1
|
Wang TY, Rukundo JL, Mao Z, Krylov SN. Maximizing the Accuracy of Equilibrium Dissociation Constants for Affinity Complexes: From Theory to Practical Recommendations. ACS Chem Biol 2024; 19:1852-1867. [PMID: 39121869 DOI: 10.1021/acschembio.4c00259] [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: 08/12/2024]
Abstract
The equilibrium dissociation constant (Kd) is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of Kd obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of Kd determination to large systematic errors, even when random errors are small. It is imperative to both minimize and quantitatively assess the systematic errors inherent in Kd determination. Traditionally, Kd values are determined through nonlinear regression of binding isotherms. This analysis utilizes three variables: concentrations of two reactants and a fraction R of unbound limiting reactant. The systematic errors in Kd arise directly from systematic errors in these variables. Therefore, to maximize the accuracy of Kd, this study thoroughly analyzes the sources of systematic errors within the three variables, including (i) non-additive signals to calculate R, (ii) mis-calibrated experimental instruments, (iii) inaccurate calibration parameters, (iv) insufficient incubation time, (v) unsaturated binding isotherm, (vi) impurities in the reactants, and (vii) solute adsorption onto surfaces. Through this analysis, we illustrate how each source contributes to inaccuracies in the determination of Kd and propose strategies to minimize these contributions. Additionally, we introduce a method for quantitatively assessing the confidence intervals of systematic errors in concentrations, a crucial step toward quantitatively evaluating the accuracy of Kd. While presenting original findings, this paper also reiterates the fundamentals of Kd determination, hence guiding researchers across all proficiency levels. By shedding light on the sources of systematic errors and offering strategies for their mitigation, our work will help researchers enhance the accuracy of Kd determination, thereby making binding studies more reliable and the conclusions drawn from such studies more robust.
Collapse
Affiliation(s)
- Tong Ye Wang
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jean-Luc Rukundo
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Zhiyuan Mao
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
2
|
Wei K, Ye Z, Dong W, Zhang L, Wang W, Li J, Eltzov E, Wang S, Mao X. Generating robust aptamers for food analysis by sequence-based configuration optimization. Talanta 2024; 275:126044. [PMID: 38626500 DOI: 10.1016/j.talanta.2024.126044] [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: 12/13/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Advanced analytical techniques are emerging in the food industry. Aptamer-based biosensors achieve rapid and highly selective analysis, thus drawing particular attention. Aptamers are oligonucleotide probes screened via in vitro Systematic Evolution of Ligands by EXponential Enrichment (SELEX), which can bind with their specific targets by folding into three-dimensional configurations and accept various modifications to be incorporated into biosensors, showing great potential in food analysis. Unfortunately, aptamers obtained by SELEX may not possess satisfactory affinity. Post-SELEX strategies were proposed to optimize aptamers' configuration and enhance the binding affinity, with specificity confirmed. Sequence-based optimization strategies exhibit great advantages in simple operation, good generalization, low cost, etc. This review summarizes the latest study (2015-2023) on generating robust aptamers for food targets by sequence-based configuration optimization, as well as the generated aptamers and aptasensors, with an expectation to provide inspirations for developing aptamer and aptasensors with high performance for food analysis and to safeguard food quality and safety.
Collapse
Affiliation(s)
- Kaiyue Wei
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ziyang Ye
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenhui Dong
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Ling Zhang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Wenjing Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Jiao Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Sai Wang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China.
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Qingdao Key Laboratory of Food Biotechnology, Qingdao, 266404, PR China; Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, 266404, PR China
| |
Collapse
|
3
|
Krylov SN. Underestimation of the Complexity of K d Determination: Causes, Implications, and Ways to Improve. ACS MEASUREMENT SCIENCE AU 2024; 4:231-232. [PMID: 38910863 PMCID: PMC11191718 DOI: 10.1021/acsmeasuresciau.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Indexed: 06/25/2024]
Affiliation(s)
- Sergey N. Krylov
- Department
of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
- Centre
for Research on Biomolecular Interactions, York University 4700
Keele Street, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
4
|
Thomas BJ, Guldenpfennig C, Daniels MA, Burke DH, Porciani D. Multiplexed In Vivo Screening Using Barcoded Aptamer Technology to Identify Oligonucleotide-Based Targeting Reagents. Nucleic Acid Ther 2024; 34:109-124. [PMID: 38752363 PMCID: PMC11250842 DOI: 10.1089/nat.2024.0010] [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: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 06/19/2024] Open
Abstract
Recent FDA approvals of mRNA vaccines, short-interfering RNAs, and antisense oligonucleotides highlight the success of oligonucleotides as therapeutics. Aptamers are excellent affinity reagents that can selectively label protein biomarkers, but their clinical application has lagged. When formulating a given aptamer for in vivo use, molecular design details can determine biostability and biodistribution; therefore, extensive postselection manipulation is often required for each new design to identify clinically useful reagents harboring improved pharmacokinetic properties. Few methods are available to comprehensively screen such aptamers, especially in vivo, constituting a significant bottleneck in the field. In this study, we introduce barcoded aptamer technology (BApT) for multiplexed screening of predefined aptamer formulations in vitro and in vivo. We demonstrate this technology by simultaneously investigating 20 aptamer formulations, each harboring different molecular designs, for targeting Non-Small Cell Lung Cancer cells and tumors. Screening in vitro identified a 45 kDa bispecific formulation as the best cancer cell targeting reagent, whereas screening in vivo identified a 30 kDa monomeric formulation as the best tumor-specific targeting reagent. The multiplexed analysis pipeline also identified biodistribution phenotypes shared among formulations with similar molecular architectures. The BApT approach we describe here has the potential for broad application to fields where oligonucleotide-based targeting reagents are desired.
Collapse
Affiliation(s)
- Brian J. Thomas
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Caitlyn Guldenpfennig
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Mark A. Daniels
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Donald H. Burke
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - David Porciani
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| |
Collapse
|
5
|
Toma L, Mattarozzi M, Ronda L, Marassi V, Zattoni A, Fortunati S, Giannetto M, Careri M. Are Aptamers Really Promising as Receptors for Analytical Purposes? Insights into Anti-Lysozyme DNA Aptamers through a Multitechnique Study. Anal Chem 2024; 96:2719-2726. [PMID: 38294352 DOI: 10.1021/acs.analchem.3c05883] [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: 02/01/2024]
Abstract
Aptamers are recognition elements increasingly used for the development of biosensing strategies, especially in the detection of proteins or small molecule targets. Lysozyme, which is recognized as an important biomarker for various diseases and a major allergenic protein found in egg whites, is one of the main analytical targets of aptamer-based biosensors. However, since aptamer-based strategies can be prone to artifacts and data misinterpretation, rigorous strategies for multifaceted characterization of the aptamer-target interaction are needed. In this work, a multitechnique approach has been devised to get further insights into the binding performance of the anti-lysozyme DNA aptamers commonly used in the literature. To study molecular interactions between lysozyme and different anti-lysozyme DNA aptamers, measurements based on a magneto-electrochemical apta-assay, circular dichroism spectroscopy, fluorescence spectroscopy, and asymmetrical flow field-flow fractionation were performed. The reliability and versatility of the approach were proved by investigating a SELEX-selected RNA aptamer reported in the literature, that acts as a positive control. The results confirmed that an interaction in the low micromolar range is present in the investigated binding buffers, and the binding is not associated with a conformational change of either the protein or the DNA aptamer. The similar behavior of the anti-lysozyme DNA aptamers compared to that of randomized sequences and polythymine, used as negative controls, showed nonsequence-specific interactions. This study demonstrates that severe testing of aptamers resulting from SELEX selection is the unique way to push these biorecognition elements toward reliable and reproducible results in the analytical field.
