1
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Pei S, Babity S, Sara Cordeiro A, Brambilla D. Integrating microneedles and sensing strategies for diagnostic and monitoring applications: The state of the art. Adv Drug Deliv Rev 2024; 210:115341. [PMID: 38797317 DOI: 10.1016/j.addr.2024.115341] [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: 02/17/2024] [Revised: 04/23/2024] [Accepted: 05/18/2024] [Indexed: 05/29/2024]
Abstract
Microneedles (MNs) offer minimally-invasive access to interstitial fluid (ISF) - a potent alternative to blood in terms of monitoring physiological analytes. This property is particularly advantageous for the painless detection and monitoring of drugs and biomolecules. However, the complexity of the skin environment, coupled with the inherent nature of the analytes being detected and the inherent physical properties of MNs, pose challenges when conducting physiological monitoring using this fluid. In this review, we discuss different sensing mechanisms and highlight advancements in monitoring different targets, with a particular focus on drug monitoring. We further list the current challenges facing the field and conclude by discussing aspects of MN design which serve to enhance their performance when monitoring different classes of analytes.
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Affiliation(s)
- Shihao Pei
- Faculté de pharmacie, Université de Montréal, 2940 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Samuel Babity
- Faculté de pharmacie, Université de Montréal, 2940 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Ana Sara Cordeiro
- Leicester Institute for Pharmaceutical Innovation, Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, United Kingdom.
| | - Davide Brambilla
- Faculté de pharmacie, Université de Montréal, 2940 Chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada.
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2
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Kumar S, Mohan A, Sharma NR, Kumar A, Girdhar M, Malik T, Verma AK. Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review. ACS OMEGA 2024; 9:26838-26862. [PMID: 38947800 PMCID: PMC11209897 DOI: 10.1021/acsomega.4c02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.
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Affiliation(s)
- Shubham Kumar
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anand Mohan
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Neeta Raj Sharma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anil Kumar
- Gene
Regulation Laboratory, National Institute
of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Madhuri Girdhar
- Division
of Research and Development, Lovely Professional
University, Phagwara 144401, Punjab, India
| | - Tabarak Malik
- Department
of Biomedical Sciences, Institute of Health, Jimma University, MVJ4+R95 Jimma, Ethiopia
| | - Awadhesh Kumar Verma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
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3
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Szatko M, Forysiak W, Kozub S, Andruniów T, Szweda R. Revealing the Effect of Stereocontrol on Intermolecular Interactions between Abiotic, Sequence-Defined Polyurethanes and a Ligand. ACS Biomater Sci Eng 2024; 10:3727-3738. [PMID: 38804015 PMCID: PMC11167595 DOI: 10.1021/acsbiomaterials.4c00456] [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: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
The development of precision polymer synthesis has facilitated access to a diverse library of abiotic structures wherein chiral monomers are positioned at specific locations within macromolecular chains. These structures are anticipated to exhibit folding characteristics similar to those of biotic macromolecules and possess comparable functionalities. However, the extensive sequence space and numerous variables make selecting a sequence with the desired function challenging. Therefore, revealing sequence-function dependencies and developing practical tools are necessary to analyze their conformations and molecular interactions. In this study, we investigate the effect of stereochemistry, which dictates the spatial location of backbone and pendant groups, on the interaction between sequence-defined oligourethanes and bisphenol A ligands. Various methods are explored to analyze the receptor-like properties of model oligomers and the ligand. The accuracy of molecular dynamics simulations and experimental techniques is assessed to uncover the impact of discrete changes in stereochemical arrangements on the structures of the resulting complexes and their binding strengths. Detailed computational investigations providing atomistic details show that the formed complexes demonstrate significant structural diversity depending on the sequence of stereocenters, thus affecting the oligomer-ligand binding strength. Among the tested techniques, the fluorescence spectroscopy data, fitted to the Stern-Volmer equation, are consistently aligned with the calculations, thus validating the developed simulation methodology. The developed methodology opens a way to engineer the structure of sequence-defined oligomers with receptor-like functionality to explore their practical applications, e.g., as sensory materials.
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Affiliation(s)
- Maksymilian Szatko
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Weronika Forysiak
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Sara Kozub
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
| | - Tadeusz Andruniów
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Roza Szweda
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Center
for Advanced Technologies, Adam Mickiewicz
University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland
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4
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Manea I, Casian M, Hosu-Stancioiu O, de-Los-Santos-Álvarez N, Lobo-Castañón MJ, Cristea C. A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules. Anal Chim Acta 2024; 1297:342325. [PMID: 38438246 DOI: 10.1016/j.aca.2024.342325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/06/2024]
Abstract
This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.
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Affiliation(s)
- Ioana Manea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania
| | - Magdolna Casian
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania; Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain
| | - Oana Hosu-Stancioiu
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
| | - Noemí de-Los-Santos-Álvarez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - Cecilia Cristea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
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5
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Wang Y, Luo C, Lou X, Li F, Huang Y, Xia F. Fluorescent Selectivity-Enhanced FRET Based on 3D Photonic Crystals for Multianalyte Sensing. Anal Chem 2024; 96:1630-1639. [PMID: 38217493 DOI: 10.1021/acs.analchem.3c04547] [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: 01/15/2024]
Abstract
Fluorescence resonance energy transfer (FRET) finds widespread utility in biochemical sensing, single-molecule experiments, cell physiology, and various other domains due to its inherent simplicity and high sensitivity. Nevertheless, the efficiency of energy transfer between the FRET donor and acceptor is significantly contingent on the local photonic environment, a factor that limits its application in complex systems or multianalyte detections. Here, a fluorescent selectivity-enhanced acridine orange (AO)-aflatoxins (AFs) FRET system based on a range of 3D topological photonic crystals (PCs) was developed with the aim of enhancing the selectivity and discrimination capabilities of FRET. By exploring the angle-dependent characteristics of the photonic stopband, the stopband distribution across different 3D topological PCs pixels was investigated. This approach led to selective fluorescence enhancement in PCs that matched the stopbands, enabling the successful discrimination of six distinct aflatoxins and facilitating complex multianalysis of moldy food samples. In particular, the stopband, which was strategically positioned within the blue-purple structural color range, exhibited a strong alignment with the fluorescence peaks of both the FRET donor and acceptor. This alignment allowed the 3D three-pointed star PCs to be effectively employed for the identification of mixed samples containing six distinct aflatoxins as well as the detection of real aflatoxin samples present in moldy potatoes, bread, oats, and peanuts. Impressively, this approach achieved a remarkable accuracy rate of 100%. This innovative strategy not only presents a novel avenue for developing a multitarget discrimination analysis system but also offers a convenient pretreatment method for the quantitative detection of various aflatoxins.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Cihui Luo
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Fengyu Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Yu Huang
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
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6
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Chowdhury MA, Collins JM, Gell DA, Perry S, Breadmore MC, Shigdar S, King AE. Isolation and Identification of the High-Affinity DNA Aptamer Target to the Brain-Derived Neurotrophic Factor (BDNF). ACS Chem Neurosci 2024; 15:346-356. [PMID: 38149631 DOI: 10.1021/acschemneuro.3c00661] [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] [Indexed: 12/28/2023] Open
Abstract
Aptamers are functional oligonucleotide ligands used for the molecular recognition of various targets. The natural characteristics of aptamers make them an excellent alternative to antibodies in diagnostics, therapeutics, and biosensing. DNA aptamers are mainly single-stranded oligonucleotides (ssDNA) that possess a definite binding to targets. However, the application of aptamers to the fields of brain health and neurodegenerative diseases has been limited to date. Herein, a DNA aptamer against the brain-derived neurotrophic factor (BDNF) protein was obtained by in vitro selection. BDNF is a potential biomarker of brain health and neurodegenerative diseases and has functions in the synaptic plasticity and survival of neurons. We identified eight aptamers that have binding affinity for BDNF from a 50-nucleotide library. Among these aptamers, NV_B12 showed the highest sensitivity and selectivity for detecting BDNF. In an aptamer-linked immobilized sorbent assay (ALISA), the NV_B12 aptamer strongly bound to BDNF protein, in a dose-dependent manner. The dissociation constant (Kd) for NV_B12 was 0.5 nM (95% CI: 0.4-0.6 nM). These findings suggest that BDNF-specific aptamers could be used as an alternative to antibodies in diagnostic and detection assays for BDNF.
