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Bruce-Tagoe TA, Bhaskar S, Kavle RR, Jeevanandam J, Acquah C, Ohemeng-Boahen G, Agyei D, Danquah MK. Advances in aptamer-based biosensors for monitoring foodborne pathogens. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2024; 61:1252-1271. [PMID: 38910921 PMCID: PMC11190136 DOI: 10.1007/s13197-023-05889-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/27/2023] [Accepted: 10/21/2023] [Indexed: 06/25/2024]
Abstract
Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05889-8.
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Affiliation(s)
| | - Shyju Bhaskar
- Department of Food Science, University of Otago, Dunedin, 9056 New Zealand
| | - Ruchita Rao Kavle
- Department of Food Science, University of Otago, Dunedin, 9056 New Zealand
| | - Jaison Jeevanandam
- CQM - Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Caleb Acquah
- Faculty of Health Sciences, University of Ottawa, Ottawa, ON K1H 8M5 Canada
| | - Godfred Ohemeng-Boahen
- Department of Chemical Engineering, Kwame Nkrumah University of Science and Technology, UPO, Kumasi, Ghana
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, 9056 New Zealand
| | - Michael K. Danquah
- Chemical Engineering Department, University of Tennessee, Chattanooga, TN 37403 USA
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2
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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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Zhao Y, Li AZ, Liu J. Capture-SELEX for Chloramphenicol Binding Aptamers for Labeled and Label-Free Fluorescence Sensing. ENVIRONMENT & HEALTH (WASHINGTON, D.C.) 2023; 1:102-109. [PMID: 37614296 PMCID: PMC10442912 DOI: 10.1021/envhealth.3c00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 08/25/2023]
Abstract
Chloramphenicol (CAP) is a potent antibiotic. Due to its side effects, CAP is currently banned in most countries, but it is still found in many food products and in the environment. Developing aptamer-based biosensors for the detection of CAP has interested many researchers. While both RNA and DNA aptamers were previously reported for CAP, they were all obtained by immobilization of the CAP base, which omitted the two chlorine atoms. In this work, DNA aptamers were selected using the library-immobilized method and free unmodified CAP. Three families of aptamers were obtained, and the best one named CAP1 showed a dissociation constant (Kd) of 9.8 μM using isothermal titration calorimetry (ITC). A fluorescent strand-displacement sensor showed a limit of detection (LOD) of 14 μM CAP. Thioflavin T (ThT) staining allowed label-free detection of CAP with a LOD of 1 μM in buffer, 1.8 μM in Lake Ontario water, and 3.6 μM in a wastewater sample. Comparisons were made with previously reported aptamers, and ITC failed to show binding of a previously reported 80-mer aptamer. Due to the small size and well-defined secondary structures of CAP1, this aptamer will find analytical applications for environmental and food monitoring.
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Affiliation(s)
- Yichen Zhao
- Department of Chemistry,
Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Albert Zehan Li
- Department of Chemistry,
Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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4
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Sharma R, Mukherjee M, Bhatt P, Raghavarao KSMS. Rational Truncation of Aptamer for Ultrasensitive Aptasensing of Chloramphenicol: Studies Using Bio-Layer Interferometry. BIOSENSORS 2023; 13:660. [PMID: 37367025 DOI: 10.3390/bios13060660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
Aptamers are an excellent choice for the selective detection of small molecules. However, the previously reported aptamer for chloramphenicol suffers from low affinity, probably as a result of steric hindrance due to its bulky nature (80 nucleotides) leading to lower sensitivity in analytical assays. The present work was aimed at improving this binding affinity by truncating the aptamer without compromising its stability and three-dimensional folding. Shorter aptamer sequences were designed by systematically removing bases from each or both ends of the original aptamer. Thermodynamic factors were evaluated computationally to provide insight into the stability and folding patterns of the modified aptamers. Binding affinities were evaluated using bio-layer interferometry. Among the eleven sequences generated, one aptamer was selected based on its low dissociation constant, length, and regression of model fitting with association and dissociation curves. The dissociation constant could be lowered by 86.93% by truncating 30 bases from the 3' end of the previously reported aptamer. The selected aptamer was used for the detection of chloramphenicol in honey samples, based on a visible color change upon the aggregation of gold nanospheres caused by aptamer desorption. The detection limit could be reduced 32.87 times (1.673 pg mL-1) using the modified length aptamer, indicating its improved affinity as well as its suitability in real-sample analysis for the ultrasensitive detection of chloramphenicol.