Collapse
Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- CNR, Institute of Biophysics, Pisa 56124, Italy
| | - Valentina Marassi
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Andrea Zattoni
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Simone Fortunati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Van Echelpoel R, Joosten F, Parrilla M, De Wael K. Progress on the Electrochemical Sensing of Illicit Drugs. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:413-442. [PMID: 38273206 DOI: 10.1007/10_2023_239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Illicit drugs are harmful substances, threatening both health and safety of societies in all corners of the world. Several policies have been developed over time to deal with this illicit drug problem, including supply reduction and harm reduction policies. Both policies require on-site detection tools to succeed, i.e. sensors that can identify illicit drugs in samples at the point-of-care. Electrochemical sensors are highly suited for this task, due to their short analysis times, low cost, high accuracy, portability and orthogonality with current technologies. In this chapter, we evaluate the latest trend in electrochemical sensing of illicit drugs, with a focus on detection of illicit drugs in seizures and body fluids. Furthermore, we will also provide an outlook on the potential of electrochemistry in wearable sensors for this purpose.
Collapse
|
8
|
Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
Collapse
Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
9
|
Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
Collapse
Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| |
Collapse
|
10
|
Thomas BJ, Guldenpfennig C, Guan Y, Winkler C, Beecher M, Beedy M, Berendzen AF, Ma L, Daniels MA, Burke DH, Porciani D. Targeting lung cancer with clinically relevant EGFR mutations using anti-EGFR RNA aptamer. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102046. [PMID: 37869258 PMCID: PMC10589377 DOI: 10.1016/j.omtn.2023.102046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023]
Abstract
A significant fraction of non-small cell lung cancer (NSCLC) cases are due to oncogenic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR). Anti-EGFR antibodies have shown limited clinical benefit for NSCLC, whereas tyrosine kinase inhibitors (TKIs) are effective, but resistance ultimately occurs. The current landscape suggests that alternative ligands that target wild-type and mutant EGFRs are desirable for targeted therapy or drug delivery development. Here we evaluate NSCLC targeting using an anti-EGFR aptamer (MinE07). We demonstrate that interaction sites of MinE07 overlap with clinically relevant antibodies targeting extracellular domain III and that MinE07 retains binding to EGFR harboring the most common oncogenic and resistance mutations. When MinE07 was linked to an anti-c-Met aptamer, the EGFR/c-Met bispecific aptamer (bsApt) showed superior labeling of NSCLC cells in vitro relative to monospecific aptamers. However, dual targeting in vivo did not improve the recognition of NSCLC xenografts compared to MinE07. Interestingly, biodistribution of Cy7-labeled bsApt differed significantly from Alexa Fluor 750-labeled bsApt. Overall, our findings demonstrate that aptamer formulations containing MinE07 can target ectopic lung cancer without additional stabilization or PEGylation and highlights the potential of MinE07 as a targeting reagent for the recognition of NSCLC harboring clinically relevant EGFRs.
Collapse
Affiliation(s)
- Brian J. Thomas
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Caitlyn Guldenpfennig
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Yue Guan
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Calvin Winkler
- Department of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Margaret Beecher
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Michaela Beedy
- Department of Biochemistry, Westminster College, Fulton, MO 65251, USA
| | - Ashley F. Berendzen
- Research Division/Biomolecular Imaging Center, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Lixin Ma
- Research Division/Biomolecular Imaging Center, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Department of Radiology, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Mark A. Daniels
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | - Donald H. Burke
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - David Porciani
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Johnson RE, Murray MT, Bycraft LJ, Myler P, Wetmore SD, Manderville RA. Harnessing a 4-Formyl-Aniline Handle to Tune the Stability of a DNA Aptamer-Protein Complex via Fluorescent Surrogates. Bioconjug Chem 2023; 34:2066-2076. [PMID: 37857354 DOI: 10.1021/acs.bioconjchem.3c00373] [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: 10/21/2023]
Abstract
Interactions between DNA aptamers and protein targets hold promise for the development of pharmaceuticals and diagnostics. As such, the utilization of fluorescent nucleobase surrogates in studying aptamer-protein interactions is a powerful tool due to their ability to provide site-specific information through turn-on fluorescence. Unfortunately, previously described turn-on probes serving as nucleobase replacements have only been strongly disruptive to the affinity of aptamer-protein interactions. Herein, we present a modified TBA15 aptamer for thrombin containing a fluorescent surrogate that provides site-specific turn-on emission with low nanomolar affinity. The modification, referred to as AnBtz, was substituted at position T3 and provided strong turn-on emission (Irel ≈ 4) and brightness (ε·Φ > 20 000 cm-1 M-1) with an apparent dissociation constant (Kd) of 15 nM to afford a limit of detection (LOD) of 10 nM for thrombin in 20% human serum. The probe was selected through a modular "on-strand" synthesis process that utilized a 4-formyl-aniline (4FA) handle. Using this platform, we were able to enhance the affinity of the final aptamer conjugate by ∼30-fold in comparison with the initial conjugate design. Molecular dynamics simulations provide insight into the structural basis for this phenomenon and highlight the importance of targeting hydrophobic protein binding sites with fluorescent nucleobase surrogates to create new contacts with protein targets.
Collapse
Affiliation(s)
- Ryan E Johnson
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Makay T Murray
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Lucas J Bycraft
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Peter Myler
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Richard A Manderville
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
13
|
Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [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: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
Collapse
Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- 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
| |
Collapse
|
14
|
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: 10] [Impact Index Per Article: 10.0] [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.