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Affiliation(s)
- Md Anisuzzaman Chowdhury
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Jessica M Collins
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - David A Gell
- Menzies Research Institute, School of Medicine, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Michael C Breadmore
- Australian Centre for Research on Separation Science (ACROSS), School of Chemistry, University of Tasmania, Sandy Bay, Hobart, Tasmania 7001, Australia
| | - Sarah Shigdar
- School of Medicine, Faculty of Health, Deakin University, Geelong, Victoria 3220, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
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7
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Porciani D, Alampi MM, Abbruzzetti S, Viappiani C, Delcanale P. Fluorescence Correlation Spectroscopy as a Versatile Method to Define Aptamer-Protein Interactions with Single-Molecule Sensitivity. Anal Chem 2024; 96:137-144. [PMID: 38124657 PMCID: PMC10782416 DOI: 10.1021/acs.analchem.3c03341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Aptamers are folded oligonucleotides that selectively recognize and bind a target and are consequently regarded as an emerging alternative to antibodies for sensing and therapeutic applications. The rational development of functional aptamers is strictly related to the accurate definition of molecular binding properties. Nevertheless, most of the methodologies employed to define binding affinities use bulk measurements. Here, we describe the use of fluorescence correlation spectroscopy (FCS) as a method with single-molecule sensitivity that quantitatively defines aptamer-protein binding. First, FCS was used to measure the equilibrium affinity between the CLN3 aptamer, conjugated with a dye, and its target, the c-Met protein. Equilibrium affinity was also determined for other functional aptamers targeting nucleolin and platelet-derived growth factors. Then, association and dissociation rates of CLN3 to/from the target protein were measured using FCS by monitoring the equilibration kinetics of the binding reaction in solution. Finally, FCS was exploited to investigate the behavior of CLN3 exposed to physiological concentrations of the most abundant serum proteins. Under these conditions, the aptamer showed negligible interactions with nontarget serum proteins while preserving its affinity for the c-Met. The presented results introduce FCS as an alternative or complementary analytical tool in aptamer research, particularly well-suited for the characterization of protein-targeting aptamers.
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Affiliation(s)
- David Porciani
- MU
Bond Life Sciences Center, University of
Missouri-Columbia, 1201 Rollins Street, Columbia, Missouri 65211-7310, United States
- Department
of Molecular Microbiology & Immunology, School of Medicine, University of Missouri-Columbia, 1 Hospital Dr, Columbia, Missouri 65212, United States
| | - Manuela Maria Alampi
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, Parma 43124, Italy
| | - Stefania Abbruzzetti
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, Parma 43124, Italy
| | - Cristiano Viappiani
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, Parma 43124, Italy
| | - Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, Parma 43124, Italy
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8
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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9
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Yu H, Zhao Q. Profiling Additional Effects of Aptamer Fluorophore Modification on Microscale Thermophoresis Characterization of Aptamer-Target Binding. Anal Chem 2023; 95:17011-17019. [PMID: 37946406 DOI: 10.1021/acs.analchem.3c03603] [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: 11/12/2023]
Abstract
Aptamers are promising affinity ligands with considerable applications, such as biosensors, disease diagnosis, therapy, etc. Characterization of aptamer-target binding is important in aptamer selection and aptamer applications. Microscale thermophoresis (MST) is an emerging optical technique for molecular interactions, which monitors fluorescence responses of fluorescent molecules in a microscopic temperature gradient. Harnessing merits in trace sample consumption, high speed, free separation, free immobilization, and ratiometric analysis, MST draws intense wide attention. MST is often applied for aptamer-target binding studies using fluorescently labeled aptamers. However, the MST signal is strongly dependent on fluorophore modifications at aptamers, which brings additional challenges and effects for MST analyzing aptamer affinity. Here, we systematically explored effects of fluorophore modifications (e.g., fluorophore types, fluorophore positions, etc.) of aptamer probes on MST characterizing aptamer-target interactions and identified gaps of MST analysis in aptamer affinity determination, taking aptamers against cadmium ions and aflatoxin B1 as two representatives. The same aptamers with different fluorophore modifications showed distinct MST signals in response magnitudes and signs as well as determined affinities, and some of them failed to respond to target binding and gave false affinity information in MST. A competitive MST method can be used to extract the affinity of unmodified aptamers, excluding effects of fluorophore modification. This work highlights that appropriate fluorophore modification is crucial in MST analysis of aptamer affinity, and caution is needed in MST applications, providing a basis for rational design of the MST method for the reliable molecular interaction study.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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10
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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11
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Yu H, Zhao Q. Rapid sensitive fluorescence detection of cadmium (II) with pyrene excimer switching aptasensor. J Environ Sci (China) 2023; 133:1-7. [PMID: 37451780 DOI: 10.1016/j.jes.2022.03.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 07/18/2023]
Abstract
Heavy metal cadmium (II) contamination often occurs, causing great health risk to human due to high toxicity of cadmium (II). Rapid, sensitive and simple detection of cadmium (II) are of great importance in environmental monitoring. Taking advantage of aptamer in specific recognition, easy modification, and capability of binding-induced structure change, here we reported a simple fluorescent sensor with rapid and sensitive response for Cd2+ using aptamer pyrene excimer switch. The aptamer was labeled with dual pyrene molecules at two ends of the sequence. The binding of Cd2+ to this aptamer probe brought the pyrene labels into close proximity and enhanced formation of a pyrene excimer, which generated increased fluorescence at 485 nm. By measuring the fluorescence of pyrene excimer, we achieved detection of Cd2+ with this aptasensor. Under the optimum experimental conditions, the detection limit of Cd2+ reached nanomolar levels. This method was selective and allowed for the detection of Cd2+ in tap water. This fluorescence aptasensor is promising for rapid detection of Cd2+ in broad applications.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China.
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12
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LeMon MB, Douma CC, Burke GS, Bowser MT. Fabrication of µFFE Devices in COC via Hot Embossing with a 3D-Printed Master Mold. MICROMACHINES 2023; 14:1728. [PMID: 37763891 PMCID: PMC10534651 DOI: 10.3390/mi14091728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/19/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
The fabrication of high-performance microscale devices in substrates with optimal material properties while keeping costs low and maintaining the flexibility to rapidly prototype new designs remains an ongoing challenge in the microfluidics field. To this end, we have fabricated a micro free-flow electrophoresis (µFFE) device in cyclic olefin copolymer (COC) via hot embossing using a PolyJet 3D-printed master mold. A room-temperature cyclohexane vapor bath was used to clarify the device and facilitate solvent-assisted thermal bonding to fully enclose the channels. Device profiling showed 55 µm deep channels with no detectable feature degradation due to solvent exposure. Baseline separation of fluorescein, rhodamine 110, and rhodamine 123, was achieved at 150 V. Limits of detection for these fluorophores were 2 nM, 1 nM, and 10 nM, respectively, and were comparable to previously reported values for glass and 3D-printed devices. Using PolyJet 3D printing in conjunction with hot embossing, the full design cycle, from initial design to production of fully functional COC µFFE devices, could be completed in as little as 6 days without the need for specialized clean room facilities. Replicate COC µFFE devices could be produced from an existing embossing mold in as little as two hours.
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Affiliation(s)
| | | | | | - Michael T. Bowser
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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13
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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14
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Wang Z, Lou X. Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors. BIOSENSORS 2023; 13:bios13040425. [PMID: 37185500 PMCID: PMC10135899 DOI: 10.3390/bios13040425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/17/2023]
Abstract
Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
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15
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Chauhan NK, Anand A, Sharma A, Dhiman K, Gosain TP, Singh P, Singh P, Khan E, Chattopadhyay G, Kumar A, Sharma D, Ashish, Sharma TK, Singh R. Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein. Microbiol Spectr 2023; 11:e0197322. [PMID: 36507689 PMCID: PMC9927256 DOI: 10.1128/spectrum.01973-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.
