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Manceau M, Farre C, Lagarde F, Mathey R, Buhot A, Vidic J, Léguillier V, Hou Y, Chaix C. Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes. ACS APPLIED MATERIALS & INTERFACES 2024; 16:29645-29656. [PMID: 38809175 DOI: 10.1021/acsami.4c02355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The cell-SELEX method enables efficient selection of aptamers that bind whole bacterial cells. However, after selection, it is difficult to determine their binding affinities using common screening methods because of the large size of the bacteria. Here we propose a simple surface plasmon resonance imaging method (SPRi) for aptamer characterization using bacterial membrane vesicles, called nanosomes, instead of whole cells. Nanosomes were obtained from membrane fragments after mechanical cell disruption in order to preserve the external surface epitopes of the bacterium used for their production. The study was conducted on Bacillus cereus (B. cereus), a Gram-positive bacterium commonly found in soil, rice, vegetables, and dairy products. Four aptamers and one negative control were initially grafted onto a biochip. The binding of B. cereus cells and nanosomes to immobilized aptamers was then compared. The use of nanosomes instead of cells provided a 30-fold amplification of the SPRi signal, thus allowing the selection of aptamers with higher affinities. Aptamer SP15 was found to be the most sensitive and selective for B. cereus ATCC14579 nanosomes. It was then truncated into three new sequences (SP15M, SP15S1, and SP15S2) to reduce its size while preserving the binding site. Fitting the results of the SPRi signal for B. cereus nanosomes showed a similar trend for SP15 and SP15M, and a slightly higher apparent association rate constant kon for SP15S2, which is the truncation with a high probability of a G-quadruplex structure. These observations were confirmed on nanosomes from B. cereus ATCC14579 grown in milk and from the clinical strain B. cereus J066. The developed method was validated using fluorescence microscopy on whole B. cereus cells and the SP15M aptamer labeled with a rhodamine. This study showed that nanosomes can successfully mimic the bacterial membrane with great potential for facilitating the screening of specific ligands for bacteria.
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Affiliation(s)
- Mathilde Manceau
- Université Claude Bernard Lyon 1, CNRS, ISA, UMR5280, 69100 Villeurbanne, France
| | - Carole Farre
- Université Claude Bernard Lyon 1, CNRS, ISA, UMR5280, 69100 Villeurbanne, France
| | - Florence Lagarde
- Université Claude Bernard Lyon 1, CNRS, ISA, UMR5280, 69100 Villeurbanne, France
| | - Raphaël Mathey
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Arnaud Buhot
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Jasmina Vidic
- Université Paris-Saclay, INRAE, AgroParisTech, UMR 1319, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Vincent Léguillier
- Université Paris-Saclay, INRAE, AgroParisTech, UMR 1319, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Yanxia Hou
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Carole Chaix
- Université Claude Bernard Lyon 1, CNRS, ISA, UMR5280, 69100 Villeurbanne, France
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2
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Guo X. Research progress on the detection of foodborne pathogens based on aptamer recognition. Mikrochim Acta 2024; 191:318. [PMID: 38727855 DOI: 10.1007/s00604-024-06375-4] [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: 01/31/2024] [Accepted: 04/20/2024] [Indexed: 05/15/2024]
Abstract
Foodborne diseases caused by bacterial contamination are a serious threat to food safety and human health. The classical plate culture method has the problems of long detection cycle, low sensitivity and specificity, and complicated operation, which cannot meet the growing demand for rapid quantitative detection of pathogenic bacteria. The frequent outbreak of foodborne diseases has put forward higher requirements for rapid and simple detection technology of foodborne pathogens. Aptamer is a kind of oligonucleotide fragment that can recognize targets with the advantages of high affinity and good specificity. The target can be range from proteins, small molecules, cells bacteria, and even viruses. Herein, the latest advances in sensitive and rapid detection of foodborne pathogens based on aptamer recognition was reviewed. Special attention has been paid to the obtained sequences of aptamers to various foodborne pathogens, the optimization of sequences, and the mechanism of aptamer recognition. Then, the research progress of biosensors for the detection of pathogenic bacteria based on aptamer recognition were summarized. Some challenges and prospects for the detection of foodborne pathogens based on aptamer recognition were prospected. In summary, with the further deepening of aptamer research and improvement of detection technology, aptamer-based recognition can meet the needs of rapid, sensitive, and accurate detection in practical applications.
