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Zhu J, Yin H, Wang Y, Wang L, Geng X, Deng Y. Conformational change-based fluorometric aptasensor for sensitive cadmium(II) detection in fruits and vegetables. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39143932 DOI: 10.1039/d4ay01333f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Cadmium (Cd2+) is a highly toxic heavy metal that can accumulate in the human body through contaminated food and water, posing great health risks. In this study, a label-free fluorescent aptasensor based on SYBR Green I (SGI) for the rapid and sensitive detection of Cd2+ in food samples was designed. The aptasensor utilizes a Cd2+-specific aptamer (Cd-(21)) and its complementary strand (CSCd-(21)) to form a double-stranded DNA (dsDNA) structure in the absence of Cd2+. SGI intercalates into the dsDNA, resulting in a strong fluorescence signal. In the presence of Cd2+, the aptamer undergoes a conformational change, preventing the formation of dsDNA and leading to a decrease in fluorescence intensity. Under optimized conditions, the aptasensor exhibited a linear response to Cd2+ concentrations ranging from 0.11 to 157.37 ng mL-1, with a limit of detection (LOD) of 0.07 ng mL-1. The aptasensor demonstrated high specificity and was successfully applied to detect Cd2+ in fruits and vegetables, with satisfactory recovery rates (95-111%). The proposed aptasensor provides a promising tool for the rapid and sensitive detection of Cd2+ in food.
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Affiliation(s)
- Jiangxiong Zhu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Hao Yin
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Yang Wang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
| | - Lumei Wang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Xueqing Geng
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
| | - Yun Deng
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
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2
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Meng M, Ma X, Yu L, Zhang X, Chen Y, Li W, Wen Q, Xu D, Chen Q, Xiong Y, Ren J. Phage-induced "one-to-many" FRET sensor for highly sensitive detection of Escherichia coli O157:H7. Biosens Bioelectron 2024; 264:116661. [PMID: 39142229 DOI: 10.1016/j.bios.2024.116661] [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: 05/09/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
As a foodborne pathogen capable of causing severe illnesses, early detection of Escherichia coli O157:H7 (E. coli O157:H7) is crucial for ensuring food safety. While Förster resonance energy transfer (FRET) is an efficient and precise detection technique, there remains a need for amplification strategies to detect low concentrations of E. coli O157:H7. In this study, we presented a phage (M13)-induced "one to many" FRET platform for sensitively detecting E. coli O157:H7. The aptamers, which specifically recognize E. coli O157:H7 were attached to magnetic beads as capture probes for separating E. coli O157:H7 from food samples. The peptide O157S, which specifically targets E. coli O157:H7, and streptavidin binding peptide (SBP), which binds to streptavidin (SA), were displayed on the P3 and P8 proteins of M13, respectively, to construct the O157S-M13K07-SBP phage as a detection probe for signal output. Due to the precise distance (≈3.2 nm) between two neighboring N-terminus of P8 protein, the SA-labeled FRET donor and acceptor can be fixed at the Förster distance on the surface of O157S-M13K07-SBP via the binding of SA and SBP, inducing FRET. Moreover, the P8 protein, with ≈2700 copies, enabled multiple FRET (≈605) occurrences, amplifying FRET in each E. coli O157:H7 recognition event. The O157S-M13K07-SBP-based FRET sensor can detect E. coli O157:H7 at concentration as low as 6 CFU/mL and demonstrates excellent performance in terms of selectivity, detection time (≈3 h), accuracy, precision, practical application, and storage stability. In summary, we have developed a powerful tool for detecting various targets in food safety, environmental monitoring, and medical diagnosis.
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Affiliation(s)
- Meng Meng
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Xiaoyong Ma
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Liping Yu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Xinfang Zhang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Yanni Chen
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Wang Li
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Qian Wen
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Dong Xu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Qi Chen
- Institute of Translational Medicine, Nanchang University, Nanchang, 330031, China
| | - Ying Xiong
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China.
| | - Jiali Ren
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, National Engineering Research Center of Rice and Byproducts Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China.