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Affiliation(s)
- Neeraj Kumar Chauhan
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Anjali Anand
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Arun Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Kanika Dhiman
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Prashant Singh
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Padam Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Eshan Khan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | - Deepak Sharma
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ashish
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
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16
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A review: Construction of aptamer screening methods based on improving the screening rate of key steps. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Analytical Perspectives in the Study of Polyvalent Interactions of Free and Surface-Bound Oligonucleotides and Their Implications in Affinity Biosensing. Int J Mol Sci 2022; 24:ijms24010175. [PMID: 36613616 PMCID: PMC9820729 DOI: 10.3390/ijms24010175] [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: 12/01/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The high affinity and/or selectivity of oligonucleotide-mediated binding offers a myriad of therapeutical and analytical applications, whose rational design implies an accurate knowledge of the involved molecular mechanisms, concurring equilibrium processes and key affinity parameters. Oligonucleotide-functionalized gold surfaces or nanostructures are regularly employed analytical platforms for the development of label-free optical or electrochemical biosensors, and recently, novel detection platform designs have been increasingly considering the synergistic effect of polyvalent binding, involving the simultaneous interaction of two or several oligonucleotide strands. Considering the general lack of studies involving ternary single-stranded DNA (ssDNA) interactions, a complementary analytical workflow involving capillary gel electrophoretic (CGE) mobility shift assay, microcalorimetry and computational modeling has been deployed for the characterization of a series of free and surface-bound binary and ternary oligonucleotide interactions. As a proof of concept, the DNA analogue of MicroRNA 21 (miR21), a well-known oncogenic short MicroRNA (miRNA) sequence, has been chosen as a target molecule, simulating limiting-case scenarios involved in dual molecular recognition models exploited in affinity (bio)sensing. Novel data for the characterization of oligonucleotide interacting modules is revealed, offering a fast and complete mapping of the specific or non-specific, often competing, binary and ternary order interactions in dynamic equilibria, occurring between various free and metal surface-bound oligonucleotides.
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18
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Yu H, Zhao Q. Aptamer Molecular Beacon Sensor for Rapid and Sensitive Detection of Ochratoxin A. Molecules 2022; 27:molecules27238267. [PMID: 36500359 PMCID: PMC9737911 DOI: 10.3390/molecules27238267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Ochratoxin A (OTA) is a carcinogenic fungal secondary metabolite which causes wide contamination in a variety of food stuffs and environments and has a high risk to human health. Developing a rapid and sensitive method for OTA detection is highly demanded in food safety, environment monitoring, and quality control. Here, we report a simple molecular aptamer beacon (MAB) sensor for rapid OTA detection. The anti-OTA aptamer has a fluorescein (FAM) labeled at the 5' end and a black hole quencher (BHQ1) labeled at the 3' end. The specific binding of OTA induced a conformational transition of the aptamer from a random coil to a duplex-quadruplex structure, which brought FAM and BHQ1 into spatial proximity causing fluorescence quenching. Under the optimized conditions, this aptamer sensor enabled OTA detection in a wide dynamic concentration range from 3.9 nM to 500 nM, and the detection limit was about 3.9 nM OTA. This method was selective for OTA detection and allowed to detect OTA spiked in diluted liquor and corn flour extraction samples, showing the capability for OTA analysis in practical applications.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- Correspondence:
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19
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Zhang H, Zhang X, Huang G, Li F, Wu F, Xie C, Liu D, Yao D. Screening ssDNA Aptamers Against Human Vascular Endothelial Factor 165 via Semirational Design. J Chem Inf Model 2022; 62:4983-4991. [PMID: 36215718 DOI: 10.1021/acs.jcim.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a valid tumor marker, vascular endothelial growth factor 165 (VEGF165) is an effective therapeutic target for anticancer treatments. Aptamers hold great promise for the development of anti-VEGF strategies. In this study, anti-VEGF165 ssDNA aptamers were screened using a semirational design and a multilevel screening strategy. Recombinant human VEGF165 protein was used as a target for the construction of an ssDNA virtual aptamer library with ssDNA that had one sole secondary structure. After silicon-assisted prescreening, circular dichroism and isothermal titration calorimetry were used to further screen for candidates. Three aptamers (nos. 524, 529, and 64) with one sole secondary and tertiary structure, showing a high affinity for VEGF165, were identified. The KD values obtained using surface plasmon resonance analysis were 36.3, 288, and 79.3 nM for aptamers 524, 529, and 64, respectively. Cytological tests revealed that the three aptamers inhibit rhVEGF165-induced proliferation of HUVECs. Specifically, aptamer 529 had the strongest inhibitory effect (nearly 100% inhibition). The screening strategy used in our study showed improved screening efficiency relative to other methods and resulted in aptamers with one sole conformation. The aptamers had an advantage in ensuring the uniqueness of aptamer targeting. This semirational design and multilevel screening strategy provide a reference for the screening of other aptamers.
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Affiliation(s)
- Haiyi Zhang
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiyao Zhang
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Guanhong Huang
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Feifei Li
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fengmei Wu
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Chunfang Xie
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Daling Liu
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Dongsheng Yao
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
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20
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Butler-Laporte G, Gonzalez-Kozlova E, Su CY, Zhou S, Nakanishi T, Brunet-Ratnasingham E, Morrison D, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg M, Langenberg C, Forgetta V, Mooser V, Marron T, Beckmann N, Kenigsberg E, Charney AW, Kim-Schulze S, Merad M, Kaufmann DE, Gnjatic S, Richards JB. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 2022; 19:34. [PMID: 36171541 PMCID: PMC9516500 DOI: 10.1186/s12014-022-09371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 08/21/2022] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION Severe COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions. METHODS We measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support. RESULTS 580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p < 3.4 × 10-4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex. CONCLUSIONS Severe COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.
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Affiliation(s)
- Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | | | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, KyotoKyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | | | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Jonathan Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Marc Afilalo
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Danielle Henry
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Julia Carrasco-Zanini
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Maik Pietzner
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nofar Kimchi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Nardin Rezk
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Meriem Bouab
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Louis Petitjean
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Charlotte Guzman
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Xiaoqing Xue
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Chris Tselios
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Branka Vulesevic
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Olumide Adeleye
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Tala Abdullah
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Noor Almamlouk
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Yara Moussa
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Chantal DeLuca
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Naomi Duggan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montréal, Québec, Canada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montréal, Québec, Canada
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario A Cedillo
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W Simons
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jocelyn Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ieisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Celia M T Greenwood
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | | | | | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- SomaLogic Inc, Boulder, CO, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Thomas Marron
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Early Phase Trials Unit, Mount Sinai Hospital, New York, NY, USA
| | - Noam Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada.
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.
- Department of Twin Research, King's College London, London, UK.
- 5 Prime Sciences, Montreal, Québec, Canada.
- McGill University, King's College London (Honorary), Jewish General Hospital, Pavilion H-4133755 Côte-Ste-Catherine, Montréal, Québec, H3T 1E2, Canada.
