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Córdova-Espinoza MG, González-Vázquez R, Barron-Fattel RR, Gónzalez-Vázquez R, Vargas-Hernández MA, Albores-Méndez EM, Esquivel-Campos AL, Mendoza-Pérez F, Mayorga-Reyes L, Gutiérrez-Nava MA, Medina-Quero K, Escamilla-Gutiérrez A. Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification. Int J Mol Sci 2024; 25:1257. [PMID: 38279257 PMCID: PMC10817072 DOI: 10.3390/ijms25021257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.
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Affiliation(s)
- María Guadalupe Córdova-Espinoza
- Immunology Laboratory, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico;
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Hospital de Especialidades, “Dr. Antonio Fraga Mouret”, National Medical Center La Raza, Mexico City 02990, Mexico
| | - Rosa González-Vázquez
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Hospital de Especialidades, “Dr. Antonio Fraga Mouret”, National Medical Center La Raza, Mexico City 02990, Mexico
| | - Rolando Rafik Barron-Fattel
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
| | - Raquel Gónzalez-Vázquez
- Laboratory of Biotechnology, Department of Biological Systems, Metropolitana Campus Xochimilco, CONAHCYT—Universidad Autonoma, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico;
| | - Marco Antonio Vargas-Hernández
- Research Department, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Exsal Manuel Albores-Méndez
- Research Department, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Ana Laura Esquivel-Campos
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - Felipe Mendoza-Pérez
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - Lino Mayorga-Reyes
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - María Angélica Gutiérrez-Nava
- Laboratory of Microbial Ecology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacan, Mexico City 04960, Mexico;
| | - Karen Medina-Quero
- Immunology Laboratory, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico;
| | - Alejandro Escamilla-Gutiérrez
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Microbiology Laboratory, Hospital General “Dr. Gaudencio González Garza”, National Medical Center La Raza, Mexico City 02990, Mexico
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Su Y, Zhu L, Wu Y, Liu Z, Xu W. Progress and challenges in bacterial whole-cell-components Aptamer advanced screening and site identification. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gan Z, Roslan MAM, Abd Shukor MY, Halim M, Yasid NA, Abdullah J, Md Yasin IS, Wasoh H. Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application. BIOSENSORS 2022; 12:bios12110922. [PMID: 36354431 PMCID: PMC9687594 DOI: 10.3390/bios12110922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 05/28/2023]
Abstract
Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.
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Affiliation(s)
- Zixuen Gan
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
| | | | - Mohd Yunus Abd Shukor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
| | - Murni Halim
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
| | - Nur Adeela Yasid
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
| | - Jaafar Abdullah
- Faculty of Science, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
| | - Ina Salwany Md Yasin
- Aquatic Animal Health and Therapeutics Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
| | - Helmi Wasoh
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, Serdang 43400, SGR, Malaysia
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Xiong L, Xia M, Wang Q, Meng Z, Zhang J, Yu G, Dong Z, Lu Y, Sun Y. DNA aptamers specific for Legionella pneumophila: systematic evolution of ligands by exponential enrichment in whole bacterial cells. Biotechnol Lett 2022; 44:777-786. [PMID: 35416565 DOI: 10.1007/s10529-022-03252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/31/2022] [Indexed: 11/30/2022]
Abstract
Legionella pneumophila is the major causative agent of Legionnaires' disease and Pontiac fever, which pose major public health problems. Rapid detection of L. pneumophila is important for global control of these diseases. Aptamers, short oligonucleotides that bind to targets with high affinity and specificity, have great potential for use in pathogenic bacterium detection, diagnostics, and therapy. Here, we used a whole-cell SELEX (systematic evolution of ligands by exponential enrichment) method to isolate and characterize single-stranded DNA (ssDNA) aptamers against L. pneumophila. A total of 60 ssDNA sequences were identified after 17 rounds of selection. Other bacterial species (Escherichia coli, Bacillus subtilis, Pseudomonas syringae, Staphylococcus aureus, Legionella quateirensis, and Legionella adelaidensis) were used for counterselection to enhance the specificity of ssDNA aptamers against L. pneumophila. Four ssDNA aptamers showed strong affinity and high selectivity for L. pneumophila, with Kd values in the nanomolar range. Bioinformatic analysis of the most specific aptamers revealed predicted conserved secondary structures that might bind to L. pneumophila cell walls. In addition, the binding of these four fluorescently labeled aptamers to the surface of L. pneumophila was observed directly by fluorescence microscopy. These aptamers identified in this study could be used in the future to develop medical diagnostic tools and public environmental detection assays for L. pneumophila.
