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Wei K, Ye Z, Dong W, Zhang L, Wang W, Li J, Eltzov E, Wang S, Mao X. Generating robust aptamers for food analysis by sequence-based configuration optimization. Talanta 2024; 275:126044. [PMID: 38626500 DOI: 10.1016/j.talanta.2024.126044] [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: 12/13/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.
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Affiliation(s)
- Kaiyue Wei
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ziyang Ye
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenhui Dong
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ling Zhang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenjing Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Jiao Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Sai Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China.
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
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Bai S, Yang Y, Sheng R, Qi Y, Jia Y, Wang X, Cui W, Zheng Y, Li H, Li J. Blood cellular membrane-coated Au/polydopamine nanoparticle-targeted NIR-II antibacterial therapy. J Colloid Interface Sci 2024; 665:855-862. [PMID: 38564949 DOI: 10.1016/j.jcis.2024.03.134] [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: 12/09/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Bacterial infections are the primary causes of infectious diseases in humans. In recent years, the abuse of antibiotics has led to the widespread enhancement of bacterial resistance. Concerns have been raised about the identification of a common treatment platform for bacterial infections. In this study, a composite nanomaterial was used for near-infrared II (NIR-II) photothermal antibacterial treatment. Red blood cell membrane was peeled and coated onto the surface of the Au/polydopamine nanoparticle-containing aptamer. The composite nanomaterials based on Au/polydopamine exhibit highest photothermal conversion capability. Moreover, these assembled nanoparticles can quickly enter the body's circular system with a specific capability to recognise bacteria. In vivo experiments demonstrated that the composites could kill bacteria from infected blood while significantly reducing the level of bacteria in various organs. Such assemblies offer a paradigm for the treatment of bacterial infections caused by the side effects of antibiotics.
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Affiliation(s)
- Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Rongtian Sheng
- School of Public Health, Jilin University, Changchun 130021, China
| | - Yanfei Qi
- School of Public Health, Jilin University, Changchun 130021, China
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaolong Wang
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Wei Cui
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yichen Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hong Li
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China.
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Qin M, Khan IM, Ding N, Qi S, Dong X, Zhang Y, Wang Z. Aptamer-modified paper-based analytical devices for the detection of food hazards: Emerging applications and future perspective. Biotechnol Adv 2024; 73:108368. [PMID: 38692442 DOI: 10.1016/j.biotechadv.2024.108368] [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: 12/28/2023] [Revised: 03/10/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Food analysis plays a critical role in assessing human health risks and monitoring food quality and safety. Currently, there is a pressing need for a reliable, portable, and quick recognition element for point-of-care testing (POCT) to better serve the demands of on-site food analysis. Aptamer-modified paper-based analytical devices (Apt-PADs) have excellent characteristics of high portability, high sensitivity, high specificity, and on-site detection, which have been widely used and concerned in the field of food safety. The article reviews the basic components and working principles of Apt-PADs, and introduces their representative applications detecting food hazards. Finally, the advantages, challenges, and future directions of Apt-PADs-based sensing performance are discussed, to provide new directions and insights for researchers to select appropriate Apt-PADs according to specific applications.
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Affiliation(s)
- Mingwei Qin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Imran Mahmood Khan
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo 315100, PR China
| | - Ning Ding
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shuo Qi
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoze Dong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China.