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Liu F, Zhang C, Duan Y, Ma J, Wang Y, Chen G. In vitro selection and characterization of a DNA aptamer targeted to Prorocentrum minimum-A common harmful algae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154771. [PMID: 35339548 DOI: 10.1016/j.scitotenv.2022.154771] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/08/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Prorocentrum minimum is a common diarrhetic shellfish toxins-producing marine microalga that may seriously endanger marine resources and cause great economic losses. The development of a novel rapid detection technique is of great importance for the prevention and control of the damage caused by P. minimum. In this study, the aptamer against P. minimum was for the first time generated from an artificially synthesized single-stranded DNA library by systematic evolution of ligand by exponential enrichment (SELEX), using P. minimum and P. minimum-related species, including Prorocentrum donghaiense, Prorocentrum lima and Prorocentrum micans as target and counter-screening species, respectively. The aptamer library was successfully obtained at the end of 18 rounds of SELEX-screening by continuously monitoring the binding ratio of the resultant ssDNA from each round. Three sequences (Apt 1, Apt 2 and Apt 3) with the highest frequency in the aptamer library resulted from high-throughput sequencing were first selected as candidate aptamers. The secondary structure of these sequences was predicted and analyzed. In addition, the specificity and affinity of these candidate aptamers were determined by flow cytometry analysis. The results indicated that these aptamers had high specificity and affinity, with a KD of (224.6 ± 8.8) nM (Apt 1), (286.6 ± 13.9) nM (Apt 2) and (388.5 ± 44.6) nM (Apt 3), respectively. Apt 1 was therefore chosen as the best aptamer against P. minimum. Finally, the fluorescence microscopic examination further confirmed that Apt 1 can well bind to P. minimum. In summary, Apt 1 may be promising for being used as a novel molecular recognition element for P. minimum.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Jinju Ma
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
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23
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Correira JM, Webb LJ. Formation and Characterization of a Stable Monolayer of Active Acetylcholinesterase on Planar Gold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3501-3513. [PMID: 35276042 DOI: 10.1021/acs.langmuir.1c03399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enzyme activity is the basis for many biosensors where a catalytic event is used to detect the presence and amount of a biomolecule of interest. To create a practical point-of-care biosensor, these enzymes need to be removed from their native cellular environments and immobilized on an abiological surface to rapidly transduce a biochemical signal into an interpretable readout. This immobilization often leads to loss of activity due to unfolded, aggregated, or improperly oriented enzymes when compared to the native state. In this work, we characterize the formation and surface packing density of a stable monolayer of acetylcholinesterase (AChE) immobilized on a planar gold surface and quantify the extent of activity loss following immobilization. Using spectroscopic ellipsometry, we determined that the surface concentration of AChE on a saturated Au surface in a buffered solution was 2.77 ± 0.21 pmol cm-2. By calculating the molecular volume of hydrated AChE, corresponding to a sphere of 6.19 nm diameter, divided by the total volume at the AChE-Au interface, we obtain a surface packing density of 33.4 ± 2.5% by volume. This corresponds to 45.1 ± 3.4% of the theoretical maximum monolayer coverage, assuming hexagonal packing. The true value, however, may be larger due to unfolding of enzymes to occupy a larger volume. The enzyme activity and kinetic measurements showed a 90.6 ± 1.4% decrease in specific activity following immobilization. Finally, following storage in a buffered solution for over 100 days at both room temperature and 4 °C, approximately 80% of this enzyme activity was retained. This contrasts with the native aqueous enzyme, which loses approximately 75% of its activity within 1 day and becomes entirely inactive within 6 days.
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Affiliation(s)
- Joshua M Correira
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J Webb
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, Texas 78712-1224, United States
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Isolation and Characterization of a ssDNA Aptamer against Major Soluble Antigen of Renibacterium salmoninarum. Molecules 2022; 27:molecules27061853. [PMID: 35335217 PMCID: PMC8951219 DOI: 10.3390/molecules27061853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/29/2022] Open
Abstract
Bacterial kidney disease (BKD) is a major health problem of salmonids, affecting both wild and cultured salmon. The disease is caused by Renibacterium salmoninarum (Rs), a fastidious, slow-growing and strongly Gram-positive diplobacillus that produces chronic, systemic infection characterized by granulomatous lesions in the kidney and other organs, often resulting in death. Fast detection of the pathogen is important to limit the spread of the disease, particularly in hatcheries or aquaculture facilities. Aptamers are increasingly replacing conventional antibodies as platforms for the development of rapid diagnostic tools. In this work, we describe the first instance of isolating and characterizing a ssDNA aptamer that binds with high affinity to p57 or major soluble antigen (MSA), the principal antigen found on the cell wall surface of Rs. Specifically, in this study a construct of the full-length protein containing a DNA binding domain (MSA-R2c) was utilized as target. Aptamers were isolated from a pool of random sequences using GO-SELEX (graphene oxide-systematic evolution of ligands by exponential enrichment) protocol. The selection generated multiple aptamers with conserved motifs in the random region. One aptamer with high frequency of occurrence in different clones was characterized and found to display a strong binding affinity to MSA-R2c with a Kd of 3.0 ± 0.6 nM. The aptamer could be potentially utilized for the future development of a sensor for rapid and onsite detection of Rs in water or in infected salmonids, replacing time-consuming and costly lab analyses.
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25
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Pearson JJ, Temenoff JS. Growth Factor Immobilization Strategies for Musculoskeletal Disorders. Curr Osteoporos Rep 2022; 20:13-25. [PMID: 35118607 PMCID: PMC10772941 DOI: 10.1007/s11914-022-00718-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE OF REVIEW Tissue regenerative solutions for musculoskeletal disorders have become increasingly important with a growing aged population. Current growth factor treatments often require high dosages with the potential for off-target effects. Growth factor immobilization strategies offer approaches towards alleviating these concerns. This review summarizes current growth factor immobilization techniques (encapsulation, affinity interactions, and covalent binding) and the effects of immobilization on growth factor loading, release, and bioactivity. RECENT FINDINGS The breadth of immobilization techniques based on encapsulation, affinity, and covalent binding offer multiple methods to improve the therapeutic efficacy of growth factors by controlling bioactivity and release. Growth factor immobilization strategies have evolved to more complex systems with the capacity to load and release multiple growth factors with spatiotemporal control. The advancements in immobilization strategies allow for development of new, complex musculoskeletal tissue treatment strategies with improved spatiotemporal control of loading, release, and bioactivity.
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Affiliation(s)
- Joseph J Pearson
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA
| | - Johnna S Temenoff
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA.
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
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A novel labeled and label-free dual electrochemical detection of endotoxin based on aptamer-conjugated magnetic reduced graphene oxide-gold nanocomposite. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116116] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
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Vogiazi V, de la Cruz A, Varughese EA, Heineman WR, White RJ, Dionysiou DD. Sensitive Electrochemical Detection of Microcystin-LR in Water Samples Via Target-Induced Displacement of Aptamer Associated [Ru(NH 3) 6] 3. ACS ES&T ENGINEERING 2021; 1:10.1021/acsestengg.1c00256. [PMID: 34988551 PMCID: PMC8722374 DOI: 10.1021/acsestengg.1c00256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In this study, we demonstrate the successful development of an electrochemical aptamer-based sensor for point-of-use detection and quantification of the highly potent microcystin-LR (MC-LR) in water. The sensor uses hexaammineruthenium(III) chloride ([Ru(NH3)6]3+) as redox mediator, because of the ability of the positively charged (3+) molecule to associate with the phosphate backbone of the nucleic acids. We quantitatively measure the target-induced displacement of aptamer associated, or surface confined, [Ru(NH3)6]3+ in the presence of MC-LR. Upon the addition of MC-LR in the water, surface-confined [Ru(NH3)6]3+ dissociates, resulting in less faradaic current from the reduction of [Ru(NH3)6]3+ to [Ru(NH3)6]2+ Sensing surfaces of highly packed immobilized aptamers were capable of recording decreasing square wave voltammetry (SWV) signals after the addition of MC-LR in buffer. As a result, SWV recorded substantial signal suppression within 15 min of target incubation. The sensor showed a calculated limit of detection (LOD) of 9.2 pM in buffer. The effects of interferents were minimal, except when high concentrations of natural organic matter (NOM) were present. Also, the sensor performed well in drinking water samples. These results indicate a sensor with potential for fast and specific quantitative determination of MC-LR in drinking water samples. A common challenge when developing electrochemical, aptamer-based sensors is the need to optimize the nucleic acid aptamer in order to achieve sensitive signaling. This is particularly important when an aptamer experiences only a small or localized conformational change that provides only a limited electrochemical signal change. This study suggests a strategy to overcome that challenge through the use of a nucleic acid-associated redox label.