Collapse
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.
| |
Collapse
|
15
|
Wang TY, Ji H, Everton D, Le ATH, Krylova SM, Fournier R, Krylov SN. Fundamental Determinants of the Accuracy of Equilibrium Constants for Affinity Complexes. Anal Chem 2023; 95:15826-15832. [PMID: 37831482 DOI: 10.1021/acs.analchem.3c03557] [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: 10/14/2023]
Abstract
The equilibrium constant of a chemical reaction is arguably the key thermodynamic parameter in chemistry; we naturally expect that equilibrium constants are determined accurately. The majority of equilibrium constants determined today are those of binding reactions that form affinity complexes, such as protein-protein, protein-DNA, and protein-small molecule. There is growing awareness that the determination of equilibrium constants for highly stable affinity complexes may be very inaccurate. However, fundamental (i.e., method-independent) determinants of accuracy are poorly understood. Here, we present a study that explicitly shows what the accuracy of equilibrium constants of affinity complexes depends on. This study reveals the critical importance of the choice of concentration of interacting components and creates a theoretical foundation for improving the accuracy of the equilibrium constants. The predicted influence of concentrations on accuracy was confirmed experimentally. The results of this fundamental study provide instructive guidance for experimentalists independently on the method they use.
Collapse
Affiliation(s)
- Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Hongchen Ji
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Daniel Everton
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - René Fournier
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
16
|
Ding Y, Liu J. Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers. Anal Chem 2023; 95:14651-14658. [PMID: 37721984 DOI: 10.1021/acs.analchem.3c02477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.
Collapse
Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
17
|
Zhao Y, Li AZ, Liu J. Capture-SELEX for Chloramphenicol Binding Aptamers for Labeled and Label-Free Fluorescence Sensing. ENVIRONMENT & HEALTH (WASHINGTON, D.C.) 2023; 1:102-109. [PMID: 37614296 PMCID: PMC10442912 DOI: 10.1021/envhealth.3c00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 08/25/2023]
Abstract
Chloramphenicol (CAP) is a potent antibiotic. Due to its side effects, CAP is currently banned in most countries, but it is still found in many food products and in the environment. Developing aptamer-based biosensors for the detection of CAP has interested many researchers. While both RNA and DNA aptamers were previously reported for CAP, they were all obtained by immobilization of the CAP base, which omitted the two chlorine atoms. In this work, DNA aptamers were selected using the library-immobilized method and free unmodified CAP. Three families of aptamers were obtained, and the best one named CAP1 showed a dissociation constant (Kd) of 9.8 μM using isothermal titration calorimetry (ITC). A fluorescent strand-displacement sensor showed a limit of detection (LOD) of 14 μM CAP. Thioflavin T (ThT) staining allowed label-free detection of CAP with a LOD of 1 μM in buffer, 1.8 μM in Lake Ontario water, and 3.6 μM in a wastewater sample. Comparisons were made with previously reported aptamers, and ITC failed to show binding of a previously reported 80-mer aptamer. Due to the small size and well-defined secondary structures of CAP1, this aptamer will find analytical applications for environmental and food monitoring.
Collapse
Affiliation(s)
- Yichen Zhao
- Department of Chemistry,
Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Albert Zehan Li
- Department of Chemistry,
Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry,
Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
18
|
Moreira G, Qian H, Datta SPA, Bliznyuk N, Carpenter J, Dean D, McLamore E, Vanegas D. A capacitive laser-induced graphene based aptasensor for SARS-CoV-2 detection in human saliva. PLoS One 2023; 18:e0290256. [PMID: 37590297 PMCID: PMC10434860 DOI: 10.1371/journal.pone.0290256] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
SARS-CoV-2 virus induced CoVID-19 pandemic has accelerated the development of diagnostic tools. Devices integrated with electrochemical biosensors may be an interesting alternative to respond to the high demand for testing, particularly in contexts where access to standard detection technologies is lacking. Aptamers as recognition elements are useful due to their stability, specificity, and sensitivity to binding target molecules. We have developed a non-invasive electrochemical aptamer-based biosensor targeting SARS-CoV-2 in human saliva. The aptamer is expected to detect the Spike protein of SARS-CoV-2 wildtype and its variants. Laser-induced graphene (LIG) electrodes coated with platinum nanoparticles were biofunctionalized with a biotin-tagged aptamer. Electrochemical Impedance Spectroscopy (EIS) for BA.1 sensing was conducted in sodium chloride/sodium bicarbonate solution supplemented with pooled saliva. To estimate sensing performance, the aptasensor was tested with contrived samples of UV-attenuated virions from 10 to 10,000 copies/ml. Selectivity was assessed by exposing the aptasensor to non-targeted viruses (hCoV-OC43, Influenza A, and RSV-A). EIS data outputs were further used to select a suitable response variable and cutoff frequency. Capacitance increases in response to the gradual loading of the attenuated BA.1. The aptasensor was sensitive and specific for BA.1 at a lower viral load (10-100 copies/ml) and was capable of discriminating between negative and positive contrived samples (with strain specificity against other viruses: OC43, Influenza A, and RSV-A). The aptasensor detected SARS-CoV-2 with an estimated LOD of 1790 copies/ml in contrived samples. In human clinical samples, the aptasensor presents an accuracy of 72%, with 75% of positive percent of agreement and 67% of negative percent of agreement. Our results show that the aptasensor is a promising candidate to detect SARS-CoV-2 during early stages of infection when virion concentrations are low, which may be useful for preventing the asymptomatic spread of CoVID-19.
Collapse
Affiliation(s)
- Geisianny Moreira
- Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina, United States of America
- Department of Agricultural Sciences, Clemson University, Clemson, South Carolina, United States of America
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lancing, Michigan, United States of America
| | - Hanyu Qian
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Shoumen Palit Austin Datta
- Department of Mechanical Engineering, MIT Auto-ID Labs, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Anesthesiology, Medical Device (MDPnP) Interoperability and Cybersecurity Labs, Biomedical Engineering Program, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Nikolay Bliznyuk
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Jeremiah Carpenter
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - Eric McLamore
- Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina, United States of America
- Department of Agricultural Sciences, Clemson University, Clemson, South Carolina, United States of America
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lancing, Michigan, United States of America
| | - Diana Vanegas
- Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina, United States of America
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lancing, Michigan, United States of America
- Interdisciplinary Group for Biotechnology Innovation and Ecosocial Change -BioNovo, Universidad del Valle, Cali, Colombia
| |
Collapse
|
19
|
Xu G, Wang C, Yu H, Li Y, Zhao Q, Zhou X, Li C, Liu M. Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer. Nucleic Acids Res 2023; 51:7666-7674. [PMID: 37351632 PMCID: PMC10415127 DOI: 10.1093/nar/gkad541] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.
