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Li D, Su Y, Li J, Liu R, Fang B, He J, Xu W, Zhu L. Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections. Biomacromolecules 2023; 24:4568-4586. [PMID: 37728999 DOI: 10.1021/acs.biomac.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.
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Affiliation(s)
- Diandian Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yuan Su
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Rong Liu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Bing Fang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jingjing He
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
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Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
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Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
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Recent progress in aptamer-based microfluidics for the detection of circulating tumor cells and extracellular vesicles. J Pharm Anal 2023; 13:340-354. [PMID: 37181295 PMCID: PMC10173182 DOI: 10.1016/j.jpha.2023.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Liquid biopsy is a technology that exhibits potential to detect cancer early, monitor therapies, and predict cancer prognosis due to its unique characteristics, including noninvasive sampling and real-time analysis. Circulating tumor cells (CTCs) and extracellular vesicles (EVs) are two important components of circulating targets, carrying substantial disease-related molecular information and playing a key role in liquid biopsy. Aptamers are single-stranded oligonucleotides with superior affinity and specificity, and they can bind to targets by folding into unique tertiary structures. Aptamer-based microfluidic platforms offer new ways to enhance the purity and capture efficiency of CTCs and EVs by combining the advantages of microfluidic chips as isolation platforms and aptamers as recognition tools. In this review, we first briefly introduce some new strategies for aptamer discovery based on traditional and aptamer-based microfluidic approaches. Then, we subsequently summarize the progress of aptamer-based microfluidics for CTC and EV detection. Finally, we offer an outlook on the future directional challenges of aptamer-based microfluidics for circulating targets in clinical applications.
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Lim H, Chang J, Kim KI, Moon Y, Lee S, Lee B, Lee JH, Lee J. On-chip selection of adenosine aptamer using graphene oxide-coated magnetic nanoparticles. BIOMICROFLUIDICS 2022; 16:044102. [PMID: 35909647 PMCID: PMC9337878 DOI: 10.1063/5.0095419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a method that is generally used for developing aptamers, which have arisen the promising alternatives for antibodies. However, conventional SELEX methods have limitations, such as a limited selection of target molecules, time-consuming and complex fabrication processes, and labor-intensive processes, which result in low selection yields. Here, we used (i) graphene oxide (GO)-coated magnetic nanoparticles in the selection process for separation and label-free detection and (ii) a multilayered microfluidic device manufactured using a three-dimensionally printed mold that is equipped with automated control valves to achieve precise fluid flows. The developed on-chip aptamer selection device and GO-coated magnetic nanoparticles were used to screen aptamer candidates for adenosine in eight cycles of the selection process within approximately 2 h for each cycle. Based on results from isothermal titration calorimetry, an aptamer with a dissociation constant of 18.6 ± 1.5 μM was selected. Therefore, the on-chip platform based on GO-coated magnetic nanoparticles provides a novel label-free screening technology for biosensors and micro/nanobiotechnology for achieving high-quality aptamers.
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Affiliation(s)
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kyung-il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Youngkwang Moon
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Saebom Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Byoungsang Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung Heon Lee
- Authors to whom correspondence should be addressed:, Tel.: +82-31-290-7404 and , Tel.: +82-31-299-4845
| | - Jinkee Lee
- Authors to whom correspondence should be addressed:, Tel.: +82-31-290-7404 and , Tel.: +82-31-299-4845
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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Screening and Identification of Specific Aptamers for Shellfish Allergen Tropomyosin with Capillary Electrophoresis-SELEX. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02211-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Xiao X, Li H, Zhao L, Zhang Y, Liu Z. Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications. Biomed Pharmacother 2021; 143:112232. [PMID: 34649356 DOI: 10.1016/j.biopha.2021.112232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/04/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.
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Affiliation(s)
- Xueran Xiao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hui Li
- Department of Urology, Peking University International Hospital, Beijing 102206, China
| | - Lijian Zhao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yanfen Zhang
- Technology Transfer Center, Hebei University, Baoding 071002, China.
| | - Zhongcheng Liu
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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Ayodele OO, Adesina AO, Pourianejad S, Averitt J, Ignatova T. Recent Advances in Nanomaterial-Based Aptasensors in Medical Diagnosis and Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:932. [PMID: 33917467 PMCID: PMC8067492 DOI: 10.3390/nano11040932] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Rapid and accurate diagnosis of various biomarkers associated with medical conditions including early detection of viruses and bacteria with highly sensitive biosensors is currently a research priority. Aptamer is a chemically derived recognition molecule capable of detecting and binding small molecules with high specificity and its fast preparation time, cost effectiveness, ease of modification, stability at high temperature and pH are some of the advantages it has over traditional detection methods such as High Performance Liquid Chromatography (HPLC), Enzyme-linked Immunosorbent Assay (ELISA), Polymerase Chain Reaction (PCR). Higher sensitivity and selectivity can further be achieved via coupling of aptamers with nanomaterials and these conjugates called "aptasensors" are receiving greater attention in early diagnosis and therapy. This review will highlight the selection protocol of aptamers based on Traditional Systematic Evolution of Ligands by EXponential enrichment (SELEX) and the various types of modified SELEX. We further identify both the advantages and drawbacks associated with the modified version of SELEX. Furthermore, we describe the current advances in aptasensor development and the quality of signal types, which are dependent on surface area and other specific properties of the selected nanomaterials, are also reviewed.