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Affiliation(s)
- Vasileia Vogiazi
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering (ChEE), University of Cincinnati, Cincinnati, Ohio, 45221-0012, USA
| | - Armah de la Cruz
- Office of Research and Development, US Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Eunice A Varughese
- Office of Research and Development, US Environmental Protection Agency, Cincinnati, Ohio, USA
| | - William R Heineman
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | - Ryan J White
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH, 45221-0030
| | - Dionysios D Dionysiou
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering (ChEE), University of Cincinnati, Cincinnati, Ohio, 45221-0012, USA
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Chen R, Kan L, Duan F, He L, Wang M, Cui J, Zhang Z, Zhang Z. Surface plasmon resonance aptasensor based on niobium carbide MXene quantum dots for nucleocapsid of SARS-CoV-2 detection. Mikrochim Acta 2021; 188:316. [PMID: 34476615 PMCID: PMC8412382 DOI: 10.1007/s00604-021-04974-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022]
Abstract
A novel label-free surface plasmon resonance (SPR) aptasensor has been constructed for the detection of N-gene of SARS-CoV-2 by using thiol-modified niobium carbide MXene quantum dots (Nb2C-SH QDs) as the bioplatform for anchoring N-gene-targeted aptamer. In the presence of SARS-CoV-2 N-gene, the immobilized aptamer strands changed their conformation to specifically bind with N-gene. It thus increased the contact area or enlarged the distance between aptamer and the SPR chip, resulting in a change of the SPR signal irradiated by the laser (He-Ne) with the wavelength (λ) of 633 nm. Nb2C QDs were derived from Nb2C MXene nanosheets via a solvothermal method, followed by functionalization with octadecanethiol through a self-assembling method. Subsequently, the gold chip for SPR measurements was modified with Nb2C-SH QDs via covalent binding of the Au-S bond also by self-assembling interaction. Nb2C-SH QDs not only resulted in high bioaffinity toward aptamer but also enhanced the SPR response. Thus, the Nb2C-SH QD-based SPR aptasensor had low limit of detection (LOD) of 4.9 pg mL−1 toward N-gene within the concentration range 0.05 to 100 ng mL−1. The sensor also showed excellent selectivity in the presence of various respiratory viruses and proteins in human serum and high stability. Moreover, the Nb2C-SH QD-based SPR aptasensor displayed a vast practical application for the qualitative analysis of N-gene from different samples, including seawater, seafood, and human serum. Thus, this work can provide a deep insight into the construction of the aptasensor for detecting SARS-CoV-2 in complex environments.
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Affiliation(s)
- Rongyuan Chen
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Lun Kan
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Fenghe Duan
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Linghao He
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Minghua Wang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Jing Cui
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Zhihong Zhang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
| | - Zhonghou Zhang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou, 450001, People's Republic of China.
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Schilling-Loeffler K, Rodriguez R, Williams-Woods J. Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers. Int J Mol Sci 2021; 22:ijms22168868. [PMID: 34445583 PMCID: PMC8396345 DOI: 10.3390/ijms22168868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022] Open
Abstract
Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.
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Heredia FL, Roche-Lima A, Parés-Matos EI. A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers. PLoS Comput Biol 2021; 17:e1009247. [PMID: 34343165 PMCID: PMC8362955 DOI: 10.1371/journal.pcbi.1009247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/13/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The selection of a DNA aptamer through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method involves multiple binding steps, in which a target and a library of randomized DNA sequences are mixed for selection of a single, nucleotide-specific molecule. Usually, 10 to 20 steps are required for SELEX to be completed. Throughout this process it is necessary to discriminate between true DNA aptamers and unspecified DNA-binding sequences. Thus, a novel machine learning-based approach was developed to support and simplify the early steps of the SELEX process, to help discriminate binding between DNA aptamers from those unspecified targets of DNA-binding sequences. An Artificial Intelligence (AI) approach to identify aptamers were implemented based on Natural Language Processing (NLP) and Machine Learning (ML). NLP method (CountVectorizer) was used to extract information from the nucleotide sequences. Four ML algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, Support Vector Machines) were trained using data from the NLP method along with sequence information. The best performing model was Support Vector Machines because it had the best ability to discriminate between positive and negative classes. In our model, an Accuracy (A) of 0.995, the fraction of samples that the model correctly classified, and an Area Under the Receiving Operating Curve (AUROC) of 0.998, the degree by which a model is capable of distinguishing between classes, were observed. The developed AI approach is useful to identify potential DNA aptamers to reduce the amount of rounds in a SELEX selection. This new approach could be applied in the design of DNA libraries and result in a more efficient and faster process for DNA aptamers to be chosen during SELEX. In this manuscript authors explain the development and validation of a novel artificial intelligence approach to support and simplify the early steps of the process from SELEX, to help discriminate binding between deoxynucleotide aptamers from those unspecified targets of DNA-binding sequences. The approach was implemented based on Natural Language Processing and Machine Learning. CountVectorizer, a Natural Language Processing method, was used to extract information from nucleotide sequences. Four Machine Learning algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, and Support Vector Machines) were trained using data from the Natural Language Processing method along with sequence information. From these four trained machine learning algorithms, the best performance and selected model was Support Vectors Machines, because it had the best discriminatory metrics (i.e., Accuracy (A) = 0.995; AUROC (AU) = 0.998). In general, all models showed good metric results for predicting DNA aptamer sequences. The Machine Learning model complexity and difficult interpretation may hinder its application into the standard practice. For this reason, the development of a web-app is already taking place to facilitate the interpretation and application of the obtained results.
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Affiliation(s)
- Frances L. Heredia
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Elsie I. Parés-Matos
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
- * E-mail:
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32
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Myres GJ, Peterson EM, Harris JM. Confocal Raman Microscopy Enables Label-Free, Quantitative, and Structurally Informative Detection of DNA Hybridization at Porous Silica Surfaces. Anal Chem 2021; 93:7978-7986. [PMID: 34037395 DOI: 10.1021/acs.analchem.1c00885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Characterization of DNA at solid/liquid interfaces remains a challenge because most surface-sensitive techniques are unable to provide quantitative insight into the base content, length, or structure. Surface-enhanced Raman scattering measurements of DNA hybridization on plasmonic-metal substrates have been used to overcome small Raman-scattering cross-sections; however, surface-enhanced Raman spectroscopy measurements are not generally quantitative due to the fall-off in the scattering signal with the decay of the electric field enhancement from the surface, which also limits the length of oligonucleotides that can be investigated. In this work, we introduce an experimental methodology in which confocal Raman microscopy is used to characterize hybridization reactions of ssDNA immobilized at the solid/liquid interface of porous silica particles. By focusing the femtoliter confocal probe volume within a single porous particle, signal enhancement arises from the ∼1500-times greater surface area detected compared to a planar substrate. Because the porous support is a purely dielectric material, the scattering signal is independent of the proximity of the oligonucleotide to the silica surface. With this technique, we characterize a 19-mer capture strand and determine its hybridization efficiency with 9-mer and 16-mer target sequences from the scattering of a structurally insensitive phosphate-stretching mode. Changes in polarizability and frequency of scattering from DNA bases were observed, which are consistent with Watson-Crick base pairing. Quantification of base content from their duplex scattering intensities allows us to discriminate between hybridization of two target strands of equivalent length but with different recognition sequences. A duplex having a single-nucleotide polymorphism could be distinguished from hybridization of a fully complementary strand based on differences in base content and duplex conformation.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Eric M Peterson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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33
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Ștefan G, Hosu O, De Wael K, Lobo-Castañón MJ, Cristea C. Aptamers in biomedicine: Selection strategies and recent advances. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.137994] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Moshari M, Koirala D, Allen PB. Electrochemical biosensors based on divinyl sulfone conjugation of DNA to graphene oxide electrodes. J Solid State Electrochem 2021. [DOI: 10.1007/s10008-021-04930-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Weaver SD, Whelan RJ. Characterization of DNA aptamer-protein binding using fluorescence anisotropy assays in low-volume, high-efficiency plates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1302-1307. [PMID: 33533761 DOI: 10.1039/d0ay02256j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aptamers have many useful attributes including specific binding to molecular targets. After aptamers are identified, their target binding must be characterized. Fluorescence anisotropy (FA) is one technique that can be used to characterize affinity and to optimize aptamer-target interactions. Efforts to make FA assays more efficient by reducing assay volume and time from mixing to measurement may save time and resources by minimizing consumption of costly reagents. Here, we use thrombin and two thrombin-binding aptamers as a model system to show that plate-based FA experiments can be performed in volumes as low as 2 μL per well with 20 minute incubations with minimal loss in assay precision. We demonstrate that the aptamer-thrombin interaction is best modelled with the Hill equation, indicating cooperative binding. The miniaturization of this assay has implications in drug development, as well as in the efficiency of aptamer selection workflows by allowing for higher throughput aptamer analysis.
