducted by the G-quadruplex library and the random library, respectively. Aptamer 45e (from the G-quadruplex library) and aptamer 75a were obtained after optimization, and aptamer 45e turned out to have a higher affinity toward STX. Furthermore, it was found that the hydrogen bonding and the van der Waals forces (VDW) played major roles in the high efficiency and specificity between STX and 45e by means of molecular docking and dynamics simulation. Based on this, aptamer 45e-1 with the Kd value of 19 nM was obtained by further optimization, which was then used to construct a simple, label-free and real-time optical BLI aptasensor for the detection of STX. This aptasensor showed good reproducibility and stability. In summary, with the advantages of screening aptamers of high efficiency and specificity toward the targets, the proposed IMC-SELEX provides a promising screening strategy for discovering aptamers, which could be used as the potential molecular recognition elements in the fields of biomedicine, food safety and environmental monitoring.
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22
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Wang J, Zhu L, Li T, Li X, Huang K, Xu W. Multiple functionalities of functional nucleic acids for developing high-performance lateral flow assays. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Ramana LN, Mathapati SS, Salvi N, Khadilkar MV, Malhotra A, Santra V, Sharma TK. A paper microfluidic device based colorimetric sensor for the detection and discrimination of elapid versus viper envenomation. Analyst 2022; 147:685-694. [PMID: 35072182 DOI: 10.1039/d1an01698a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Snake bites are a neglected tropical disease, causing mortality and severe damage to various vital organs like the nervous system, kidneys and heart. There is increasing interest in designing new antivenom treatments that are more specific to particular groups (either taxonomic or regional) of species, given the increasing evidence that current polyvalent Indian antivenom is ineffective in many situations. Under these circumstances, being able to detect the species, or a group of species, responsible for the envenomation becomes important. Unfortunately, no such diagnostic tool is available in the Indian market. Such a tool will need to be rapid, sensitive and affordable. To address this need, we have combined the power of nanotechnology and paper microfluidics and herein report a device that has the ability to detect and differentiate viper venom from elapid and scorpion venom. In principle, this assay is based on the release of the dye from the stimuli-responsive glutaraldehyde cross-linked methylene blue-loaded gelatin (GMG) nanoparticles in the presence of snake venom metalloproteases and serine proteases. The developed equipment-free assay can detect and discriminate viper venom from that of elapids and scorpions. The low-end detection limit of the sensor is ∼3.0 ng for the saw-scaled viper Echis carinatus, while the same for Russell's viper Daboia russelii is ∼6.0 ng. The performance of the sensor remains unaltered for different batches of GMG nanoparticles. Altogether, this finding establishes the role of nanotechnology and paper microfluidics in the rapid and accurate detection of viper venom.
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Affiliation(s)
- Lakshmi Narashimhan Ramana
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India.
| | - Santosh S Mathapati
- Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | - Nitin Salvi
- Premium Serums and Vaccines Pvt. Ltd, Maharashtra, 410504, India
| | - M V Khadilkar
- Premium Serums and Vaccines Pvt. Ltd, Maharashtra, 410504, India
| | - Anita Malhotra
- School of Natural sciences, College of Environment sciences and Engineering, Bangor University, Bangor LL57 2UW, UK
| | - Vishal Santra
- Society for Nature Conservation, Research and Community Engagement (CONCERN), Nalikul, Hooghly, 712407, West Bengal, India
- Captive and Field Herpetology, 13 Hirfron, Anglesey, LL65 1YU, Wales, UK
| | - Tarun Kumar Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India.
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24
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Xie M, Zhao F, Zhang Y, Xiong Y, Han S. Recent advances in aptamer-based optical and electrochemical biosensors for detection of pesticides and veterinary drugs. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108399] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Das S, Jain S, Ilyas M, Anand A, Kumar S, Sharma N, Singh K, Mahlawat R, Sharma TK, Atmakuri K. Development of DNA Aptamers to Visualize Release of Mycobacterial Membrane-Derived Extracellular Vesicles in Infected Macrophages. Pharmaceuticals (Basel) 2021; 15:ph15010045. [PMID: 35056102 PMCID: PMC8779091 DOI: 10.3390/ph15010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/08/2021] [Accepted: 12/19/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) have emerged into a novel vaccine platform, a biomarker and a nano-carrier for approved drugs. Their accurate detection and visualization are central to their utility in varied biomedical fields. Owing to the limitations of fluorescent dyes and antibodies, here, we describe DNA aptamer as a promising tool for visualizing mycobacterial EVs in vitro. Employing SELEX from a large DNA aptamer library, we identified a best-performing aptamer that is highly specific and binds at nanomolar affinity to EVs derived from three diverse mycobacterial strains (pathogenic, attenuated and avirulent). Confocal microscopy revealed that this aptamer was not only bound to in vitro-enriched mycobacterial EVs but also detected EVs that were internalized by THP-1 macrophages and released by infecting mycobacteria. To the best of our knowledge, this is the first study that detects EVs released by mycobacteria during infection in host macrophages. Within 4 h, most released mycobacterial EVs spread to other parts of the host cell. We predict that this tool will soon hold huge potential in not only delineating mycobacterial EVs-driven pathogenic functions but also in harboring immense propensity to act as a non-invasive diagnostic tool against tuberculosis in general, and extra-pulmonary tuberculosis in particular.