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3
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Costanzo H, Gooch J, Tungsirisurp S, Frascione N. The Development and Characterisation of ssDNA Aptamers via a Modified Cell-SELEX Methodology for the Detection of Human Red Blood Cells. Int J Mol Sci 2024; 25:1814. [PMID: 38339091 PMCID: PMC10855528 DOI: 10.3390/ijms25031814] [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: 12/11/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Blood is one of the most commonly found biological fluids at crime scenes, with the detection and identification of blood holding a high degree of evidential value. It can provide not only information about the nature of the crime but can also lead to identification via DNA profiling. Presumptive tests for blood are usually sensitive but not specific, so small amounts of the substrate can be detected, but false-positive results are often encountered, which can be misleading. Novel methods for the detection of red blood cells based on aptamer-target interactions may be able to overcome these issues. Aptamers are single-stranded DNA or RNA sequences capable of undergoing selective antigen association due to three-dimensional structure formation. The use of aptamers as a target-specific moiety poses several advantages and has the potential to replace antibodies within immunoassays. Aptamers are cheaper to produce, display no batch-to-batch variation and can allow for a wide range of chemical modifications. They can help limit cross-reactivity, which is a hindrance to current forensic testing methods. Within this study, a modified Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process was used to generate aptamers against whole red blood cells. Obtained aptamer pools were analysed via massively parallel sequencing to identify viable sequences that demonstrate a high affinity for the target. Using bioinformatics platforms, aptamer candidates were identified via their enrichment profiles. Binding characterisation was also conducted on two selected aptamer candidates via fluorescent microscopy and qPCR to visualise and quantify aptamer binding. The potential for these aptamers is broad as they can be utilised within a range of bioassays for not only forensic applications but also other analytical science and medical applications. Potential future work includes the incorporation of developed aptamers into a biosensing platform that can be used at crime scenes for the real-time detection of human blood.
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Affiliation(s)
| | | | | | - Nunzianda Frascione
- Department of Analytical, Environmental & Forensic Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE1 9NH, UK; (H.C.); (J.G.); (S.T.)
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Bohrmann L, Burghardt T, Rodríguez-Rodríguez C, Herth MM, Saatchi K, Häfeli UO. Quantitative Evaluation of a Multimodal Aptamer-Targeted Long-Circulating Polymer for Tumor Targeting. ACS OMEGA 2023; 8:11003-11020. [PMID: 37008162 PMCID: PMC10061651 DOI: 10.1021/acsomega.2c07762] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Aptamers are promising targeting agents for imaging and therapy of numerous diseases, including cancer. However, a significant shortcoming of aptamers is their poor stability and fast excretion, limiting their application in vivo. Common strategies to overcome these challenges is to chemically modify aptamers in order to increase their stability and/or to apply formulation technologies such as conjugating them to polymers or nanocarriers in order to increase their circulation half-life. This is expected to result in improved cellular uptake or retention to passively targeted nanomedicines. Herein, we report a modular conjugation strategy based on click chemistry between functionalized tetrazines and trans-cyclooctene (TCO), for the modification of high molecular weight hyperbranched polyglycerol (HPG) with sgc8 aptamer, fluorescent dyes, and 111In. Our data indicate strong affinity of sgc8 against a range of solid tumor-derived cell lines that have previously not been tested with this aptamer. Nevertheless, nonspecific uptake of scrambled ssDNA-functionalized HPG in cells highlights inherent challenges of aptamer-targeted probes that remain to be solved for clinical translation. We validate HPG-sgc8 as a nontoxic nanoprobe with high affinity against MDA-MB-468 breast and A431 lung cancer cells and show significantly increased plasma stability compared to free sgc8. In vivo quantitative SPECT/CT imaging indicates EPR-mediated tumor uptake of HPG-sgc8 and nontargeted or scrambled ssDNA-conjugated HPG but no statistically significant difference between these formulations in terms of total tumor uptake or retention. Our study emphasizes the need for stringent controls and quantification in the evaluation of aptamer-targeted probes. For this purpose, our versatile synthesis strategy provides a simple approach for the design and evaluation of long-circulating aptamer-conjugated nanoformulations.