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4
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Oliveira R, Pinho E, Barros MM, Azevedo NF, Almeida C. In vitro selection of DNA aptamers against staphylococcal enterotoxin A. Sci Rep 2024; 14:11345. [PMID: 38762575 PMCID: PMC11102521 DOI: 10.1038/s41598-024-61094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/30/2024] [Indexed: 05/20/2024] Open
Abstract
Staphylococcal enterotoxin A (SEA) is the most frequently reported in staphylococcal food poisoning (SFP) outbreaks. Aptamers are single-stranded nucleic acids that are seen as promising alternatives to antibodies in several areas, including diagnostics. In this work, systematic evolution of ligands by exponential enrichment (SELEX) was used to select DNA aptamers against SEA. The SELEX protocol employed magnetic beads as an immobilization matrix for the target molecule and real-time quantitative PCR (qPCR) for monitoring and optimizing sequence enrichment. After 10 selection cycles, the ssDNA pool with the highest affinity was sequenced by next generation sequencing (NGS). Approximately 3 million aptamer candidates were identified, and the most representative cluster sequences were selected for further characterization. The aptamer with the highest affinity showed an experimental dissociation constant (KD) of 13.36 ± 18.62 nM. Increased temperature negatively affected the affinity of the aptamer for the target. Application of the selected aptamers in a lateral flow assay demonstrated their functionality in detecting samples containing 100 ng SEA, the minimum amount capable of causing food poisoning. Overall, the applicability of DNA aptamers in SEA recognition was demonstrated and characterized under different conditions, paving the way for the development of diagnostic tools.
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Affiliation(s)
- Ricardo Oliveira
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal.
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
| | - Eva Pinho
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Maria Margarida Barros
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Carina Almeida
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Araújo D, Silva AR, Fernandes R, Serra P, Barros MM, Campos AM, Oliveira R, Silva S, Almeida C, Castro J. Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals. Pathogens 2024; 13:320. [PMID: 38668275 PMCID: PMC11054384 DOI: 10.3390/pathogens13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
The importance of addressing the problem of biofilms in farm, wild, and companion animals lies in their pervasive impact on animal health and welfare. Biofilms, as resilient communities of microorganisms, pose a persistent challenge in causing infections and complicating treatment strategies. Recognizing and understanding the importance of mitigating biofilm formation is critical to ensuring the welfare of animals in a variety of settings, from farms to the wild and companion animals. Effectively addressing this issue not only improves the overall health of individual animals, but also contributes to the broader goals of sustainable agriculture, wildlife conservation, and responsible pet ownership. This review examines the current understanding of biofilm formation in animal diseases and elucidates the complex processes involved. Recognizing the limitations of traditional antibiotic treatments, mechanisms of resistance associated with biofilms are explored. The focus is on alternative therapeutic strategies to control biofilm, with illuminating case studies providing valuable context and practical insights. In conclusion, the review highlights the importance of exploring emerging approaches to mitigate biofilm formation in animals. It consolidates existing knowledge, highlights gaps in understanding, and encourages further research to address this critical facet of animal health. The comprehensive perspective provided by this review serves as a foundation for future investigations and interventions to improve the management of biofilm-associated infections in diverse animal populations.
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Affiliation(s)
- Daniela Araújo
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Ana Rita Silva
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Rúben Fernandes
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Patrícia Serra
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Maria Margarida Barros
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Ana Maria Campos
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Ricardo Oliveira
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- AliCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Sónia Silva
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Carina Almeida
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- AliCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana Castro
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [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: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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Yang G, Liu W, Zhao Y, Jiang G, Zhu C, Qu F. Induction of binding sites for RecA aptamers by differentiated-competition capillary Electrophoresis-SELEX. Talanta 2024; 267:125213. [PMID: 37757693 DOI: 10.1016/j.talanta.2023.125213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
The binding site-oriented SELEX strategy is an effective way to promote the functional evolution of aptamers. Here we report a novel aptamer screening strategy (Differentiated-competition Capillary Electrophoresis-SELEX), which enables candidate aptamers to be directionally induced to bind to different active sites of RecA. In this strategy, we introduce two competing binding factors into the "binding - dissociation" dynamic equilibrium system of RecA and ssDNA libraries. Due to the completely different binding mechanism of the competitive factor and the ssDNA library, it exerts different interference on the binding of RecA and the ssDNA library, which directed the binding site of aptamer candidates during the SELEX process. Multifunctional aptamers with high affinity and specificity were found to inhibit RecA activity by binding to different active sites. In conclusion, the SELEX method developed in our current study have identified a variety of biologically functional aptamers with relatively well-defined binding sites that regulate RecA protein activity, which has potential applications and future prospects for accurate screening of biological functional aptamers.