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Affiliation(s)
- Soonjyoti Das
- Aptamer Technology and Diagnostics Laboratory (ATDL), Multidisciplinary Clinical and Translational Research Group (MCTR), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.D.); (A.A.); (N.S.); (K.S.); (R.M.)
| | - Sapna Jain
- Bacterial Pathogenesis Laboratory, Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.J.); (M.I.); (S.K.)
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Mohd Ilyas
- Bacterial Pathogenesis Laboratory, Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.J.); (M.I.); (S.K.)
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
| | - Anjali Anand
- Aptamer Technology and Diagnostics Laboratory (ATDL), Multidisciplinary Clinical and Translational Research Group (MCTR), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.D.); (A.A.); (N.S.); (K.S.); (R.M.)
| | - Saurabh Kumar
- Bacterial Pathogenesis Laboratory, Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.J.); (M.I.); (S.K.)
| | - Nishant Sharma
- Aptamer Technology and Diagnostics Laboratory (ATDL), Multidisciplinary Clinical and Translational Research Group (MCTR), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.D.); (A.A.); (N.S.); (K.S.); (R.M.)
- Department of Biotechnology, Jamia Hamdard, New Delhi 110062, Delhi, India
| | - Kuljit Singh
- Aptamer Technology and Diagnostics Laboratory (ATDL), Multidisciplinary Clinical and Translational Research Group (MCTR), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.D.); (A.A.); (N.S.); (K.S.); (R.M.)
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 18001, Jammu and Kashmir, India
| | - Rahul Mahlawat
- Aptamer Technology and Diagnostics Laboratory (ATDL), Multidisciplinary Clinical and Translational Research Group (MCTR), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.D.); (A.A.); (N.S.); (K.S.); (R.M.)
| | - Tarun Kumar Sharma
- Aptamer Technology and Diagnostics Laboratory (ATDL), Multidisciplinary Clinical and Translational Research Group (MCTR), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.D.); (A.A.); (N.S.); (K.S.); (R.M.)
- Correspondence: (T.K.S.); (K.A.)
| | - Krishnamohan Atmakuri
- Bacterial Pathogenesis Laboratory, Infection and Immunology Group, Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India; (S.J.); (M.I.); (S.K.)
- Correspondence: (T.K.S.); (K.A.)
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26
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Li G, Li H, Chen W, Chen H, Wu G, Tan M, Liang J, Zhou Z. Highly Sensitive Electrochemical Aptasensor for Detection of Glypican-3 Using Hemin-Reduced Graphene Oxide-Platinum Nanoparticles Coupled with Conductive Reduced Graphene Oxide-Gold Nanoparticles. J Biomed Nanotechnol 2021; 17:2444-2454. [PMID: 34974867 DOI: 10.1166/jbn.2021.3215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An electrochemical aptasensor for quantitatively detecting glypican-3 (GPC3) was constructed by combining hemin-reduced graphene oxide-platinum (H-rGO-Pt) nanoparticles (NPs) with reduced graphene oxide-gold (rGO-Au) nanoparticles (NPs). Herein, the rGO-Au NPs deposited onto screen-printed electrodes resulted in signal amplification due to their large surface areas. Meanwhile, highly conductive H-rGO-Pt NPs acted as a sensing medium that improved electrical conductivity and as an indicator for monitoring peak current for determination. A GPC3 aptamer (GPC3apt) with a low equilibrium dissociation constant was used as a bio-recognition molecule. GPC3apt specifically captured GPC3 proteins and formed aptamer-GPC3 complexes, which impeded electron transfer and thus hampered the redox signal of hemin in H-rGO-Pt NPs. This developed electrochemical aptasensor showed a linear response to GPC3 (from 0.001 μg/mL to 10 μg/mL) and had a detection limit of 0.001 μg/mL. This work provides a low-cost and highly sensitive detection with and good recovery for GPC3 and holds great promise for the clinical diagnosis of hepatocellular carcinoma.