Collapse
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Chen Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| |
Collapse
|
20
|
Anbiaee G, Khoshbin Z, Zamanian J, Samie A, Ramezani M, Alibolandi M, Danesh NM, Taghdisi SM, Abnous K. A fluorescent aptasensor for quantification of cocaine mediated by signal amplification characteristics of UiO-66/AuNPs nanocomposite. Anal Biochem 2023:115193. [PMID: 37257736 DOI: 10.1016/j.ab.2023.115193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/10/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Due to the detrimental effects of cocaine on the human body such as organ damage, paranoia, immunodeficiency, cardiovascular disease, blood pressure, and stress, it is highly required to develop sensing approaches for its rapid and facile determination. Based on the signal enhancement capability of the UiO-66/AuNPs nanocomposite and acting as a capture agent, we designed a cost-effective fluorescent aptasensor for cocaine detection. The cocaine presence in the sample would cause a considerable escalation in the quenching of the fluorescence signal. The aptasensor achieved the linear response range over 0.5 μM-20 μM with a low detection limit of 0.178 μM. The selectivity of the designed aptasensing assay was successfully confirmed by examining several analgesic drugs. The aptasensor was employed for cocaine determination in human serum as the real samples. This method has a substantial benefit the for development of a low-cost and facile tool in medicine and forensic science.
Collapse
Affiliation(s)
- Ghasem Anbiaee
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Javad Zamanian
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Samie
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Noor Mohammd Danesh
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
21
|
Han J, Ma P, Khan IM, Zhang Y, Wang Z. Study of binding mechanism of aptamer to kanamycin and the development of fluorescent aptasensor in milk detection. Talanta 2023; 260:124530. [PMID: 37116356 DOI: 10.1016/j.talanta.2023.124530] [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: 01/11/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
Aptasensors being versatile sensing platforms presented higher sensitivity toward target detection. However, lacking theoretical basis of recognition between most targets and their corresponding aptamers has impeded their applications. Herein, we conducted a study to explore the binding mechanism of aptamer to kanamycin (Kana) and developed rapid fluorescent aptasensing methods. Based on the fluorescence polarization results, base mutations were performed at different sites of the aptamer. The key binding nucleotides of Kana was identified as T7, T8, C13 and A15 by using isothermal titration calorimetry (ITC). The Kmut3 (2.18 μM) with lower dissociation constants (Kd), one-third of the native aptamer (6.91 μM), was also obtained. In addition, the lower K+ concentration and temperature were found to be conducive to Kana binding. Circular dichroism (CD) results revealed that the binding of Kana can trigger the change of base stacking force and helix force. On the aforementioned basis, a fluorescent sensor was designed with the native aptamer and Kmut3 as recognition elements. The comparison results proved that the Kmut3 presented a 3 times lower limit of detection of 59 nM compared to the native aptamer (148 nM). Notably, this developed aptasensor can be finished in 45 min and was convenient to operate.
Collapse
Affiliation(s)
- Jing Han
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Pengfei Ma
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China; School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212004, China.
| |
Collapse
|
22
|
Bohrmann L, Burghardt T, Rodríguez-Rodríguez C, Herth MM, Saatchi K, Häfeli UO. Quantitative Evaluation of a Multimodal Aptamer-Targeted Long-Circulating Polymer for Tumor Targeting. ACS OMEGA 2023; 8:11003-11020. [PMID: 37008162 PMCID: PMC10061651 DOI: 10.1021/acsomega.2c07762] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Aptamers are promising targeting agents for imaging and therapy of numerous diseases, including cancer. However, a significant shortcoming of aptamers is their poor stability and fast excretion, limiting their application in vivo. Common strategies to overcome these challenges is to chemically modify aptamers in order to increase their stability and/or to apply formulation technologies such as conjugating them to polymers or nanocarriers in order to increase their circulation half-life. This is expected to result in improved cellular uptake or retention to passively targeted nanomedicines. Herein, we report a modular conjugation strategy based on click chemistry between functionalized tetrazines and trans-cyclooctene (TCO), for the modification of high molecular weight hyperbranched polyglycerol (HPG) with sgc8 aptamer, fluorescent dyes, and 111In. Our data indicate strong affinity of sgc8 against a range of solid tumor-derived cell lines that have previously not been tested with this aptamer. Nevertheless, nonspecific uptake of scrambled ssDNA-functionalized HPG in cells highlights inherent challenges of aptamer-targeted probes that remain to be solved for clinical translation. We validate HPG-sgc8 as a nontoxic nanoprobe with high affinity against MDA-MB-468 breast and A431 lung cancer cells and show significantly increased plasma stability compared to free sgc8. In vivo quantitative SPECT/CT imaging indicates EPR-mediated tumor uptake of HPG-sgc8 and nontargeted or scrambled ssDNA-conjugated HPG but no statistically significant difference between these formulations in terms of total tumor uptake or retention. Our study emphasizes the need for stringent controls and quantification in the evaluation of aptamer-targeted probes. For this purpose, our versatile synthesis strategy provides a simple approach for the design and evaluation of long-circulating aptamer-conjugated nanoformulations.
Collapse
Affiliation(s)
- Lennart Bohrmann
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Tobias Burghardt
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Matthias M. Herth
- Department
of Drug Design and Pharmacology, Faculty of Health and Medicinal Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Department
of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej
9, 2100 Copenhagen, Denmark
| | - Katayoun Saatchi
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Urs O. Häfeli
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| |
Collapse
|
23
|
Aptamer-functionalized capacitive biosensors. Biosens Bioelectron 2023; 224:115014. [PMID: 36628826 DOI: 10.1016/j.bios.2022.115014] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/17/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
The growing use of aptamers as target recognition elements in label-free biosensing necessitates corresponding transducers that can be used in relevant environments. While popular in many fields, capacitive sensors have seen relatively little, but growing use in conjunction with aptamers for sensing diverse targets. Few reports have shown physiologically relevant sensitivity in laboratory conditions and a cohesive picture on how target capture modifies the measured capacitance has been lacking. In this review, we assess the current state of the field in three areas: small molecule, protein, and cell sensing. We critically analyze the proposed hypotheses on how aptamer-target capture modifies the capacitance, as many mechanistic postulations appear to conflict between published works. As the field matures, we encourage future works to investigate individual aptamer-target interactions and to interrogate the physical mechanisms leading to measured changes in capacitance. To this point, we provide recommendations on best practices for developing aptasensors with a particular focus on considerations for biosensing in clinical settings.
