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Schäfer L, Miskey C, Hein S, Völker E, Reuter A, Beyer K, Ahrens B, Mayer G, Holzhauser T. DNA Meets Protein─Development, Characterization, and Application of Aptamers against Peanut Allergen. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18225-18233. [PMID: 39079057 DOI: 10.1021/acs.jafc.4c03948] [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: 08/15/2024]
Abstract
Allergen detection methods support food labeling and quality assessment at the allergen component level of allergen preparations used for allergy diagnosis and immunotherapy (AIT). Commonly applied enzyme-linked immunosorbent assay (ELISA) requires animal antibodies but potentially shows batch variations. We developed synthetic aptamers as alternative binders in allergen detection to meet the replacement, reduction, and refinement (3R) principle on animal protection in science. ssDNA aptamers were specifically selected against the major peanut allergen Ara h 1 and identified by next-generation sequencing. Application in various detection systems (ELISA-like assays, western blot, and surface plasmon resonance) was demonstrated. The ELISA-like assay comprised a sensitivity of 10 ng/mL Ara h 1, comparable to published antibody-based ELISA, and allowed Ara h 1 detection in various peanut flours, similar to those used in peanut AIT as well as in processed food. This ELISA-like aptamer-based assay proofs antibody-free allergen detection for food labeling or quality assessment of diagnostic and therapeutic allergen products.
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Affiliation(s)
- Laura Schäfer
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Csaba Miskey
- Division of Hematology, Cell and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Sascha Hein
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
- Division of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Elke Völker
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Andreas Reuter
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Kirsten Beyer
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Birgit Ahrens
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
- Department of Pediatrics, Division of Pneumology, Allergology, Infectious Diseases and Gastroenterology, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Günter Mayer
- Life and Medical Sciences, University of Bonn, 53121 Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, 53121 Bonn, Germany
| | - Thomas Holzhauser
- Division of Allergology, Paul-Ehrlich-Institut, 63225 Langen, Germany
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2
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Lin C, Li Q, Liu D, Feng Q, Zhou H, Shi B, Zhang X, Hu Y, Jiang X, Sun X, Wang D. Recent research progress in tetrodotoxin detection and quantitative analysis methods. Front Chem 2024; 12:1447312. [PMID: 39206441 PMCID: PMC11349515 DOI: 10.3389/fchem.2024.1447312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
Tetrodotoxin (TTX) is a highly potent and widely distributed ion-channel marine neurotoxin; it has no specific antidote and poses a great risk to human health. Therefore, detecting and quantifying TTX to effectively implement prevention strategies is important for food safety. The development of novel and highly sensitive, highly specific, rapid, and simple techniques for trace TTX detection has attracted widespread attention. This review summarizes the latest advances in the detection and quantitative analysis of TTX, covering detection methods based on biological and cellular sensors, immunoassays and immunosensors, aptamers, and liquid chromatography-mass spectrometry. It further discusses the advantages and applications of various detection technologies developed for TTX and focuses on the frontier areas and development directions of TTX detection, providing relevant information for further investigations.
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Affiliation(s)
- Chao Lin
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Qirong Li
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Dong Liu
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Hengzong Zhou
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Bohe Shi
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Xinxin Zhang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Yurui Hu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Xinmiao Jiang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Xiaoming Sun
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
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3
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Singh NK, Wang Y, Wen C, Davis B, Wang X, Lee K, Wang Y. High-affinity one-step aptamer selection using a non-fouling porous hydrogel. Nat Biotechnol 2024; 42:1224-1231. [PMID: 37798416 DOI: 10.1038/s41587-023-01973-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023]
Abstract
Aptamers, commonly referred to as chemical antibodies, are used in a wide range of applications including drug delivery and biosensing. However, the process of aptamer selection poses a substantial challenge, as it requires numerous cycles of enrichment and involves issues with nonspecific binding. We present a simple, fast instrument-free method for aptamer enrichment and selection based on a diffusion-binding process in a three-dimensional non-fouling porous hydrogel with immobilized target proteins. Low-affinity aptamer candidates can be rapidly released from the hydrogel, whereas high-affinity candidates are restricted due to their strong binding to the immobilized protein targets. Consequently, a one-step enriched aptamer pool can strongly bind the protein targets. This enrichment is consistent across five proteins with isoelectric points in varying ranges. With thrombin as a representative model, the anti-thrombin aptamer identified from an enriched aptamer pool has been found to have a binding affinity that is comparable to those identified over ten cycles of selection using traditional methods.
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Affiliation(s)
- Naveen K Singh
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, Delhi, New Delhi, India
| | - Yixun Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Connie Wen
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Brandon Davis
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Xuelin Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA.
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4
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Galvan S, Teixeira AP, Fussenegger M. Enhancing cell-based therapies with synthetic gene circuits responsive to molecular stimuli. Biotechnol Bioeng 2024. [PMID: 38867466 DOI: 10.1002/bit.28770] [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: 10/13/2023] [Revised: 04/21/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Synthetic biology aims to contribute to the development of next-generation patient-specific cell-based therapies for chronic diseases especially through the construction of sophisticated synthetic gene switches to enhance the safety and spatiotemporal controllability of engineered cells. Indeed, switches that sense and process specific cues, which may be either externally administered triggers or endogenous disease-associated molecules, have emerged as powerful tools for programming and fine-tuning therapeutic outputs. Living engineered cells, often referred to as designer cells, incorporating such switches are delivered to patients either as encapsulated cell implants or by infusion, as in the case of the clinically approved CAR-T cell therapies. Here, we review recent developments in synthetic gene switches responsive to molecular stimuli, spanning regulatory mechanisms acting at the transcriptional, translational, and posttranslational levels. We also discuss current challenges facing clinical translation of cell-based therapies employing these devices.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana P Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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Le Dortz LL, Rouxel C, Polack B, Boulouis HJ, Lagrée AC, Deshuillers PL, Haddad N. Tick-borne diseases in Europe: Current prevention, control tools and the promise of aptamers. Vet Parasitol 2024; 328:110190. [PMID: 38714064 DOI: 10.1016/j.vetpar.2024.110190] [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: 10/27/2023] [Revised: 04/03/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
In Europe, tick-borne diseases (TBDs) cause significant morbidity and mortality, affecting both human and animal health. Ticks can transmit a wide variety of pathogens (bacteria, viruses, and parasites) and feed on many vertebrate hosts. The incidence and public health burden of TBDs are tending to intensify in Europe due to various factors, mainly anthropogenic and often combined. Early detection of tick-borne pathogens (TBPs), preventive measures and treatment are of great importance to control TBDs and their expansion. However, there are various limitations in terms of the sensitivity and/or specificity of detection and prevention methods, and even in terms of feasibility. Aptamers are single-stranded DNA or RNA that could address these issues as they are able to bind with high affinity and specificity to a wide range of targets (e.g., proteins, small compounds, and cells) due to their unique three-dimensional structure. To date, aptamers have been selected against TBPs such as tick-borne encephalitis virus, Francisella tularensis, and Rickettsia typhi. These studies have demonstrated the benefits of aptamer-based assays for pathogen detection and medical diagnosis. In this review, we address the applications of aptamers to TBDs and discuss their potential for improving prevention measures (use of chemical acaricides, vaccination), diagnosis and therapeutic strategies to control TBDs.
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Affiliation(s)
- Lisa Lucie Le Dortz
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Clotilde Rouxel
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Bruno Polack
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Henri-Jean Boulouis
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Anne-Claire Lagrée
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Pierre Lucien Deshuillers
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Nadia Haddad
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France.