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Affiliation(s)
- Guiyin Li
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
| | - HaiMei Li
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
| | - Wei Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
| | - Huijiang Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
| | - Guanxiong Wu
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
| | - Mingxiong Tan
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin Normal University, Yulin, Guangxi, 537000, People's Republic of China
| | - Jintao Liang
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
| | - Zhide Zhou
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi, 541004, People's Republic of China
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27
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Yagati AK, Behrent A, Tomanek V, Chavan SG, Go A, Park SR, Jin Z, Baeumner AJ, Lee MH. Polypyrrole-palladium nanocomposite as a high-efficiency transducer for thrombin detection with liposomes as a label. Anal Bioanal Chem 2021; 414:3205-3217. [PMID: 34617153 DOI: 10.1007/s00216-021-03673-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022]
Abstract
Sensitive and selective determination of protein biomarkers with high accuracy often remains a great challenge due to their existence in the human body at an exceptionally low concentration level. Therefore, sensing mechanisms that are easy to use, simple, and capable of accurate quantification of analyte are still in development to detect biomarkers at a low concentration level. To meet this end, we demonstrated a methodology to detect thrombin in serum at low concentration levels using polypyrrole (PPy)-palladium (Pd)nanoparticle-based hybrid transducers using liposomes encapsulated redox marker as a label. The morphology of Ppy-Pd composites was characterized by scanning electron microscopy, and the hybrid structure provided excellent binding and detection platform for thrombin detection in both buffer and serum solutions. For quantitative measurement of thrombin in PBS and serum, the change in current was monitored using differential pulse voltammetry, and the calculated limit of quantification (LOQ) and limit of detection (LOD) for the linear segment (0.1-1000 nM of thrombin) were 1.1 pM and 0.3 pM, in serum, respectively. The sensors also exhibited good stability and excellent selectivity towards the detection of thrombin, and thus make it a strong candidate for adopting its sensing applications in biomarker detection technologies.
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Affiliation(s)
- Ajay Kumar Yagati
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-Gu, 06974, Seoul, Republic of Korea
- Institute of Analytical Chemistry, Chemo-and Biosensors, Faculty of Chemistry and Pharmacy, University of Regensburg, 31, 93053, Regensburg, Germany
| | - Arne Behrent
- Institute of Analytical Chemistry, Chemo-and Biosensors, Faculty of Chemistry and Pharmacy, University of Regensburg, 31, 93053, Regensburg, Germany
| | - Vanessa Tomanek
- Institute of Analytical Chemistry, Chemo-and Biosensors, Faculty of Chemistry and Pharmacy, University of Regensburg, 31, 93053, Regensburg, Germany
| | - Sachin Ganpat Chavan
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Anna Go
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Sung Ryul Park
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Zhengzhi Jin
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Antje J Baeumner
- Institute of Analytical Chemistry, Chemo-and Biosensors, Faculty of Chemistry and Pharmacy, University of Regensburg, 31, 93053, Regensburg, Germany.
| | - Min-Ho Lee
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-Gu, 06974, Seoul, Republic of Korea.
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28
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Kim DM, Go MJ, Lee J, Na D, Yoo SM. Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies. Molecules 2021; 26:5187. [PMID: 34500620 PMCID: PMC8434002 DOI: 10.3390/molecules26175187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.
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Affiliation(s)
- Dong-Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea;
| | - Myeong-June Go
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Seung-Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
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29
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Complex target SELEX-based identification of DNA aptamers against Bungarus caeruleus venom for the detection of envenomation using a paper-based device. Biosens Bioelectron 2021; 193:113523. [PMID: 34333364 DOI: 10.1016/j.bios.2021.113523] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/30/2021] [Accepted: 07/18/2021] [Indexed: 11/20/2022]
Abstract
Complex target SELEX always have been an intriguing approach to the scientific community, as it offers the potential discovery of novel biomarkers. We herein successfully performed SELEX on Bungarus caeruleus venom to develop a panel of highly affine aptamers that specifically recognizes the B. caeruleus (common krait) venom and was able to discriminate the B. caeruleus venom from Cobra, Russell's, and Saw-scaled viper's venom. The aptamers generated against the crude venom also lead to the identification of the specific component of the venom, which is β-Bungarotoxin, a toxin uniquely present in the B. caeruleus venom. The best performing aptamer candidates were used as a molecular recognition element in a paper-based device and were able to detect as low as 2 ng krait venom in human serum background. The developed aptamer-based paper device can be used for potential point-of-care venom detection applications due to its simplicity and affordability.