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Affiliation(s)
- Richa Sharma
- Department of Food Engineering, CSIR-Central Food Technological Research Institute (CFTRI), Mysore 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Monali Mukherjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute (CFTRI), Mysore 570020, India
| | - Praveena Bhatt
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute (CFTRI), Mysore 570020, India
| | - K S M S Raghavarao
- Department of Food Engineering, CSIR-Central Food Technological Research Institute (CFTRI), Mysore 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Chemical Engineering, Indian Institute of Technology (IIT)-Tirupati, Tirupati 517619, India
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5
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Liu Y, Deng Y, Li S, Wang-Ngai Chow F, Liu M, He N. Monitoring and detection of antibiotic residues in animal derived foods: Solutions using aptamers. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Ye H, Yang Z, Khan IM, Niazi S, Guo Y, Wang Z, Yang H. Split aptamer acquisition mechanisms and current application in antibiotics detection: a short review. Crit Rev Food Sci Nutr 2022; 63:9098-9110. [PMID: 35507474 DOI: 10.1080/10408398.2022.2064810] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Antibiotic contamination is becoming a prominent global issue. Therefore, sensitive, specific and simple technology is desirable the demand for antibiotics detection. Biosensors based on split aptamer has gradually attracted extensive attention for antibiotic detection due to its higher sensitivity, lower cost, false positive/negative avoidance and flexibility in sensor design. Although many of the reported split aptamers are antibiotics aptamers, the acquisition and mechanism of splitting is still unknow. In this review, six reported split aptamers in antibiotics are outlined, including Enrofloxacin, Kanamycin, Tetracycline, Tobramycin, Neomycin, Streptomycin, which have contributed to promote interest, awareness and thoughts into this emerging research field. The study introduced the pros and cons of split aptamers, summarized the assembly principle of split aptamer and discussed the intermolecular binding of antibiotic-aptamer complexes. In addition, the recent application of split aptamers in antibiotic detection are introduced. Split aptamers have a promising future in the design and development of biosensors for antibiotic detection in food and other field. The development of the antibiotic split aptamer meets many challenges including mechanism discovery, stability improvement and new biosensor development. It is believed that split aptamer could be a powerful molecular probe and plays an important role in aptamer biosensor.
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Affiliation(s)
- Hua Ye
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhixin Yang
- Department of Food Science & Technology, National University of Singapore, Singapore, Singapore
| | | | - Sobia Niazi
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yuanxin Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhouping Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hongshun Yang
- Department of Food Science & Technology, National University of Singapore, Singapore, Singapore
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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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8
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Duan N, Song M, Mi W, Wang Z, Wu S. Effectively Selecting Aptamers for Targeting Aromatic Biogenic Amines and Their Application in Aptasensing Establishment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14671-14679. [PMID: 34809428 DOI: 10.1021/acs.jafc.1c05934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
It is necessary to detect the biogenic amine (BA) content in food due to their toxicological effects and their role as an index of freshness for protein-rich foods. Aptamer-based techniques have the potential to provide alternative methods for sensitive and efficient monitoring of BAs. Herein, we described the selection and characterization of DNA aptamers for tyramine (TYR) and β-phenethylamine (PHE) using a one-pot coupled with separate selection strategy. During the selection process, melting curve analysis was developed to monitor the enrichment of the aptamer species, and a saturation of the selection was found at the 14th round. Based on the fluorescence assay, aptamers TYR-2 and PHE-2 showed high affinity to TYR and PHE with the dissociation constant values of 64.28 ± 10.4 and 71.64 ± 11.47 nM, respectively. The circular dichromatic and molecular docking technologies were employed for the preliminary binding mechanism analysis. The obtained aptamers TYR-2 and PHE-2 were used in a fluorescence method for the TYR and PHE determination with limits of detection of 0.34 and 0.39 ng/mL, respectively. In addition, the developed aptasensor was further applied to the TYR and PHE detection in pork and beer samples, and the recovery rate was between 95.6 and 104.2%. It was demonstrated that the selected aptamers had enormous potential as a molecular probe for the identification and determination of BAs.