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Affiliation(s)
- Simon D Weaver
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, USA
| | - Rebecca J Whelan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
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36
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Chen X, Lisi F, Bakthavathsalam P, Longatte G, Hoque S, Tilley RD, Gooding JJ. Impact of the Coverage of Aptamers on a Nanoparticle on the Binding Equilibrium and Kinetics between Aptamer and Protein. ACS Sens 2021; 6:538-545. [PMID: 33296177 DOI: 10.1021/acssensors.0c02212] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Knowledge of the interaction between aptamer and protein is integral to the design and development of aptamer-based biosensors. Nanoparticles functionalized with aptamers are commonly used in these kinds of sensors. As such, studies into how the number of aptamers on the nanoparticle surface influence both kinetics and thermodynamics of the binding interaction are required. In this study, aptamers specific for interferon gamma (IFN-γ) were immobilized on the surface of gold nanoparticles (AuNPs), and the effect of surface coverage of aptamer on the binding interaction with its target was investigated using fluorescence spectroscopy. The number of aptamers were adjusted from an average of 9.6 to 258 per particle. The binding isotherm between AuNPs-aptamer conjugate and protein was modeled with the Hill-Langmuir equation, and the determined equilibrium dissociation constant (K'D) decreased 10-fold when increasing the coverage of aptamer. The kinetics of the reaction as a function of coverage of aptamer were also investigated, including the association rate constant (kon) and the dissociation rate constant (koff). The AuNPs-aptamer conjugate with 258 aptamers per particle had the highest kon, while the koff was similar for AuNPs-aptamer conjugates with different surface coverages. Therefore, the surface coverage of aptamers on AuNPs affects both the thermodynamics and the kinetics of the binding. The AuNPs-aptamer conjugate with the highest surface coverage is the most favorable in biosensors considering the limit of detection, sensitivity, and response time of the assay. These findings deepen our understanding of the interaction between aptamer and target protein on the particle surface, which is important to both improve the scientific design and increase the application of aptamer-nanoparticle based biosensor.
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Affiliation(s)
- Xueqian Chen
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Fabio Lisi
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Padmavathy Bakthavathsalam
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Guillaume Longatte
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Sharmin Hoque
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D. Tilley
- School of Chemistry and Electron Microscope Unit a Microscopy Australia Node, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for Nanomedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales 2052, Australia
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Wang H, Li X, Lai LA, Brentnall TA, Dawson DW, Kelly KA, Chen R, Pan S. X-aptamers targeting Thy-1 membrane glycoprotein in pancreatic ductal adenocarcinoma. Biochimie 2021; 181:25-33. [PMID: 33242496 PMCID: PMC7863625 DOI: 10.1016/j.biochi.2020.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/26/2020] [Accepted: 11/20/2020] [Indexed: 12/15/2022]
Abstract
Modified DNA aptamers incorporated with amino-acid like side chains or drug-like ligands can offer unique advantages and enhance specificity as affinity ligands. Thy-1 membrane glycoprotein (THY1 or CD90) was previously identified as a biomarker candidate of neovasculature in pancreatic ductal adenocarcinoma (PDAC). The current study developed and evaluated modified DNA X-aptamers targeting THY1 in PDAC. The expression and glycosylation of THY1 in PDAC tumor tissues were assessed using immunohistochemistry and quantitative proteomics. Bead-based X-aptamer library that contains 108 different sequences was used to screen for high affinity THY1 X-aptamers. The sequences of the X-aptamers were analyzed with the next-generation sequencing. The affinities of the selected X-aptamers to THY1 were quantitatively evaluated with flow cytometry. Three high affinity THY1 X-aptamers, including XA-B217, XA-B216 and XA-A9, were selected after library screening and affinity binding evaluation. These three X-aptamers demonstrated a high binding affinity and specificity to THY1 protein and the THY1 expressing cell lines, using THY1 antibody as a comparison. The development of these X-aptamers provides highly specific and non-immunogenic affinity ligands for THY1 binding in the context of biomarker development and clinical applications. They could be further exploited to assist molecular imaging of PDAC targeting THY1.
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Affiliation(s)
- Hongyu Wang
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA; Department of Diagnostic and Interventional Imaging, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Xin Li
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Lisa A Lai
- Division of Gastroenterology, Department of Medicine, The University of Washington, Seattle, WA, 98195, USA
| | - Teresa A Brentnall
- Division of Gastroenterology, Department of Medicine, The University of Washington, Seattle, WA, 98195, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kimberly A Kelly
- Department of Biomedical Engineering, University of Virginia School of Engineering and Applied Sciences, Charlottesville, VA, 22908, USA
| | - Ru Chen
- Division of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sheng Pan
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA; Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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38
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Aptamer-Target-Gold Nanoparticle Conjugates for the Quantification of Fumonisin B1. BIOSENSORS-BASEL 2021; 11:bios11010018. [PMID: 33430067 PMCID: PMC7827823 DOI: 10.3390/bios11010018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
Fumonisin B1 (FB1), a mycotoxin classified as group 2B hazard, is of high importance due to its abundance and occurrence in varied crops. Conventional methods for detection are sensitive and selective; however, they also convey disadvantages such as long assay times, expensive equipment and instrumentation, complex procedures, sample pretreatment and unfeasibility for on-site analysis. Therefore, there is a need for quick, simple and affordable quantification methods. On that note, aptamers (ssDNA) are a good alternative for designing specific and sensitive biosensing techniques. In this work, the assessment of the performance of two aptamers (40 and 96 nt) on the colorimetric quantification of FB1 was determined by conducting an aptamer-target incubation step, followed by the addition of gold nanoparticles (AuNPs) and NaCl. Although MgCl2 and Tris-HCl were, respectively, essential for aptamer 96 and 40 nt, the latter was not specific for FB1. Alternatively, the formation of Aptamer (96 nt)-FB1-AuNP conjugates in MgCl2 exhibited stabilization to NaCl-induced aggregation at increasing FB1 concentrations. The application of asymmetric flow field-flow fractionation (AF4) allowed their size separation and characterization by a multidetection system (UV-VIS, MALS and DLS online), with a reduction in the limit of detection from 0.002 µg/mL to 56 fg/mL.