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Affiliation(s)
- Xianglin Guo
- School of Food Science and Technology, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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3
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Zhang Z, Deng X, Zhang W, Chen K, Su Y, Gao C, Gong D, Zhu L, Cai J. Manipulation of magnetic beads for actively capturing Vibrio parahaemolyticus and nucleic acid based on microfluidic system. BIOMICROFLUIDICS 2024; 18:034104. [PMID: 38737753 PMCID: PMC11088461 DOI: 10.1063/5.0193442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/27/2024] [Indexed: 05/14/2024]
Abstract
Rapid biological detection of pathogen micro-organisms has attracted much attention for practical biomedical applications. Despite the development in this field, it is still challenging to achieve simple and rapid biological detection using the microfluidic method. Herein, we propose a novel strategy of biological detection that combines precise detection control of the capillary microfluidic chip and versatile manipulation of magnetic beads. The microfluidic chip was fabricated via laser cutting, which utilized capillary pressure to realize rapid passive injection of liquid samples. Under an external magnetic field, the aptamer-modified magnetic beads were actuated to mix with Vibrio parahaemolyticus (V. parahaemolyticus) and its nucleic acid in the capillary microfluidic chip for rapid selective capture and detection, which could be achieved within 40 min. The experimental results demonstrated that V. parahaemolyticus could be captured using on-chip immunomagnetic beads with a high efficiency and significantly enhanced detection value. Due to these superior performances, the capillary microfluidic system, based on the manipulation of magnetic beads, demonstrated great potential for automatic biological detection.
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Affiliation(s)
- Zhaoxuan Zhang
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xue Deng
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Kehan Chen
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yuan Su
- Key Laboratory of Precision Nutrition and Quality Control of Food, Ministry of Education, Department of Nutrition and Health (Institute of Nutrition and Health), China Agricultural University, Beijing 100083, China
| | - Chao Gao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - De Gong
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Quality Control of Food, Ministry of Education, Department of Nutrition and Health (Institute of Nutrition and Health), China Agricultural University, Beijing 100083, China
| | - Jun Cai
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
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4
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Liu Q, Zheng J, Xie A, Chen M, Gong RY, Sheng Y, Chen HL, Qi CB. Exosome, a Rising Biomarkers in Liquid Biopsy: Advances of Label-Free and Label Strategy for Diagnosis of Cancer. Crit Rev Anal Chem 2024:1-12. [PMID: 38669199 DOI: 10.1080/10408347.2024.2339961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Cancer is commonly considered as one of the most severe diseases, posing a significant threat to human health and society due to various serious challenges. These challenges include difficulties in accurate diagnosis and a high propensity to form metastasis. Tissue biopsy remains the gold standard for diagnosing and subtyping cancer. However, concerns arise from its invasive nature and the potential risk of metastasis during these complex diagnostic procedures. Meanwhile, liquid biopsy has recently witnessed the rapid advancements with the emergence of three prominent detection biomarkers: circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. Whereas, the very low abundance of CTCs combined with the instability of ctDNA intensify the challenges and decrease the accuracy of these two biomarkers for cancer diagnosis. While exosomes have gained widespread recognition as a promising biomarker in liquid biopsy due to their relatively low-invasive detection method, excellent biostability, rich resources, high abundance, and ability to provide valuable information about cancer. Therefore, it is crucial to systematically summarize recent advancements mainly in exosome-based detection methods for early cancer diagnosis. Specifically, this review will primarily focus on label-based and label-free strategies for detecting cancer using exosomes. We anticipate that this comprehensive analysis will enhance readers' understanding of the significance and value of exosomes in the fields of cancer diagnosis and therapy.