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Affiliation(s)
- Lina Xiong
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Mingchen Xia
- Guangzhou Saite Testing Co., LTD, Guangzhou, China
| | - Qinglin Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhen Meng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China
| | - Jie Zhang
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China
| | - Zhangyong Dong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yunhao Sun
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China. .,College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, No. 24, Dongsha Street, Guangzhou, China.
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5
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Research progress of whole-cell-SELEX selection and the application of cell-targeting aptamer. Mol Biol Rep 2022; 49:7979-7993. [PMID: 35274201 DOI: 10.1007/s11033-022-07317-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Aptamers refer to the artificially synthesized nucleic acid sequences (DNA/RNA) that can bind to a wide range of targets with high affinity and specificity, which are generally generated from systematic evolution of ligands by exponential enrichment (SELEX). As a novel method of aptamers screening, whole-cell-SELEX (WC-SELEX) has gained more and more attention in many fields such as biomedicine, analytical chemistry, and molecular diagnostics due to its ability to screen multiple potential aptamers without knowing the detailed structural information of target molecules. METHODS AND RESULTS In recent years, with the deepening of research on application of aptamers, the traditional WC-SELEX cannot meet the practical application because of long experimental period, complicated operation process and low specificity, etc. Therefore, the development of more efficient methods for screening aptamer is always on the road. This paper summarizes the current research status of WC-SELEX for bacteria, parasites and animal cells, and reviews the latest advances of WC-SELEX techniques that are dependent on novel instruments, materials and microelectronics, including fluorescence-activated cell sorting-assisted SELEX, three-dimensional assisted WC-SELEX, and microfluidic chip system-assisted WC-SELEX. In addition, the application of aptamers targeting cells was discussed. CONCLUSION Taken together, this review is aimed at providing a reference for WC-SELEX selection and application of aptamer targeting cells.
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Yu Q, Liu M, Wu S, Xiao H, Qin X, Li P. Generation and characterization of aptamers against grass carp reovirus infection for the development of rapid detection assay. JOURNAL OF FISH DISEASES 2021; 44:33-44. [PMID: 32959408 DOI: 10.1111/jfd.13265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/20/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Grass carp reovirus (GCRV) causes devastating viral haemorrhagic disease in farmed grass carp (Ctenopharyngon idellus). As novel molecular probes, aptamers have been widely applied in rapid diagnosis and efficient therapies against virus or diseases. In this study, three single-stranded DNA (ssDNA) aptamers were selected against GCRV-infected CIK cells via SELEX (systematic evolution of ligands by exponential enrichment technology). Secondary structures predicted by MFOLD indicated that aptamers formed stem-loop structures, and GVI-11 had the lowest ΔG value of -30.84 KJ/mol. Three aptamers could specifically recognize GCRV-infected CIK cells, with calculated dissociation constants (Kd) of 220.86, 176.63 and 278.66 nM for aptamers GVI-1, GVI-7 and GVI-11, respectively, which indicated that they could serve as specific delivery system for antiviral therapies. The targets of aptamers GVI-1, GVI-7 and GVI-11 on the surface of GCRV-infected cells could be membrane proteins, which were trypsin-sensitive. Furthermore, FAM-labelled aptamer GVI-7 could be applied to detect GCRV infection in vivo. It is the first time to generate and characterize aptamers against GCRV-infected cells. These aptamers have great potentials in development of rapid diagnosis technology and antiviral agents against GCRV infection in aquaculture.