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Affiliation(s)
| | | | | | | | - Tetyana Ignatova
- Nanoscience Department, The Joint School of Nanoscience & Nanoengineering, University of North Carolina, Greensboro, NC 27401, USA; (O.O.A.); (A.O.A.); (S.P.); (J.A.)
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Guo X, Chen GH. Capillary electrophoresis-based methodology for screening of oligonucleotide aptamers. Biomed Chromatogr 2021; 35:e5109. [PMID: 33660332 DOI: 10.1002/bmc.5109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/28/2023]
Abstract
As a new molecular recognition element, oligonucleotide aptamer not only has higher affinity and specificity to target molecules, but also has the advantages of wide recognition range, in vitro synthesis and chemical stability compared with conventional antibodies. Since a kind of screening method termed systematic evolution of ligands by exponential enrichment (SELEX) was reported, scientists have extensively researched the methodology of how to highly and efficiently screen out aptamers from a library consisting of a large number of random oligonucleotides. Certainly capillary electrophoresis-based screening methodologies, including nonequilibrium capillary electrophoresis of equilibrium mixtures, equilibrium capillary electrophoresis of equilibrium mixtures, non-SELEX, ideal-filter capillary electrophoresis, capillary transient isotachophoresis, etc., are revolutionary. Compared with conventional SELEX, these capillary electrophoresis-based methodologies show incomparable advantages such as the single-round screening of aptamers and increased successful screening rate. Methodology studies on the screening process of aptamers are comprehensively reviewed.
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Affiliation(s)
- Xin Guo
- College of Food and Bioengineering, Jiangsu University, Zhenjiang, China.,Periodicals Agency of Jiangsu University, Zhenjiang, China
| | - Guan-Hua Chen
- College of Food and Bioengineering, Jiangsu University, Zhenjiang, China
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Advances in Gold Nanoparticles-Based Colorimetric Aptasensors for the Detection of Antibiotics: An Overview of the Past Decade. NANOMATERIALS 2021; 11:nano11040840. [PMID: 33806173 PMCID: PMC8066193 DOI: 10.3390/nano11040840] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022]
Abstract
Misuse of antibiotics has recently been considered a global issue because of its harmful effects on human health. Since conventional methods have numerous limitations, it is necessary to develop fast, simple, sensitive, and reproducible methods for the detection of antibiotics. Among numerous recently developed methods, aptasensors are fascinating because of their good specificity, sensitivity and selectivity. These kinds of biosensors combining aptamer with colorimetric applications of gold nanoparticles to recognize small molecules are becoming more popular owing to their advantageous features, for example, low cost, ease of use, on-site analysis ability using naked eye and no prerequisite for modern equipment. In this review, we have highlighted the recent advances and working principle of gold nanoparticles based colorimetric aptasensors as promising methods for antibiotics detection in different food and environmental samples (2011–2020). Furthermore, possible advantages and disadvantages have also been summarized for these methods. Finally, the recent challenges, outlook, and promising future perspectives for developing novel aptasensors are also considered.
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Saito S. SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques. ANAL SCI 2021; 37:17-26. [PMID: 33132238 DOI: 10.2116/analsci.20sar18] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo Sakura, Saitama, 338-8570, Japan.
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Shoaib M, Shehzad A, Mukama O, Raza H, Niazi S, Khan IM, Ali B, Akhtar W, Wang Z. Selection of potential aptamers for specific growth stage detection of Yersinia enterocolitica. RSC Adv 2020; 10:24743-24752. [PMID: 35516186 PMCID: PMC9055141 DOI: 10.1039/d0ra00683a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/17/2020] [Indexed: 11/28/2022] Open
Abstract
Yersinia enterocolitica remains a threat to public health, and a sensitive detection method is a prerequisite due to its complicated diagnosis associated with slow growth. Recently, aptamer-based detection systems have played a vital role in the development of simple, rapid, sensitive, and specific detection methods. Herein, highly specific ssDNA aptamers were screened against Y. enterocolitica at the different growth stages by whole cell-SELEX. Cells at different growth stages were harvested and incubated with an ssDNA library to get an enriched pool of specific aptamer candidates. After the 10th round of SELEX, the enriched pool was sequenced and grouped into seven families based on homology and similarity of the secondary structure. Flow cytometry analysis revealed that the aptamers M1, M5, and M7 with K d values of 37.93 ± 7.88 nM, 74.96 ± 21.34 nM, and 73.02 ± 18.76 nM had the highest affinity and specificity to the target, respectively. The selected aptamers showed binding to the different growth stages of Y. enterocolitica with a significant increase in the gated fluorescence. Our aptamer selection strategy is convenient, and the developed aptamer can be useful for an accurate and reliable detection system.