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39
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Ducongé F. Aptamers for Molecular Imaging. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00034-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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40
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Karanja CW, Yeboah KS, Ong WWS, Sintim HO. A STING-based fluorescent polarization assay for monitoring activities of cyclic dinucleotide metabolizing enzymes. RSC Chem Biol 2020; 2:206-214. [PMID: 34458783 PMCID: PMC8341399 DOI: 10.1039/d0cb00187b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/29/2020] [Indexed: 12/17/2022] Open
Abstract
Cyclic dinucleoties, such as cGAMP, c-di-GMP and c-di-AMP, are fascinating second messengers with diverse roles in both prokaryotes and eukaryotes. Consequently there is a need for simple and inexpensive methods for profiling these compounds in biological media, monitoring their synthesis or degradation by enzymes and for identifying inhibitors of proteins that metabolize or bind to these dinucleotides. Since 2011, when we reported the first simple method to detect c-di-GMP (S. Nakayama, I. Kelsey, J. Wang, K. Roelofs, B. Stefane, Y. Luo, V. T. Lee and H. O. Sintim, J. Am. Chem. Soc., 2011, 133, 4856) or in 2014 when we revealed another surprisingly simple assay to detect c-di-AMP (J. Zhou, D. A. Sayre, Y. Zheng, H. Szmacinski and H. O. Sintim, Anal. Chem., 2014, 86, 2412), there have been efforts to develop assays to detect cyclic dinucleotides by others. However a unified and simple assay, which can be used for all cyclic dinucleotides is lacking. Here, we investigate STING binding by various fluorescein-labeled c-di-GMP, c-di-AMP and cGAMP, using fluorescent polarization (FP). Fluorescein-labeled c-di-GMP (F-c-di-GMP) was found to be the best binder of STING. This probe could be displaced by unlabeled cGAMP, c-di-AMP or c-di-GMP and hence it is a universal probe, which can be used to monitor all three dinucleotides. HPLC analysis was used to validate the new F-c-di-GMP-based FP assay. Cyclic dinucleoties, such as cGAMP, c-di-GMP and c-di-AMP, are fascinating second messengers with diverse roles in both prokaryotes and eukaryotes.![]()
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Affiliation(s)
- Caroline W Karanja
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
| | - Kofi S Yeboah
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
| | - Wilson W S Ong
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
| | - Herman O Sintim
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA.,Institute for Drug Discovery, Purdue University 720 Clinic Drive West Lafayette IN 47907 USA .,Purdue Institute of Inflammation, Immunology, and Infectious Disease West Lafayette IN 47907 USA
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41
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Koudrina A, O'Brien J, Garcia R, Boisjoli S, Kan PTM, Tsai EC, DeRosa MC. Assessment of Aptamer-Targeted Contrast Agents for Monitoring of Blood Clots in Computed Tomography and Fluoroscopy Imaging. Bioconjug Chem 2020; 31:2737-2749. [PMID: 33232126 DOI: 10.1021/acs.bioconjchem.0c00525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Objective: Random formation of thrombi is classified as a pathological process that may result in partial or complete obstruction of blood flow and limited perfusion. Further complications include pulmonary embolism, thrombosis-induced myocardial infraction, ischemic stroke, and others. Location and full delineation of the blood clot are considered to be two clinically relevant aspects that could streamline proper diagnosis and treatment follow-up. In this work, we prepared two types of X-ray attenuating contrast formulations, using fibrinogen aptamer as the clot-seeking moiety. Methods: Two novel aptamer-targeted formulations were designed. Iodine-modified bases were directly incorporated into a fibrinogen aptamer (iodo-FA). Isothermal titration calorimetry was used to confirm that these modifications did not negatively impact target binding. Iodo-FA was tested for its ability to produce concentration-dependent contrast enhancement in a phantom CT. It was subsequently tested in vitro with clotted human and swine blood. This allowed for translation into ex vivo testing, using fluoroscopy. FA was also used to functionalize gold nanoparticles (FA-AuNPs), and contrast capabilities were confirmed. This formulation was tested in vitro using clotted human blood in a CT scan. Results: Unmodified FA and iodo-FA demonstrated a nearly identical affinity toward fibrin, confirming that base modifications did not impact target binding. Iodo-FA and FA-AuNPs both demonstrated excellent concentration-dependent contrast enhancement capabilities (40.5 HU mM-1 and 563.6 HU μM-1, respectively), which were superior to the clinically available agent, iopamidol. In vitro CT testing revealed that iodo-FA is able to penetrate into the blood clots, producing contrast enhancement throughout, while FA-AuNPs only accumulated on the surface of the clot. Iodo-FA was thereby translated to ex vivo testing, confirming target-binding associated accumulation of the contrast material at the location of the clot within the dilation of the external carotid artery. This resulted in a 34% enhancement of the clot. Conclusions: Both iodo-FA and FA-AuNPs were confirmed to be effective contrast formulations in CT. Targeting of fibrin, a major structural constituent of thrombi, with these novel contrast agents would allow for higher contrast enhancement and better clot delineation in CT and fluoroscopy.
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Affiliation(s)
- Anna Koudrina
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | | | - Roberto Garcia
- Department of Neurosurgery, The University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Spencer Boisjoli
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Peter T M Kan
- Department of Neurosurgery, The University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Eve C Tsai
- The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada.,Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada.,Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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42
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Kim SM, Kim J, Noh S, Sohn H, Lee T. Recent Development of Aptasensor for Influenza Virus Detection. BIOCHIP JOURNAL 2020; 14:327-339. [PMID: 33224441 PMCID: PMC7670017 DOI: 10.1007/s13206-020-4401-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022]
Abstract
In nowadays, we have entered the new era of pandemics and the significance of virus detection deeply impacts human society. Viruses with genetic mutations are reported nearly every year, and people have prepared tools to detect the virus and vaccines to ensure proper treatments. Influenza virus (IV) is one of the most harmful viruses reporting various mutations, sub-types, and rapid infection speed for humans and animals including swine and poultry. Moreover, IV infection presents several harmful symptoms including cough, fever, diarrhea, chills, even causing death. To reduce the IV-induced harm, its proper and rapid detection is highly required. Conventional techniques were used against various IV sub-types including H1N1, H3N2, and H5N1. However, some of the techniques are time-consuming, expensive, or labor-intensive for detecting IV. Recently, the nucleic acid-based aptamer has gained attention as a novel bioprobe for constructing a biosensor. In this review, the authors discuss the recent progress in aptasensors for detecting IV in terms of an electrochemical and an optical biosensor.
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Affiliation(s)
- Soo Min Kim
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01899 Republic of Korea
| | - Jinmyeong Kim
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01899 Republic of Korea
| | - Seungwoo Noh
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01899 Republic of Korea
| | - Hiesang Sohn
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01899 Republic of Korea
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01899 Republic of Korea
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43
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Naghian E, Marzi Khosrowshahi E, Sohouli E, Pazoki-Toroudi HR, Sobhani-Nasab A, Rahimi-Nasrabadi M, Ahmadi F. Electrochemical Oxidation and Determination of Antiviral Drug Acyclovir by Modified Carbon Paste Electrode With Magnetic CdO Nanoparticles. Front Chem 2020; 8:689. [PMID: 33134244 PMCID: PMC7511707 DOI: 10.3389/fchem.2020.00689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022] Open
Abstract
With the development of nanomaterials in electrochemical sensors, the use of nanostructures to modify the electrode surface has been shown to improve the kinetics of the electron transfer process. In this study, a sensor was developed for the electrochemical determination of Acyclovir (ACV) based on the modified carbon paste electrode (CPE) by CdO/Fe3O4. The magnetic CdO nanoparticles characterization was studied by energy-dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD). To study of the modified CPE surface morphology, scanning electron microscopy (SEM) was used. At the optimal conditions, a noteworthy enhancement in the electrochemical behavior of ACV was observed at the surface of the modified CPE compared to the unmodified CPE. A detection limit of 300 nM and a linear range of 1–100 μM were obtained for the quantitative monitoring of ACV at the modified CPE surface using differential pulse voltammetry (DPV) in phosphate buffer. The RSD% (relative standard deviation) of the electrode response was <4.3% indicating the development of a high precision method. Also, satisfactory results were obtained in the determination of ACV with the modified electrode in tablet, blood serum, and urine samples with a satisfactory relative recovery (RR%) in the range of 94.0–104.4%.
