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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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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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Du S, Ge Y, Lu Z, Du W, Zhang Z, Zhang H. Selection and application of highly specific Salmonella typhimurium aptamers against matrix interference. Biosens Bioelectron 2024; 249:116013. [PMID: 38211466 DOI: 10.1016/j.bios.2024.116013] [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: 10/30/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
In practical applications, the structure and performance of aptamers can be influenced by the presence of sample matrices, which interferes with the specific binding between the aptamer and its target. In this work, to obtain aptamer chains resistant to matrix interference, four typical food matrices were introduced as negative selection targets and selection environments in the process of selecting aptamers for Salmonella typhimurium using the systematic evolution of ligands by exponential enrichment (SELEX) technology. As a result, some highly specific candidate aptamers for Salmonella typhimurium (BB-34, BB-37, ROU-8, ROU-9, ROU-14, ROU-24, DAN-3, NAI-12, and NAI-21) were successfully obtained. Based on the characterization results of secondary structure, affinity, and specificity of these candidate aptamers, ROU-24 selected in the pork matrix and BB-34 selected in the binding buffer were chosen to develop label-free fluorescence aptasensors for the sensitive and rapid detection of the Salmonella typhimurium and verify the performance against matrix interference. The ROU-24-based aptasensor demonstrated a larger linear range and better specificity compared to the BB-34-based aptasensor. Meanwhile, the recovery rate of the ROU-24-based aptasensor in real sample detection (ranging from 94.2% to 110.7%) was significantly higher than that of the BB-34-based aptasensor. These results illustrated that the negative selection of food matrices induced in SELEX could enhance specific binding between the aptamer and its target and the performance against matrix interference. Overall, the label-free fluorescence aptasensors were developed and successfully validated in different foodstuffs, demonstrating a theoretical and practical basis for the study of aptamers against matrix interference.
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Affiliation(s)
- Shuyuan Du
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, PR China
| | - Yuanyuan Ge
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, PR China
| | - Zhang Lu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, PR China
| | - Wenjing Du
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, PR China
| | - Zhen Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, PR China
| | - Hongyan Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Science, Shandong Normal University, Jinan, 250014, PR China.
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Sajjad B, Hussain S, Rasool K, Hassan M, Almomani F. Comprehensive insights into advances in ambient bioaerosols sampling, analysis and factors influencing bioaerosols composition. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122473. [PMID: 37659632 DOI: 10.1016/j.envpol.2023.122473] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/20/2023] [Accepted: 08/27/2023] [Indexed: 09/04/2023]
Abstract
While the study of bioaerosols has a long history, it has garnered heightened interest in the past few years, focusing on both culture-dependent and independent sampling and analysis approaches. Observations have been made regarding the seasonal fluctuations in microbial communities and their connection to particular ambient atmospheric factors. The study of airborne microbial communities is important in public health and atmospheric processes. Nevertheless, the establishment of standardized protocols for evaluating airborne microbial communities and utilizing microbial taxonomy as a means to identify distinct bioaerosols sources and seasonal patterns remains relatively unexplored. This article discusses the challenges and limitations of ambient bioaerosols sampling and analysis, including the lack of standardized methods and the heterogeneity of sources. Future prospects in the field of bioaerosols, including the use of high-throughput sequencing technologies, omics studies, spectroscopy and fluorescence-based monitoring to provide comprehensive incite on metabolic capacity, and activity are also presented. Furthermore, the review highlights the factors that affect bioaerosols composition, including seasonality, atmospheric conditions, and pollution levels. Overall, this review provides a valuable resource for researchers, policymakers, and stakeholders interested in understanding and managing bioaerosols in various environments.
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Affiliation(s)
- Bilal Sajjad
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 5825, Doha, Qatar; Department of Chemical Engineering, Qatar University, P. O. Box 2713, Doha, Qatar
| | - Sabir Hussain
- Department of Environmental Science, Institute of Space Technology, Islamabad, Pakistan
| | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 5825, Doha, Qatar.