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Affiliation(s)
- Muhammad Shoaib
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Aamir Shehzad
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
- UniLaSalle, Univ. Artois, EA7519 - Transformations & Agro-ressources, Normandie Université F-76130 Mont-Saint-Aignan France
| | - Omar Mukama
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Department of Biology, College of Science and Technology, University of Rwanda Avenue de l'armée, P. O. Box: 3900 Kigali Rwanda
| | - Husnain Raza
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- School of Food and Biological Engineering, Jiangsu University Zhenjiang Jiangsu 212013 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Sobia Niazi
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Imran Mahmood Khan
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Barkat Ali
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
| | - Wasim Akhtar
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
- National Institute of Food Science and Technology, FFNHS, University of Agriculture Faisalabad 38040 Pakistan
| | - Zhouping Wang
- School of Food Science and Technology, Jiangnan University Wuxi 214122 People's Republic of China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University Wuxi 214122 People's Republic of China
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JIANG H, LV XF, ZHAO KX. Progress of Aptamer Screening Techniques Based on Microfluidic Chips. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60015-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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ZHU C, ZHAO XY, YANG G, QU F. Capillary Electrophoresis Involving in High Efficiency Screening for Aptamers. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [PMCID: PMC7219368 DOI: 10.1016/s1872-2040(20)60014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a universal technology for aptamer' screening. Accurate and efficient screening methods and strategy design are the key to success. This review briefly summarizes capillary electrophoresis (CE) involving in the efficient screening for aptamers in our group since 2007, including the application of CE in pre-screening, screening and post-screening process, classification and screening strategies against different protein targets, multiple screening modes, and screening for multi-scale targets. Finally, combined with the current progresses of aptamer screening, some remaining issues are discussed and the development prospects are proposed.
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LI LS, ZHU C, ZHAO Y, YANG G, QU F. Investigation of Library Input on Aptamers Selection Efficiency Using Capillary Electrophoresis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60017-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Zhu C, Yang G, Ghulam M, Li L, Qu F. Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers. Biotechnol Adv 2019; 37:107432. [PMID: 31437572 DOI: 10.1016/j.biotechadv.2019.107432] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/24/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023]
Abstract
Aptamers have drawn considerable attention as newly emerging molecular recognition elements in clinical diagnostics, drug delivery, therapeutics, environmental monitoring, and food safety analyses. As the in vitro screening antibody analogs, aptamers are enabled to recognize various types of targets with high affinity and specificity like or even superior to antibodies. However, the restrictions and inefficiency of selection have been hampering their wider application. Among various modified systematic evolution of ligands by exponential enrichment (SELEX) methods, capillary electrophoresis (CE)-SELEX holds multiple functions and advantages with the powerful qualitative and quantitative analysis capabilities, less consumption of sample and analytical reagent, natural binding environment, higher screening efficiency, and availability in multiple modes. This review summarizes the key developments in the area of CE-SELEX by leading research groups, including our teams' ten years of research and experience to help researchers fully understand and utilize CE-SELEX. Aptamers' history, applications, as well as the SELEX developments, have been briefly described; the advantages of CE-SELEX are highlighted compared with the conventional SELEX methods. Further, we describe some essential CE-SELEX models and provide an overview of the CE-SELEX, including the targets and ssDNA library, every technical point in the selection process, and post-SELEX protocol. We expect this review will inspire more researchers to have insight into the screening problems from CE-SELEX viewpoint and will help to improve the selection efficiency and probability of success to meet the growing needs of aptamers' discovery in bioanalytical and medical fields.
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Affiliation(s)
- Chao Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Murtaza Ghulam
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China.
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Zhang GQ, Zhong LP, Yang N, Zhao YX. Screening of aptamers and their potential application in targeted diagnosis and therapy of liver cancer. World J Gastroenterol 2019; 25:3359-3369. [PMID: 31341361 PMCID: PMC6639558 DOI: 10.3748/wjg.v25.i26.3359] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/02/2019] [Accepted: 06/08/2019] [Indexed: 02/06/2023] Open
Abstract
Aptamers are a class of single oligonucleotide molecules (DNA or RNA) that are screened from random DNA or RNA oligonucleotide chain libraries by the systemic evolution of ligands by exponential enrichment technology. The selected aptamers are capable of specifically binding to different targeting molecules, which is achieved by the three-dimensional structure of aptamers. Aptamers are similar in function to monoclonal antibodies, and therefore, they are also referred to as "chemical antibodies". Due to their high affinity and specificity and low immunogenicity, aptamers are topics of intense interest in today's biological targeting research especially in tumor research. They not only have high potential for clinical advances in tumor targeting detection but also are highly promising as targeted tumor drug carriers for use in tumor therapy. Various experimental studies have shown that aptamer-based diagnostic and therapeutic methods for liver cancer have great potential for application. This paper summarizes the structure, characteristics, and screening methods of aptamers and reviews the recent research progress on nucleic acid aptamers in the targeted diagnosis and treatment of liver cancer.