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6
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Le Dortz LL, Rouxel C, Leroy Q, Ducongé F, Boulouis HJ, Haddad N, Deshuillers PL, Lagrée AC. Aptamer selection against cell extracts containing the zoonotic obligate intracellular bacterium, Anaplasma phagocytophilum. Sci Rep 2024; 14:2465. [PMID: 38291133 PMCID: PMC10828505 DOI: 10.1038/s41598-024-52808-8] [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: 11/14/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
A. phagocytophilum is a zoonotic and tick-borne bacterium, threatening human and animal health. Many questions persist concerning the variability of strains and the mechanisms governing the interactions with its different hosts. These gaps can be explained by the difficulty to cultivate and study A. phagocytophilum because of its strict intracellular location and the lack of specific tools, in particular monoclonal antibodies, currently unavailable. The objective of our study was to develop DNA aptamers against A. phagocytophilum, or molecules expressed during the infection, as new study and/or capture tools. Selecting aptamers was a major challenge due to the strict intracellular location of the bacterium. To meet this challenge, we set up a customized selection protocol against an enriched suspension of A. phagocytophilum NY18 strain, cultivated in HL-60 cells. The implementation of SELEX allowed the selection of three aptamers, characterized by a high affinity for HL-60 cells infected with A. phagocytophilum NY18 strain. Interestingly, the targets of these three aptamers are most likely proteins expressed at different times of infection. The selected aptamers could contribute to increase our understanding of the interactions between A. phagocytophilum and its hosts, as well as permit the development of new diagnostic, therapeutic or drug delivery appliances.
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Affiliation(s)
- Lisa Lucie Le Dortz
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France.
| | - Clotilde Rouxel
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France
| | - Quentin Leroy
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France
| | - Frédéric Ducongé
- CEA, Fundamental Research Division (DRF), Institute of Biology François Jacob, Molecular Imaging Research Center, CNRS UMR9199, Paris-Saclay University, 92265, Fontenay-Aux-Roses, France
| | - Henri-Jean Boulouis
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France
| | - Nadia Haddad
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France.
| | - Pierre Lucien Deshuillers
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France
| | - Anne-Claire Lagrée
- Anses, INRAe, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratory of Animal Health, 94700, Maisons-Alfort, France
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7
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Wang X, Jia B, Lee K, Davis B, Wen C, Wang Y, Zheng H, Wang Y. Biomimetic Bacterial Capsule for Enhanced Aptamer Display and Cell Recognition. J Am Chem Soc 2024; 146:868-877. [PMID: 38153404 DOI: 10.1021/jacs.3c11208] [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: 12/29/2023]
Abstract
Great effort has been made to encapsulate or coat living mammalian cells for a variety of applications ranging from diabetes treatment to three-dimensional printing. However, no study has reported the synthesis of a biomimetic bacterial capsule to display high-affinity aptamers on the cell surface for enhanced cell recognition. Therefore, we synthesized an ultrathin alginate-polylysine coating to display aptamers on the surface of living cells with natural killer (NK) cells as a model. The results show that this coating-mediated aptamer display is more stable than direct cholesterol insertion into the lipid bilayer. The half-life of the aptamer on the cell surface can be increased from less than 1.5 to over 20 h. NK cells coated with the biomimetic bacterial capsule exhibit a high efficiency in recognizing and killing target cells. Therefore, this work has demonstrated a promising cell coating method for the display of aptamers for enhanced cell recognition.
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Affiliation(s)
- Xuelin Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bei Jia
- Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Brandon Davis
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Connie Wen
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yixun Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hong Zheng
- Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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8
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Cai S, Ren R, He J, Wang X, Zhang Z, Luo Z, Tan W, Korchev Y, Edel JB, Ivanov AP. Selective Single-Molecule Nanopore Detection of mpox A29 Protein Directly in Biofluids. NANO LETTERS 2023; 23:11438-11446. [PMID: 38051760 PMCID: PMC10755749 DOI: 10.1021/acs.nanolett.3c02709] [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: 07/20/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.
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Affiliation(s)
- Shenglin Cai
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Ren Ren
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Jiaxuan He
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Zheng Zhang
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Zhaofeng Luo
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Weihong Tan
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Yuri Korchev
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
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9
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Shin I, Kang K, Kim J, Sel S, Choi J, Lee JW, Kang HY, Song G. AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders. BMC Bioinformatics 2023; 24:447. [PMID: 38012571 PMCID: PMC10680337 DOI: 10.1186/s12859-023-05577-6] [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: 08/24/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evolution of ligands by exponential enrichment (SELEX) method is a critical in vitro technique employed to identify aptamers that bind specifically to target proteins. While advanced SELEX-based methods such as Cell- and HT-SELEX are available, they often encounter issues such as extended time consumption and suboptimal accuracy. Several In silico aptamer discovery methods have been proposed to address these challenges. These methods are specifically designed to predict aptamer-protein interaction (API) using benchmark datasets. However, these methods often fail to consider the physicochemical interactions between aptamers and proteins within tertiary structures. RESULTS In this study, we propose AptaTrans, a pipeline for predicting API using deep learning techniques. AptaTrans uses transformer-based encoders to handle aptamer and protein sequences at the monomer level. Furthermore, pretrained encoders are utilized for the structural representation. After validation with a benchmark dataset, AptaTrans has been integrated into a comprehensive toolset. This pipeline synergistically combines with Apta-MCTS, a generative algorithm for recommending aptamer candidates. CONCLUSION The results show that AptaTrans outperforms existing models for predicting API, and the efficacy of the AptaTrans pipeline has been confirmed through various experimental tools. We expect AptaTrans will enhance the cost-effectiveness and efficiency of SELEX in drug discovery. The source code and benchmark dataset for AptaTrans are available at https://github.com/pnumlb/AptaTrans .
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Affiliation(s)
- Incheol Shin
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Keumseok Kang
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Juseong Kim
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Sanghun Sel
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Jeonghoon Choi
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Jae-Wook Lee
- Research & Development, NuclixBio, Seoul, Republic of Korea
| | - Ho Young Kang
- Research & Development, NuclixBio, Seoul, Republic of Korea
| | - Giltae Song
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea.
- School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea.
- Center for Artificial Intelligence Research, Pusan National University, Busan, Republic of Korea.
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10
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Lin Y, Chen CY, Ku YC, Wang LC, Hung CC, Lin ZQ, Chen BH, Hung JT, Sun YC, Hung KF. A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen. RSC Adv 2023; 13:32681-32693. [PMID: 37936644 PMCID: PMC10626974 DOI: 10.1039/d3ra04686a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
Aptamers have sparked significant interest in cell recognition because of their superior binding specificity and biocompatibility. Cell recognition can be mediated by targeting the major histocompatibility complex (MHC) that presents short peptides derived from intracellular antigens. Although numerous antibodies have demonstrated a specific affinity for the peptide-MHC complex, the number of aptamers that exhibit comparable characteristics is limited. Aptamers are usually selected from large libraries via the Systemic Evolution of Ligands by Exponential Enrichment (SELEX), an iterative process of selection and PCR amplification to enrich a pool of aptamers with high affinity. However, the success rate of aptamer identification is low, possibly due to the presence of complementary sequences or sequences rich in guanine and cytosine that are less accessible for primers. Here, we modified SELEX by employing systemic consecutive selections with minimal PCR amplification. We also modified the analysis by selecting aptamers that were identified in multiple selection rounds rather than those that are highly enriched. Using this approach, we were able to identify two aptamers with binding specificity to cells expressing the ovalbumin alloantigen as a proof of concept. These two aptamers were also discovered among the top 150 abundant candidates, despite not being highly enriched, by performing conventional SELEX. Additionally, we found that highly enriched aptamers tend to contain fractions of the primer sequence and have minimal target affinity. Candidate aptamers are easily missed in the conventional SELEX process. Therefore, our modification for SELEX may facilitate the identification of aptamers for more application in diverse biomedical fields. Significance: we modify the conventional method to improve the efficiency in the identification of the aptamer, a single strand of nucleic acid with binding specificity to the target molecule, showing as a proof of concept that this approach is particularly useful to select aptamers that can selectively bind to cells presenting a particular peptide by the major histocompatibility complex (MHC) on the cell surface. Given that cancer cells may express mutant peptide-MHC complexes that are distinct from those expressed by normal cells, this study sheds light on the potential application of aptamers to cancer cell targeting.