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Affiliation(s)
- Qian Liu
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Jing Zheng
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - An Xie
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Min Chen
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Rui-Yue Gong
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Yuan Sheng
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Hong-Lei Chen
- Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Chu-Bo Qi
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
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Kavruk M, Babaie Z, Kibar G, Çetin B, Yeşilkaya H, Amrani Y, Dursun AD, Özalp VC. Aptamer decorated PDA@magnetic silica microparticles for bacteria purification. Mikrochim Acta 2024; 191:285. [PMID: 38652174 PMCID: PMC11039557 DOI: 10.1007/s00604-024-06322-3] [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: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.
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Affiliation(s)
- Murat Kavruk
- Department of Medical Biology, Faculty of Medicine, İstanbul Aydın University, İstanbul, 34295, Türkiye
| | - Zahra Babaie
- Microfluidics & Lab-on-a-chip Research Group, İ.D. Bilkent University, Ankara, 06800, Türkiye
- UNAM-National Nanotech, Research Center and Institute Materials Science & Nanotech, İ.D. Bilkent University, Ankara, 06800, Türkiye
| | - Güneş Kibar
- Microfluidics & Lab-on-a-chip Research Group, İ.D. Bilkent University, Ankara, 06800, Türkiye
- UNAM-National Nanotech, Research Center and Institute Materials Science & Nanotech, İ.D. Bilkent University, Ankara, 06800, Türkiye
- Micro Nano Particles (MNP) Research Group, Materials Science and Engineering Department, Adana Alparslan Turkes Science and Technology University, Adana, 01250, Türkiye
| | - Barbaros Çetin
- Department of Medical Biology, Faculty of Medicine, İstanbul Aydın University, İstanbul, 34295, Türkiye
- Microfluidics & Lab-on-a-chip Research Group, İ.D. Bilkent University, Ankara, 06800, Türkiye
| | - Hasan Yeşilkaya
- Department Respiratory Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Yassine Amrani
- Department Respiratory Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Ali Doğan Dursun
- Department of Physiology, School of Medicine, Atilim University, Ankara, 06830, Türkiye
| | - V Cengiz Özalp
- Department of Medical Biology, School of Medicine, Atilim University, Ankara, 06830, Türkiye.
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Léguillier V, Heddi B, Vidic J. Recent Advances in Aptamer-Based Biosensors for Bacterial Detection. BIOSENSORS 2024; 14:210. [PMID: 38785684 PMCID: PMC11117931 DOI: 10.3390/bios14050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.
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Affiliation(s)
- Vincent Léguillier
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Brahim Heddi
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Jasmina Vidic
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
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7
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Jin Z, Wei Z. Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends. Compr Rev Food Sci Food Saf 2024; 23:e13280. [PMID: 38284571 DOI: 10.1111/1541-4337.13280] [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: 08/07/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024]
Abstract
In recent years, investigations on molecular interaction mechanisms between food proteins and ligands have attracted much interest. The interaction mechanisms can supply much useful information for many fields in the food industry, including nutrient delivery, food processing, auxiliary detection, and others. Molecular simulation has offered extraordinary insights into the interaction mechanisms. It can reflect binding conformation, interaction forces, binding affinity, key residues, and other information that physicochemical experiments cannot reveal in a fast and detailed manner. The simulation results have proven to be consistent with the results of physicochemical experiments. Molecular simulation holds great potential for future applications in the field of food protein-ligand interactions. This review elaborates on the principles of molecular docking and molecular dynamics simulation. Besides, their applications in food protein-ligand interactions are summarized. Furthermore, challenges, perspectives, and trends in molecular simulation of food protein-ligand interactions are proposed. Based on the results of molecular simulation, the mechanisms of interfacial behavior, enzyme-substrate binding, and structural changes during food processing can be reflected, and strategies for hazardous substance detection and food flavor adjustment can be generated. Moreover, molecular simulation can accelerate food development and reduce animal experiments. However, there are still several challenges to applying molecular simulation to food protein-ligand interaction research. The future trends will be a combination of international cooperation and data sharing, quantum mechanics/molecular mechanics, advanced computational techniques, and machine learning, which contribute to promoting food protein-ligand interaction simulation. Overall, the use of molecular simulation to study food protein-ligand interactions has a promising prospect.