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Affiliation(s)
- Lennart Bohrmann
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Tobias Burghardt
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Matthias M. Herth
- Department
of Drug Design and Pharmacology, Faculty of Health and Medicinal Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Department
of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej
9, 2100 Copenhagen, Denmark
| | - Katayoun Saatchi
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Urs O. Häfeli
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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Su Y, Zhu L, Wu Y, Liu Z, Xu W. Progress and challenges in bacterial whole-cell-components Aptamer advanced screening and site identification. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Dhingra S, Siddiqui I, Gupta SP, Jayakumar J, Jou JH, Pal SK. Solution-processable organic light-emitting diodes utilizing electroluminescent perylene tetraester-based columnar liquid crystals. SOFT MATTER 2022; 18:8850-8855. [PMID: 36374203 DOI: 10.1039/d2sm01235a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herein, we reveal a homologous series of liquid crystals involving perylene tetraesters as the core connected to the four trialkoxyphenyl units at the periphery using the triazole moiety as the linker. A thorough analysis using differential scanning calorimetry, polarized optical microscopy, and small- and wide-angle X-ray scattering studies confirm that all the mesogens 1a-c hold a stable enantiotropic columnar mesophase. Suitable molecular orbital levels and excellent material photophysical and thermal properties encouraged the study of their electroluminescent properties. Due to this, a well designed solution-processable organic light emitting diode device structure is configured as ITO (125 nm)/poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) (35 nm)/host: x wt% emitter (x = 0.5, 1.0, 3.0, 5.0) (20 nm)/2,2'2''-(1,3,5-benzinetriyl)tris(1-phenyl-1-H-benzimidazole) (TPBi) (40 nm)/lithium fluoride (LiF) (1 nm)/aluminium (Al) (200 nm) using compounds 1a-c as emitters. 4,4',4''-Tris[phenyl(m-tolyl)amino]triphenylamine (m-MTDATA) and 4,4'-bis(N-carbazolyl)-1,1'-biphenyl (CBP) were chosen as two different host materials. The current density-voltage-luminance and current efficacy-luminance-power efficacy plots suggest that m-MTDATA is a better host than CBP. Amongst, device based on 1 wt% emitter 1c doped in the m-MTDATA host matrix displayed the best performance, with a maximum power efficacy of 17.2 lm W-1, current efficacy of 18.5 cd A-1, and external quantum efficiency of 6.3%.
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Affiliation(s)
- Shallu Dhingra
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector-81, SAS Nagar, Knowledge City, Manauli, 140306, India.
| | - Iram Siddiqui
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | | | - Jayachandran Jayakumar
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Jwo-Huei Jou
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Santanu Kumar Pal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector-81, SAS Nagar, Knowledge City, Manauli, 140306, India.
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da Silva AG, Goulart LR, Löffler P, Code C, Neves AF. Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples. Int J Mol Sci 2022; 23:ijms232213866. [PMID: 36430340 PMCID: PMC9693377 DOI: 10.3390/ijms232213866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Limitations in the detection of cocirculating flaviviruses such as Dengue and Zika lead us to propose the use of aptameric capture of the viral RNA in combination with RT-PCR (APTA-RT-PCR). Aptamers were obtained via SELEX and next-generation sequencing, followed by colorimetric and fluorescent characterizations. An APTA-RT-PCR assay was developed, optimized, and tested against the viral RNAs in 108 serum samples. After selection, sequence APTAZC10 was designed as a bifunctional molecular beacon (APTAZC10-MB), exhibiting affinity for the viral targets. APTA-RT-PCR was able to detect Dengue and Zika RNA in 43% and 8% of samples, respectively. Our results indicate that APTAZC10-MB and APTA-RT-PCR will be useful to improve the detection of Dengue and Zika viruses in a fast molecular assay for the improvement of infectious disease surveillance.
