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Torregrosa D, Jauset-Rubio M, Serrano R, Svobodová M, Grindlay G, O'Sullivan CK, Mora J. Ultrasensitive determination of β-conglutin food allergen by means an aptamer assay based on inductively coupled plasma mass spectrometry detection. Anal Chim Acta 2023; 1252:341042. [PMID: 36935136 DOI: 10.1016/j.aca.2023.341042] [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: 11/24/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
The overall objective of this work is the evaluation of different competitive aptamer assays based on inductively coupled plasma mass spectrometry (ICP-MS) detection for the determination of β-conglutin (food protein allergen from lupin) in flour samples. To this end, two competitive aptamer assay schemes were developed using either thiolated aptamers chemisorbed onto gold nanoparticles (AuNPs) or biotinylated aptamers linked to streptavidin-AuNPs. The influence of ICP-MS detection mode (i.e., conventional vs single particle) on assay performance was explored. In the case of the thiolated aptamer, the limit of detection (LoD) obtained using the single particle mode was improved 2-fold as compared to the LoD provided by the conventional mode. With regards to the biotinylated aptamer, the use of the conventional mode provided a 5-fold improvement of LoD as compared to that obtained for the single particle one. Using the optimized conditions, the best LoD of 2 pM was obtained with the biotinylated aptamer operating with conventional ICP-MS detection. When compared to previous reports using the same aptamer in a competitive assay, the developed method significantly improved the LoD by at least an order of magnitude. Different flour samples containing lupin were successfully analyzed according to European Conformity guidelines for the analysis of food contaminants.
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Affiliation(s)
- Daniel Torregrosa
- University of Alicante, Department of Analytical Chemistry, Nutrition and Food Sciences, PO Box 99, 03080, Alicante, Spain
| | - Miriam Jauset-Rubio
- INTERFIBIO Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Raquel Serrano
- University of Alicante, Department of Analytical Chemistry, Nutrition and Food Sciences, PO Box 99, 03080, Alicante, Spain
| | - Marketa Svobodová
- INTERFIBIO Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Guillermo Grindlay
- University of Alicante, Department of Analytical Chemistry, Nutrition and Food Sciences, PO Box 99, 03080, Alicante, Spain.
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain; Institució Catalana de Recerca i Estudis Avancats (ICREA), 08010, Barcelona, Spain
| | - Juan Mora
- University of Alicante, Department of Analytical Chemistry, Nutrition and Food Sciences, PO Box 99, 03080, Alicante, Spain
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2
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Jauset-Rubio M, Ortiz M, O’Sullivan CK. Exploiting the Nucleic Acid Nature of Aptamers for Signal Amplification. BIOSENSORS 2022; 12:972. [PMID: 36354481 PMCID: PMC9688535 DOI: 10.3390/bios12110972] [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: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Aptamer-based assays and sensors are garnering increasing interest as alternatives to antibodies, particularly due to their increased flexibility for implementation in alternative assay formats, as they can be employed in assays designed for nucleic acids, such as molecular aptamer beacons or aptamer detection combined with amplification. In this work, we took advantage of the inherent nucleic acid nature of aptamers to enhance sensitivity in a rapid and facile assay format. An aptamer selected against the anaphylactic allergen β-conglutin was used to demonstrate the proof of concept. The aptamer was generated by using biotinylated dUTPs, and the affinity of the modified aptamer as compared to the unmodified aptamer was determined by using surface plasmon resonance to calculate the dissociation constant (KD), and no significant improvement in affinity due to the incorporation of the hydrophobic biotin was observed. The modified aptamer was then applied in a colorimetric competitive enzyme-linked oligonucleotide assay, where β-conglutin was immobilized on the wells of a microtiter plate, competing with β-conglutin free in solution for the binding to the aptamer. The limit of detection achieved was 68 pM, demonstrating an improvement in detection limit of three orders of magnitude as compared with the aptamer simply modified with a terminal biotin label. The concept was then exploited by using electrochemical detection and screen-printed electrodes where detection limits of 326 fM and 7.89 fM were obtained with carbon and gold electrodes, respectively. The assay format is generic in nature and can be applied to all aptamers, facilitating an easy and cost-effective means to achieve lower detection limits.