Collapse
|
24
|
Chovelon B, Peyrin E, Ragot M, Salem N, Nguyen TG, Auvray B, Henry M, Petrillo MA, Fiore E, Bessy Q, Faure P, Ravelet C. Nile blue as reporter dye in salt aggregation based-colorimetric aptasensors for peptide, small molecule and metal ion detection. Anal Chim Acta 2023; 1243:340840. [PMID: 36697182 DOI: 10.1016/j.aca.2023.340840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/21/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Herein, we report a novel approach for the design of a colorimetric aptasensor, relying on a Dye Salt Aggregation-based Colorimetric Oligonucleotide assay (DYSACO assay). This method is based on the use of an intercalating agent, Nile Blue (NB), whose aggregation capacities (and thus modification of its absorption spectrum) are drastically amplified by adding salts to the working solution. The presence of an aptamer could protect NB from such aggregation process due to its intercalation into double-stranded DNA and/or interaction with nucleobases. In response to the addition of the specific ligand, the competition between NB and the target for binding to the aptamer occurs, resulting in an increase in the dye salt aggregation and then in the blue-to-blank color change of the solution. The proof-of-principle was demonstrated by employing the anti-l-tyrosinamide aptamer and the assay was successfully applied to the trace enantiomer detection, allowing the detection of an enantiomeric impurity down to approximately 2% in a non-racemic sample. Through a reversed mechanism based on the increased capture of NB by DNA upon analyte binding, the sensing platform was further demonstrated for the Hg(II) detection. Water samples of different origin were spiked with Hg(II) analyte at final range concentrations comprised between (0.5-15 μM). An excellent overall recovery of 122 ± 14%; 105 ± 14%; 99 ± 9%; was respectively obtained from river, tap and mineral water, suggesting that the sensor can be used under real sample conditions. The assay was also shown to work for sensing the ochratoxin A and d-arginine vasopressin compounds, revealing its simplicity and generalizability potentialities.
Collapse
Affiliation(s)
- Benoît Chovelon
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041, Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France.
| | - Mailys Ragot
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Nassim Salem
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Truong Giang Nguyen
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Benjamin Auvray
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Mickael Henry
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Mel-Alexandre Petrillo
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Quentin Bessy
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Patrice Faure
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041, Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France.
| |
Collapse
|
25
|
Rukundo JL, Latimer J, Jain S, Kochmann S, Krylov SN. Streamlined Data Processing for Determination of Equilibrium Dissociation Constants with Accurate Constant via Transient Incomplete Separation (ACTIS). Anal Chem 2023; 95:3563-3568. [PMID: 36763923 DOI: 10.1021/acs.analchem.2c05607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The determination of accurate equilibrium dissociation constants, Kd, of protein-small molecule complexes is important but challenging as all established methods have inherent sources of inaccuracy. Accurate Constant via Transient Incomplete Separation (ACTIS) is a new method for Kd determination using transient incomplete separation of the complex from the unbound small molecule in a pressure-driven flow inside a capillary. ACTIS is accurate, and its accuracy is invariant to variations in geometries of both the fluidic system and the flow. Furthermore, ACTIS is implemented using a simple fluidic system supporting its accuracy and providing a simple-to-follow/copy template for instrumentation. Despite the simple and robust instrumentation/acquisition, the current data processing workflow is cumbersome, time consuming, and prone to hard-to-trace human errors therefore hindering ACTIS' ability to become a practical reference method for Kd determination. This technical note describes a streamlined workflow for processing ACTIS data; the workflow is implemented as a set of open-source software tools called prACTISed (https://github.com/prACTISedProgram/prACTISed). These tools allow all steps of data processing to be performed in a fast and straightforward fashion. These practical software tools complement the simple instrumentation serving both developers and users of ACTIS.
Collapse
Affiliation(s)
- Jean-Luc Rukundo
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jessica Latimer
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Shiv Jain
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sven Kochmann
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
26
|
Bennett HA, Li Y, Yan H. Thermal treatment affects aptamers' structural profiles. Bioorg Med Chem Lett 2023; 82:129150. [PMID: 36693483 DOI: 10.1016/j.bmcl.2023.129150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Using anion-exchange high performance liquid chromatography under non-denaturing conditions, the conformational flexibility of adenosine-, ampicillin-, and quinine aptamers were studied. It was found that all three aptamers showed more than one species when not subjected to thermal anneal. Addition of ligand to untreated aptamers did not significantly change the structural distribution. Upon heating followed by slow cooling, however, all three aptamers were found to exist virtually solely in one structure, presumably the partial hairpin species. It was also found that sonication of quinine aptamer, but not adenosine and ampicillin aptamer, led to its elution off HPLC as virtually a single species. These changes in conformational distribution as a result of thermal anneal or sonication were further confirmed by UV/vis and circular dichroism spectroscopy, as well as melt curves. The findings provided basis for future optimization of aptamer selection and preparation, where thermal anneal can help optimize selection efficiency and improve the consistency in the interpretation of results.
Collapse
Affiliation(s)
- Hayley-Ann Bennett
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Yifeng Li
- Department of Computer Science and Department of Biological Sciences, Brock University, Canada.
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada.
| |
Collapse
|
27
|
Qi X, Zhang L, Wang X, Chen S, Wang X. A label-free colorimetric aptasensor based on an engineered chimeric aptamer and Au@FeP nanocomposites for the detection of kanamycin. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
|
28
|
Perez Tobia J, Huang PJJ, Ding Y, Saran Narayan R, Narayan A, Liu J. Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures. ACS Synth Biol 2023; 12:186-195. [PMID: 36594697 DOI: 10.1021/acssynbio.2c00462] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.
Collapse
Affiliation(s)
- Javier Perez Tobia
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran Narayan
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Apurva Narayan
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada.,Department of Computer Science, Western University, London, Ontario N6A 3K7, Canada.,Systems Design Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
29
|
Huang Y, Ryssy J, Nguyen MK, Loo J, Hällsten S, Kuzyk A. Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes. Anal Chem 2022; 94:17577-17586. [PMID: 36480745 PMCID: PMC9773176 DOI: 10.1021/acs.analchem.2c04034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (KD) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.
Collapse
Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,E-mail:
| | - Joonas Ryssy
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City700000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City700000, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Susanna Hällsten
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,E-mail:
| |
Collapse
|
30
|
Lu C, Lopez A, Zheng J, Liu J. Using the Intrinsic Fluorescence of DNA to Characterize Aptamer Binding. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227809. [PMID: 36431910 PMCID: PMC9692703 DOI: 10.3390/molecules27227809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
The reliable, readily accessible and label-free measurement of aptamer binding remains a challenge in the field. Recent reports have shown large changes in the intrinsic fluorescence of DNA upon the formation of G-quadruplex and i-motif structures. In this work, we examined whether DNA intrinsic fluorescence can be used for studying aptamer binding. First, DNA hybridization resulted in a drop in the fluorescence, which was observed for A30/T30 and a 24-mer random DNA sequence. Next, a series of DNA aptamers were studied. Cortisol and Hg2+ induced fluorescence increases for their respective aptamers. For the cortisol aptamer, the length of the terminal stem needs to be short to produce a fluorescence change. However, caffeine and adenosine failed to produce a fluorescence change, regardless of the stem length. Overall, using the intrinsic fluorescence of DNA may be a reliable and accessible method to study a limited number of aptamers that can produce fluorescence changes.