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Affiliation(s)
- Guo-Qing Zhang
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Li-Ping Zhong
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Nuo Yang
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yong-Xiang Zhao
- National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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High-efficiency selection of aptamers for bovine lactoferrin by capillary electrophoresis and its aptasensor application in milk powder. Talanta 2019; 205:120088. [PMID: 31450439 DOI: 10.1016/j.talanta.2019.06.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/14/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
Abstract
Capillary electrophoresis-based systematic evolution of ligands by exponential enrichment (CE-SELEX) is a high-efficient technique for aptamers selection, and has been evolved into many modes. In this study, we obtained the aptamer against bovine lactoferrin (BLF) with high affinity (dissociation constant, Kd = 20.74 ± 6.89 nM) and good specificity (>1000 folds) using single step CE-SELEX (ssCE-SELEX) mode. In the selection process, ssCE demonstrated high-efficiency selection with bulk Kd reaching at 0.19 ± 0.04 μM by only two rounds, as compared to capillary zone electrophoresis (CZE) mode with Kd of 0.39 ± 0.03 μM. Next-generation sequencing (NGS) was performed by two methods of high output (Hiseq) and medium output (Miseq) with different sequencing depths, and their same results of high-frequency sequences confirmed the reliability of the obtained sequences. Through affinity analysis, the primer region and single base mutation (SBM) were observed to affect the sequence structure and to result in affinity change. Besides, molecular dynamics (MD) simulation was performed to validate the binding affinity of the candidates with BLF by analyzing binding sites, interaction forces, and binding free energy. Moreover, BLF detection in milk powder matrices was completed successfully with the optimized CE-aptasensor. The signal response was in a good linear relationship (R2 = 0.9930) with 4-128 nM of BLF and the detection limit was 1 nM. The obtained results of BLF in four milk powder samples were in an acceptable agreement with the labeled concentrations. This study presented a completed CE based process including aptamers selection, affinity characterization, and detection application, which also validated the high-efficiency selection of ssCE-SELEX mode.
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Foret F, Datinská V, Voráčová I, Novotný J, Gheibi P, Berka J, Astier Y. Macrofluidic Device for Preparative Concentration Based on Epitachophoresis. Anal Chem 2019; 91:7047-7053. [DOI: 10.1021/acs.analchem.8b05860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- František Foret
- Czech Academy of Sciences, Institute of Analytical Chemistry, Brno 61142, Czech Republic
- CEITEC Masaryk University Brno 60177, Czech Republic
| | - Vladimíra Datinská
- Czech Academy of Sciences, Institute of Analytical Chemistry, Brno 61142, Czech Republic
- Roche Sequencing Solutions, Incorporated, Pleasanton, California 94588, United States
| | - Ivona Voráčová
- Czech Academy of Sciences, Institute of Analytical Chemistry, Brno 61142, Czech Republic
| | - Jakub Novotný
- Czech Academy of Sciences, Institute of Analytical Chemistry, Brno 61142, Czech Republic
| | - Pantea Gheibi
- Roche Sequencing Solutions, Incorporated, Pleasanton, California 94588, United States
| | - Jan Berka
- Roche Sequencing Solutions, Incorporated, Pleasanton, California 94588, United States
| | - Yann Astier
- Roche Sequencing Solutions, Incorporated, Pleasanton, California 94588, United States
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Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection. Anal Chim Acta 2019; 1070:112-122. [PMID: 31103164 DOI: 10.1016/j.aca.2019.04.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 12/29/2022]
Abstract
Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has proven to be an effective technique for aptamers selection. In this study, we present an online reaction based convenient single-step CE-SELEX (ssCE-SELEX) mode with human thrombin (H-Thr) as a model target. The selection progress was monitored through bulk Kd analysis, which showed more than a 1000-fold improvement over the initial library after two rounds of selection. Three selected candidate sequences presented high binding affinities against H-Thr with nanomolar (nM) Kd determined by nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM, 56.4-177.1 nM) and CE based non-linear fitting (CE-NLF, 98.2-199.7 nM). They also exhibited high specificities towards H-Thr compared with bovine thrombin, IgG, lysozyme, and lactoferrin. Meanwhile, the Kd results by isothermal titration calorimetry (ITC) confirmed the effective CE in measuring the aptamer affinity. In addition, three candidates were applied as aptasensors in the AuNPs based colorimetric assay, which showed visible color change and good linear relationships (R2 > 0.93) with H-Thr concentration. Furthermore, molecular dynamics (MD) simulation was performed to validate the binding of the three candidates with H-Thr by binding sites and binding free energy. The ssCE-SELEX method avoids off-line incubation, saves time and sample, and may provide a universal and convenient method for aptamers selection.