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Affiliation(s)
- Amanda Gabrielle da Silva
- Institute of Physics, Postgraduate Program in Exact and Technological Sciences, Universidade Federal de Catalão, Catalão 75704-020, Brazil
| | - Luiz Ricardo Goulart
- Nanobiotechnology Laboratory, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia 38402-022, Brazil
| | - Philipp Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Christian Code
- Dianox ApS, Fruebjergvej 3, 2100 København, Denmark
- PhyLife Physical Life Sciences, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Adriana Freitas Neves
- Institute of Biotechnology, Molecular Biology Laboratory, Universidade Federal de Catalão, Catalão 75704-020, Brazil
- Correspondence:
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A sequential toggle cell-SELEX DNA aptamer for targeting Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli bacteria. J Genet Eng Biotechnol 2022; 20:95. [PMID: 35776386 PMCID: PMC9249959 DOI: 10.1186/s43141-022-00374-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/02/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND Mastitis is an inflammation of the mammary glands caused by a microbial infection. The common bacteria causing this infection in dairy farms are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The aptamer is a new biosensor platform for detecting pathogens; however, its use for simultaneous detection of S. aureus, S. agalactiae, and E. coli bacteria has not been reported. This study's objective is to isolate and characterize polyclonal DNA aptamer with broad reactivity to the mastitis bacteria S. aureus, S. agalactiae, and E. coli using a sequential toggle cell-SELEX. METHODS AND RESULTS The DNA aptamer pool from SELEX 15 was inserted into the pGEM-T easy plasmid. Furthermore, the transformant clones were selected by PCR colony, plasmid isolation, and sequencing. Six DNA aptamers, consisting of S15K3, S15K4, S15K6, S15K13, S15K15, and S15K20 with a constant region and the right size of 81 bp were derived from the sequencing analysis. The secondary structure of the DNA was predicted using Mfold software. The DNA was analyzed with binding characteristics, including binding capacity and affinity (Kd), using qPCR. The results indicated aptamer S15K15 has the highest binding ability into S. agalactiae, while S15K13 performed binding capacity most to E. coli EPEC 4, and S15K3 has the highest capacity of binding to S. aureus BPA-12. CONCLUSION Aptamer S15K3 has the best binding characteristics on all three bacterial targets.
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El-Husseini DM, Sayour AE, Melzer F, Mohamed MF, Neubauer H, Tammam RH. Generation and Selection of Specific Aptamers Targeting Brucella Species through an Enhanced Cell-SELEX Methodology. Int J Mol Sci 2022; 23:ijms23116131. [PMID: 35682807 PMCID: PMC9180945 DOI: 10.3390/ijms23116131] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
Brucellae are Gram-negative, aerobic, non-motile coccobacilli causing brucellosis in man and animals. The disease is one of the most significant yet neglected global zoonoses. Especially in developing countries, brucellosis is causing public health problems and economic losses to private animal owners and national revenues. Composed of oligonucleotides, aptamers are chemical analogues of antibodies that are promising components for developing aptamer-based rapid, sensitive, and specific tests to identify the Brucella group of bacteria. For this purpose, aptamers were generated and selected by an enhanced protocol of cell systematic evolution of ligands by exponential enrichment (cell-SELEX). This enhanced cell-SELEX procedure involved the combination of both conventional and toggle cell-SELEX to boost the specificity and binding affinity to whole Brucella cells. This procedure, combined with high-throughput sequencing of the resulting aptamer pools, comprehensive bioinformatics analysis, and wet lab validation assays, led to the selection of a highly sensitive and specific aptamer for those Brucella species known to circulate in Egypt. The isolated candidate aptamer showed dissociation constant (KD) values of 43.5 ± 11, 61.5 ± 8, and 56 ± 10.8 nM for B. melitensis, B. abortus, and B. suis, respectively. This is the first development of a Brucella-specific aptamer using an enhanced combination of conventional and toggle cell-SELEX to the authors’ best knowledge.