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Affiliation(s)
- Miriam Jauset-Rubio
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, 43007 Tarragona, Spain
| | - Mayreli Ortiz
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, 43007 Tarragona, Spain
| | - Ciara K. O’Sullivan
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, 43007 Tarragona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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3
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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4
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Jia W, Wang Z, Lu Z, Ding B, Li Z, Xu D. The discovery of lactoferrin dual aptamers through surface plasmon resonance imaging combined with a bioinformation analysis. Analyst 2021; 145:6298-6306. [PMID: 32940261 DOI: 10.1039/d0an01513j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An analytical method for screening aptamers for different recognition sites in lactoferrin (Lac) molecules has been developed based on Surface Plasmon Resonance imaging (SPRi), combined with the cluster classification calculation of a quasi-aptamer library strategy and molecular docking simulation analysis. Using the software simulation, a homology analysis was performed on the selected quasi-aptamer sequences, which could be divided into 8 different families. Based on the principle of biomolecular recognition, a label-free, high-throughput dual immune site screening method was established, in which the nucleic acid aptamers of recognizing ability for lactoferrin molecules were fixed onto the surface of the SPRi sensor chip and could bind to the lactoferrin molecules. Then, the aptamer candidates to be paired were introduced, and the recognition event of the second immune site was judged by observing the binding signal of SPRi. The paired SPRi signal was generated only when the site identified by the second nucleic acid molecule was different from the first immune site. Based on this principle, a pair of Lac nucleic acid aptamers (Lac-8 and Lac-25) was finally screened and confirmed using computerized simulation, and has been employed to assay Lac in milk by ELONA (Enzyme-Linked Oligonucleotide Assay).
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Affiliation(s)
- Wenchao Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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Al Hamoui Dit Banni G, Nasreddine R, Fayad S, Colas C, Marchal A, Nehmé R. Investigation of lipase-ligand interactions in porcine pancreatic extracts by microscale thermophoresis. Anal Bioanal Chem 2021; 413:3667-3681. [PMID: 33797603 DOI: 10.1007/s00216-021-03314-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
The evaluation of binding affinities between large biomolecules and small ligands is challenging and requires highly sensitive techniques. Microscale thermophoresis (MST) is an emerging biophysical technique used to overcome this limitation. This work describes the first MST binding method to evaluate binding affinities of small ligands to lipases from crude porcine pancreatic extracts. The conditions of the MST assay were thoroughly optimized to successfully evaluate the dissociation constant (Kd) between pancreatic lipases (PL) and triterpenoid compounds purified from oakwood. More precisely, the fluorescent labeling of PL (PL*) using RED-NHS dye was achieved via a buffer exchange procedure. The MST buffer was composed of 20 mM NaH2PO4 + 77 mM NaCl (pH 6.6) with 0.05% Triton-X added to efficiently prevent protein aggregation and adsorption, even when using only standard, uncoated MST capillaries. Storage at -20 °C ensured stability of PL* and its fluorescent signal. MST results showed that crude pancreatic extracts were suitable as a source of PL for the evaluation of binding affinities of small ligands. Quercotriterpenoside-I (QTT-I) demonstrated high PL* binding affinity (31 nM) followed by 3-O-galloylbarrinic acid (3-GBA) (500 nM) and bartogenic acid (BA) (1327 nM). To enrich the 50 kDa lipase responsible for the majority of hydrolysis activity in the crude pancreatic extracts, ammonium sulfate precipitation was attempted and its efficiency confirmed using capillary electrophoresis (CE)-based activity assays and HRMS. Moreover, to accurately explain enzyme modulation mechanism, it is imperative to complement binding assays with catalytic activity ones.