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Affiliation(s)
- Nuo Duan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Mingqian Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Weiyu Mi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Cen Y, Wang Z, Ke P, Zhu W, Yuan Z, Feng S, Chen Y, Lin C, Liu X, Li Y, Yan P. Development of a novel ssDNA aptamer targeting cardiac troponin I and its clinical applications. Anal Bioanal Chem 2021; 413:7043-7053. [PMID: 34673993 DOI: 10.1007/s00216-021-03667-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Cardiac troponin I (cTnI) is a specific biomarker of acute myocardial infarction (AMI). However, cTnI detection kits prepared with antibodies have many defects. Nucleic acid aptamers are sequences of single-strand DNA or RNA that can overcome the deficiency of antibodies. Herein, sandwich ELONA methods were established based on aptamers. Two selected ssDNA aptamers (Apt3 and Apt6) showed high binding affinity and sensibility (Apt3: Kd = 1.01 ± 0.07 nM, Apt6: k = 0.68 ± 0.05) and did not bind to the same domain of cTnI. Therefore, these two aptamers can be applied to the ELONA methods. The detection range of cTnI using the dual-aptamer sandwich ELONA method was 0.05-200 ng/mL, and the bioanalytical method verification results can meet the national standard of Chinese Pharmacopoeia (2020 Edition). There was no difference between results of the dual-aptamer sandwich ELONA method and the diagnostic results of serum obtained from 243 people (P = 0.39, P ˃ 0.05). The sensitivity and specificity of the ELONA with cTnI in serum were 96.46% and 93.85%, respectively. Compared with the FICA kit, which is clinically used, the consequences of ELONA method are closer to the diagnostic results. This study suggests that the aptamers Apt3 and Apt6 have high affinity and strong specificity and that the dual-aptamer sandwich ELONA method has a wide detection range and can be used to determine cTnI in serum, with potential applications in the diagnosis of AMIs.
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Affiliation(s)
- Yi Cen
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhongping Wang
- Tongpeng Zhongxu Pharmaceutical Technology Company, Guangzhou, Guangdong, China
| | - Peixiong Ke
- Department of Pharmacology, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenting Zhu
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhongwen Yuan
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Senling Feng
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yiqing Chen
- Tongpeng Zhongxu Pharmaceutical Technology Company, Guangzhou, Guangdong, China
| | - Caiyan Lin
- Tongpeng Zhongxu Pharmaceutical Technology Company, Guangzhou, Guangdong, China
| | - Xiaomin Liu
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuting Li
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Pengke Yan
- Department of Pharmacy, Biomedicine Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
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Fan H, Liu Y, Dong J, Luo Z. Screening Aptamers that Are Specific for Beclomethasone and the Development of Quantum Dot-Based Assay. Appl Biochem Biotechnol 2021; 193:3139-3150. [PMID: 34085169 DOI: 10.1007/s12010-021-03585-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/28/2021] [Indexed: 12/16/2022]
Abstract
We developed an aptamer that was specific for beclomethasone (BEC) via systematic evolution of ligands by exponential enrichment (SELEX). Development was monitored by real-time quantitative PCR (Q-PCR) and the enriched library was sequenced by high-throughput sequencing. Forty-seven aptamer candidates were obtained; of these, BEC-6 showed the highest affinity (Kd = 0.15 ± 0.02 μM) and did not cross-react with other BEC analogs. We also developed a quantum dot-based assay (QDA) for the detection of BEC that was based upon a quantum dot (QD) composite probe. Under optimized reaction conditions, the linear range of this method for BEC was 0.1 to 10 μM with a low detection limit (LOD) of 0.1 μM. Subsequently, the method was used to detect BEC in Traditional Chinese Medicine (TCM) with a mean recovery of 81.72-91.84%. This is the first report to describe the development of an aptamer against BEC; BEC-6 can also be engineered into QDA for the detection of BEC.
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Affiliation(s)
- Hongli Fan
- Institute of Mathematical Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yaxiong Liu
- NMPA Key Laboratory for Rapid Testing Technology of Drugs, Guangdong Institute for Drug Control, Guangzhou, 510663, China
| | - Jiamei Dong
- Institute of Mathematical Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Zhuoya Luo
- NMPA Key Laboratory for Rapid Testing Technology of Drugs, Guangdong Institute for Drug Control, Guangzhou, 510663, China.
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Xu Y, Jiang X, Zhou Y, Ma M, Wang M, Ying B. Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases. Front Bioeng Biotechnol 2021; 9:704077. [PMID: 34447741 PMCID: PMC8383106 DOI: 10.3389/fbioe.2021.704077] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023] Open
Abstract
Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.