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Affiliation(s)
- Qing Yu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Advanced Technology R & D Center, Beibu Gulf Marine Industrial Research Institute, Guangxi Academy of Sciences, Nanning, China
| | - Mingzhu Liu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Advanced Technology R & D Center, Beibu Gulf Marine Industrial Research Institute, Guangxi Academy of Sciences, Nanning, China
| | - Siting Wu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Advanced Technology R & D Center, Beibu Gulf Marine Industrial Research Institute, Guangxi Academy of Sciences, Nanning, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Hehe Xiao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Advanced Technology R & D Center, Beibu Gulf Marine Industrial Research Institute, Guangxi Academy of Sciences, Nanning, China
| | - Xinling Qin
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
| | - Pengfei Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Advanced Technology R & D Center, Beibu Gulf Marine Industrial Research Institute, Guangxi Academy of Sciences, Nanning, China
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, China
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Selection and Identification of Common Aptamers against Both Vibrio Harveyi and Vibrio Alginolyticus. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60018-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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YU Q, LIU MZ, XIAO HH, YI Y, CHENG H, Putra DF, LI SQ, LI PF. Selection and Characterization of Aptamers for Specific Detection of Iridovirus Disease in Cultured Hybrid Grouper (Epinephelus Fuscoguttatus♀ × E. Lanceolatus♂). CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60021-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Liu D, Hu B, Peng D, Lu S, Gao S, Li Z, Wang L, Jiao B. Isolation ssDNA aptamers specific for both live and viable but nonculturable stateVibrio vulnificususing whole bacteria-SEILEX technology. RSC Adv 2020; 10:15997-16008. [PMID: 35493682 PMCID: PMC9052868 DOI: 10.1039/c9ra10733a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/05/2020] [Indexed: 11/23/2022] Open
Abstract
Vibrio vulnificus is a ubiquitous marine bacterium that may cause rapid and deadly infection, threatening lives of people living around natural bodies of water, especially in coastal regions. However, traditional culture-based methods are time-consuming and unable to detect Viable But Non-Culturable (VBNC) V. vulnificus cells. In this work, we isolated a batch of detection aptamers specifically binding to V. vulnificus in all culture status. With traditional whole bacteria-SELEX (Systematic Evolution of Ligands by EXponential enrichment), flow cytometer analysis and imaging, we identify 18 candidates and validated two of them (V8 and V13) as applicable aptamers. Their truncated sequences also showed comparable performance. The dissociation constant (KD) value of V8 is shown to be as low as 11.22 ± 1.32 nM. Optimal aptamers V8 and V13 are also validated to be effective to detect different Vibrio vulnificus strains under different binding environments using flow cytometry. As for detection parameters, the LOD of the V8 from cytometry is 29.96 CFU mL−1, and the linear range is 102–5 × 105 CFU mL−1. This is the first case demonstrating that aptamers can detect the existence of VBNC bacteria as well as live bacteria. With whole-bacteria SELEX, we got aptamers that can bind to V. vulnificus in VBNC Status for the first time.![]()
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Affiliation(s)
- Dejing Liu
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
| | - Bo Hu
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
| | - Dingfa Peng
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
| | - Shan Lu
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
| | - Shunxiang Gao
- Eye & ENT Hospital
- State Key Laboratory of Medical Neurobiology
- Institutes of Brain Science and Collaborative Innovation Center for Brain Science
- Shanghai Medical College
- Fudan University
| | - Zhengang Li
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology
- College of Basic Medical Sciences
- Second Military Medical University
- Shanghai
- People's Republic of China
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Yu Q, Liu M, Xiao H, Wu S, Qin X, Ke K, Li S, Mi H, Shi D, Li P. Development of novel aptamer-based enzyme-linked apta-sorbent assay (ELASA) for rapid detection of mariculture pathogen Vibrio alginolyticus. JOURNAL OF FISH DISEASES 2019; 42:1523-1529. [PMID: 31448425 DOI: 10.1111/jfd.13066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
As the major opportunistic pathogen to both marine animals and humans, Vibrio alginolyticus (V. alginolyticus) has caused heavy economic losses to mariculture. ssDNA aptamer VA2 targeting live V. alginolyticus was generated by systematic evolution of ligands by exponential enrichment (SELEX) technology in our previous study. In this study, we first developed aptamer (VA2)-based enzyme-linked apta-sorbent assay (VA2-ELASA) for rapid detection of mariculture pathogen V. alginolyticus. The VA2-ELASA could achieve the rapid detection for V. alginolyticus infection with high specificity and sensitivity. The VA2-ELASA could specifically identify V. alginolyticus, but not other non-target bacterial strains. VA2-ELASA could detect V. alginolyticus at the concentration of 5 × 104 /ml, the incubation time short to 1 min and the incubation temperature as high as 45°C, which proved sensitivity and stability of the novel VA2-ELASA in this study. It took less than one hour to accomplish the detection process by VA2-ELASA. The characteristics of specificity, sensitivity and easy operation make VA2-ELASA a novel useful technology for the rapid diagnosis of pathogen V. alginolyticus in mariculture.