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Affiliation(s)
- Ghassan Al Hamoui Dit Banni
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France
| | - Rouba Nasreddine
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France
| | - Syntia Fayad
- Institut des Sciences de la Vigne et du Vin (ISVV), EA 5477, Unité de recherche Œnologie, USC 1366 INRA, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Cyril Colas
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France.,Centre de Biophysique Moléculaire, CNRS-Université d'Orléans, UPR 4311, 45071, Orléans CEDEX 2, France
| | - Axel Marchal
- Institut des Sciences de la Vigne et du Vin (ISVV), EA 5477, Unité de recherche Œnologie, USC 1366 INRA, Université de Bordeaux, 33882, Villenave d'Ornon, France
| | - Reine Nehmé
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708 - UMR 7311, Université d'Orléans, 45067, Orléans, France.
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Zara L, Achilli S, Chovelon B, Fiore E, Toulmé JJ, Peyrin E, Ravelet C. Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants. Anal Chim Acta 2021; 1159:338382. [PMID: 33867041 DOI: 10.1016/j.aca.2021.338382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/28/2023]
Abstract
Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.
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Affiliation(s)
- Lorena Zara
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Novaptech, 2 Allée Du Doyen Georges Brus, 33600, Pessac, France
| | - Silvia Achilli
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | - Benoît Chovelon
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Service de Biochimie, Biologie Moléculaire, Toxicologie Environnementale, CHU de Grenoble-Alpes Site Nord- Institut de Biologie et de Pathologie, La Tronche, France
| | | | | | - Eric Peyrin
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France.
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Biophysical Characterization of Aptamer-Target Interactions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:1-15. [PMID: 31375847 DOI: 10.1007/10_2019_103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Aptamers are single-stranded nucleic acid molecules forming well-defined 3D structures. Aptamers typically bind to their ligands with high affinity and specificity. They are capable of interacting with various kinds of ligands: ions, small molecules, peptides, proteins, viruses, bacteria, and even cells. Therefore, aptamers are in widespread use as sensor molecules or as targeting agents in diagnostics and pharmaceutics. As a prerequisite for their use in these economic high-value areas, aptamers must be studied in detail with respect to different biophysical characteristics. Of central importance are basic binding parameters of the aptamer-target interaction, such as binding affinity and kinetics. Numerous biophysical methods with different features, characteristics, and capabilities are used in the field today for this purpose.This chapter provides an overview of the current state-of-the-art technologies for studying interactions between aptamers and targets and discusses their advantages as well as drawbacks. Furthermore, essential aspects influencing any aptamer characterization strategy will be presented. Finally, issues of comparability of binding data between different aptamer characterization technologies will be discussed. Graphical Abstract.
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Mairal Lerga T, Jauset-Rubio M, Skouridou V, Bashammakh AS, El-Shahawi MS, Alyoubi AO, O'Sullivan CK. High Affinity Aptamer for the Detection of the Biogenic Amine Histamine. Anal Chem 2019; 91:7104-7111. [PMID: 31042376 DOI: 10.1021/acs.analchem.9b00075] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The importance of histamine in various physiological functions and its involvement in allergenic responses make this small molecule one of the most studied biogenic amines. Even though a variety of chromatography-based methods have been described for its analytical determination, the disadvantages they present in terms of cost, analysis time, and low portability limit their suitability for in situ routine testing. In this work, we sought to identify histamine-binding aptamers that could then be exploited for the development of rapid, facile, and sensitive assays for histamine detection suitable for point-of-need analysis. A classic SELEX process was designed employing magnetic beads for target immobilization and the selection was completed after ten rounds. Following Next Generation Sequencing of the last selection rounds from both positive and counter selection magnetic beads, several sequences were identified and initially screened using an apta-PCR affinity assay (APAA). Structural and functional characterization of the candidates resulted in the identification of the H2 aptamer. The high binding affinity of the H2 aptamer to histamine was validated using four independent assays ( KD of 3-34 nM). Finally, the H2 aptamer was used for the development of a magnetic beads-based competitive assay for the detection of histamine in both buffer and synthetic urine, achieving very low limits of detection of 18 pM and 76 pM, respectively, while no matrix effects were observed. These results highlight the suitability of the strategy followed for identifying small molecule-binding aptamers and the compatibility of the selected H2 aptamer with the analysis of biological samples, thus facilitating the development of point-of-care devices for routine testing. Ongoing work is focused on extending the application of the H2 aptamer to the detection of spoilage in meat, fish, and beverages, as well as evaluating the affinity of truncated forms of the aptamer.