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Screening of Oligonucleotide Aptamers and Application in Detection of Pesticide and Veterinary Drug Residues. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61153-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Zhang Y, Lai BS, Juhas M. Recent Advances in Aptamer Discovery and Applications. Molecules 2019; 24:molecules24050941. [PMID: 30866536 PMCID: PMC6429292 DOI: 10.3390/molecules24050941] [Citation(s) in RCA: 335] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.
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Affiliation(s)
- Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen 518055, China.
| | - Bo Shiun Lai
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Mario Juhas
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, CH-8006 Zurich, Switzerland.
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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Zhu C, Wang X, Li L, Hao C, Hu Y, Rizvi AS, Qu F. Online reaction based single-step CE for Protein-ssDNA complex obtainment to assist aptamer selection. Biochem Biophys Res Commun 2018; 506:169-175. [PMID: 30340834 DOI: 10.1016/j.bbrc.2018.08.189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/07/2023]
Abstract
CE application in aptamer selection (CE-SELEX) shows more advantages than other selection methods. In this study, an online reaction based single-step CE (ssCE) mode was employed for fast obtaining protein-ssDNA complex. Using human thrombin (H-Thr) and its aptamer Apt29 as models, we accomplished the procedures of mixing, reaction, separation, detection and complex collection in single step online process, which took about 10 min to obtain the H-Thr/Apt29 complex. Important factors, affecting the aptamer and H-Thr interaction (buffer, ratio of aptamer and H-Thr amount), and complex separation and collection (voltage and temperature) were discussed. Later, the online reaction of H-Thr with an 80 nt ssDNA library was realized under optimized conditions, and the H-Thr/ssDNA complex was collected and subjected to PCR. By analyzing the PCR product through capillary gel electrophoresis, the resulting approximative 80 nt DNA length validated the ssDNA sequence in complex. To confirm the availability of ssCE mode, two ssDNA libraries with different lengths (56 nt and 82 nt ssDNA) and three proteins (platelet derived growth factor, PDGF-BB; lactoferrin protein, LF; and single-strand DNA binding protein, SSB) were utilized. Their complex peaks were also observed in electropherograms as expected. Additionally, the online incubation of ssDNA and H-Thr was achieved by stopping the separation voltage for some time when ssDNA passed the H-Thr zone. Our results show the ssCE mode has apparent merits of saving time and sample cost for aptamer selection against protein targets.
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Affiliation(s)
- Chao Zhu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Xiaoqian Wang
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Linsen Li
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Chenxu Hao
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Youhao Hu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Aysha Sarfraz Rizvi
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Feng Qu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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Wang L, Wang R, Wei H, Li Y. Selection of aptamers against pathogenic bacteria and their diagnostics application. World J Microbiol Biotechnol 2018; 34:149. [PMID: 30220026 DOI: 10.1007/s11274-018-2528-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
Aptamers are short nucleotide sequences which can specifically bind to a variety of targets with high affinity. They are identified and selected via systematic evolution of ligands by exponential enrichment (SELEX). Compared to antibodies, aptamers offer several advantages including easy labeling, high stability and lower cost. Those advantages make it possible to be a potential for use as a recognition probe to replace antibody in the diagnostic field. This article is intended to provide a comprehensive review, which is focused on systemizing recent advancements concerning SELEX procedures, with special emphasis on the key steps in SELEX procedures. The principles of various aptamer-based detections of pathogenic bacteria and their application are discussed in detail, including colorimetric detection, fluorescence detection, electrochemical detection, lateral flow strip test, mass sensitive detection and PCR-based aptasensor. By discussing recent research and future trends based on many excellent publications and reviews, we attempt to give the readers a comprehensive view in the field of aptamer selection against pathogenic bacteria and their diagnostics application. Authors hope that this review will promote lively and valuable discussions in order to generate new ideas and approaches towards the development of aptamer-based methods for application in pathogenic bacteria diagnosis.
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Affiliation(s)
- Lijun Wang
- School of Food and Bioengineering, Xihua University, Chengdu, 610039, China.,Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ronghui Wang
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Hua Wei
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang, 330047, China
| | - Yanbin Li
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA. .,Center of Excellence for Poultry Science, University of Arkansas, 203 Engineering Hall, Fayetteville, AR, 72701, USA.