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Affiliation(s)
- Yang Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Yu-Chia Ku
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Li-Chin Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Chia-Chien Hung
- School of Computer Science, Georgia Institute of Technology Atlanta GA USA
| | - Zhi-Qian Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Bing-Hong Chen
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | | | - Yi-Chen Sun
- School of Medicine, Tzu-Chi University Hualien Taiwan
- Department of Ophthalmology, Taipei Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation New Taipei City Taiwan
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University Taipei Taiwan
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11
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Zasedateleva OA, Surzhikov SA, Kuznetsova VE, Shershov VE, Barsky VE, Zasedatelev AS, Chudinov AV. Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency. Int J Mol Sci 2023; 24:13643. [PMID: 37686447 PMCID: PMC10487964 DOI: 10.3390/ijms241713643] [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: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase-DNA-dNTP complexes. The dUTPs were C5-modified with bulky functional groups (the Cy5 dye analogs) or lighter aromatic groups. Comparing the experimental data and the results of molecular modeling revealed the decrease in PCR efficiency in the presence of modified dUTPs with an increase in the number of non-covalent bonds between the substituents and the DNA polymerase (about 15% decrease per one extra non-covalent bond). Generalization of the revealed patterns to all the studied polymerases of the A and B families is discussed herein. The number of non-covalent bonds between the substituents and polymerase amino acid residues is proposed to be a potentially variable parameter for regulating enzyme activity.
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Affiliation(s)
- Olga A. Zasedateleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
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12
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Jiang M, Fang X, Diao H, Lv S, Zhang Z, Zhang X, Chen Z, Luo Z. Semi-automated and efficient parallel SELEX of aptamers for multiple targets. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2039-2043. [PMID: 37066673 DOI: 10.1039/d3ay00367a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this study, we constructed and optimized a semi-automatic instrument to perform aptamer SELEX targeting multiple proteins simultaneously. Our work provides a simple SELEX platform characterized by real-time feedback, which is time efficient and can reduce human intervention. A number of aptamers were rapidly screened by this method. Moreover, the binding affinities of these aptamers were verified by various methods, including SPR and flow cytometry, which supports the applicability and reliability of our newly established aptamer SELEX system.
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Affiliation(s)
- Meng Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China.
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Han Diao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Shaokang Lv
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Zheng Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Xiang Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Zhiwei Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China.
- Institute of Food and Nutrition Science, Shandong University of Technology, Zibo, 255049, P. R. China
- School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255049, P. R. China
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
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13
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [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: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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14
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Shraim AS, Abdel Majeed BA, Al-Binni M, Hunaiti A. Therapeutic Potential of Aptamer-Protein Interactions. ACS Pharmacol Transl Sci 2022; 5:1211-1227. [PMID: 36524009 PMCID: PMC9745894 DOI: 10.1021/acsptsci.2c00156] [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: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded oligonucleotides (RNA or DNA) with a typical length between 25 and 100 nucleotides which fold into three-dimensional structures capable of binding to target molecules. Specific aptamers can be isolated against a large variety of targets through efficient and relatively cheap methods, and they demonstrate target-binding affinities that sometimes surpass those of antibodies. Consequently, interest in aptamers has surged over the past three decades, and their application has shown promise in advancing knowledge in target analysis, designing therapeutic interventions, and bioengineering. With emphasis on their therapeutic applications, aptamers are emerging as a new innovative class of therapeutic agents with promising biochemical and biological properties. Aptamers have the potential of providing a feasible alternative to antibody- and small-molecule-based therapeutics given their binding specificity, stability, low toxicity, and apparent non-immunogenicity. This Review examines the general properties of aptamers and aptamer-protein interactions that help to understand their binding characteristics and make them important therapeutic candidates.
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Affiliation(s)
- Ala’a S. Shraim
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Bayan A. Abdel Majeed
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Maysaa’
Adnan Al-Binni
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
| | - Abdelrahim Hunaiti
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
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15
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Le Dortz LL, Rouxel C, Leroy Q, Brosseau N, Boulouis HJ, Haddad N, Lagrée AC, Deshuillers PL. Optimized Lambda Exonuclease Digestion or Purification Using Streptavidin-Coated Beads: Which One Is Best for Successful DNA Aptamer Selection? Methods Protoc 2022; 5:mps5060089. [PMID: 36412811 PMCID: PMC9680285 DOI: 10.3390/mps5060089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 12/14/2022] Open
Abstract
The high failure rate of the in vitro aptamer selection process by SELEX (Systematic Evolution of Ligands by EXponential enrichment) limits the production of these innovative oligonucleotides and, consequently, limits their potential applications. The generation of single-stranded DNA (ssDNA) is a critical step of SELEX, directly affecting the enrichment and the selection of potential binding sequences. The main goal of this study was to confirm the best method for generating ssDNA by comparing the purification of ssDNA, using streptavidin-coated beads, and lambda exonuclease digestion, and by improving ssDNA recovery through protocol improvements. In addition, three techniques for quantifying the ssDNA generated (Qubit vs. NanodropTM vs. gel quantification) were compared, and these demonstrated the accuracy of the gel-based quantification method. Lambda exonuclease digestion was found to be more efficient for ssDNA recovery than purification using streptavidin-coated beads, both quantitatively and qualitatively. In conclusion, this work provides a detailed and rigorous protocol for generating ssDNA, improving the chances of a successful aptamer selection process.
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16
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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17
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Onaş AM, Dascălu C, Raicopol MD, Pilan L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. BIOSENSORS 2022; 12:816. [PMID: 36290952 PMCID: PMC9599214 DOI: 10.3390/bios12100816] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.
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Affiliation(s)
- Andra Mihaela Onaş
- Advanced Polymer Materials Group, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Constanţa Dascălu
- Faculty of Applied Sciences, University ‘Politehnica’ of Bucharest, 313 Splaiul Independenţei, District 6, 060042 Bucharest, Romania
| | - Matei D. Raicopol
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Luisa Pilan
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
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18
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Chang TC, Sun AY, Huang YC, Wang CH, Wang SC, Chau LK. Integration of Power-Free and Self-Contained Microfluidic Chip with Fiber Optic Particle Plasmon Resonance Aptasensor for Rapid Detection of SARS-CoV-2 Nucleocapsid Protein. BIOSENSORS 2022; 12:bios12100785. [PMID: 36290923 PMCID: PMC9599074 DOI: 10.3390/bios12100785] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 05/31/2023]
Abstract
The global pandemic of COVID-19 has created an unrivalled need for sensitive and rapid point-of-care testing (POCT) methods for the detection of infectious viruses. For the novel coronavirus SARS-CoV-2, the nucleocapsid protein (N-protein) is one of the most abundant structural proteins of the virus and it serves as a useful diagnostic marker for detection. Herein, we report a fiber optic particle plasmon resonance (FOPPR) biosensor which employed a single-stranded DNA (ssDNA) aptamer as the recognition element to detect the SARS-CoV-2 N-protein in 15 min with a limit of detection (LOD) of 2.8 nM, meeting the acceptable LOD of 106 copies/mL set by the WHO target product profile. The sensor chip is a microfluidic chip based on the balance between the gravitational potential and the capillary force to control fluid loading, thus enabling the power-free auto-flowing function. It also has a risk-free self-contained design to avoid the risk of the virus leaking into the environment. These findings demonstrate the potential for designing a low-cost and robust POCT device towards rapid antigen detection for early screening of SARS-CoV-2 and its related mutants.
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Affiliation(s)
- Ting-Chou Chang
- Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 621301, Taiwan
| | - Aileen Y. Sun
- Instant NanoBiosensors, Co., Ltd., Taipei 115010, Taiwan
| | - Yu-Chung Huang
- Instant NanoBiosensors, Co., Ltd., Taipei 115010, Taiwan
| | - Chih-Hui Wang
- Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 621301, Taiwan
| | - Shau-Chun Wang
- Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 621301, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi 62102, Taiwan
| | - Lai-Kwan Chau
- Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 621301, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi 62102, Taiwan
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19
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Graßhoff H, Fourlakis K, Comdühr S, Riemekasten G. Autoantibodies as Biomarker and Therapeutic Target in Systemic Sclerosis. Biomedicines 2022; 10:biomedicines10092150. [PMID: 36140251 PMCID: PMC9496142 DOI: 10.3390/biomedicines10092150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Systemic sclerosis (SSc) is a rare connective tissue disorder characterized by immune dysregulation evoking the pathophysiological triad of inflammation, fibrosis and vasculopathy. In SSc, several alterations in the B-cell compartment have been described, leading to polyclonal B-cell hyperreactivity, hypergammaglobulinemia and autoantibody production. Autoreactive B cells and autoantibodies promote and maintain pathologic mechanisms. In addition, autoantibodies in SSc are important biomarkers for predicting clinical phenotype and disease progression. Autoreactive B cells and autoantibodies represent potentially promising targets for therapeutic approaches including B-cell-targeting therapies, as well as strategies for unselective and selective removal of autoantibodies. In this review, we present mechanisms of the innate immune system leading to the generation of autoantibodies, alterations of the B-cell compartment in SSc, autoantibodies as biomarkers and autoantibody-mediated pathologies in SSc as well as potential therapeutic approaches to target these.