Collapse
Affiliation(s)
- Chang Lu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jinkai Zheng
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Correspondence:
| |
Collapse
|
31
|
Liu J, Li T, Wang G, Chen J, Yao Q, Li Q, Zhao X. Aptamer-assisted two-point immobilized agonist-bound angiotensin II type 1 receptor for a second-site modulator discovery. iScience 2022; 25:105361. [DOI: 10.1016/j.isci.2022.105361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 10/12/2022] [Indexed: 12/01/2022] Open
|
32
|
Are aptamer-based biosensing approaches a good choice for female fertility monitoring? A comprehensive review. Biosens Bioelectron 2022; 220:114881. [DOI: 10.1016/j.bios.2022.114881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/23/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
|
33
|
Wang TY, Rukundo JL, Le ATH, Ivanov NA, Le Blanc JCY, Gorin BI, Krylov SN. Transient Incomplete Separation of Species with Close Diffusivity to Study the Stability of Affinity Complexes. Anal Chem 2022; 94:15415-15422. [DOI: 10.1021/acs.analchem.2c03313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | - Jean-Luc Rukundo
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | - An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | - Nikita A. Ivanov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | | | - Boris I. Gorin
- Eurofins CDMO Alphora, 2395 Speakman Drive #2001, Mississauga, OntarioL5K 1B3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| |
Collapse
|
34
|
Zhang P, Qin K, Lopez A, Li Z, Liu J. General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers. Anal Chem 2022; 94:15456-15463. [DOI: 10.1021/acs.analchem.2c03564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pengbo Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ke Qin
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
35
|
Liu L, Yu H, Zhao Q. The Characterization of Binding between Aptamer and Bisphenol A and Developing Electrochemical Aptasensors for Bisphenol A with Rationally Engineered Aptamers. BIOSENSORS 2022; 12:bios12110913. [PMID: 36354422 PMCID: PMC9688307 DOI: 10.3390/bios12110913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/12/2023]
Abstract
Bisphenol A (BPA) is widely used in the manufacture of polycarbonate and epoxy-resin-based products, and BPA contamination often happens in a variety of types of environment and food stuffs. BPA can cause many harmful effects to health due to its high toxicity. The rapid detection of BPA is of great significance in environmental monitoring and food safety. Nucleic acid aptamers show advantages in biosensors due to good chemical stability, the ease of labeling functional groups, and target binding that induces conformation change. Here, we performed a thorough characterization of the binding performance of one 60-nt anti-BPA DNA aptamer with isothermal titration calorimetry (ITC). We found the crucial region of the aptamer sequence for affinity binding with BPA, and the aptamer was able to be truncated to 29-nt DNA without losing affinity. We then developed a simple reagent-less electrochemical aptamer-based sensor for rapid BPA detection with this engineered aptamer. The truncated aptamer with a redox tag methylene blue (MB) was immobilized on a gold electrode. BPA-binding induced the conformation change of the MB-labeled aptamer, moving the MB close to the electrode surface and causing a significant current increase in MB in square wave voltammetry (SWV). Under optimized conditions, we achieved the quantitative detection of BPA with a detection limit of BPA at 0.1 μM. This sensor showed quick response to BPA and could be regenerated by washing with deionized water. This sensor was selective, and it allowed detecting BPA in complex samples, showing its potential in practice. This study will help in further applications of the aptamers of BPA.
Collapse
Affiliation(s)
- Liying Liu
- 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
| | - 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
| |
Collapse
|
36
|
Zamanian J, Khoshbin Z, Hosseinzadeh H, Danesh NM, Khakshour Abdolabadi A, Abnous K, Taghdisi SM. An ultrasensitive detection platform for cocaine: Aptasensing strategy in capillary tube. Front Chem 2022; 10:996358. [PMID: 36339038 PMCID: PMC9626653 DOI: 10.3389/fchem.2022.996358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/10/2022] [Indexed: 09/16/2023] Open
Abstract
Cocaine as a detrimental addictive drug threats human health through inducing heart problem, blood pressure, anxiety, immunodeficiency, paranoia, and organ damage. Thus, the quantification of cocaine in the biological samples by a simple, high specificity, and fast method is highly urgent to decrease the harmful effect of the misuse of this drug. In this study, we constructed a novel fluorescent aptasensor by combining the fluorescein (FAM)-modified specific aptamer and AuNPs in a capillary tube as the sensing substrate for the first time. The presence of cocaine recovered the fluorescence response of the aptasensor through interaction with the aptamer and differentiation of the aptamer@AuNPs complex. By fluorescence microscopy imaging of the aptasensor substrate and its quantitative analysis, a remarkable linear range from 100 pM to 600 µM and the ultra-low limit of detection (LOD) as 0.31 pM were achieved for the target detection. Cocaine was successfully quantified in the real samples (human serum and urine) by using the aptasensor. The aptasensor is simple, easy-to-use, favorable applicability, and cost-effective; and to the best of our knowledge, it is the first use of the capillary tube as a sensing platform just by using about 3 μl of the samples. It is also an easy-to-carry tool, promising for the on-site target detection. Besides, it can be a portable device for monitoring cocaine by using a handheld single-beam fluorescence microscope. It can be an appropriate detection tool in forensic science and medicine.
Collapse
Affiliation(s)
- Javad Zamanian
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Hosseinzadeh
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Noor Mohammd Danesh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Institute of Science and New Technologies, Tehran, Iran
| | - Ali Khakshour Abdolabadi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
37
|
Yan X, Du G, Chen H, Zhao Q, Guo Q, Wang J, Wang Z, Song W, Sheng Q, Luo Y, Yuan Y, Yue T. Label-free fluorescence aptasensor for the detection of patulin using target-induced DNA gates and TCPP/BDC-NH 2 mixed ligands functionalized Zr-MOF systems. Biosens Bioelectron 2022; 217:114723. [PMID: 36150324 DOI: 10.1016/j.bios.2022.114723] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 11/02/2022]
Abstract
Patulin (PAT) is an unsaturated lactone mycotoxin primarily produced by Penicillium expansum and Aspergillus clavatus. Given the potential health risks and economic losses associated with PAT, the rapid detection of PAT using fluorescent aptasensors is of significant importance in evaluating food safety. However, it easily increases the cost and complexity caused by signal labeling. We combined TCPP/BDC-NH2 mixed ligands functionalized Zr metal-organic frameworks (Zr-MOFmix) and terminated three-stranded DNA gates (ttsDNA gates) to fabricate a label-free fluorescent aptasensor for PAT detection. The Zr-MOFmix system was synthesized via a one-pot strategy and could be used to address the problem of pore size limitation and increase the loading amounts of dyes. TtsDNA gate was integrated into the Zr-MOFmix system to control the release of dyes, exhibiting a high signal-to-background ratio. The single-stranded aptamer region in ttsDNA gate situated away from the surface of the Zr-MOFmix, resulting in a natural release of dyes in the absence of PAT. While binding to PAT resulted in target-induced conformational changes that helped form the hairpin structure of the aptamer. This structure hindered the release of dyes from the pores of Zr-MOFmix, thus reducing the fluorescence signals intensity. The stimuli-responsive DNA-gated material provides a platform for PAT analysis under conditions of a low limit of detection (0.871 pg/mL). Furthermore, the excellent specificity and anti-interference of the fluorescent aptasensor make the system suitable for the analysis of apple juice samples. This label-free strategy is cheaper and simper compared with labeled detection, especially for the development of multi-target-detection.