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Affiliation(s)
- Teresa Mairal Lerga
- Nanobiotechnology & Bioanalysis Group, INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Quimica , Universitat Rovira I Virgili , Avinguda Paı̈sos Catalans 26 , 43007 Tarragona , Spain
| | - Miriam Jauset-Rubio
- Nanobiotechnology & Bioanalysis Group, INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Quimica , Universitat Rovira I Virgili , Avinguda Paı̈sos Catalans 26 , 43007 Tarragona , Spain
| | - Vasso Skouridou
- Nanobiotechnology & Bioanalysis Group, INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Quimica , Universitat Rovira I Virgili , Avinguda Paı̈sos Catalans 26 , 43007 Tarragona , Spain
| | - Abdulaziz S Bashammakh
- Department of Chemistry, Faculty of Science , King Abdulaziz University , P.O. Box 80203, 21589 Jeddah , Saudi Arabia
| | - Mohammad S El-Shahawi
- Department of Chemistry, Faculty of Science , King Abdulaziz University , P.O. Box 80203, 21589 Jeddah , Saudi Arabia
| | - Abdulrahman O Alyoubi
- Department of Chemistry, Faculty of Science , King Abdulaziz University , P.O. Box 80203, 21589 Jeddah , Saudi Arabia
| | - Ciara K O'Sullivan
- Nanobiotechnology & Bioanalysis Group, INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Quimica , Universitat Rovira I Virgili , Avinguda Paı̈sos Catalans 26 , 43007 Tarragona , Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys 23 , 08010 Barcelona , Spain
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9
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Nakatsuka N, Cao HH, Deshayes S, Melkonian AL, Kasko AM, Weiss PS, Andrews AM. Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23490-23500. [PMID: 29851335 PMCID: PMC6087467 DOI: 10.1021/acsami.8b02837] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or l-tryptophan were selectively recognized by previously identified dopamine or l-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though, slightly greater than the previously determined solution dissociation constant. Using prefunctionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with l-3,4-dihydroxyphenylalanine, l- threo-dihydroxyphenylserine, and l-5-hydroxytryptophan enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons and future identification and characterization of novel aptamers targeting neurotransmitters or other important small molecules.
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Affiliation(s)
- Nako Nakatsuka
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Huan H. Cao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Stephanie Deshayes
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Arin L. Melkonian
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Andrea M. Kasko
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Paul S. Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Anne M. Andrews
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, CA 90095, United States
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10
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Wu Z, He D, Xu E, Jiao A, Chughtai MFJ, Jin Z. Rapid detection of β-conglutin with a novel lateral flow aptasensor assisted by immunomagnetic enrichment and enzyme signal amplification. Food Chem 2018; 269:375-379. [PMID: 30100448 DOI: 10.1016/j.foodchem.2018.07.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/27/2018] [Accepted: 07/01/2018] [Indexed: 12/29/2022]
Abstract
A simple, rapid and economic lateral flow immunochromatographic assay (LFICA) was designed for ultrasensitive detection of β-conglutin. Instead of antibodies and gold nanoparticles (AuNPs) used in conventional LFICA, a cognate aptamer duo, binding to β-conglutin and Fe3O4@Au core-shell nanoparticles, was applied in this study. An enzyme signal amplification strategy was used to enhance sensitivity. In addition, a new magnetic enrichment strategy was employed to further enhance sensitivity of the assay, slowing down movement of the capture probe (i.e., Fe3O4@Au nanostructures) using an external magnetic field. The novel LFICA assay can be completed within 20 min and achieved a detection limit of 8 fM, a thousand-times lower than similar assays without magnetic focusing. Overall, our results demonstrated the potential for the proposed LFICA sensor in rapid detection of β-conglutin without any special analytical expertise or instrumentations.