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Selection and Identification of Novel Aptamers Specific for Clenbuterol Based on ssDNA Library Immobilized SELEX and Gold Nanoparticles Biosensor. Molecules 2018; 23:molecules23092337. [PMID: 30216975 PMCID: PMC6225122 DOI: 10.3390/molecules23092337] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 11/17/2022] Open
Abstract
We describe a multiple combined strategy to discover novel aptamers specific for clenbuterol (CBL). An immobilized ssDNA library was used for the selection of specific aptamers using the systematic evolution of ligands by exponential enrichment (SELEX). Progress was monitored using real-time quantitative PCR (Q-PCR), and the enriched library was sequenced by high-throughput sequencing. Candidate aptamers were picked and preliminarily identified using a gold nanoparticles (AuNPs) biosensor. Bioactive aptamers were characterized for affinity, circular dichroism (CD), specificity and sensitivity. The Q-PCR amplification curve increased and the retention rate was about 1% at the eighth round. Use of the AuNPs biosensor and CD analyses determined that six aptamers had binding activity. Affinity analysis showed that aptamer 47 had the highest affinity (Kd = 42.17 ± 8.98 nM) with no cross reactivity to CBL analogs. Indirect competitive enzyme linked aptamer assay (IC-ELAA) based on a 5′-biotin aptamer 47 indicated the limit of detection (LOD) was 0.18 ± 0.02 ng/L (n = 3), and it was used to detect pork samples with a mean recovery of 83.33–97.03%. This is the first report of a universal strategy including library fixation, Q-PCR monitoring, high-throughput sequencing, and AuNPs biosensor identification to select aptamers specific for small molecules.
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In vivo biosensors: mechanisms, development, and applications. ACTA ACUST UNITED AC 2018; 45:491-516. [DOI: 10.1007/s10295-018-2004-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/30/2017] [Indexed: 01/09/2023]
Abstract
Abstract
In vivo biosensors can recognize and respond to specific cellular stimuli. In recent years, biosensors have been increasingly used in metabolic engineering and synthetic biology, because they can be implemented in synthetic circuits to control the expression of reporter genes in response to specific cellular stimuli, such as a certain metabolite or a change in pH. There are many types of natural sensing devices, which can be generally divided into two main categories: protein-based and nucleic acid-based. Both can be obtained either by directly mining from natural genetic components or by engineering the existing genetic components for novel specificity or improved characteristics. A wide range of new technologies have enabled rapid engineering and discovery of new biosensors, which are paving the way for a new era of biotechnological progress. Here, we review recent advances in the design, optimization, and applications of in vivo biosensors in the field of metabolic engineering and synthetic biology.
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Silver decahedral nanoparticles empowered SPR imaging-SELEX for high throughput screening of aptamers with real-time assessment. Biosens Bioelectron 2018; 109:206-213. [PMID: 29567565 DOI: 10.1016/j.bios.2018.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 01/16/2023]
Abstract
A highly efficient method for aptamer screening with real-time monitoring of the SELEX process was described by silver decahedra nanoparticles (Ag10-NPs) enhanced surface plasmon resonance imaging (SPRI). A microarray chip was developed by immobilization of target protein (Lactoferrin (Lac)) and control proteins (α-lactalbumin (α), β-lactoglobulin (β), casein, and bovine serum albumin (BSA)) on the biochip surface. Ag10-NPs were conjugated with an ssDNA library (lib) (Ag10-NPs-library) that consisted of a central 40 nt randomized sequence and a 20 nt fixed primer sequence. Introduction of the Ag10-NPs-library to the SPRI flow channels drastically increased the sensitivity of SPRI signal for real-time monitoring of SELEX. The work allows rapid screening of potential targets, and yields nine aptamers with high affinity (nanomolar range) for Lac after only six-rounds of selection. The aptamer Lac 13-26 was then further tested by SPRI, and the results demonstrated that the aptamer had the capacity to be ultra-sensitive for specific detection of Lac. The novel SPRI-SELEX method demonstrated here showed many advantages of real-time evaluation, high throughput, and high efficiency.
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Ric A, Ecochard V, Iacovoni JS, Boutonnet A, Ginot F, Ong-Meang V, Poinsot V, Paquereau L, Couderc F. G-quadruplex aptamer selection using capillary electrophoresis-LED-induced fluorescence and Illumina sequencing. Anal Bioanal Chem 2018; 410:1991-2000. [PMID: 29380016 DOI: 10.1007/s00216-018-0865-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/28/2017] [Accepted: 01/08/2018] [Indexed: 01/15/2023]
Abstract
One of the major difficulties that arises when selecting aptamers containing a G-quadruplex is the correct amplification of the ssDNA sequence. Can aptamers containing a G-quadruplex be selected from a degenerate library using non-equilibrium capillary electrophoresis (CE) of equilibrium mixtures (NECEEM) along with high-throughput Illumina sequencing? In this article, we present some mismatches of the G-quadruplex T29 aptamer specific to thrombin, which was PCR amplified and sequenced by Illumina sequencing. Then, we show the proportionality between the number of sequenced molecules of T29 added to the library and the number of sequences obtained in Illumina sequencing, and we find that T29 sequences from this aptamer can be detected in a random library of ssDNA after the sample is fractionated by NECEEM, amplified by PCR, and sequenced. Treatment of the data by the counting of double-stranded DNA T29 sequences containing a maximum of two mismatches reveals a good correlation with the enrichment factor (fE). This factor is the ratio of the number of aptamer sequences found in the collected complex sample divided by the total number of sequencing reads (aptamer and non-aptamer) plus the quantity of T29 molecules (spiked into a DNA library) injected into CE.