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Affiliation(s)
- Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ming Ma
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,The First People's Hospital of Shuangliu District, Chengdu/West China (Airport)Hospital Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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12
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Selection and identification of diethylstilbestrol-specific aptamers based on magnetic-bead SELEX. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105354] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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Lan X, Zhu L, Xu W. Novel immuno-nucleic acid cooperative detection technology for food safety. FOOD AGR IMMUNOL 2020. [DOI: 10.1080/09540105.2020.1763261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Xinyue Lan
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, People’s Republic of China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture and Rural Affairs, Beijing, People’s Republic of China
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14
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Majdinasab M, Mishra RK, Tang X, Marty JL. Detection of antibiotics in food: New achievements in the development of biosensors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115883] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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WANG ZJ, CHEN EN, YANG G, ZHAO XY, QU F. Research Advances of Aptamers Selection for Small Molecule Targets. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60013-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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16
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John Ho LS, Fogel R, Limson JL. Generation and screening of histamine-specific aptamers for application in a novel impedimetric aptamer-based sensor. Talanta 2020; 208:120474. [DOI: 10.1016/j.talanta.2019.120474] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 01/29/2023]
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17
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Song S, Wang X, Xu K, Ning L, Yang X. Rapid identification and quantitation of the viable cells of Lactobacillus casei in fermented dairy products using an aptamer-based strategy powered by a novel cell-SELEX protocol. J Dairy Sci 2019; 102:10814-10824. [DOI: 10.3168/jds.2019-16693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/08/2019] [Indexed: 01/12/2023]
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Wang C, Du X, Xie T, Li H. Label- and modification-free-based in situ selection of bovine serum albumin specific aptamer. J Sep Sci 2019; 42:3571-3578. [PMID: 31550414 DOI: 10.1002/jssc.201900620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Systematic evolution of ligands by exponential enrichment is a traditional approach to select aptamer, which has a great potential in biosensing field. However, chemical modifications of DNA library or targets before selection might block the real recognition and binding sites between aptamers and their targets. In this study, a label- and modification-free-based in situ selection strategy was developed to overcome this limitation. The strategy is an attempt to screen bovine serum albumin aptamers according to the principle of electrophoretic mobility shift assay, and allowed single-stranded DNA sequence to be fully exposed to interact with bovine serum albumin which was mixed with the agarose gel beforehand. After eight rounds of selection, specific aptamer with low dissociation constant (Kd ) value of 69.44 ± 7.60 nM was selected and used for subsequent establishment of fluorescence biosensor. After optimization, the optimal aptasensor exhibited a high sensitivity toward bovine serum albumin with a limit of detection of 0.24 ng/mL (linear range from 1 to 120 ng/mL). These results indicated that the label- and modification-free-based in situ selection strategy proposed in this work could effectively select specific aptamer to develop aptasensor for sensitive detection of bovine serum albumin or other targets in actual complicated samples.
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Affiliation(s)
- Chuchu Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Xiaoyan Du
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Tiantian Xie
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Hao Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
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19
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Wang L, Wang C, Li H. Selection of DNA aptamers and establishment of an effective aptasensor for highly sensitive detection of cefquinome residues in milk. Analyst 2019; 143:3202-3208. [PMID: 29872833 DOI: 10.1039/c8an00709h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cefquinome (CFQ), which is a fourth-generation cephalosporin approved for veterinary use only, has been widely used for treating porcine or bovine respiratory infection, bovine mastitis and other diseases. However, the antibacterial effect of CFQ is based on the duration of drug concentration remaining in excess of the minimum inhibitory concentration in serum or tissues, thereby inevitably leading to CFQ residues with high levels in animal-sourced food. In this paper, four CFQ-specific ssDNA aptamers were selected via a magnetic bead-based systematic evolution of ligands by the exponential enrichment (SELEX) method. Aptamer W1 with the lowest dissociation constant (Kd) value of 40.13 ± 22.11 nM was chosen for establishing a fluorescence aptasensor based on magnetic separation and release of molecular beacons for detection of CFQ residues. This aptasensor exhibited a high sensitivity toward CFQ with a limit of detection (LOD) of 0.09 ng mL-1 (linear range from 0.5 to 150 ng mL-1). Moreover, the present aptasensor also showed high selectivity against ampicillin and CFQ's structural analogs (i.e., cefpirome sulfate and cefixime). Finally, this aptasensor was used to detect CFQ in real spiked milk. The recovery rate of CFQ from spiked milk samples ranged from 96.6% to 103.2%. These results indicated that the developed aptasensor is a promising, highly sensitive and specific method for CFQ residue detection in animal-sourced food.