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20
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Kazemi Y, Dehghani S, Nosrati R, Taghdisi SM, Abnous K, Alibolandi M, Ramezani M. Recent progress in the early detection of cancer based on CD44 biomarker; nano-biosensing approaches. Life Sci 2022; 300:120593. [PMID: 35500679 DOI: 10.1016/j.lfs.2022.120593] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/06/2023]
Abstract
CD44 is a cell matrix adhesion molecule overexpressed on the cell surfaces of the major cancers. CD44 as a cancer-related biomarker has an essential role in the invasion and metastasis of cancer. The detection and quantification of CD44 can provide essential information useful for clinical cancer diagnosis. In this regard, biosensors with sensitive and specific properties, give prominence to the development of CD44 detection platforms. To date, various aptamer-based sensitive-enhancers together with nanoparticles (NPs) have been combined into the biosensors systems to provide an innovative biosensing method (aptasensors/nano-aptasensors) with substantially improved detection limit. This review article discusses the recent advances in the field of biosensors, nanobiosensors, and aptasensors for the quantitative determination of CD44 and the detection of CD44-expressing cancer cells.
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Affiliation(s)
- Youkabed Kazemi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Dehghani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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21
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Singh N, Hutson R, Milton NGN, Javid FA. Ovarian cancer and KiSS-1 gene expression: A consideration of the use of Kisspeptin plus Kisspeptin aptamers in diagnostics and therapy. Eur J Pharmacol 2022; 917:174752. [PMID: 35026192 DOI: 10.1016/j.ejphar.2022.174752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/22/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022]
Abstract
Gynaecological cancers continue to present a significant health burden upon the health of the global female population. This deficit is most prominent with ovarian cancer which possesses the lowest survival rate compared to all other cancers occurring within this anatomical region, with an annual UK-mortality of 7,300. The poor tolerability and selectively of the treatment options that are currently available is likely to have contributed to this high mortality rate thus, demonstrating the need for the development of enhanced therapeutic approaches. Aptamer technology would involve the engineering of specifically sequenced oligonucleotide chains, which bind to macromolecular targets with a high degree of affinity and selectively. Recent in-vitro studies conducted upon the clinical utility of this technique have supported its superiority in targeting individual therapeutic drug targets compared to various other targeting moieties currently within therapeutic use such as, monoclonal antibodies. For this reason, the employment of this technique is likely to be favourable in reducing the incidence of non-specific, chemotherapy-associated adverse effects. Kisspeptin is a naturally expressed polypeptide with an established role in the development of the reproductive system and other proposed roles in influencing the ability of ovarian cancer growths to exhibit the metastasis hallmark. This distinctive feature would indicate the potential for the manipulation of this pathway through the application of aptamer structures in developing a novel prophylactic strategy and improve the long-term outcome for ovarian cancer patients.
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Affiliation(s)
- Navinder Singh
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom
| | - Richard Hutson
- St James's Leeds University Teaching Hospital, Beckett Street, Leeds, LS9 7TF, United Kingdom
| | - Nathaniel G N Milton
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, City Campus, Leeds, LS1 3HE, United Kingdom
| | - Farideh A Javid
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom.
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22
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Torres-Vázquez B, María de Lucas A, García-Crespo C, Antonio García-Martín J, Fragoso A, Fernández-Algar M, Perales C, Domingo E, Moreno M, Briones C. In vitro selection of high affinity DNA and RNA aptamers that detect hepatitis C virus core protein of genotypes 1 to 4 and inhibit virus production in cell culture. J Mol Biol 2022; 434:167501. [DOI: 10.1016/j.jmb.2022.167501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
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23
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Abstract
Magnetic cell separation has become a key methodology for the isolation of target cell populations from biological suspensions, covering a wide spectrum of applications from diagnosis and therapy in biomedicine to environmental applications or fundamental research in biology. There now exists a great variety of commercially available separation instruments and reagents, which has permitted rapid dissemination of the technology. However, there is still an increasing demand for new tools and protocols which provide improved selectivity, yield and sensitivity of the separation process while reducing cost and providing a faster response. This review aims to introduce basic principles of magnetic cell separation for the neophyte, while giving an overview of recent research in the field, from the development of new cell labeling strategies to the design of integrated microfluidic cell sorters and of point-of-care platforms combining cell selection, capture, and downstream detection. Finally, we focus on clinical, industrial and environmental applications where magnetic cell separation strategies are amongst the most promising techniques to address the challenges of isolating rare cells.
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24
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Lupu LM, Wiegand P, Holdschick D, Mihoc D, Maeser S, Rawer S, Völklein F, Malek E, Barka F, Knauer S, Uth C, Hennermann J, Kleinekofort W, Hahn A, Barka G, Przybylski M. Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination. Int J Mol Sci 2021; 22:12832. [PMID: 34884636 PMCID: PMC8657952 DOI: 10.3390/ijms222312832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (KD) of a protein-antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled ("conformational") antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA-aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.
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Affiliation(s)
- Loredana-Mirela Lupu
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Pascal Wiegand
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Daria Holdschick
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Delia Mihoc
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stefan Maeser
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stephan Rawer
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Friedemann Völklein
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Ebrahim Malek
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Frederik Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Sascha Knauer
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Christina Uth
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Julia Hennermann
- Department of Pediatrics, Universitätsmedizin Mainz, 55130 Mainz, Germany;
| | - Wolfgang Kleinekofort
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, Feulgenstraße 10-12, 35389 Giessen, Germany;
| | - Günes Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Michael Przybylski
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
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25
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Xiao X, Li H, Zhao L, Zhang Y, Liu Z. Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications. Biomed Pharmacother 2021; 143:112232. [PMID: 34649356 DOI: 10.1016/j.biopha.2021.112232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/04/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.
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Affiliation(s)
- Xueran Xiao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hui Li
- Department of Urology, Peking University International Hospital, Beijing 102206, China
| | - Lijian Zhao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yanfen Zhang
- Technology Transfer Center, Hebei University, Baoding 071002, China.
| | - Zhongcheng Liu
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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26
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Drees A, Fischer M. High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers. Int J Mol Sci 2021; 22:9202. [PMID: 34502110 PMCID: PMC8431662 DOI: 10.3390/ijms22179202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. 'High-throughput sequencing fluorescent ligand interaction profiling' (HiTS-FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS-FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS-FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.
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Affiliation(s)
- Alissa Drees
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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27
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Cleri F, Lensink MF, Blossey R. DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2. Front Mol Biosci 2021; 8:713003. [PMID: 34458322 PMCID: PMC8397481 DOI: 10.3389/fmolb.2021.713003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/28/2021] [Indexed: 12/22/2022] Open
Abstract
DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of DNA aptamers to interact with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and subsequent fusioning of the virus membrane with the host cell membrane. In order to achieve this, the S1 domain of one protomer switches between a closed conformation, in which the binding site is inaccessible to the cell receptors, and an open conformation, in which ACE2 can bind, thereby initiating the entry process of the viral genetic material in the host cell. Here we show, by means of state-of-the-art molecular simulations, that small DNA aptamers experimentally identified can recognize the S-protein of SARS-CoV-2, and characterize the details of the binding process. We find that their interaction with different subdomains of the S-protein can effectively block, or at least considerably slow down the opening process of the S1 domain, thereby significantly reducing the probability of virus-cell binding. We provide evidence that, as a consequence, binding of the human ACE2 receptor may be crucially affected under such conditions. Given the facility and low cost of fabrication of specific aptamers, the present findings could open the way to both an innovative viral screening technique with sub-nanomolar sensitivity, and to an effective and low impact curative strategy.