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Affiliation(s)
- Zhengzong Wu
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Deyun He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Enbo Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Aiquan Jiao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Muhammad Farhan Jahangir Chughtai
- NUR International Universities, Lahore, Pakistan; National Institute of Food Science & Technology, University of Agriculture, Faisalabad, Pakistan
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.
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11
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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12
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Cao C, Zhang F, Goldys EM, Gao F, Liu G. Advances in structure-switching aptasensing towards real time detection of cytokines. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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Identification and characterization of nucleobase-modified aptamers by click-SELEX. Nat Protoc 2018; 13:1153-1180. [PMID: 29700486 DOI: 10.1038/nprot.2018.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aptamers are single-stranded oligonucleotides that are in vitro-selected to recognize their target molecule with high affinity and specificity. As they consist of the four canonical nucleobases, their chemical diversity is limited, which in turn limits the addressable target spectrum. Introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of the DNA and thereby the target spectrum. Here, we describe a protocol to select nucleobase-modified aptamers by using click chemistry (CuAAC) to introduce the preferred chemical modification. The use of click chemistry to modify the DNA library enables the introduction of a wide range of possible functionalities, which can be customized to the requirements of the target molecule and the desired application. This protocol yields modified DNA aptamers with extended interaction properties that are not accessible with the canonical set of nucleotides. After synthesis of the starting library containing a commercially available, alkyne-modified uridine (5-ethynyl-deoxyuridine (EdU)) instead of thymidine, the library is functionalized with the modification of choice by CuAAC. The thus-modified DNA is incubated with the target molecule and the best binding sequences are recovered. The chemical modification is removed during the amplification process. Therefore, this protocol is compatible with conventional amplification procedures and avoids enzymatic incompatibility problems associated with more extensive nucleobase modifications. After single-strand generation, the modification is reintroduced into the enriched library, which can then be subjected to the subsequent selection cycle. The duration of each selection cycle as outlined in the protocol is ∼1 d.
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15
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Malekzad H, Jouyban A, Hasanzadeh M, Shadjou N, de la Guardia M. Ensuring food safety using aptamer based assays: Electroanalytical approach. Trends Analyt Chem 2017; 94:77-94. [PMID: 32287541 PMCID: PMC7112916 DOI: 10.1016/j.trac.2017.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aptamers, are being increasingly employed as favorable receptors for constructing highly sensitive biosensors, for their remarkable affinities towards certain targets including a wide scope of biological or chemical substances, and their superiority over other biologic receptors. The selectivity and affinity of the aptamers have been integrated with the wise design of the assay, applying suitable modifications, such as nanomaterials on the electrode surface, employing oligonucleotide-specific amplification strategies or, their combinations. After successful performance of the electrochemical aptasensors for biomedical applications, the food sector with its direct implication for human health, which demands rapid and sensitive and economic analytical solutions for determination of health threatening contaminants in all stages of production process, is the next field of research for developing efficient electrochemical aptasensors. The aim of this review is to categorize and introduce food hazards and summarize the recent electrochemical aptasensors that have been developed to address these contaminants.
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Affiliation(s)
- Hedieh Malekzad
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Kimia Idea Pardaz Azarbayjan (KIPA) Science Based Company, Tabriz University of Medical Sciences, Tabriz 51664, Iran
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasrin Shadjou
- Department of Nanochemistry, Nano Technology Research Center, Urmia University, Urmia, Iran
- Department of Nanochemistry, Faculty of Science, Urmia University, Urmia, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, Burjassot 46100, Valencia, Spain
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16
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Skouridou V, Schubert T, Bashammakh AS, El-Shahawi MS, Alyoubi AO, O'Sullivan CK. Aptatope mapping of the binding site of a progesterone aptamer on the steroid ring structure. Anal Biochem 2017; 531:8-11. [PMID: 28499498 DOI: 10.1016/j.ab.2017.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/19/2023]
Abstract
In this work we report the mapping of the binding site of the only progesterone aptamer published to date, in an approach referred to as aptatope mapping. By linking the binding data obtained from microscale thermophoresis analysis to the structural differences on the ring structure of a range of steroids, we elucidated the moieties involved in aptamer-progesterone binding. This approach can be further exploited for the characterization of aptamer specificity and ultimately facilitate the development of aptamer-based assays depending on the desired specificity.