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Affiliation(s)
- Ge Yang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wenjing Liu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Guangyu Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - 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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8
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Wang M, Hao MC, Huangfu Y, Yang KZ, Zhang XQ, Zhang Y, Chen J, Zhang ZL. A Universal Aptamer for Influenza A Viruses: Selection, Recognition, and Infection Inhibition. ACS Pharmacol Transl Sci 2024; 7:249-258. [PMID: 38230279 PMCID: PMC10789145 DOI: 10.1021/acsptsci.3c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
It is crucial to develop universal inhibitors for viral inhibition due to the rapid mutation of viruses. Herein, a universal aptamer inhibitor was developed that enabled a single DNA molecule to recognize several hemeagglutinin (HA) protein subtypes, inducing broad neutralization against influenza A viruses (IAVs). Through a multi-channel enrichment (MCE) strategy, a high-affinity aptamer named UHA-2 was obtained, with its dissociation constants (Kd) for three different HA proteins being 1.5 ± 0.2 nM (H5N1), 3.7 ± 0.4 nM (H7N9), and 10.1 ± 1.1 nM (H9N2). The UHA-2 aptamer had a universal inhibition effect, by which it could broadly neutralize influenza A H5N1, H7N9, H9N2, H1N1, and H3N2 viruses. Universal aptamer inhibitors have the advantages of acquisition in vitro, stability, simple structure, small size, etc. This study not only develops a novel universal aptamer to achieve a broad inhibition effect on various IAVs, but also opens up an efficient strategy for the development of universal inhibitors against viruses.
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Affiliation(s)
- Meng Wang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
| | - Meng-Chan Hao
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueyue Huangfu
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
| | - Ke-Zhu Yang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
| | - Xiao-Qing Zhang
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Zhang
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianjun Chen
- Key
Laboratory of Special Pathogens and Biosafety, Wuhan Institute of
Virology, Center for Biosafety Mega-Science,
Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Ling Zhang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan, Hubei 430072, China
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9
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Berzal-Herranz A, Romero-López C. Aptamers' Potential to Fill Therapeutic and Diagnostic Gaps. Pharmaceuticals (Basel) 2024; 17:105. [PMID: 38256938 PMCID: PMC10818422 DOI: 10.3390/ph17010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
More than 30 years ago, in 1990, three independent research groups published several papers demonstrating that genetics could be performed in vitro in the absence of living organisms or cells [...].
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Affiliation(s)
- Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas. PTS Granada, Av. del Conocimiento 17, 18016 Granada, Spain
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas. PTS Granada, Av. del Conocimiento 17, 18016 Granada, Spain
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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11
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Kohn EM, Konovalov K, Gomez CA, Hoover GN, Yik AKH, Huang X, Martell JD. Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS Chem Biol 2023; 18:1976-1984. [PMID: 37531184 DOI: 10.1021/acschembio.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirill Konovalov
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christian A Gomez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gillian N Hoover
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew Kai-Hei Yik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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12
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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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Yang H, Xia L, Zheng J, Xie Z, Zhou J, Wu Y. Screening and identification of a DNA aptamer to construct the label-free fluorescent aptasensor for ultrasensitive and selective detection of clothianidin residue in agricultural products. Talanta 2023; 262:124712. [PMID: 37244242 DOI: 10.1016/j.talanta.2023.124712] [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: 02/21/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Clothianidin pesticide not only pollutes the ecological environment, but also poses a potential threat to human health. Thus, it is of great importance to develop efficient and accurate methods to recognize and detect clothianidin residues in agricultural products. Aptamer has the advantages of easy modification, high affinity and good stability, which is particularly suitable as a recognition biomolecule for pesticide detection. However, the aptamer against clothianidin has not been reported. Herein, the aptamer (named CLO-1) had good selectivity and strong affinity (Kd = 40.66 ± 3.47 nM) to clothianidin pesticide, which was screened for the first time by Capture-SELEX strategy. The binding effect of CLO-1 aptamer to clothianidin was further studied by circular dichroism (CD) spectroscopy and molecular docking technique. Finally, the CLO-1 aptamer was used as the recognition molecule to construct a label-free fluorescent aptasensor using GeneGreen dye as sensing signal for the highly sensitive detection of clothianidin pesticide. The constructed fluorescent aptasensor had the limit of detection (LOD) as low as 5.527 μg L-1 for clothianidin, and displayed good selectivity against other competitive pesticides. The aptasensor was applied to detect the clothianidin spiked in tomatoes, pears and cabbages, and the recovery rate was good in the range of 81.99%-106.64%. This study provides a good application prospect for the recognition and detection of clothianidin.