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Affiliation(s)
- Fabrizio Cleri
- University of Lille, CNRS UMR8520 IEMN, Institut d’Electronique, Microélectronique et Nanotechnologie, Lille, France
- University of Lille, Departement de Physique, Villeneuve d’Ascq, France
| | - Marc F. Lensink
- University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Ralf Blossey
- University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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28
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Martin DR, Sibuyi NR, Dube P, Fadaka AO, Cloete R, Onani M, Madiehe AM, Meyer M. Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care. Diagnostics (Basel) 2021; 11:1352. [PMID: 34441287 PMCID: PMC8391981 DOI: 10.3390/diagnostics11081352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.
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Affiliation(s)
- Darius Riziki Martin
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Nicole Remaliah Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Phumuzile Dube
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Adewale Oluwaseun Fadaka
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Martin Onani
- Department of Chemistry, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Abram Madimabe Madiehe
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
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29
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Han C, Li Q, Ji H, Xing W, Zhang L, Zhang L. Aptamers: The Powerful Molecular Tools for Virus Detection. Chem Asian J 2021; 16:1298-1306. [PMID: 33851522 DOI: 10.1002/asia.202100242] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Indexed: 01/23/2023]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides selected by the technique of systematic evolution of ligands by exponential enrichment (SELEX). Aptamers have been demonstrated to bind various targets from small-molecule to cells or even tissues in the way of antibodies. Thus, they are called chemical antibodies. We summarize and evaluate recent developments in aptamer-based sensors (for short aptasensors) for virus detection in this review. These aptasensors are mainly classified into optical and electronic aptasensors based on the type of transducer. Nowadays, the smartphone has become the most widely used mobile device with billions of users worldwide. Considering the ongoing COVID-19 outbreak, smartphone-based aptasensors for a portable and point-of-care test (POCT) of COVID-19 detection will be of great importance in the future.
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Affiliation(s)
- Cong Han
- State Key Laboratory of Medicinal Chemical biology, College of Life Sciences, Nankai University, Tianjin, 300350, P. R. China
| | - Qian Li
- State Key Laboratory of Medicinal Chemical biology, College of Pharmacy, Nankai University, Tianjin, 300350, P. R. China
| | - Haishuo Ji
- State Key Laboratory of Medicinal Chemical biology, College of Pharmacy, Nankai University, Tianjin, 300350, P. R. China
| | - Wenping Xing
- State Key Laboratory of Medicinal Chemical biology, College of Pharmacy, Nankai University, Tianjin, 300350, P. R. China
| | - Limin Zhang
- Department of Internal Medicine, Leling Hospital of Traditional Chinese Medicine, Shandong, 253600, P. R. China
| | - Liyun Zhang
- State Key Laboratory of Medicinal Chemical biology, College of Life Sciences, Nankai University, Tianjin, 300350, P. R. China
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30
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Zara L, Achilli S, Chovelon B, Fiore E, Toulmé JJ, Peyrin E, Ravelet C. Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants. Anal Chim Acta 2021; 1159:338382. [PMID: 33867041 DOI: 10.1016/j.aca.2021.338382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/28/2023]
Abstract
Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.
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Affiliation(s)
- Lorena Zara
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Novaptech, 2 Allée Du Doyen Georges Brus, 33600, Pessac, France
| | - Silvia Achilli
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | - Benoît Chovelon
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Service de Biochimie, Biologie Moléculaire, Toxicologie Environnementale, CHU de Grenoble-Alpes Site Nord- Institut de Biologie et de Pathologie, La Tronche, France
| | | | | | - Eric Peyrin
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France.
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31
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Cataldo R, De Nunzio G, Millithaler JF, Alfinito E. Aptamers Which Target Proteins: What Proteotronics Suggests to Pharmaceutics. Curr Pharm Des 2020; 26:363-371. [PMID: 31942851 DOI: 10.2174/1381612826666200114095027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Abstract
Aptamers represent a challenging field of research, relevant for diagnosis in macular degeneration, cancer, thrombosis and many inflammatory diseases, and promising in drug discovery and development. Their selection is currently performed by a stable in vitro technology, namely, SELEX. Furthermore, computationalstatistical tools have been developed to complement the SELEX selection; they work both in the preliminary stage of selection, by designing high affinity aptamers for the assigned target, and also in the final stage, analyzing the features of the best performers to implement the selection technique further. A massive use of the in silico approach is, at present, only restricted by the limited knowledge of the specific aptamer-target topology. Actually, only about fifty X-ray structures of aptamer-protein complexes have been experimentally resolved, highlighting how this knowledge has to be improved. The structure of biomolecules like aptamer-protein complexes can be represented by networks, from which several parameters can be extracted. This work briefly reviews the literature, discussing if and how general network parameters in the framework of Proteotronics and graph theory (such as electrical features, link number, free energy change, and assortativity), are important in characterizing the complexes, anticipating some features of the biomolecules. To better explain this topic, a case-study is proposed, constituted by a set of anti-angiopoietin (Ang2) aptamers, whose performances are known from the experiments, and for which two different types of conformers were predicted. A topological indicator is proposed, named Möbius (M), which combines local and global information, and seems able to discriminate between the two possible types of conformers, so that it can be considered as a useful complement to the in vitro screening for pharmaceutical aims.
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Affiliation(s)
- Rosella Cataldo
- Department of Mathematics and Physics "Ennio De Giorgi", University of Salento, Lecce, Italy.,Laboratory of Interdisciplinary Research Applied to Medicine (DReAM), University of Salento and ASL (Local Health Authority), Lecce, Italy
| | - Giorgio De Nunzio
- Department of Mathematics and Physics "Ennio De Giorgi", University of Salento, Lecce, Italy.,Laboratory of Interdisciplinary Research Applied to Medicine (DReAM), University of Salento and ASL (Local Health Authority), Lecce, Italy
| | - Jean-Francois Millithaler
- Electrical and Computer Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, United States
| | - Eleonora Alfinito
- Department of Innovation Engineering, University of Salento, Lecce, Italy
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32
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Zhang L, Fang X, Liu X, Ou H, Zhang H, Wang J, Li Q, Cheng H, Zhang W, Luo Z. Discovery of sandwich type COVID-19 nucleocapsid protein DNA aptamers. Chem Commun (Camb) 2020; 56:10235-10238. [PMID: 32756614 DOI: 10.1039/d0cc03993d] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Here, we report for the first time DNA aptamers targeted toward the COVID-19 nucleocapsid protein (Np). Np is one of the most abundant structural proteins and it serves as a diagnostic marker for the accurate and sensitive detection of COVID-19. After five rounds of selection, we obtained four DNA sequences with an affinity below 5 nM. The best one displayed a superb binding performance toward Np with a Kd value of 0.49 nM. Interestingly, we found that the four pairs of aptamers could bind to Np successively, suggesting a sandwich-type interaction. Using these sandwiched aptamers in ELISA and colloidal gold immunochromatographic strips, we were able to detect Np at the tens of pM level. The results demonstrate that aptamers are powerful molecular tools for virus detection, diagnosis, and antiviral therapy.
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Affiliation(s)
- Liyun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, 300350, P. R. China.
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33
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Oteng EK, Gu W, McKeague M. High-efficiency enrichment enables identification of aptamers to circulating Plasmodium falciparum-infected erythrocytes. Sci Rep 2020; 10:9706. [PMID: 32546848 PMCID: PMC7298056 DOI: 10.1038/s41598-020-66537-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Plasmodium falciparum is the causative agent of the deadliest human malaria. New molecules are needed that can specifically bind to erythrocytes that are infected with P. falciparum for diagnostic purposes, to disrupt host-parasite interactions, or to deliver chemotherapeutics. Aptamer technology has the potential to revolutionize biological diagnostics and therapeutics; however, broad adoption is hindered by the high failure rate of the systematic evolution of ligands by exponential enrichment (SELEX). Here we performed parallel SELEX experiments to compare the impact of two different methods for single-strand recovery on the efficiency of aptamer enrichment. Our experimental results and analysis of SELEX publications spanning 13 years implicate the alkaline denaturation step as a significant cause for inefficient aptamer selection. Thus, we applied an exonuclease single-strand recovery step in our SELEX to direct aptamers to the surface of erythrocytes infected with P. falciparum. The selected aptamers bind with high affinity (low nanomolar Kd values) and selectivity to exposed surface proteins of both laboratory parasite strains as well isolates from patients in Asia and Africa with clinical malaria. The results obtained in this study potentially open new approaches to malaria diagnosis and surveillance.