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Affiliation(s)
- Audrey Ric
- Laboratoire des IMRCP, UMR 5623, Université de Toulouse, Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, 31077, Toulouse, France
- Picometrics Technologies, 478 Rue de la Découverte, 31670, Labège, France
| | - Vincent Ecochard
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, 31077, Toulouse, France
| | - Jason S Iacovoni
- I2MC, UMR1048, 1 Avenue du Professeur Jean Poulhès, 31432, Toulouse Cedex 4, France
| | - Audrey Boutonnet
- Picometrics Technologies, 478 Rue de la Découverte, 31670, Labège, France
| | - Frédéric Ginot
- Picometrics Technologies, 478 Rue de la Découverte, 31670, Labège, France
| | - Varravaddheay Ong-Meang
- Laboratoire des IMRCP, UMR 5623, Université de Toulouse, Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
| | - Véréna Poinsot
- Laboratoire des IMRCP, UMR 5623, Université de Toulouse, Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
| | - Laurent Paquereau
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, 31077, Toulouse, France
| | - François Couderc
- Laboratoire des IMRCP, UMR 5623, Université de Toulouse, Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France.
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An aptamer-based PCR method coupled with magnetic immunoseparation for sensitive detection of Salmonella Typhimurium in ground turkey. Anal Biochem 2017. [PMID: 28645756 DOI: 10.1016/j.ab.2017.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aptamers are single-stranded oligonucleotide ligands that can bind to targets with high affinity and specificity. They have been widely studied in the field of diagnostics as alternatives to antibodies due to their favorable features such as easy labeling, temperature tolerance, lower cost and recognition of a wide variety of targets. In this study, an aptamer-based PCR method coupled with magnetic immunoseparation was developed to detect S. Typhimurium from ground turkey. Firstly, biotinylated polyclonal anti-S. Typhimurium antibody was immobilized on streptavidin-coated magnetic nanobeads to capture S. Typhimurium. Secondly, the aptamers were added and bound to the surface of S. Typhimurium after blocking the magnetic nanobeads with short ssDNA. Finally, the aptamers were released by heating and amplified by PCR. After optimization, this assay was able to detect 102 CFU/mL of S. Typhimurium in pure culture, and 103 CFU/mL of S. Typhimurium in ground turkey. This study demonstrated the feasibility and application of an aptamer-based PCR method coupled with magnetic immunoseparation for sensitive detection of S. Typhimurium in ground turkey.
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Platella C, Riccardi C, Montesarchio D, Roviello GN, Musumeci D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim Biophys Acta Gen Subj 2017; 1861:1429-1447. [PMID: 27865995 PMCID: PMC7117017 DOI: 10.1016/j.bbagen.2016.11.027] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | | | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Napoli, Italy.
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Wang L, Wang R, Chen F, Jiang T, Wang H, Slavik M, Wei H, Li Y. QCM-based aptamer selection and detection of Salmonella typhimurium. Food Chem 2016; 221:776-782. [PMID: 27979272 DOI: 10.1016/j.foodchem.2016.11.104] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/11/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022]
Abstract
In this study, quartz crystal microbalance (QCM) was used to select aptamers against Salmonella typhimurium. To increase the success rate of Systematic Evolution of Ligands Exponential Enrichment (SELEX), the affinity of DNA pool in each round was simultaneously tracked using QCM in order to avoid the loss of high-quality aptamers. When the frequency change reached a maximum value after several rounds of selection and counter-selection, the candidate pool was cloned and sequenced. Out of three aptamer candidates, aptamer B5 showed high specificity and binding affinity with dissociation constant (Kd value) of 58.5nM, and was chosen for further studies. Subsequently, a QCM-based aptasensor was developed to detect S. typhimurium. This aptasensor was able to detect 103CFU/mL of S. typhimurium with less than 1h. This study demonstrated QCM-based selection could be more effective selection of aptamers and QCM-based aptasensor could be more sensitive in detecting S. typhimurium.
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Affiliation(s)
- Lijun Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ronghui Wang
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Fang Chen
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Tieshan Jiang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hong Wang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Michael Slavik
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hua Wei
- Jiangxi-OAI Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Yanbin Li
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA; Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA.