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Affiliation(s)
- Lihui Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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20
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A competitive colorimetric chloramphenicol assay based on the non-cross-linking deaggregation of gold nanoparticles coated with a polyadenine-modified aptamer. Mikrochim Acta 2018; 185:534. [PMID: 30406418 DOI: 10.1007/s00604-018-3067-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/20/2018] [Indexed: 12/28/2022]
Abstract
A competitive colorimetric assay has been established to detect chloramphenicol (CAP). It is based on the use of colloidal and electrostatically stabilized aptamer-modified gold nanoparticles (GNPs). The CAP aptamer is modified by a sequence of 5 adenosine groups to anchor it on the surface of GNPs. It can competitively capture two compounds, viz. D-(-)-threo-2-amino-1-(4-nitrophenyl)-1,3-propanediol (CAP-base, with a positive charge) and CAP (which is uncharged). The capture of the positively charged CAP-base triggers the aggregation of modified GNPs in salt-containing solution, and this causes a color change from red to purple. However, in the presence of CAP and CAP-base, the capture of the uncharged CAP weakens this color change by a competing process for capture. Thus, the concentration of CAP is associated with the degree of deaggregation of GNPs and can be quantified by the ratio of absorbances at 620 nm and 520 nm. The assay has a 22 nM limit of detection in acidic solution, and the response is linear in the range of 0.20 to 3.20 μM CAP concentration. This assay was successfully applied to the determination of CAP in spiked environmental water samples. Conceivably, this method has a wide scope in that it may be applied to a wide range of analytes if respective aptamers are available. Graphical abstract Schematic presentation of a competitive non-cross linking deaggregating method for detecting chloramphenicol. The surface charge of polyA-Apt@GNPs and its aggregation degree (purple) are determined by the charge of target. (CAP-base: precursor of CAP; PolyA-Apt@GNPs: 5'-polyA-modified DNA aptamer functionalized gold nanoparticles.).
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21
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Zhao L, Huang Y, Dong Y, Han X, Wang S, Liang X. Aptamers and Aptasensors for Highly Specific Recognition and Sensitive Detection of Marine Biotoxins: Recent Advances and Perspectives. Toxins (Basel) 2018; 10:E427. [PMID: 30366456 PMCID: PMC6265707 DOI: 10.3390/toxins10110427] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/13/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023] Open
Abstract
Marine biotoxins distribute widely, have high toxicity, and can be easily accumulated in water or seafood, exposing a serious threat to consumer health. Achieving specific and sensitive detection is the most effective way to prevent emergent issues caused by marine biotoxins; however, the previous detection methods cannot meet the requirements because of ethical or technical drawbacks. Aptamers, a kind of novel recognition element with high affinity and specificity, can be used to fabricate various aptasensors (aptamer-based biosensors) for sensitive and rapid detection. In recent years, an increasing number of aptamers and aptasensors have greatly promoted the development of marine biotoxins detection. In this review, we summarized the recent aptamer-related advances for marine biotoxins detection and discussed their perspectives. Firstly, we summarized the sequences, selection methods, affinity, secondary structures, and the ion conditions of all aptamers to provide a database-like information; secondly, we summarized the reported aptasensors for marine biotoxins, including principles, detection sensitivity, linear detection range, etc.; thirdly, on the basis of the existing reports and our own research experience, we forecast the development prospects of aptamers and aptasensors for marine biotoxins detection. We hope this review not only provides a comprehensive summary of aptamer selection and aptasensor development for marine biotoxins, but also arouses a broad readership amongst academic researchers and industrial chemists.
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Affiliation(s)
- Lianhui Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Yunfei Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Yiyang Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xutiange Han
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Sai Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China.