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Affiliation(s)
- Eugene K Oteng
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, 20852, USA.
| | - Wenjuan Gu
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA
| | - Maureen McKeague
- Department of Pharmacology and Therapeutics, McGill University, 3655 Prom. Sir-William-Osler, Montreal, Quebec, H3G 1Y6, Canada.,Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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34
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Azri FA, Eissa S, Zourob M, Chinnappan R, Sukor R, Yusof NA, Raston NHA, Alhoshani A, Jinap S. Electrochemical determination of zearalenone using a label-free competitive aptasensor. Mikrochim Acta 2020; 187:266. [PMID: 32279134 DOI: 10.1007/s00604-020-4218-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/06/2020] [Indexed: 11/25/2022]
Abstract
An electrochemical aptasensor is described for determination of the phytohormone of zearalenone (ZEA). The gold electrode was modified with ZEA via covalent attachment using cysteamine-hydrochloride and 1,4-phenylene diisocyanate linker. A truncated ZEA aptamer with a dissociation constant of 13.4 ± 2.1 nM was used in an aptasensor. The electrochemical property was investigated using square wave voltammetry for monitoring the change in the electron transfer using the ferro/ferricyanide system as redox probe. Under optimal experimental conditions, the response was best measured at a potential of 0.20 V (vs. Ag/AgCl). The signals depended on the competitive mechanism between the immobilised ZEA and free ZEA for the aptamer binding site. The aptasensor works in the range 0.01 to 1000 ng·mL-1 ZEA concentration, with a detection limit of 0.017 ng·mL-1. High degree of cross-reactivity with the other analogues of ZEA was observed, whereas none towards other mycotoxins. The aptasensor was further applied for the determination of ZEA in the extract of maize grain and showed good recovery percentages between 87 and 110%. Graphical abstract Schematic representation of the electrochemical determination of zearalenone based on indirect competitive assay. Step a Immobilisation of ZEA on the surface of gold electrode via covalent attachment, b competition for the ZEA aptamer binding site between immobilised and free ZEA, and c current signal of the binding event based on SWV technique.
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Affiliation(s)
- Farah Asilah Azri
- Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Shimaa Eissa
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi, Riyadh, 11533, Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi, Riyadh, 11533, Saudi Arabia
| | - Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi, Riyadh, 11533, Saudi Arabia
| | - Rashidah Sukor
- Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.,Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Nurul Hanun Ahmad Raston
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ali Alhoshani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11533, Saudi Arabia
| | - Selamat Jinap
- Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia. .,Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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35
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PCR incorporation of dUMPs modified with aromatic hydrocarbon substituents of different hydrophilicities: Synthesis of C5-modified dUTPs and PCR studies using Taq, Tth, Vent (exo-) and Deep Vent (exo-) polymerases. Bioorg Chem 2020; 99:103829. [PMID: 32299018 DOI: 10.1016/j.bioorg.2020.103829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/25/2020] [Accepted: 04/05/2020] [Indexed: 02/07/2023]
Abstract
Deoxyuridine triphosphate derivatives (dUTPs) modified at the C5 position of the pyrimidine ring with various aromatic hydrocarbon substituents of different hydrophilicities have been synthesized. The aromatic hydrocarbon substituents were attached to dUTPs via a CHCHCH2NHCOCH2 linker. The efficiency of the PCR incorporation of modified dUMPs using Taq, Tth, Vent (exo-) and Deep Vent (exo-) polymerases and a model DNA template containing one, two and three adjacent adenine nucleotides at three different sites within the sequence was investigated. For all the polymerases used, the yield of the modified PCR product was significantly increased with increasing hydrophilicity of the aromatic hydrocarbon substituent. In particular, for the above polymerases, the efficiency of the incorporation of dUMPs modified with the most hydrophilic of the studied aromatic hydrocarbon substituents, a 4-hydroxyphenyl residue, was 60-85% of the efficiency of dTMP incorporation. At the same time, the relative efficiencies of the incorporation of dUMPs modified with 2-, 4-methoxyphenyl, phenyl and 4-nitrophenyl substituents ranged from 20 to 50% and were 2-18% for the 1-naphthalene and 4-biphenyl groups, which were the most hydrophobic of the studied aromatic hydrocarbon substituents.
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36
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Zheng Y, Geng X, Yang X, Li S, Liu Y, Liu X, Wang Q, Wang K, Jia R, Xu Y. Exploring Interactions of Aptamers with Aβ 40 Amyloid Aggregates and Its Application: Detection of Amyloid Aggregates. Anal Chem 2020; 92:2853-2858. [PMID: 31916749 DOI: 10.1021/acs.analchem.9b05493] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The exhaustive investigating interactions between recognition probes and amyloid aggregates, especially simultaneous recognition events, are challenging and crucial for the design of biosensing probes and further diagnosis of amyloid diseases. In the present work, the interactions of aptamers (Apts) with β-amyloid (Aβ) aggregates were explored thoroughly by single-molecule force spectroscopy (SMFS). Indeed, it was found that the interaction of aptamer1 (Apt1)-amyloid aggregates was different from that of aptamer2 (Apt2)-Aβ40 aggregates at the single-molecule level. Especially, the interaction force of Apt1-Aβ40 fibril showed a double distinguishing Gaussian fitting. The only unimodal distribution of the force histogram was displayed for the interactions of Apt2-Aβ40 oligomer, Apt2-Aβ40 fibril, and Apt1-Aβ40 oligomer. More intriguingly, two Apts could bind to amyloid aggregates simultaneously. With the assistance of two Apts recognition, a novel sensitive dual Apt-based surface plasmon resonance (SPR) sensor using Au nanoparticles (AuNPs) was developed for quantifying Aβ40 aggregates. The dual Apt-based SPR sensor not only avoided the limitation of steric hindrance and epitope but also employed simple operation as well as inexpensive recognition probes. A detection limit as low as 0.2 pM for Aβ40 oligomer and 0.05 pM for Aβ40 fibril could be achieved. Moreover, the established sensor could be successfully applied to detect Aβ40 aggregates in artificial cerebrospinal fluid (CSF) and undiluted real CSF. This work could provide a strategy to monitor a simultaneous recognition event using SMFS and broaden the application of Apts in the diagnosis of neurodegenerative diseases.
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Affiliation(s)
- Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Xiuhua Geng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Shaoyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Yaqin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Xiaofeng Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Ruichen Jia
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province , Hunan University , Changsha 410082 , P. R. China
| | - Yao Xu
- Huaihe Hospital of Henan University , Henan University , Kaifeng 475001 , P. R. China
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Ye W, Liu T, Zhang W, Zhu M, Liu Z, Kong Y, Liu S. Marine Toxins Detection by Biosensors Based on Aptamers. Toxins (Basel) 2019; 12:E1. [PMID: 31861315 PMCID: PMC7020455 DOI: 10.3390/toxins12010001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 12/11/2022] Open
Abstract
Marine toxins cause great harm to human health through seafood, therefore, it is urgent to exploit new marine toxins detection methods with the merits of high sensitivity and specificity, low detection limit, convenience, and high efficiency. Aptasensors have emerged to replace classical detection methods for marine toxins detection. The rapid development of molecular biological approaches, sequencing technology, material science, electronics and chemical science boost the preparation and application of aptasensors. Taken together, the aptamer-based biosensors would be the best candidate for detection of the marine toxins with the merits of high sensitivity and specificity, convenience, time-saving, relatively low cost, extremely low detection limit, and high throughput, which have reduced the detection limit of marine toxins from nM to fM. This article reviews the detection of marine toxins by aptamer-based biosensors, as well as the selection approach for the systematic evolution of ligands by exponential enrichment (SELEX), the aptamer sequences. Moreover, the newest aptasensors and the future prospective are also discussed, which would provide thereotical basis for the future development of marine toxins detection by aptasensors.