Collapse
Affiliation(s)
- Xiaohai Yan
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Gengan Du
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Hong Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Qiannan Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Qi Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Wei Song
- College of Food Science and Technology, Northwest University, Xi'an, 710067, China
| | - Qinglin Sheng
- College of Food Science and Technology, Northwest University, Xi'an, 710067, China
| | - Yane Luo
- College of Food Science and Technology, Northwest University, Xi'an, 710067, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China; College of Food Science and Technology, Northwest University, Xi'an, 710067, China.
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China; College of Food Science and Technology, Northwest University, Xi'an, 710067, China.
| |
Collapse
|
38
|
Zhu C, Zhang F, Li H, Chen Z, Yan M, Li L, Qu F. CRISPR/Cas Systems Accelerating the Development of Aptasensors. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
39
|
Li T, Wang J, Zhu L, Li C, Chang Q, Xu W. Advanced screening and tailoring strategies of pesticide aptamer for constructing biosensor. Crit Rev Food Sci Nutr 2022; 63:10974-10994. [PMID: 35699641 DOI: 10.1080/10408398.2022.2086210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rapid development of aptamers has helped address the challenges presented by the wide existed pesticides contaminations. Screening of aptamers with excellent performance is a prerequisite for successfully constructing biosensors, while further tailoring of aptamers with enhanced activity greatly improved the assay performance. Firstly, this paper reviewed the advanced screening strategies for pesticides aptamers, including immobilization screening that preserves the native structures of targets, non-immobilized screening based on nanomaterials, capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX), virtual screening in silico, high-throughput selection, and rational secondary library generation methods, which contributed significantly to improve the success rate of screening, reduce the screening time, and ensure aptamer binding affinity. Secondly, the precise tailoring strategies for pesticides aptamers were modularly elaborated, containing deletion, splitting, elongation, and fusion, which provided various advantages like cost-efficiency, enhanced binding affinity, and new derived functional motifs. Thirdly, the developed aptamer-based biosensors (aptasensors) for pesticide detection were systematically reviewed according to the different signal output modes. Finally, the challenges and future perspectives of pesticide detection are discussed comprehensively.
Collapse
Affiliation(s)
- Tianshun Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jia Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Chenwei Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qiaoying Chang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| |
Collapse
|
40
|
Xu G, Zhao J, Yu H, Wang C, Huang Y, Zhao Q, Zhou X, Li C, Liu M. Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer. J Am Chem Soc 2022; 144:7731-7740. [PMID: 35442665 DOI: 10.1021/jacs.2c00478] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg2+ and Na+ ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through π-π stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.
Collapse
Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,Xi'an Modern Chemistry Research Institute, Xi'an, 710065, People's Republic of China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Chen Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yangyu Huang
- Shaoyang University, Shaoyang, 422000, People's Republic of China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310000, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| |
Collapse
|
41
|
Zhao Y, Yavari K, Wang Y, Pi K, Van Cappellen P, Liu J. Deployment of functional DNA-based biosensors for environmental water analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
42
|
Ding Y, Liu X, Huang PJJ, Liu J. Homogeneous assays for aptamer-based ethanolamine sensing: no indication of target binding. Analyst 2022; 147:1348-1356. [PMID: 35244657 DOI: 10.1039/d2an00145d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethanolamine is an important analyte for environmental chemistry and biological sciences. A few DNA aptamers were previously reported for binding ethanolamine with a dissociation constant (Kd) as low as 9.6 nM. However, most of the previous binding assays and sensing work used either immobilized ethanolamine or immobilized aptamers. In this work, we studied three previously reported DNA sequences, two of which were supposed to bind ethanolamine while the other could not bind. Isothermal titration calorimetry revealed no binding for any of these sequences. In addition, due to their guanine-rich sequences, thioflavin T was used as a probe. Little fluorescence change was observed with up to 1 μM ethanolamine. Responses within the millimolar range of ethanolamine were attributed to the general fluorescence quenching effect of ethanolamine instead of aptamer binding. Finally, after studying the adsorption of ethanolamine to gold nanoparticles (AuNPs), we confirmed the feasibility of using AuNPs as a probe when the concentration of ethanolamine was below 0.1 mM. However, no indication of specific aptamer binding was observed by comparing the three DNA sequences for their color changing trends. This work articulates the importance of careful homogeneous binding assays using free target molecules.
Collapse
Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Xun Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| |
Collapse
|
43
|
Martínez-Jarquín S, Begley A, Lai YH, Bartolomeo GL, Pruška A, Rotach C, Zenobi R. Aptapaper─An Aptamer-Functionalized Glass Fiber Paper Platform for Rapid Upconcentration and Detection of Small Molecules. Anal Chem 2022; 94:5651-5657. [PMID: 35343676 DOI: 10.1021/acs.analchem.2c00035] [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
We tested a paper-based platform ("Aptapaper") for the upconcentration and analysis of small molecules from complex matrices for two well-characterized aptamers, quinine and serotonin binding aptamers (QBA and SBA, respectively). After incubating the aptapaper under conditions that ensure correct aptamer folding, the aptapaper was used to upconcentrate target analytes from complex matrices. Aptapaper was rinsed, dried, and the target analyte was detected immediately or up to 4 days later by paper spray ionization coupled to high-resolution mass spectrometry (PS-MS). The minimum concentrations detectable were 81 pg/mL and 1.8 ng/mL for quinine and serotonin, respectively, from 100 mM AmAc or water. Complementary characterization of the QBA aptapaper system was performed using an orthogonal fluorescence microscopy method. Random adsorption was analyte-specific and observed for quinine, but not serotonin. This aptapaper approach is a semiquantitative (10-20% RSD) platform for upconcentration of small metabolites by mass spectrometry.
Collapse
Affiliation(s)
| | - Alina Begley
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Yin-Hung Lai
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.,Department of Chemical Engineering, National United University, Miaoli 360302, Taiwan.,Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | | | - Adam Pruška
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Christian Rotach
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| |
Collapse
|
44
|
Huang Y, Nguyen MK, Nguyen VH, Loo J, Lehtonen AJ, Kuzyk A. Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2954-2960. [PMID: 35212547 PMCID: PMC8908738 DOI: 10.1021/acs.langmuir.1c03434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Aptamers have emerged as versatile affinity ligands and as promising alternatives to protein antibodies. However, the inconsistency in the reported affinities and specificities of aptamers has greatly hindered the development of aptamer-based applications. Herein, we present a strategy to characterize aptamers by using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. We demonstrate the characterization of several DNA aptamers, including aptamers for small molecules and macromolecules, as well as aptamers with high and low affinities. The presented characterization scheme can be readily adapted to a wide selection of aptamers. We anticipate that our approach will advance the development of aptamer-based applications by enabling reliable and reproducible characterization of aptamers.