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Affiliation(s)
- Ebrahim Naghian
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Department of Chemistry, South Tehran Branch Islamic Azad University, Tehran, Iran
| | | | - Esmail Sohouli
- Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Ali Sobhani-Nasab
- Social Determinants of Health (SDH) Research Center, Kashan University of Medical Sciences, Kashan, Iran.,Core Research Lab, Kashan University of Medical Sciences, Kashan, Iran
| | - Mehdi Rahimi-Nasrabadi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Farhad Ahmadi
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
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44
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Amiri M, Nekoueian K, Saberi RS. Graphene-family materials in electrochemical aptasensors. Anal Bioanal Chem 2020; 413:673-699. [PMID: 32939567 DOI: 10.1007/s00216-020-02915-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/02/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
The study of graphene-based carbon nanocomposites has remarkably increased in recent years. Functionalized graphene-based nanostructures, including graphene oxide and reduced graphene oxide, have great potential as new innovative electrode materials in the fabrication of novel electrochemical sensors. Electrochemical sensors based on aptamers attracted great attention because of their high sensitivity and selectivity, and simple instrumentation, as well as low production cost. Aptamers as a potent alternative to antibodies are functional nucleic acids with a high tendency to specific analytes. Electrochemical aptasensors show specific recognition ability for a wide range of analytes. Although aptamers are selected in vitro in contrast to antibodies, they are interesting due to advantages like high stability, easy chemical modifications, and the potential to be employed in nanostructured device fabrication or electrochemical sensing devices. Recently, new nanomaterials have shown a significant impact on the production of electrochemical sensors with high efficiency and performance. This review aims to give an outline of electrochemical aptasensors based on the graphene family materials and discuss the detection mechanism in this type of aptasensors. The present review summarizes some of the recent achievements in graphene-based aptasensors and includes their recent electroanalytical applications. Graphical Abstract Graphical Abstract.
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Affiliation(s)
- Mandana Amiri
- Department of Chemistry, University of Mohaghegh Ardabili, Daneshgah Street, Ardabil, 56199-11367, Iran.
| | - Khadijeh Nekoueian
- Department of Chemistry, University of Mohaghegh Ardabili, Daneshgah Street, Ardabil, 56199-11367, Iran
| | - Reyhaneh Sadat Saberi
- East Sage Investigative Corporation, Isfahan Science and Technology Town, Isfahan, 8415683111, Iran
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45
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Scheepers MRW, Haenen SRR, Coers JM, van IJzendoorn LJ, Prins MWJ. Inter-particle biomolecular reactivity tuned by surface crowders. NANOSCALE 2020; 12:14605-14614. [PMID: 32614022 DOI: 10.1039/d0nr03125a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The rate at which colloidal particles can form biomolecular bonds controls the kinetics of applications such as particle-based biosensing, targeted drug delivery and directed colloidal assembly. Here we study how the reactivity of the particle surface depends on its molecular composition, quantified by the inter-particle rate of aggregation in an optomagnetic cluster experiment. Particles were functionalized with DNA or with proteins for specific binding, and with polyethylene glycol as a passive surface crowder. The data show that the inter-particle binding kinetics are dominated by specific interactions, which surprisingly can be tuned by the passive crowder molecules for both the DNA and the protein system. The experimental results are interpreted using model simulations, which show that the crowder-induced decrease of the particle surface reactivity can be described as a reduced reactivity of the specific binder molecules on the particle surface.
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Affiliation(s)
- M R W Scheepers
- Eindhoven University of Technology, Department of Applied Physics, PO Box 513, 5600 MB Eindhoven, The Netherlands
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46
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Mamer SB, Page P, Murphy M, Wang J, Gallerne P, Ansari A, Imoukhuede PI. The Convergence of Cell-Based Surface Plasmon Resonance and Biomaterials: The Future of Quantifying Bio-molecular Interactions-A Review. Ann Biomed Eng 2020; 48:2078-2089. [PMID: 31811474 PMCID: PMC8637426 DOI: 10.1007/s10439-019-02429-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022]
Abstract
Cell biology is driven by complex networks of biomolecular interactions. Characterizing the kinetic and thermodynamic properties of these interactions is crucial to understanding their role in different physiological processes. Surface plasmon resonance (SPR)-based approaches have become a key tool in quantifying biomolecular interactions, however conventional approaches require isolating the interacting components from the cellular system. Cell-based SPR approaches have recently emerged, promising to enable precise measurements of biomolecular interactions within their normal biological context. Two major approaches have been developed, offering their own advantages and limitations. These approaches currently lack a systematic exploration of 'best practices' like those existing for traditional SPR experiments. Toward this end, we describe the two major approaches, and identify the experimental parameters that require exploration, and discuss the experimental considerations constraining the optimization of each. In particular, we discuss the requirements of future biomaterial development needed to advance the cell-based SPR technique.
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Affiliation(s)
- Spencer B Mamer
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Jiaojiao Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pierrick Gallerne
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Ecole Centrale de Lille, Villeneuve d'Ascq, Hauts-De-France, France
| | - Ali Ansari
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - P I Imoukhuede
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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47
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Smith MH, Fologea D. Kinetic Exclusion Assay of Biomolecules by Aptamer Capture. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3442. [PMID: 32570818 PMCID: PMC7348807 DOI: 10.3390/s20123442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of aptamers titrated with thrombin were fitted with a 1:1 binding model and provided an effective Kd of the binding in the sub-nanomolar range. However, our experimental results suggest that this simple model does not satisfactorily describe the binding process; therefore, the possibility that the aptamer is composed of a mixture of two or more distinct Kd populations is discussed. The same standard curves, together with a four-parameter logistic equation, were used to determine "unknown" concentrations of thrombin in mock samples. The ability to identify and characterize complex binding stoichiometry, together with the determination of target analyte concentrations in the pM-nM range, supports the adoption of this technology for kinetics, equilibrium, and analytical purposes by employing aptamers as biorecognition elements.
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Affiliation(s)
- Mark H. Smith
- Department of Physics, Boise State University, 1910 University Drive, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Programs, Boise State University, 1910 University Drive, Boise, ID 83725, USA
| | - Daniel Fologea
- Department of Physics, Boise State University, 1910 University Drive, Boise, ID 83725, USA;
- Biomolecular Sciences Graduate Programs, Boise State University, 1910 University Drive, Boise, ID 83725, USA
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48
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Krasitskaya VV, Goncharova NS, Biriukov VV, Bashmakova EE, Kabilov MR, Baykov IK, Sokolov AE, Frank LA. The Ca 2+ -Regulated Photoprotein Obelin as a Tool for SELEX Monitoring and DNA Aptamer Affinity Evaluation. Photochem Photobiol 2020; 96:1041-1046. [PMID: 32304233 DOI: 10.1111/php.13274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/29/2020] [Indexed: 12/11/2022]
Abstract
Bioluminescent solid-phase analysis was proposed to monitor the selection process and to determine binding characteristics of the aptamer-target complexes during design and development of the specific aptamers. The assay involves Ca2+ -regulated photoprotein obelin as a simple, sensitive and fast reporter. Applicability and the prospects of the approach were exemplified by identification of DNA aptamers to cardiac troponin I, a highly specific early biomarker for acute myocardial infarction. Two structurally different aptamers specific to various epitopes of troponin I were obtained and then tested in a model bioluminescent assay.
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Affiliation(s)
| | | | | | - Eugenia E Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Ivan K Baykov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Aleksey E Sokolov
- Siberian Federal University, Krasnoyarsk, Russia.,Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Ludmila A Frank
- Institute of Biophysics SB RAS, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia
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Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review. Anal Chim Acta 2020; 1125:267-278. [PMID: 32674773 DOI: 10.1016/j.aca.2020.05.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 12/26/2022]
Abstract
Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.
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50
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The Use of Aptamers and Molecularly Imprinted Polymers in Biosensors for Environmental Monitoring: A Tale of Two Receptors. CHEMOSENSORS 2020. [DOI: 10.3390/chemosensors8020032] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Effective molecular recognition remains a major challenge in the development of robust receptors for biosensing applications. Over the last three decades, aptamers and molecularly imprinted polymers (MIPs) have emerged as the receptors of choice for use in biosensors as viable alternatives to natural antibodies, due to their superior stability, comparable binding performance, and lower costs. Although both of these technologies have been developed in parallel, they both suffer from their own unique problems. In this review, we will compare and contrast both types of receptor, with a focus on the area of environmental monitoring. Firstly, we will discuss the strategies and challenges involved in their development. We will also discuss the challenges that are involved in interfacing them with the biosensors. We will then compare and contrast their performance with a focus on their use in the detection of environmental contaminants, namely, antibiotics, pesticides, heavy metals, and pathogens detection. Finally, we will discuss the future direction of these two technologies.
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