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Affiliation(s)
- Dalia M. El-Husseini
- Biotechnology Department, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Ashraf E. Sayour
- Molecular Biomimetics Research Group, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt;
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Magda F. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
| | - Reham H. Tammam
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
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Isolation and Characterization of a ssDNA Aptamer against Major Soluble Antigen of Renibacterium salmoninarum. Molecules 2022; 27:molecules27061853. [PMID: 35335217 PMCID: PMC8951219 DOI: 10.3390/molecules27061853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/29/2022] Open
Abstract
Bacterial kidney disease (BKD) is a major health problem of salmonids, affecting both wild and cultured salmon. The disease is caused by Renibacterium salmoninarum (Rs), a fastidious, slow-growing and strongly Gram-positive diplobacillus that produces chronic, systemic infection characterized by granulomatous lesions in the kidney and other organs, often resulting in death. Fast detection of the pathogen is important to limit the spread of the disease, particularly in hatcheries or aquaculture facilities. Aptamers are increasingly replacing conventional antibodies as platforms for the development of rapid diagnostic tools. In this work, we describe the first instance of isolating and characterizing a ssDNA aptamer that binds with high affinity to p57 or major soluble antigen (MSA), the principal antigen found on the cell wall surface of Rs. Specifically, in this study a construct of the full-length protein containing a DNA binding domain (MSA-R2c) was utilized as target. Aptamers were isolated from a pool of random sequences using GO-SELEX (graphene oxide-systematic evolution of ligands by exponential enrichment) protocol. The selection generated multiple aptamers with conserved motifs in the random region. One aptamer with high frequency of occurrence in different clones was characterized and found to display a strong binding affinity to MSA-R2c with a Kd of 3.0 ± 0.6 nM. The aptamer could be potentially utilized for the future development of a sensor for rapid and onsite detection of Rs in water or in infected salmonids, replacing time-consuming and costly lab analyses.
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11
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Xiao S, Sun L, Lu J, Dong Z. A label-free aptasensor for rapid detection of clenbuterol based on SYBR GREEN I. NEW J CHEM 2022. [DOI: 10.1039/d2nj01959k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free fluorescent biosensor based on clenbuterol binding aptamer and the fluorescent intercalator SYBR Green I (SGI) was established for the sensitive and selective detection of clenbuterol. In the absence...
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12
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Tapp M, Dennis P, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9043-9052. [PMID: 34279112 DOI: 10.1021/acs.langmuir.1c01053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.
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Affiliation(s)
| | - Patrick Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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BipD of Burkholderia pseudomallei: Structure, Functions, and Detection Methods. Microorganisms 2021; 9:microorganisms9040711. [PMID: 33808203 PMCID: PMC8067316 DOI: 10.3390/microorganisms9040711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 01/13/2023] Open
Abstract
Melioidosis is a severe disease caused by Burkholderia pseudomallei (B. pseudomallei), a Gram-negative environmental bacterium. It is endemic in Southeast Asia and Northern Australia, but it is underreported in many other countries. The principal routes of entry for B. pseudomallei are skin penetration, inhalation, and ingestion. It mainly affects immunocompromised populations, especially patients with type 2 diabetes mellitus. The laboratory diagnosis of melioidosis is challenging due to its non-specific clinical manifestations, which mimic other severe infections. The culture method is considered an imperfect gold standard for the diagnosis of melioidosis due to its low sensitivity. Antibody detection has low sensitivity and specificity due to the high seropositivity among healthy people in endemic regions. Antigen detection using various proteins has been tested for the rapid determination of B. pseudomallei; however, it presents certain limitations in terms of its sensitivity and specificity. Therefore, this review aims to frame the present knowledge of a potential target known as the Burkholderia invasion protein D (BipD), including future directions for its detection using an aptamer-based sensor (aptasensor).
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