Collapse
Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dist. 10, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University Ho Chi Minh City,
Linh Trung Ward, Thu Duc District, 700000 Ho Chi Minh City, Vietnam
| | - Vu Hoang Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Arttu J. Lehtonen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Department
of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| |
Collapse
|
45
|
Assays to Estimate the Binding Affinity of Aptamers. Talanta 2022; 238:122971. [PMID: 34857318 DOI: 10.1016/j.talanta.2021.122971] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.
Collapse
|
46
|
Abnous K, Abdolabadi AK, Ramezani M, Alibolandi M, Nameghi MA, Zavvar T, Khoshbin Z, Lavaee P, Taghdisi SM, Danesh NM. A highly sensitive electrochemical aptasensor for cocaine detection based on CRISPR-Cas12a and terminal deoxynucleotidyl transferase as signal amplifiers. Talanta 2022; 241:123276. [PMID: 35121546 DOI: 10.1016/j.talanta.2022.123276] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/23/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022]
Abstract
Cocaine is one of the mainly used illegal drugs in the world. Using the signal amplification elements of terminal deoxynucleotidyl transferase (TdT) and CRISPR-Cas12a, a highly sensitive and simple electrochemical aptasensor was introduced for cocaine quantification. When, no cocaine existed in the sample, the 3'-end of complementary strand of aptamer (CS) was extended by TdT, leading to the activation of CRISPR-Cas12a and remaining of very short oligonucleotides on the working electrode. So, the current signal was remarkably promoted. With the presence of cocaine, CS left the electrode surface. Thus, nothing changed following the incubation of TdT and CRISPR-Cas12a and the Aptamer/Cocaine complex presented on the electrode. Consequently, the [Fe(CN)6]3-/4- could not freely reach the electrode surface and the signal response was weak. Under optimal situations, the biosensor revealed a wide linear relation from 40 pM to 150 nM with detection limit of 15 pM for cocaine. The sensitivity of the analytical system was comparable and even better than other reported methods for cocaine detection. The designed method displayed excellent cocaine selectivity. The aptasensor could work well for cocaine assay in serum samples. So, the aptasensor is expected to be an efficient analytical method with broad applications in the determination of diverse analytes.
Collapse
Affiliation(s)
- Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morteza Alinezhad Nameghi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - TaranehSadat Zavvar
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parirokh Lavaee
- Academic Center for Education, Culture and Research, Research Institute for Industrial Biotechnology, Industrial Biotechnology on Microorganisms, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Noor Mohammad Danesh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Institute of Science and New Technologies, Tehran, Iran.
| |
Collapse
|
47
|
Xia F, He A, Zhao H, Sun Y, Duan Q, Abbas SJ, Liu J, Xiao Z, Tan W. Molecular Engineering of Aptamer Self-Assemblies Increases in Vivo Stability and Targeted Recognition. ACS NANO 2022; 16:169-179. [PMID: 34935348 DOI: 10.1021/acsnano.1c05265] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Functionally modified aptamer conjugates are promising tools for targeted imaging or treatment of various diseases. However, broad applications of aptamer molecules are limited by their in vivo instability. To overcome this challenge, current strategies mostly rely on covalent chemical modification of aptamers, a complicated process that requires case-by-case sequence design, multiple-step synthesis, and purification. Herein, we report a covalent modification-free strategy to enhance the in vivo stability of aptamers. This strategy simply utilizes one-step molecular engineering of aptamers with gold nanoclusters (GNCs) to form GNCs@aptamer self-assemblies. Using Sgc8 as a representative aptamer, the resulting GNCs@Sgc8 assemblies enhance cancer-cell-specific binding and sequential internalization by a receptor-mediated endocytosis pathway. Importantly, the GNCs@aptamer self-assemblies resist nuclease degradation for as long as 48 h, compared to the degradation of aptamer alone at 3 h. In parallel, the tumor-targeted recognition and retention of GNCs@aptamer self-assemblies are dramatically enhanced, indicated by a 9-fold signal increase inside the tumor compared to the aptamer alone. This strategy is to avoid complicated chemical modification of aptamers and can be extended to all aptamers. Our work provides a simple, effective, and universal strategy for enhancing the in vivo stability of any aptamer or its conjugates, thus expanding their imaging and therapeutic applications.
Collapse
Affiliation(s)
- Fangfang Xia
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Axin He
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haitao Zhao
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiao Duan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sk Jahir Abbas
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| |
Collapse
|
48
|
|
49
|
Cánovas R, Daems E, Campos R, Schellinck S, Madder A, Martins JC, Sobott F, De Wael K. Novel electrochemiluminescent assay for the aptamer-based detection of testosterone. Talanta 2021; 239:123121. [PMID: 34942485 DOI: 10.1016/j.talanta.2021.123121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/19/2022]
Abstract
This work presents a proof-of-concept assay for the detection and quantification of small molecules based on aptamer recognition and electrochemiluminescence (ECL) readout. The testosterone-binding (TESS.1) aptamer was used to demonstrate the novel methodology. Upon binding of the target, the TESS.1 aptamer is released from its complementary capture probe - previously immobilized at the surface of the electrode - producing a decrease in the ECL signal after a washing step removing the released (labeled) TESS.1 aptamer. The analytical capability of the ECL assay towards testosterone detection was investigated displaying a linear range from 0.39 to 1.56 μM with a limit of detection of 0.29 μM. The selectivity of the proposed assay was assessed by performing two different negative control experiments; i) detection of testosterone with a randomized ssDNA sequence and ii) detection of two other steroids, i.e. deoxycholic acid and hydrocortisone with the TESS.1 aptamer. In parallel, complementary analytical techniques were employed to confirm the suggested mechanism: i) native nano-electrospray ionization mass spectrometry (native nESI-MS) was used to determine the stoichiometry of the binding, and to characterize aptamer-target interactions; and, ii) isothermal titration calorimetry (ITC) was carried out to elucidate the dissociation constant (Kd) of the complex of testosterone and the TESS.1 aptamer. The combination of these techniques provided a complete understanding of the aptamer performance, the binding mechanism, affinity and selectivity. Furthermore, this important characterization carried out in parallel validates the real functionality of the aptamer (TESS.1) ensuring its use towards selective testosterone binding in further biosensors. This research will pave the way for the development of new aptamer-based assays coupled with ECL sensing for the detection of relevant small molecules.
Collapse
Affiliation(s)
- Rocío Cánovas
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Elise Daems
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; BAMS Research Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Rui Campos
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Sofie Schellinck
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - José C Martins
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Frank Sobott
- BAMS Research Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Karolien De Wael
- A-Sense Lab, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.
| |
Collapse
|
50
|
Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
Collapse
Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|