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Affiliation(s)
- Qing Yu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Mingzhu Liu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Hehe Xiao
- College of Life Science, Henan Normal University, Xinxiang, China
- Guangxi Key Lab for Marine Biotechnology, Beihai, China
| | - Siting Wu
- Guangxi Key Lab for Marine Biotechnology, Beihai, China
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xianling Qin
- Guangxi Key Laboratory of Marine Environmental Science, Nanning, China
| | - Ke Ke
- Guangxi Key Laboratory of Marine Environmental Science, Nanning, China
| | - Siqiao Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Huizhi Mi
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Deqiang Shi
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Pengfei Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
- Guangxi Key Lab for Marine Biotechnology, Beihai, China
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Yu Q, Liu M, Su H, Xiao H, Wu S, Qin X, Li S, Mi H, Lu Z, Shi D, Li P. Selection and characterization of ssDNA aptamers specifically recognizing pathogenic Vibrio alginolyticus. JOURNAL OF FISH DISEASES 2019; 42:851-858. [PMID: 30859598 DOI: 10.1111/jfd.12985] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
Vibrio alginolyticus (V. alginolyticus) is a major opportunistic pathogen to both marine animals and humans, which has also caused heavy economic losses to mariculture. The aim of this study was to develop highly specific aptamers for V. alginolyticus. Single-stranded DNA (ssDNA) aptamers with high binding affinity to viable V. alginolyticus were generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and identified by flow cytometric analysis in this study. The selected aptamers showed high specificity for V. alginolyticus and low apparent binding for other bacteria. The aptamers formed distinct stem-loop structures, which could form the basis of aptamers' specific binding to the target V. alginolyticus. Aptamer VA2 and VA8 showed particularly high binding affinity constant (Kd) of 14.31 ± 4.26 and 90.00 ± 13.51 nM, respectively. The aptamers produced no cytotoxic effects in vitro and in vivo. ssDNA aptamers were successfully selected against the viable bacteria pathogen V. alginolyticus by SELEX. The aptamers selected in this study could be not only applied as specific chemical molecular probes for studying V. alginolyticus pathogenesis to Trachinotus ovatus, but also developing rapid convenient diagnosis assay for V. alginolyticus infection, even when applied to the complex sample matrix, such as food and environment samples.
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Affiliation(s)
- Qing Yu
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
| | - Mingzhu Liu
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
| | - Hongfei Su
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, College of Marine Sciences, Guangxi University, Nanning, China
| | - Hehe Xiao
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Siting Wu
- Guangxi Key Lab for Marine Biotechnology, Guangxi Institute of Oceanography, Beihai, China
| | - Xianling Qin
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
| | - Siqiao Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Huizhi Mi
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Zijun Lu
- College of Marine Sciences, Guangxi University for Nationalities, Nanning, China
| | - Deqiang Shi
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
| | - Pengfei Li
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
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12
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Aptamer-assisted novel technologies for detecting bacterial pathogens. Biomed Pharmacother 2017; 93:737-745. [PMID: 28700978 DOI: 10.1016/j.biopha.2017.07.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/18/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Nowadays, all people are at risk of infectious diseases that are mainly caused by bacteria causing infection. There is a permanent demand for an appropriate detection method that is affordable, practical, careful, rapid, sensitive, efficient and economical. Aptamers are single stranded DNA or RNA oligonucleotides, which can be recognized specifically and bind to their target molecules and also, be exploited in diagnostic applications. Recently, aptamer-based systems have offered great potentials in applications for the recognition of several important bacterial pathogens from clinical and food specimens. There are several reports appraising the diagnostic applicability of aptamer-based systems for the detection of pathogens. As for its excellent sensitivity, as well as its rapid and efficient detectability, this technique may be practical to indicate bacterial targets with less sample size and may consume less time than traditional methods These systems offer a promising approach for the sensitive and quick detection of food-borne and clinical agents. This review provides an overview of aptamer-based methods as a novel approach for detecting bacterial pathogens.