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30
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Lee ES, Kim EJ, Park TK, Bae DW, Cha SS, Kim TW, Kim YP. Gold nanoparticle-assisted SELEX as a visual monitoring platform for the development of small molecule-binding DNA aptasensors. Biosens Bioelectron 2021; 191:113468. [PMID: 34233257 DOI: 10.1016/j.bios.2021.113468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/09/2021] [Accepted: 06/26/2021] [Indexed: 02/07/2023]
Abstract
To resolve time-consuming and imperceptible monitoring problems in the traditional systematic evolution of ligands by exponential enrichment (SELEX), we report gold nanoparticle-assisted SELEX (GNP-SELEX) as a visual, proofreading, and self-monitoring platform and its application to small molecule-binding single-stranded DNA (ssDNA) aptasensors. Through the colorimetric changes between rounds, GNP-SELEX enabled the rapid determination of target-specific aptamer library enrichment with neither target modification nor extra monitoring process. We identified ssDNA aptamers with high selectivity and binding affinity by targeting two small molecules (brassinolide; BL and bisphenol A; BPA) as a model. The rational design of selected aptamers by 3D molecular simulation increased their ability to detect BL or BPA in real samples as bioreceptors. These results suggest that GNP-SELEX is useful as a self-monitoring platform to discover ssDNA aptamers as well as to develop aptasensors for diverse targets in a rapid and simple way.
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Affiliation(s)
- Eun-Song Lee
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Eun-Ji Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Tae-Ki Park
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Da-Woon Bae
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Tae-Wuk Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Department of HY-KIST Bio-Convergence, Hanyang University, Seoul, 04763, Republic of Korea.
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31
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Guo W, Zhang C, Ma T, Liu X, Chen Z, Li S, Deng Y. Advances in aptamer screening and aptasensors' detection of heavy metal ions. J Nanobiotechnology 2021; 19:166. [PMID: 34074287 PMCID: PMC8171055 DOI: 10.1186/s12951-021-00914-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Heavy metal pollution has become more and more serious with industrial development and resource exploitation. Because heavy metal ions are difficult to be biodegraded, they accumulate in the human body and cause serious threat to human health. However, the conventional methods to detect heavy metal ions are more strictly to the requirements by detection equipment, sample pretreatment, experimental environment, etc. Aptasensor has the advantages of strong specificity, high sensitivity and simple preparation to detect small molecules, which provides a new direction platform in the detection of heavy metal ions. This paper reviews the selection of aptamers as target for heavy metal ions since the 21th century and aptasensors application for detection of heavy metal ions that were reported in the past five years. Firstly, the selection methods for aptamers with high specificity and high affinity are introduced. Construction methods and research progress on sensor based aptamers as recognition element are also introduced systematically. Finally, the challenges and future opportunities of aptasensors in detecting heavy metal ions are discussed.
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Affiliation(s)
- Wenfei Guo
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Chuanxiang Zhang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Tingting Ma
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Xueying Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
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32
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Phopin K, Tantimongcolwat T. Pesticide Aptasensors-State of the Art and Perspectives. SENSORS 2020; 20:s20236809. [PMID: 33260648 PMCID: PMC7730859 DOI: 10.3390/s20236809] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023]
Abstract
Contamination by pesticides in the food chain and the environment is a worldwide problem that needs to be actively monitored to ensure safety. Unfortunately, standard pesticide analysis based on mass spectrometry takes a lot of time, money and effort. Thus, simple, reliable, cost-effective and field applicable methods for pesticide detection have been actively developed. One of the most promising technologies is an aptamer-based biosensor or so-called aptasensor. It utilizes aptamers, short single-stranded DNAs or RNAs, as pesticide recognition elements to integrate with various innovative biosensing technologies for specific and sensitive detection of pesticide residues. Several platforms for aptasensors have been dynamically established, such as colorimetry, fluorometry, electrochemistry, electrochemiluminescence (ECL) and so forth. Each platform has both advantages and disadvantages depending on the purpose of use and readiness of technology. For example, colorimetric-based aptasensors are more affordable than others because of the simplicity of fabrication and resource requirements. Electrochemical-based aptasensors have mainly shown better sensitivity than others with exceedingly low detection limits. This paper critically reviews the progression of pesticide aptasensors throughout the development process, including the selection, characterization and modification of aptamers, the conceptual frameworks of integrating aptamers and biosensors, the ASSURED (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free and deliverable to end users) criteria of different platforms and the future outlook.
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Affiliation(s)
- Kamonrat Phopin
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakorn Pathom 73170, Thailand;
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Tanawut Tantimongcolwat
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakorn Pathom 73170, Thailand;
- Correspondence:
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