| | - Mujtaba Hassan
- Department of Environmental Science, Institute of Space Technology, Islamabad, Pakistan
| | - Fares Almomani
- Department of Chemical Engineering, Qatar University, P. O. Box 2713, Doha, Qatar
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Ning W, Hu S, Zhou C, Luo J, Li Y, Zhang C, Luo Z, Li Y. An ultrasensitive J-shaped optical fiber LSPR aptasensor for the detection of Helicobacter pylori. Anal Chim Acta 2023; 1278:341733. [PMID: 37709468 DOI: 10.1016/j.aca.2023.341733] [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: 05/31/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
The development of label-free and sensitive detection of pathogenic bacteria is of great significance for disease prevention and public health protection. In this study, an originally bent structure, named as J-shaped optical fiber probe, was first designed to engineer a localized surface plasmon resonance (LSPR) aptamer biosensor for the rapid and ultrasensitive detection of Helicobacter pylori (H. pylori). The J-shaped optical fiber probe exhibited a significant improvement in refractive index sensitivity (RIS) and LSPR signal response. Meantime, the original sequence of aptamer was truncated in order to effectively capture H. pylori on the optical fiber surface. Besides, a spacer nucleic acid with short stem-loop structure was adopted to control the aptamer density on gold nanoparticles (AuNPs) on the surface of the J-shaped optical fiber probe, which displayed a further enhancement in LSPR signal response. Benefitting from these creative designs, the proposed LSPR biosensor can realize label-free and sensitive detection of H. pylori with a detection limit as low as 45 CFU/mL and a wide linear range from 1.0 × 102 CFU/mL to 1.0 × 108 CFU/mL. At the same time, the sensing strategy can detect the pathogenic bacteria from actual water samples in one step just in 30 min without any sample pretreatment. Due to the advantages of ease-to-preparation, high sensitivity, and rapid analysis, this proposed J-shaped optical fiber LSPR aptasensor can provide a potential strategy for point-of-caring detection of pathogenic bacteria in environmental monitoring and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chen Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Luo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yu Li
- Research Center of Analytical Instrumentation, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Chuyan Zhang
- Center for Med+X Manufacturing, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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Hou J, Xianyu Y. Tailoring the Surface and Composition of Nanozymes for Enhanced Bacterial Binding and Antibacterial Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302640. [PMID: 37322391 DOI: 10.1002/smll.202302640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Indexed: 06/17/2023]
Abstract
With the advantages of diverse structures, tunable enzymatic activity, and high stability, nanozymes are widely used in medicine, chemistry, food, environment, and other fields. As an alternative to traditional antibiotics, nanozymes attract more and more attention from the scientific researchers in recent years. Developing nanozymes-based antibacterial materials opens up a new avenue for the bacterial disinfection and sterilization. In this review, the classification of nanozymes and their antibacterial mechanisms are discussed. The surface and composition of nanozymes are critical for the antibacterial efficacy, which can be tailored to enhance both the bacterial binding and the antibacterial activity. On the one hand, the surface modification of nanozymes enables binding and targeting of bacteria that improves the antibacterial performance of nanozymes including the biochemical recognition, the surface charge, and the surface topography. On the other hand, the composition of nanozymes can be modulated to achieve enhanced antibacterial performance including the single nanozyme-mediated synergistic and multiple nanozymes-mediated cascade catalytic antibacterial applications. In addition, the current challenges and future prospects of tailoring nanozymes for antibacterial applications are discussed. This review can provide insights into the design of future nanozymes-based materials for the antibacterial treatments.
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Affiliation(s)
- Jinjie Hou
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yunlei Xianyu
- State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou, 310016, P. R. China
- Ningbo Research Institute, Zhejiang University, Ningbo, 315100, P. R. China
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Discovery and translation of functional nucleic acids for clinically diagnosing infectious diseases: Opportunities and challenges. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Development of aptamers for rapid airborne bacteria detection. Anal Bioanal Chem 2022; 414:7763-7771. [PMID: 36071267 DOI: 10.1007/s00216-022-04308-9] [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: 05/24/2022] [Revised: 08/11/2022] [Accepted: 08/27/2022] [Indexed: 11/01/2022]
Abstract
Airborne microbes can rapidly spread and cause various infectious diseases worldwide. This necessitates the determination of a fast and highly sensitive detection method. There have been no studies on receptors targeting Citrobacter braakii (C. braakii), a pathogenic bacterium which can exist in the air. In this study, we rapidly isolate an aptamer, a nucleic acid molecule that can specifically bind to C. braakii by centrifugation-based partitioning method (CBPM) reported previously by our groups as omitting the repeated rounds of binding incubation, separation, and amplification that are indispensable for SELEX. The binding affinity and specificity of isolated aptamers are checked using bacteria in liquid culture and recollection solution from aerosolized bacteria. Recollection solutions of the recovered bacteria are obtained by nebulizing, drying, and recapturing with a biosampler. The CB-5 aptamer shows high affinity and specificity for C. braakii (Kd: 16.42 in liquid culture and 26.91 nM in recollection from aerosolized sample). Our results indicate the current protocol can be employed for the rapid development of reliable diagnostic receptors targeting airborne bacteria.
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