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22
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Ladju RB, Pascut D, Massi MN, Tiribelli C, Sukowati CHC. Aptamer: A potential oligonucleotide nanomedicine in the diagnosis and treatment of hepatocellular carcinoma. Oncotarget 2017; 9:2951-2961. [PMID: 29416827 PMCID: PMC5788695 DOI: 10.18632/oncotarget.23359] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/01/2017] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers with a high mortality rate. Late diagnosis and poor prognosis are still a major drawback since curative therapies such as liver resection and liver transplantation are effective only for an early stage HCC. Development of novel molecular targeting therapies against HCC may provide new options that will improve the efficiency of the diagnosis and the success of the therapy, thus ameliorating the life expectancy of the patients. The aptamer is an oligonucleotide nanomedicine that has high binding affinity and specificity to small and large target molecules in the intracellular and extracellular environment with agonist or antagonist function. Currently, several aptamers for diagnostic and therapeutic purposes are under development to recognize different molecules of HCC. In in vitro models, the aptamer has been shown to be able to reduce the growth of HCC cells and increase the sensitivity to conventional chemotherapies. In in vivo mouse models, aptamer could induce cell apoptosis with antitumor activity. Overall data had shown that aptamer has limited toxicity and might be safe in clinical application. This review summarizes recent information of aptamer as a potential oligonucleotide nanomedicine tool, in diagnostics, targeted therapy, and as drug delivery nano-vehicles.
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Affiliation(s)
- Rusdina Bte Ladju
- Fondazione Italiana Fegato, AREA Science Park Basovizza, Trieste, Italy.,Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Devis Pascut
- Fondazione Italiana Fegato, AREA Science Park Basovizza, Trieste, Italy
| | | | - Claudio Tiribelli
- Fondazione Italiana Fegato, AREA Science Park Basovizza, Trieste, Italy
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Han X, Zhang Y, Nie J, Zhao S, Tian Y, Zhou N. Gold nanoparticle based photometric determination of tobramycin by using new specific DNA aptamers. Mikrochim Acta 2017; 185:4. [PMID: 29594665 DOI: 10.1007/s00604-017-2568-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 11/09/2017] [Indexed: 12/26/2022]
Abstract
A magnetic bead-based SELEX was applied to identify 37 single-stranded DNA aptamers specific for tobramycin after ten rounds of selection. The aptamers were classified into nine families according to sequence analysis. Among them, several aptamers with typical sequences were selected and their dissociation constants (Kds) were determined by a fluorescent method. An aptamer termed "Ap 32", with a Kd value of 56.8 ± 4.6 nM, possesses the highest affinity and satisfactory specificity. Theoretical modeling showed that nucleotides 14-18 and 26-29 play a most significant role in the interaction between aptamer and tobramycin. Subsequently, the sequence of Ap 32 was optimized through rationally designed truncation. The truncated aptamer Ap 32-2 consists of 34 nucleotides and has a Kd that is similar to the original one. It was chosen as the optimal aptamer for use in the assay and was immobilized on gold nanoparticles. On addition of tobramycin, the color turns from red to purple. The findings were used to design a photometric assay (best performed at 520 nm) that has a linear response in the 100 nM to 1.4 μM concentration range, with a 37.9 nM detection limit. The method was successfully applied to the determination of tobramycin in (spiked) honey samples. Graphical abstract A 34-nucleotide aptamer specific for tobramycin was obtained through magnetic beads-based systematic evolution of ligands by exponential enrichment (SELEX) and structural analysis-based rational post-SELEX truncation, and then applied to the determination of tobramycin using a gold nanoparticle-based photometric assay.
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Affiliation(s)
- Xuyan Han
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yuhong Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jingjing Nie
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Songyin Zhao
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yaping Tian
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Comparison of Flow Cytometry and ELASA for Screening of Proper Candidate Aptamer in Cell-SELEX Pool. Appl Biochem Biotechnol 2017; 184:444-452. [PMID: 28721653 DOI: 10.1007/s12010-017-2548-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/25/2017] [Indexed: 02/07/2023]
Abstract
Aptamers are single-stranded RNA or DNA, which bind to their target with high affinity and specificity. Method of isolating aptamers against cell surface protein is called cell-SELEX. Common approach for monitoring cell-SELEX developed aptamers is flow cytometry. Since flow cytometry is costly and requires sophisticated equipments, we suggested implementing easy access, high throughput enzyme-link apta-sorbent assay test (ELASA) to confirm the specificity of aptamers selected through cell-SELEX process. In this regard, we compared ELASA and flow cytometry techniques in order to screen potent candidate aptamers against A2780 Rcis cell line, which were selected by cell-SELEX. The obtained results demonstrated that both ELASA and flow cytometry are identical in terms of sensivity and precision for aptamers selection. Then it could be concluded that ELASA method could be used as a versatile, inexpensive procedure for in vito evaluation of isolated aptamers from cell-SELEX based process.