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Li X, He Y, Ma Y, Bie Z, Liu B, Liu Z. Hybrid Approach Combining Boronate Affinity Magnetic Nanoparticles and Capillary Electrophoresis for Efficient Selection of Glycoprotein-Binding Aptamers. Anal Chem 2016; 88:9805-9812. [PMID: 27579807 DOI: 10.1021/acs.analchem.6b02907] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Capillary electrophoresis (CE) and magnetic beads have been widely used for the selection of aptamers owing to their efficient separation ability. However, these methods alone are associated with some apparent drawbacks. CE suffers from small injection volumes and thereby only a limited amount of aptamer can be collected at each round. While the magnetic beads approach is often associated with tedious procedure and nonspecific binding. Herein we present a hybrid approach that combines the above two classical aptamer selection methods to overcome the drawbacks associated with these methods alone. In this hybrid method, one single round selection by boronate affinity magnetic nanoparticles (BA-MNPs) was first performed and then followed by a CE selection of a few rounds. The BA-MNPs-based selection eliminated nonbinding sequences, enriching effective sequences in the nucleic acid library. While the CE selection, which was carried out in free solutions, eliminated steric hindrance effects in subsequent selection. Two typical glycoproteins, Ribonuclease B (RNase B) and alkaline phosphatase (ALP), were used as targets. This hybrid method allowed for efficient selection of glycoprotein-binding aptamers within 4 rounds (1 round of BA-MNPs-based selection and 3 rounds of CE selection) and the dissociation constants reached 10-8 M level. The hybrid selection approach exhibited several significant advantages, including speed, affinity, specificity, and avoiding negative selection. Using one of the selected ALP-binding aptamers as an affinity ligand, feasibility for real application of the selected aptamers was demonstrated through constructing an improved enzyme activity assay.
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Affiliation(s)
- Xinglin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Yunjie He
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University , 321 Zhongshan Road, Nanjing 210008, China
| | - Yanyan Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Zijun Bie
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Baorui Liu
- Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University , 321 Zhongshan Road, Nanjing 210008, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
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Acousto-microfluidics for screening of ssDNA aptamer. Sci Rep 2016; 6:27121. [PMID: 27272884 PMCID: PMC4897735 DOI: 10.1038/srep27121] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022] Open
Abstract
We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8th round of the acoustophoretic systematic evolution of ligands by exponential enrichment (SELEX) and following sequence analysis with NGS, 7 PSA binding ssDNA aptamer-candidates were obtained and characterized with surface plasmon resonance (SPR) for affinity and specificity. As a result of the new SELEX method with PSA as the model target protein, the best PSA binding aptamer showed specific binding to PSA with a dissociation constant (Kd) of 0.7 nM.
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McKeague M, Wong RS, Smolke CD. Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res 2016; 44:2987-99. [PMID: 26969733 PMCID: PMC4838379 DOI: 10.1093/nar/gkw151] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022] Open
Abstract
The past decade of synthetic biology research has witnessed numerous advances in the development of tools and frameworks for the design and characterization of biological systems. Researchers have focused on the use of RNA for gene expression control due to its versatility in sensing molecular ligands and the relative ease by which RNA can be modeled and designed compared to proteins. We review the recent progress in the field with respect to RNA-based genetic devices that are controlled through small molecule and protein interactions. We discuss new approaches for generating and characterizing these devices and their underlying components. We also highlight immediate challenges, future directions and recent applications of synthetic RNA devices in engineered biological systems.
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Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Remus S Wong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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Saito S, Hirose K, Tsuchida M, Wakui K, Yoshimoto K, Nishiyama Y, Shibukawa M. Rapid acquisition of high-affinity DNA aptamer motifs recognizing microbial cell surfaces using polymer-enhanced capillary transient isotachophoresis. Chem Commun (Camb) 2015; 52:461-4. [PMID: 26525483 DOI: 10.1039/c5cc07268a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present a polymer-enhanced capillary transient isotachophoresis (PectI) selection methodology for acquisition of high-affinity (kinetically inert) DNA aptamers capable of recognizing distinct microbial cell surfaces, which requires only a single electrophoretic separation between particles (free cells and cells bound with aptamers) and molecules (unbound or dissociated DNA) in free solution.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.
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A Highlight of Recent Advances in Aptamer Technology and Its Application. Molecules 2015; 20:11959-80. [PMID: 26133761 PMCID: PMC6331864 DOI: 10.3390/molecules200711959] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/10/2023] Open
Abstract
Aptamers and SELEX (systematic evolution of ligands by exponential enrichment) technology have gained increasing attention over the past 25 years. Despite their functional similarity to protein antibodies, oligonucleotide aptamers have many unique properties that are suitable for clinical applications and industrialization. Aptamers may be superior to antibodies in fields such as biomarker discovery, in vitro and in vivo diagnosis, precisely controlled drug release, and targeted therapy. However, aptamer commercialization has not occurred as quickly as expected, and few aptamer-based products have yet successfully entered clinical and industrial use. Thus, it is important to critically review some technical barriers of aptamer and SELEX technology per se that may impede aptamer development and application. To date, how to rapidly obtain aptamers with superior bioavailability over antibodies remains the key issue. In this review, we discuss different chemical and structural modification strategies aimed to enhance aptamer bioavailability. We also discuss improvements to SELEX process steps to shorten the selection period and improve the SELEX process success rate. Applications in which aptamers are particularly suited and perform differently or superior to antibodies are briefly introduced.
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