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Affiliation(s)
| | | | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China; (W.Y.); (T.L.); (M.Z.); (Z.L.); (Y.K.); (S.L.)
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38
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Moez E, Noel D, Brice S, Benjamin G, Pascaline A, Didier M. Aptamer assisted ultrafiltration cleanup with high performance liquid chromatography-fluorescence detector for the determination of OTA in green coffee. Food Chem 2019; 310:125851. [PMID: 31767477 DOI: 10.1016/j.foodchem.2019.125851] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
One of the most common mycotoxin contaminating feed and foodstuffs is Ochratoxin A (OTA). OTA has a chronic toxic effect and proved to be mutagenic, nephrotoxic, teratogenic, immunosuppressive, and carcinogenic. Aptamer with their specific affinity for OTA was used in this paper to create an analytical technique. Several methods have been reported for the determination of OTA in foods. However, most of these methods could not be applied to a complex food as green coffee because the interfering native fluorescent products made the quantification very difficult. In this work, we mixed two separations based techniques to identify and quantify OTA in green coffee. Aptamer assisted ultrafiltration as separation technique based on the size of molecules was applied to separate the free OTA, the quantification of OTA was established by a high-performance liquid chromatography (HPLC-FD) with a limit of detection (LOD) of 0.05 ng/mL for OTA. Artificially contaminated green coffee displayed a good range of OTA recoveries up to 97.7%. This method can be applied to the quantitative determination of OTA in green coffee at levels below the maximum levels proposed by the European Commission for green coffee. It also confirm that aptamers can be used as biorecognition element in diagnostic assays with commercial application for mycotoxin analysis.
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Affiliation(s)
- Elsaadani Moez
- Cirad, UMR Qualisud, TA B-95/16, 73, rue JF Breton, 34398 Montpellier Cedex 5, France; UMR 95 QualiSud, Université de Montpellier, CIRAD, Montpellier SupAgro, Université d'Avignon, Université de la Réunion, Montpellier, France; Faculty of Biotechnology, Misr University for Science and Technology, 6th 13 October City, Egypt; IES, UMR CNRS 5214, Montpellier University, France.
| | - Durand Noel
- Cirad, UMR Qualisud, TA B-95/16, 73, rue JF Breton, 34398 Montpellier Cedex 5, France; UMR 95 QualiSud, Université de Montpellier, CIRAD, Montpellier SupAgro, Université d'Avignon, Université de la Réunion, Montpellier, France
| | - Sorli Brice
- IES, UMR CNRS 5214, Montpellier University, France
| | - Guibert Benjamin
- Cirad, UMR Qualisud, TA B-95/16, 73, rue JF Breton, 34398 Montpellier Cedex 5, France
| | - Atelier Pascaline
- Cirad, UMR Qualisud, TA B-95/16, 73, rue JF Breton, 34398 Montpellier Cedex 5, France
| | - Montet Didier
- Cirad, UMR Qualisud, TA B-95/16, 73, rue JF Breton, 34398 Montpellier Cedex 5, France; UMR 95 QualiSud, Université de Montpellier, CIRAD, Montpellier SupAgro, Université d'Avignon, Université de la Réunion, Montpellier, France
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39
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Li W, Luo Y, Gao T, Yang L, Wang J, Pei R. In Vitro Selection of DNA Aptamers for a Small-Molecule Porphyrin by Gold Nanoparticle-Based SELEX. J Mol Evol 2019; 87:231-239. [PMID: 31432230 DOI: 10.1007/s00239-019-09905-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/01/2019] [Indexed: 12/24/2022]
Abstract
In this study, a new strategy for the selection of aptamers against small-molecule target was established using gold nanoparticles (AuNPs) as the separation matrix and Zinc(II)-Protoporphyrin IX (ZnPPIX) as the target molecule without the immobilization step due to the absorption of ssDNA on AuNPs. The progress of the selection process was monitored by the recovery rate and the fluorescence enhancement of N-methyl mesoporphyrin IX (NMM) after reacting with each selected pool. After 11 rounds of selection, a truncated aptamer ZnP1.2 with a low-micromolar dissociation constant was obtained, and it also showed good fluorescence enhancement for NMM and the enhanced peroxidase activity after binding with hemin, indicating this functional aptamer has potential to be a light-up fluorescent probe and a DNAzyme which could be used as an alternative to peroxidases for many colorimetric or chemiluminescent detections in biosensing events. The experimental results show that the simple and convenient AuNP-based SELEX is very conducive to the selection of aptamers for small-molecule targets.
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Affiliation(s)
- Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.,Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, 215123, China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Tian Gao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.
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Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.
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Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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41
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Milisavljevič N, Perlíková P, Pohl R, Hocek M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org Biomol Chem 2019; 16:5800-5807. [PMID: 30063056 DOI: 10.1039/c8ob01498a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We synthesized a small library of eighteen 5-substituted pyrimidine or 7-substituted 7-deazapurine nucleoside triphosphates bearing methyl, ethynyl, phenyl, benzofuryl or dibenzofuryl groups through cross-coupling reactions of nucleosides followed by triphosphorylation or through direct cross-coupling reactions of halogenated nucleoside triphosphates. We systematically studied the influence of the modification on the efficiency of T7 RNA polymerase catalyzed synthesis of modified RNA and found that modified ATP, UTP and CTP analogues bearing smaller modifications were good substrates and building blocks for the RNA synthesis even in difficult sequences incorporating multiple modified nucleotides. Bulky dibenzofuryl derivatives of ATP and GTP were not substrates for the RNA polymerase. In the case of modified GTP analogues, a modified procedure using a special promoter and GMP as initiator needed to be used to obtain efficient RNA synthesis. The T7 RNA polymerase synthesis of modified RNA can be very efficiently used for synthesis of modified RNA but the method has constraints in the sequence of the first three nucleotides of the transcript, which must contain a non-modified G in the +1 position.
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Affiliation(s)
- Nemanja Milisavljevič
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic.
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42
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Saraf N, Villegas M, Willenberg BJ, Seal S. Multiplex Viral Detection Platform Based on a Aptamers-Integrated Microfluidic Channel. ACS OMEGA 2019; 4:2234-2240. [PMID: 30729227 PMCID: PMC6358057 DOI: 10.1021/acsomega.8b03277] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/11/2019] [Indexed: 05/02/2023]
Abstract
A polydimethylsiloxane-based microfluidic device has been developed for the multiplex detection of viral envelope proteins such as Zika and chikungunya on a single platform using aptamer-analyte interactions. The channel is integrated with microsized pillars that increase the surface area allowing more aptamers to attach to the incoming envelope protein molecules, thus increasing the overall sensitivity of the system. The working of the device depends on the formation of protein-mediated sandwich morphology that is obtained using an aptamer and aptamer-functionalized gold nanoparticle (AuNP) pair. The colorimetric signal is obtained upon introduction of silver reagents into the channel, which are selectively deposited on the AuNP surface, providing a gray contrast in the testing zone. The microfluidic channel approach successfully detected clinically relevant concentrations of Zika and chikungunya envelope proteins in phosphine-buffered saline (1 pM) and calf blood (100 pM) with high specificity using gold-decorated aptamers integrated in a microfluidic channel.