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Rasoulinejad S, Gargari SLM. Aptamer-nanobody based ELASA for specific detection of Acinetobacter baumannii isolates. J Biotechnol 2016; 231:46-54. [PMID: 27234880 DOI: 10.1016/j.jbiotec.2016.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/12/2016] [Accepted: 05/19/2016] [Indexed: 11/26/2022]
Abstract
Acinetobacter baumannii has turned into an important threat in nosocomial outbreak infections and multidrug resistance leading to high mortality rates in the 21st century. In recent years its mortality has increased by 15% which in part could be due to lack of a rapid and sensitive diagnostic test. In this work we introduced a new detection test for A. baumannii with two highly specific aptamer and nanobody molecules. High binding affinity DNA oligonucleotide aptamers toward A. baumannii were selected through 12 rounds of whole cell System Evolution of Ligands by EXponential enrichment process (SELEX). The SELEX procedures was monitored by flow cytometry. The dissociation constant and binding efficiency of the selected aptamer Aci49 was 7.547±1:353pM and 47.50%, respectively. A sandwich enzyme linked aptamer sorbent assay (ELASA) was designed with the biotinylated Aci49 aptamer and our previously developed nanobody against biofilm associated protein (Bap). The assay system was optimized with A. baumannii (ATCC 19606) and 47 clinical isolates of A. baumannii were tested. The threshold of detection in sandwich ELASA process was10(3) CFU/ml. The sensitivity of test toward the clinical isolates was 95.47%. Our results reveal that the sandwich ELASA is sensitive and specific enough for the rapid detection of A. baumannii from clinical isolates.
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Marton S, Cleto F, Krieger MA, Cardoso J. Isolation of an Aptamer that Binds Specifically to E. coli. PLoS One 2016; 11:e0153637. [PMID: 27104834 PMCID: PMC4841571 DOI: 10.1371/journal.pone.0153637] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/01/2016] [Indexed: 01/24/2023] Open
Abstract
Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. Aptamers are short oligonucleotides that bind to targets with high affinity and specificity, and have great potential for use in diagnostics and therapy. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. Fluorescently labeled aptamers label the surface of E. coli cells, as viewed by fluorescent microscopy. Specificity tests with twelve different bacterial species showed that one of the aptamers–called P12-31—is highly specific for E. coli. Importantly, this aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies.
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Affiliation(s)
- Soledad Marton
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Fernanda Cleto
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Marco Aurélio Krieger
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil.,Instituto Carlos Chagas, Laboratório de Genomica Functional, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Josiane Cardoso
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
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Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26199940 PMCID: PMC4493287 DOI: 10.1155/2015/419318] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.
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Aptasensor and genosensor methods for detection of microbes in real world samples. Methods 2013; 64:229-40. [PMID: 23872322 DOI: 10.1016/j.ymeth.2013.07.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 12/31/2022] Open
Abstract
The increasing concerns about food and environmental safety have prompted the desire to develop rapid, specific, robust and highly sensitive methods for the detection of microorganisms to ensure public health. Although traditional microbiological methods are available, they are labor intensive, unsuitable for on-site and high throughput analysis, and need well-trained personnel. To circumvent these drawbacks, many efforts have been devoted towards the development of biosensors, using nucleic acid as bio-recognition element. In this review, we will focus on recent significant advances made in two types of DNA-based biosensors, namely genosensors, and aptasensors. In genosensor approach, DNA or RNA target is detected through the hybridization reaction between DNA or RNA and ssDNA sensing element, while in aptasensor method, DNA or RNA aptamer, capable of binding to a target molecule with high affinity and specificity, plays the role of receptor. The goal of this article is to review the innovative methods that have been emerged in genosensor and aptasensor during recent years. Particular attention is given to recent advances and trends in selection of biorecognition element, DNA immobilization strategies and sensing formats.
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