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Affiliation(s)
- Zihan Jin
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zihao Wei
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
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8
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Li D, Su Y, Li J, Liu R, Fang B, He J, Xu W, Zhu L. Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections. Biomacromolecules 2023; 24:4568-4586. [PMID: 37728999 DOI: 10.1021/acs.biomac.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.
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Affiliation(s)
- Diandian Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yuan Su
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Rong Liu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Bing Fang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jingjing He
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
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Xiao F, Li W, Wang Z, Xu Q, Song Y, Huang J, Bai X, Xu H. Smartphone-assisted biosensor based on broom-like bacteria-specific magnetic enrichment platform for colorimetric detection of Listeria monocytogenes. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132250. [PMID: 37567141 DOI: 10.1016/j.jhazmat.2023.132250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Pathogenic bacteria contamination poses a major threat to human health. The detection of low-abundance bacteria in complex samples has always been a knotty problem, and high-sensitivity bacterial detection remains challenging. In this work, a novel magnetic platform with high enrichment efficiency for L. monocytogenes was developed. The magnetic platform was designed by branched polyglutamic acid-mediated indirect coupling of cefepime on magnetic nanoparticles (Cefe-PGA-MNPs), and the specific enrichment of low-abundance L. monocytogenes in real samples was achieved by an external magnet, with a capture efficiency over 90%. A controllable and highly active platinum-palladium nanozyme was synthesized and further introduced in the magnetic nanoplatform for the construction of enzymatic colorimetric biosensor. The total detection time for L. monocytogenes was within 100 min. The colorimetric signals generated by labelled nanozyme were corresponding to different concentrations of L. monocytogenes, with a limit of detection (LOD) of 3.1 × 101 CFU/mL, and high reliability and accuracy (with a recovery rate ranging from 96.5% to 116.4%) in the test of real samples. The concept of the developed method is applicable to various fields of biosensing that rely on magnetic separation platforms.
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Affiliation(s)
- Fangbin Xiao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Weiqiang Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Zhixing Wang
- Zhejiang Rural Commercial Digital Technology Co., Ltd., Hangzhou 310016, PR China
| | - Qian Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Yang Song
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Jin Huang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Xuekun Bai
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China.
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Zhang Y, Zhu L, Ma X, Zhu S, Ma Y, Hussain S, He X, Xu W. An Effective Docking-Guided Strategy for Rational Tailoring of Fluorescent Aptamer Switches of Dimethylindole Red Analogue. Anal Chem 2023; 95:7076-7081. [PMID: 37114824 DOI: 10.1021/acs.analchem.3c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The light-up aptamer-dimethylindole red (DIR) complexes have been applied in biochemistry analysis as promising signal transduction tools. However, the unfavorable repulsions between DIR and the long-sequence aptamer switch hinder the complex's further development, and it is urgent to engineer a feasible and efficient strategy for synchronously and rationally adjusting the DIR chemical structure and the DIR aptamer performance. Herein, we communicate a versatile docking-guided rational tailoring strategy to effectively upgrade a DNA aptamer which specifically turns on the fluorescence of a synthesized amino-functionalized DIR analogue (NH2-DIR). After optimizing with three-level tailoring strategies including molecule docking-guided tailoring, coarse tailoring, and fine tailoring, the NH2-DIR aptamer switch with higher binding affinity and specificity, considerable fluorescence-activation ability, and 40% shortened length was obtained. Integrating the experimental and docking results, the binding mechanism between NH2-DIR and the tailored aptamer was deciphered via three types of interactions.
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Affiliation(s)
- Yangzi Zhang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Food Laboratory of Zhongyuan, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Xuan Ma
- Food Laboratory of Zhongyuan, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Siyue Zhu
- College of Science, China Agricultural University, Beijing 100083, China
| | - Yongqiang Ma
- College of Science, China Agricultural University, Beijing 100083, China
| | - Sabir Hussain
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xiaoyun He
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Food Laboratory of Zhongyuan, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
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11
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Wang A, Feng X, He G, Xiao Y, Zhong T, Yu X. Recent advances in digital microfluidic chips for food safety analysis: Preparation, mechanism and application. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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