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Affiliation(s)
- Vasso Skouridou
- Nanobiotechnology & Bioanalysis Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, Tarragona 43007, Spain.
| | | | - Abdulaziz S Bashammakh
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mohammad S El-Shahawi
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Abdulrahman O Alyoubi
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Ciara K O'Sullivan
- Nanobiotechnology & Bioanalysis Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, Tarragona 43007, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain.
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17
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Qin S, Chen N, Yang X, Wang Q, Wang K, Huang J, Liu J, Zhou M. Development of Dual-Aptamers for Constructing Sandwich-Type Pancreatic Polypeptide Assay. ACS Sens 2017; 2:308-315. [PMID: 28723135 DOI: 10.1021/acssensors.6b00836] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pancreatic polypeptide (PP) is a specific biomarker of nonfunctional pancreatic neuroendocrine tumors (NF-pNETs). Clinical significance of PP inspires researchers to make great efforts in developing sensitive and specific sensors. However, there is no existing biosensor for detecting PP that combines facility and functionality. Addressing this challenge, a pair of aptamers which could be used to develop a sandwich assay for PP is reported. First, several high affinity aptamers are screened through graphene oxide-based SELEX, and appropriate dual-aptamers which could bind to different epitopes of PP are identified through fluorescence assays. Then the feasibility of the dual-aptamers for constructing the sandwich assay is validated via dynamic light scattering. This sandwich assay shows considerable sensitivity and specificity. The above results imply that the dual-aptamers have the potential toward developing novel sensors for PP in clinical samples.
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Affiliation(s)
- Shiya Qin
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Nandi Chen
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Xiaohai Yang
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Qing Wang
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Jianbo Liu
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Maogui Zhou
- State Key Laboratory
of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
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18
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Entzian C, Schubert T. Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis. J Vis Exp 2017. [PMID: 28117825 DOI: 10.3791/55070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Characterization of molecular interactions in terms of basic binding parameters such as binding affinity, stoichiometry, and thermodynamics is an essential step in basic and applied science. MicroScale Thermophoresis (MST) is a sensitive biophysical method to obtain this important information. Relying on a physical effect called thermophoresis, which describes the movement of molecules through temperature gradients, this technology allows for the fast and precise determination of binding parameters in solution and allows the free choice of buffer conditions (from buffer to lysates/sera). MST uses the fact that an unbound molecule displays a different thermophoretic movement than a molecule that is in complex with a binding partner. The thermophoretic movement is altered in the moment of molecular interaction due to changes in size, charge, and hydration shell. By comparing the movement profiles of different molecular ratios of the two binding partners, quantitative information such as binding affinity (pM to mM) can be determined. Even challenging interactions between molecules of small sizes, such as aptamers and small compounds, can be studied by MST. Using the well-studied model interaction between the DH25.42 DNA aptamer and ATP, this manuscript provides a protocol to characterize aptamer-small molecule interactions. This study demonstrates that MST is highly sensitive and permits the mapping of the binding site of the 7.9 kDa DNA aptamer to the adenine of ATP.