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25
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Duan Y, Wang L, Gao Z, Wang H, Zhang H, Li H. An aptamer-based effective method for highly sensitive detection of chloramphenicol residues in animal-sourced food using real-time fluorescent quantitative PCR. Talanta 2016; 165:671-676. [PMID: 28153315 DOI: 10.1016/j.talanta.2016.12.090] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/28/2016] [Accepted: 12/30/2016] [Indexed: 12/17/2022]
Abstract
Chloramphenicol (CAP) residues can not only harm human health through entering food chain, but also cause the spreading of drug-resistant bacteria, thereby leading to secondary environmental pollution. Therefore, it is in urgent need of establishing an efficient technology to detect CAP residues in animal-sourced food. In this study, a novel sensitive approach for detection of CAP was designed based on a CAP specific aptamer and real-time fluorescent quantitative PCR (qRT-PCR). The CAP specific aptamer was firstly hybridized with a biotin modified complementary probe, and then was immobilized on streptavidin conjugated magnetic beads through biotin. When CAP was added, the aptamer would specifically bind with CAP by forming a hairpin structure and be released from the magnetic beads for CAP detection by qRT-PCR. Factors (i.e., probe strand length, aptamer concentration, NaCl concentration and incubation time) that would influence the determination accuracy of this aptamer-based detection system were optimized. Under the optimized conditions, the present detection system exhibited a high sensitivity toward CAP with a limit of detection of 0.1ng/mL (linear range from 0.1 to 20ng/mL). Moreover, this detection system also showed high selectivity against thiamphenicol (TAP) and florfenicol (FF), which are CAP's structure analogs. Eventually, this detection system was applied for detecting CAP in real spiked milk. The recovery rate of CAP from spiked milk samples ranged from 94.0-102.0%. These results indicated this developed detection system a promising high sensitive and specific method of CAP residues detection in animal-sourced food.
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Affiliation(s)
- Ye Duan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lihui Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhiqiang Gao
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing 100026, China
| | - Huishan Wang
- Beijing Senkang Biotechnology Development Co., Ltd, Beijing 101400, China
| | - Hexiao Zhang
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing 100026, China.
| | - Hao Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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26
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Aeksiri N, Warakulwit C, Hannongbua S, Unajak S, Choowongkomon K. Use of Capillary Electrophoresis to Study the Binding Interaction of Aptamers with Wild-Type, K103N, and Double Mutant (K103N/Y181C) HIV-1 RT : Studying the Binding Interaction of Wild-Type, K103N, and Double Mutant (K103N/Y181C) HIV-1 RT with Aptamers by Performing the Capillary Electrophoresis. Appl Biochem Biotechnol 2016; 182:546-558. [PMID: 27900665 DOI: 10.1007/s12010-016-2343-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/24/2016] [Indexed: 12/22/2022]
Abstract
A number of nucleic acid aptamers with high affinities to human immunodeficiency virus reverse transcriptase (HIV-1 RT) are currently known. They can potentially be developed as broad-spectrum antiviral drugs, but there is little known about their binding interaction with mutant HIV-1 RT. Therefore, we utilized non-equilibrium capillary electrophoresis of equilibrium mixture (NECEEM) to study the interaction of three HIV-1 RTs (wild type, K103N, and double mutant (K103N/Y181C)) with RT1t49 and RT12 aptamers. This approach was used to study and evaluate the K d values of these molecules. The results showed that the K d values of the tested aptamers were lower than that of the DNA substrate. The results also pointed out that RT1t49 could bind with all HIV-1 RTs and compete with the DNA substrate at the active site. Moreover, we studied the binding stoichiometry of HIV-1 RT using aptamers as probes. The findings showed evidence of two binding stoichiometries with HIV-1 RT and the RT12 aptamer but only one binding stoichiometry for RT1t49. In addition, RT1t49 could bind specifically with the wild-type, K103N, and double mutants in Escherichia coli lysate. This result also indicated that the aptamer could detect HIV-1 RT in the presence of E. coli lysate.
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Affiliation(s)
- Niran Aeksiri
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok, 65000, Thailand
| | - Chompunuch Warakulwit
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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