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Affiliation(s)
- Nileshi Saraf
- Advanced
Materials Processing and Analysis Centre, Department of
Materials Science and Engineering, Department of Internal Medicine, College of
Medicine, and Nanoscience Technology Centre, University
of Central Florida, Orlando, Florida 32827, United States
| | - Michael Villegas
- University
of Florida, Gainesville, Florida 32611, United
States
| | - Bradley Jay Willenberg
- Advanced
Materials Processing and Analysis Centre, Department of
Materials Science and Engineering, Department of Internal Medicine, College of
Medicine, and Nanoscience Technology Centre, University
of Central Florida, Orlando, Florida 32827, United States
| | - Sudipta Seal
- Advanced
Materials Processing and Analysis Centre, Department of
Materials Science and Engineering, Department of Internal Medicine, College of
Medicine, and Nanoscience Technology Centre, University
of Central Florida, Orlando, Florida 32827, United States
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43
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Liu S, Chen Q, Wang Z, Cao T, Zhao G, Zhou Y. Monitoring 2,3',5,5'-tetrachlorobiphenyl with a rapid and sensitive environmental aptamer sensor. Analyst 2019; 144:4841-4847. [PMID: 31290489 DOI: 10.1039/c9an00848a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Polychlorinated biphenyl (PCB) detection in the environment is significant for both environmental protection and human health. Herein, a highly sensitive aptamer sensor has been established by employing a 2,3',5,5'-tetrachlorobiphenyl (PCB72) targeting aptamer as a highly specific recognition element and a gold/silver (Au@Ag) nanocomposite as the surface-enhanced Raman spectroscopy (SERS) substrate for detecting environmental PCB72. The Au@Ag nanoparticles (NPs) exhibit a strong SERS enhancement and provide an efficient substrate for immobilizing the PCB72 aptamer and Raman signal labelled molecule, 4-mercaptobenzoic acid (4-MBA). The targeted PCB72 could competitively bind with the PCB72 aptamer, resulting in a few aptamers sticking to the Au@Ag NPs and the "hot spot" strengthening effect of the substrate. Under optimal conditions, this aptamer sensor exhibits great performance with high sensitivity, excellent selectivity and stability for the monitoring of PCB72, which shows an excellent linear correlation ranging from 1 to 1000 pg mL-1 with a limit of detection of 0.3 pg mL-1. Furthermore, this aptamer assay exhibits high specificity and selectivity for PCB72 with the detection error of less than 0.27 for other PCBs and 0.21 for other interfering species, even if the coexisting interferents are 100-fold concentration in the system. Additionally, the recognition mechanism of the binding of aptamers to PCB72 is analyzed via UV-vis spectroscopy and molecular docking simulations, which suggest that PCB72 could insert into the aptamers. Furthermore, this method is successfully utilized for PCB72 detection in real water samples with a simple pre-treatment. In general, this work provides a new and effective method using an environmental aptamer sensor for rapid and sensitive PCB72 detection.
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Affiliation(s)
- Siyao Liu
- Department of Cardio-Thoracic Surgery, Institute of Translational Research, Tongji Hospital, Tongji University School of medicine, Shanghai 200065, People's Republic of China.
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44
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Wang T, Chen C, Larcher LM, Barrero RA, Veedu RN. Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development. Biotechnol Adv 2018; 37:28-50. [PMID: 30408510 DOI: 10.1016/j.biotechadv.2018.11.001] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/28/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023]
Abstract
Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.
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Affiliation(s)
- Tao Wang
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia; School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Changying Chen
- School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Leon M Larcher
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia.
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Gu H, Duan N, Xia Y, Hun X, Wang H, Wang Z. Magnetic Separation-Based Multiple SELEX for Effectively Selecting Aptamers against Saxitoxin, Domoic Acid, and Tetrodotoxin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9801-9809. [PMID: 30153406 DOI: 10.1021/acs.jafc.8b02771] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, a novel magnetic separation-based multiple systematic evolution of ligands by exponential enrichment (SELEX) was applied to select aptamers simultaneously against three kinds of marine biotoxins, including domoic acid (DA), saxitoxin (STX), and tetrodotoxin (TTX). Magnetic reduced graphene oxide (MRGO) was prepared to adsorb unbound ssDNAs and simplify the separation step. In the multiple SELEX, after the initial twelve rounds of selection against mixed targets and the subsequent four respective rounds of selection against each single target, the three resulting ssDNA pools were cloned, sequenced, and analyzed. Several aptamer candidates were selected and subjected to the binding affinity and specificity test. Finally, DA-06 ( Kd = 62.07 ± 19.97 nM), TTX-07 ( Kd = 44.12 ± 15.38 nM), and STX-41 ( Kd = 61.44 ± 23.18 nM) showed high affinity and good specificity for DA, TTX, and STX, respectively. They were also applied to detect and quantify DA, TTX, and STX successfully. The other two multitarget aptamers, DA-01 and TTX-27, were also obtained, which can bind with either DA or TTX. These aptamers provide alternative recognition molecules to antibodies for biosensor applications.
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Affiliation(s)
- Huajie Gu
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , China
- School of Chemical Biology and Materials Engineering , Suzhou University of Science and Technology , Suzhou 215009 , China
- Synergetic Innovation Center of Food Safety and Quality Control of Jiangsu Province , Jiangnan University , Wuxi 214122 , China
| | - Nuo Duan
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , China
- Synergetic Innovation Center of Food Safety and Quality Control of Jiangsu Province , Jiangnan University , Wuxi 214122 , China
| | - Yu Xia
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , China
- Synergetic Innovation Center of Food Safety and Quality Control of Jiangsu Province , Jiangnan University , Wuxi 214122 , China
| | - Xu Hun
- College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Haitao Wang
- National National of Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , China
| | - Zhouping Wang
- School of Food Science and Technology , Jiangnan University , Wuxi 214122 , China
- National National of Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , China
- Synergetic Innovation Center of Food Safety and Quality Control of Jiangsu Province , Jiangnan University , Wuxi 214122 , China
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Petukhov AE, Petrykina EA, Tereshkina OI, Ramenskaya GV, Antipova OM, Turashev AD, Zav’yalova EG, Golovin AV, Pavlova GV, Kopylov AM. Standardization of Thrombaptanib Drug Substance for Residual Organic Solvents. Pharm Chem J 2018. [DOI: 10.1007/s11094-018-1823-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Xu X, Ma X, Wang H, Wang Z. Aptamer based SERS detection of Salmonella typhimurium using DNA-assembled gold nanodimers. Mikrochim Acta 2018; 185:325. [PMID: 29896641 DOI: 10.1007/s00604-018-2852-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/25/2018] [Indexed: 11/26/2022]
Abstract
The authors describe a surface-enhanced Raman scattering (SERS) based aptasensor for Salmonella typhimurium (S. typhimurium). Gold nanoparticles (AuNPs; 35 nm i.d.) were functionalized with the aptamer (ssDNA 1) and used as the capture probe, while smaller (15 nm) AuNPs were modified with a Cy3-labeled complementary sequence (ssDNA 2) and used as the signalling probe. The asymmetric gold nanodimers (AuNDs) were assemblied with the Raman signal probe and the capture probe via hybridization of the complementary ssDNAs. The gap between two nanoparticles is a "hot spot" in which the Raman reporter Cy3 is localized. It experiences a strong enhancement of the electromagnetic field around the particle. After addition of S. typhimurium, it will be bound by the aptamer which therefore is partially dehybridized from its complementary sequence. Hence, Raman intensity drops. Under the optimal experimental conditions, the SERS signal at 1203 cm-1 increases linearly with the logarithm of the number of colonies in the 102 to 107 cfu·mL-1 concentration range, and the limit of detection is 35 cfu·mL-1. The method can be performed within 1 h and was successfully applied to the analysis of spiked milk samples and performed very well and with high specificity. Graphical abstract DNA-assembled asymmetric gold nanodimers (AuNDs) were synthesized and appllied in a SERS-based aptasensor for S. typhimurium. Capture probe was preferentially combined with S. typhimurium and the structure of the AuNDs was destroyed. The "hot spot" vanished partly, this resulting in the decreased Raman intensity of Cy3.
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Affiliation(s)
- Xumin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| | - Haitao Wang
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116000, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116000, China.
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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Huang Y, Xu W, Liu G, Tian L. A pure DNA hydrogel with stable catalytic ability produced by one-step rolling circle amplification. Chem Commun (Camb) 2018; 53:3038-3041. [PMID: 28239729 DOI: 10.1039/c7cc00636e] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A rolling-circle-amplification method was developed to produce DNA hydrogels with horseradish-peroxidase-like catalytic capability. The catalytic hydrogel exhibits highly improved stability at elevated temperatures or during a long-term storage. Integrated with glucose oxidase, the complex hydrogel can be applied to the sensitive and reliable detection of glucose.
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Affiliation(s)
- Yishun Huang
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Wanlin Xu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
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