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Ultrasensitive and rapid detection of β-conglutin combining aptamers and isothermal recombinase polymerase amplification. Anal Bioanal Chem 2016; 409:143-149. [PMID: 27766362 DOI: 10.1007/s00216-016-9973-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/14/2016] [Accepted: 09/23/2016] [Indexed: 02/07/2023]
Abstract
Lupin is increasingly being used in a variety of food products due to its nutritional, functional and nutraceutical properties. However, several examples of severe and even fatal food-associated anaphylaxis due to lupin inhalation or ingestion have been reported, resulting in the lupin subunit β-conglutin, being defined as the Lup an 1 allergen by the International Union of Immunological Societies (IUIS) in 2008. Here, we report an innovative method termed aptamer-recombinase polymerase amplification (Apta-RPA) exploiting the affinity and specificity of a DNA aptamer selected against the anaphylactic β-conglutin allergen termed β-conglutin binding aptamer II (β-CBA II), facilitating ultrasensitive detection via isothermal amplification. Combining magnetic beads as the solid phase with Apta-RPA detection, the total assay time was reduced from 210 min to just 25 min, with a limit of detection of 3.5 × 10-11 M, demonstrating a rapid and ultrasensitive generic methodology that can be used with any aptamer. Future work will focus on further simplification of the assay to a lateral flow format. Graphical Abstract Schematic representation of the rapid and novel bead-based Apta-RPA assay.
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Jauset-Rubio M, Svobodová M, Mairal T, McNeil C, Keegan N, El-Shahawi MS, Bashammakh AS, Alyoubi AO, O'Sullivan CK. Aptamer Lateral Flow Assays for Ultrasensitive Detection of β-Conglutin Combining Recombinase Polymerase Amplification and Tailed Primers. Anal Chem 2016; 88:10701-10709. [PMID: 27753473 DOI: 10.1021/acs.analchem.6b03256] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this work, different methodologies were evaluated in search of robust, simple, rapid, ultrasensitive, and user-friendly lateral flow aptamer assays. In one approach, we developed a competitive based lateral flow aptamer assay, in which β-conglutin immobilized on the test line of a nitrocellulose membrane and β-conglutin in the test sample compete for binding to AuNP labeled aptamer. The control line exploits an immobilized DNA probe complementary to the labeled aptamer, forcing displacement of the aptamer from the β-conglutin-aptamer complex. In a second approach, the competition for aptamer binding takes place off-strip, and following competition, aptamer bound to the immobilized β-conglutin is eluted and used as a template for isothermal recombinase polymerase amplification, exploiting tailed primers, resulting in an amplicon of a duplex flanked by single stranded DNA tails. The amplicon is rapidly and quantitatively detected using a nucleic acid lateral flow with an immobilized capture probe and a gold nanoparticle labeled reporter probe. The competitive lateral flow is completed in just 5 min, achieving a detection limit of 55 pM (1.1 fmol), and the combined competitive-amplification lateral flow requires just 30 min, with a detection limit of 9 fM (0.17 amol).
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Affiliation(s)
- Miriam Jauset-Rubio
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira I Virgili , 43007 Tarragona, Spain
| | - Markéta Svobodová
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira I Virgili , 43007 Tarragona, Spain
| | - Teresa Mairal
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira I Virgili , 43007 Tarragona, Spain
| | - Calum McNeil
- Institute of Cellular Medicine, Diagnostic and Therapeutic Technologies Group, Newcastle University , Newcastle upon Tyne, NE2 4HH, U.K
| | - Neil Keegan
- Institute of Cellular Medicine, Diagnostic and Therapeutic Technologies Group, Newcastle University , Newcastle upon Tyne, NE2 4HH, U.K
| | - Mohammad S El-Shahawi
- Department of Chemistry, Faculty of Science, King Abdulaziz University , P.O. Box 80203, Jeddah 21589, Kingdom of Saudi Arabia
| | - Abdulaziz S Bashammakh
- Department of Chemistry, Faculty of Science, King Abdulaziz University , P.O. Box 80203, Jeddah 21589, Kingdom of Saudi Arabia
| | - Abdulrahman O Alyoubi
- Department of Chemistry, Faculty of Science, King Abdulaziz University , P.O. Box 80203, Jeddah 21589, Kingdom of Saudi Arabia
| | - Ciara K O'Sullivan
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira I Virgili , 43007 Tarragona, Spain.,Institució Catalana de Recerca I Estudis Avancats , Passeig Lluís Companys 23, 08010 Barcelona, Spain
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21
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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