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Affiliation(s)
- Hongqin Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Lian Xia
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Jia Zheng
- Wuliangye Yibin Co., Ltd, Yibin, 644000, Sichuan Province, China
| | - Zhengmin Xie
- Wuliangye Yibin Co., Ltd, Yibin, 644000, Sichuan Province, China
| | - Jianli Zhou
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, China
| | - Yuangen Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, 550025, China; Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, School of Liquor and Food Engineering, Guizhou University, Guiyang, 550025, China.
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Jingwen W, Jingxin W, Ye Z, Yan Z, Caozhi L, Yanyu C, Fanli Z, Su C, Yucheng W. Building an improved transcription factor-centered yeast one hybrid system to identify DNA motifs bound by protein comprehensively. BMC PLANT BIOLOGY 2023; 23:236. [PMID: 37142946 PMCID: PMC10158250 DOI: 10.1186/s12870-023-04241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Identification of the motifs bound by a transcription factor (TF) is important to reveal the function of TF. Previously, we built a transcription factor centered yeast one hybrid (TF-Centered Y1H) that could identify the motifs bound by a target TF. However, that method was difficult to comprehensively identify all the motifs bound by a TF. RESULTS Here, we build an improved TF-Centered Y1H to comprehensively determine the motifs bound by a target TF. Recombination-mediated cloning in yeast was performed to construct a saturated prey library that contains 7 random base insertions. After TF-Centered Y1H screening, all the positive clones were pooled together to isolate pHIS2 vector. The insertion regions of pHIS2 were PCR amplified and the PCR product was subjected to high-throughput sequencing. The insertion sequences were then retrieved and analyzed using MEME program to identify the potential motifs bound by the TF. Using this technology, we studied the motifs bound by an ethylene-responsive factor (BpERF2) from birch. In total, 22 conserved motifs were identified, and most of them are novel cis-acting elements. Both the yeast one hybrid and electrophoretic mobility shift assay verified that the obtained motifs could be bound by BpERF2. In addition, chromatin immunoprecipitation (ChIP) study further suggested that the identified motifs can be bound by BpERF2 in cells of birch. These results together suggested that this technology is reliable and has biological significance. CONCLUSION This method will have wide application in DNA-protein interaction studies.
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Affiliation(s)
- Wang Jingwen
- Key Laboratory Forest Tree Genetics & Breeding of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wang Jingxin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhu Ye
- Nanjing Ruiyuan Biotechnology Company Limited, Nanking, 210000, China
| | - Zhu Yan
- Key Laboratory Forest Tree Genetics & Breeding of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Liu Caozhi
- Nanjing Ruiyuan Biotechnology Company Limited, Nanking, 210000, China
| | - Chen Yanyu
- Nanjing Ruiyuan Biotechnology Company Limited, Nanking, 210000, China
| | - Zeng Fanli
- Nanjing Ruiyuan Biotechnology Company Limited, Nanking, 210000, China
| | - Chen Su
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
| | - Wang Yucheng
- Key Laboratory Forest Tree Genetics & Breeding of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China.
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15
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Biao L, Liu J, Hu X, Xiang W, Hou W, Li C, Wang J, Yao K, Tang J, Long Z, Long W, Liu J. Recent advances in aptamer-based therapeutic strategies for targeting cancer stem cells. Mater Today Bio 2023; 19:100605. [PMID: 36969696 PMCID: PMC10034522 DOI: 10.1016/j.mtbio.2023.100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Cancer stem cells (CSCs) are believed to be the main cause of chemotherapy resistance and tumor relapse. Various therapeutic strategies to eliminate CSCs have been developed recently. Aptamers, also called "chemical antibodies", can specifically bind with their molecular targets through special tertiary structures. The advantages of aptamers, such as lower immunogenicity and smaller size, make them superior to conventional antibodies. Therefore, aptamers have been used widely as targeting ligands for CSC-targeted therapeutic strategies in different tumor types. To date, various therapeutic cargoes have been conjugated to aptamers to kill CSCs, such as chemotherapy drugs, small interfering RNAs, and microRNAs. Aptamer-based targeted therapies for CSCs have made great progress in recent years, especially the development of multifunctional aptamer-based therapeutic strategies. Besides, cell-systematic evolution of ligands by exponential enrichment has been applied to screen new aptamers that might have a higher binding ability for CSCs. In this review, we focus on recent advances and introduce some new modalities of aptamer-drug conjugates against CSCs. Some considerations of the advantages and limitations of different aptamer-based targeted therapies for CSCs are also discussed.
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Liu Y, Guan B, Xu Z, Wu Y, Wang Y, Ning G. A fluorescent assay for sensitive detection of kanamycin by split aptamers and DNA-based copper/silver nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121953. [PMID: 36242838 DOI: 10.1016/j.saa.2022.121953] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Kanamycin was a group of essential antibiotics generally served in treating infections of animals which leached into the environment residual in food, causing health concerns. Thus, selective and sensitive monitoring of kanamycin was significant for food safety. In this work, split aptamers were used as templates to prepare fluorescent Cu/Ag NCs for detection of kanamycin. According to the impressive affinity of the aptamer to kanamycin, two different detection modes were designed using kanamycin aptamer as a recognition molecule, in which one was to combine split aptamer Apt-1 with Apt-2 to form an entangled DNA as a Cu/Ag NCs template, the other was to associate the normal aptamer after encirclement to form Cu/Ag NCs templates. After the addition of kanamycin, the fluorescence signals of the Cu/Ag NCs synthesized in the two modes were both enhanced, but the approach with split aptamer exhibited a superior observable sensitivity than that of the normal type. The detection range showed a well linear relationship between 80 nM and 10 μM when the emission wavelength was 560 nm, and the detection limit was 13.3 nM. In addition, when streptomycin, oxytetracycline, chloramphenicol and chlortetracycline were involved in the selective interference experiment under the same conditions, the fluorescence intensity of the system performed no significant changes. The results demonstrated that this method possessed favorable specificity and selectivity for the assay of kanamycin, proficiently achieving efficient, rapid and sensitive evaluation of kanamycin in the milk samples.
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Affiliation(s)
- Yan Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, 410004 Changsha, China; School of Biology and Biological Engineering, South China University of Technology, 510006 Guangzhou, China
| | - Baibing Guan
- Hunan Provincial Key Laboratory for Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, 410004 Changsha, China
| | - Ziqi Xu
- Hunan Provincial Key Laboratory for Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, 410004 Changsha, China
| | - Yaohui Wu
- Hunan Provincial Key Laboratory for Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, 410004 Changsha, China
| | - Yonghong Wang
- Hunan Provincial Key Laboratory for Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, 410004 Changsha, China.
| | - Ge Ning
- International Education Institute, Hunan University of Chinese Medicine, 410208 Changsha, China.
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Mei LC, Hao GF, Yang GF. Thermodynamic database supports deciphering protein-nucleic acid interactions. Trends Biotechnol 2023; 41:140-143. [PMID: 36272818 DOI: 10.1016/j.tibtech.2022.09.018] [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: 07/13/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023]
Abstract
The thermodynamics of protein-nucleic acid interactions (PNIs) is crucial for elucidating the mechanisms of molecular recognition and pathological consequences. The Protein-Nucleic Acid Thermodynamics Database (PNATDB) is a database containing experimentally determined thermodynamic parameters along with sequence, structural, and function data, which is available free online.
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Affiliation(s)
- Long-Can Mei
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550000, China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.
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