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Armero L, Plou J, Valera PS, Serna S, García I, Liz-Marzán LM. Multiplex Determination of Glycan Profiles on Urinary Prostate-Specific Antigen by Quartz-Crystal Microbalance Combined with Surface-Enhanced Raman Scattering. ACS Sens 2024. [PMID: 39213515 DOI: 10.1021/acssensors.4c01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Prostate cancer remains a major health concern, with prostate-specific antigen (PSA) being a key biomarker for its detection and monitoring. However, PSA levels often fall into a "gray zone", where PSA levels are not clearly indicative of cancer, thus complicating early diagnosis and treatment decisions. Glycosylation profiles, which often differ between healthy and diseased cells, have emerged as potential biomarkers to enhance the specificity and sensitivity of cancer diagnosis in these ambiguous cases. We propose the integration of two complementary techniques, namely quartz-crystal microbalance with dissipation (QCM-D) and surface-enhanced Raman scattering (SERS) to study PSA glycan profiles. QCM-D offers real-time operation, PSA mass quantification, and label-free detection with high sensitivity, as well as enhanced specificity and reduced cross-reactivity when using nucleic acid aptamers as capture ligands. Complementary SERS sensing enables the determination of the glycosylation pattern on PSA, at low concentrations and without the drawbacks of photobleaching, thereby facilitating multiplexed glycosylation pattern analysis. This integrated setup could retrieve a data set comprising analyte concentrations and associated glycan profiles in relevant biological samples, which may eventually improve early disease detection and monitoring. Prostate-specific antigen (PSA), a glycoprotein secreted by prostate epithelial cells, serves as our proof-of-concept analyte. Our platform allows multiplex targeting of PSA multiplex glycosylation profiles of PSA at "gray zone" concentrations for prostate cancer diagnosis. We additionally show the use of SERS for glycan analysis in PSA secreted from prostate cancer cell lines after androgen-based treatment. Differences in PSA glycan profiles from resistant cell lines after androgen-based treatment may eventually improve cancer treatment.
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Affiliation(s)
- Laura Armero
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Department of Applied Chemistry, University of the Basque Country, Donostia-San Sebastián 20018, Spain
| | - Javier Plou
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- CIC nanoGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20018, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián 20014, Spain
| | - Pablo S Valera
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Department of Applied Chemistry, University of the Basque Country, Donostia-San Sebastián 20018, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián 20014, Spain
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Spain
| | - Sonia Serna
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
| | - Isabel García
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián 20014, Spain
| | - Luis M Liz-Marzán
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Donostia-San Sebastián 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48009, Spain
- Cinbio, Universidade de Vigo, Vigo 36310, Spain
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2
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Gao L, Li H, Dong X, Li W, Deng H. High-sensitivity QCM humidity sensor based on chitosan/carboxymethylated multiwalled carbon nanotubes composite for non-contact respiratory monitoring. Int J Biol Macromol 2024; 279:135156. [PMID: 39214201 DOI: 10.1016/j.ijbiomac.2024.135156] [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: 04/02/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Respiratory humidity is an important indicator that can reflect respiratory disorders and is easily accessible in daily life, thus attracting attention in non-contact home respiratory monitoring systems. In this work, a high-sensitivity quartz crystal microbalance (QCM) humidity sensor based on a chitosan/carboxymethylated multiwalled carbon nanotubes composite coating is developed with a response time of 36 s and a recovery time of 38 s. The humidity variations from 11 to 97 % can be detected while the wet hysteresis is 0.95 % RH. The sensor also exhibits good repeatability and stability. The physicochemical characterizations of the materials reveal the mechanism of the rapid humidity response, i.e., compared to the physically blended CS with MWCNT, the crosslinking CS-MWCNT formed the new intercalation by stronger hydrogen and amide bonding, which leads to the homogeneous coverage of CS on MWCNT, exposing more active sites and facilitating the binding rate of water molecules. Combined with respiration monitoring, the sensor is able to accurately monitor human respiration rate and depth in real time, effectively predicting and differentiating between different types of obstructive sleep apnea syndromes, providing a fast and reliable solution for daily health monitoring.
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Affiliation(s)
- Lingfei Gao
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China
| | - Hao Li
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China
| | - Xiangyang Dong
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China
| | - Wei Li
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China.
| | - Hongbing Deng
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China.
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3
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Domsicova M, Korcekova J, Poturnayova A, Breier A. New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers. Int J Mol Sci 2024; 25:6833. [PMID: 38999943 PMCID: PMC11240909 DOI: 10.3390/ijms25136833] [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: 05/30/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches.
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Affiliation(s)
- Michaela Domsicova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Jana Korcekova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Alexandra Poturnayova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Albert Breier
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 81237 Bratislava, Slovakia
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4
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Brosel-Oliu S, Rius G, Aviñó A, Nakatsuka N, Illa X, Del Corro E, Delgà-Fernández M, Masvidal-Codina E, Rodríguez N, Merino JP, Criado A, Prato M, Tkatchenko R, Eritja R, Godignon P, Garrido JA, Villa R, Guimerà A, Prats-Alfonso E. Single-Step Functionalization Strategy of Graphene Microtransistor Array with Chemically Modified Aptamers for Biosensing Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308857. [PMID: 38072781 DOI: 10.1002/smll.202308857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Indexed: 05/03/2024]
Abstract
Graphene solution-gated field-effect transistors (gSGFETs) offer high potential for chemical and biochemical sensing applications. Among the current trends to improve this technology, the functionalization processes are gaining relevance for its crucial impact on biosensing performance. Previous efforts are focused on simplifying the attachment procedure from standard multi-step to single-step strategies, but they still suffer from overreaction, and impurity issues and are limited to a particular ligand. Herein, a novel strategy for single-step immobilization of chemically modified aptamers with fluorenylmethyl and acridine moieties, based on a straightforward synthetic route to overcome the aforementioned limitations is presented. This approach is benchmarked versus a standard multi-step strategy using thrombin as detection model. In order to assess the reliability of the functionalization strategies 48-gSGFETs arrays are employed to acquire large datasets with multiple replicas. Graphene surface characterization demonstrates robust and higher efficiency in the chemical coupling of the aptamers with the single-step strategy, while the electrical response evaluation validates the sensing capability, allowing to implement different alternatives for data analysis and reduce the sensing variability. In this work, a new tool capable of overcome the functionalization challenges of graphene surfaces is provided, paving the way toward the standardization of gSGFETs for biosensing purposes.
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Affiliation(s)
- Sergi Brosel-Oliu
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Gemma Rius
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona, 08034, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, 8092, Switzerland
| | - Xavi Illa
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Elena Del Corro
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Marta Delgà-Fernández
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Eduard Masvidal-Codina
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Natalia Rodríguez
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Juan Pedro Merino
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro Criado
- CICA-Centro Interdisciplinar de Química e Bioloxía, Rúa as Carballeiras, Universidade da Coruña, A Coruña, 15071, Spain
| | - Maurizio Prato
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, Trieste, 3412 7, Italy
| | - Raphaela Tkatchenko
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Ramón Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona, 08034, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Philippe Godignon
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - José Antonio Garrido
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
| | - Rosa Villa
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Anton Guimerà
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Elisabet Prats-Alfonso
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, 28029, Spain
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5
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Stuber A, Douaki A, Hengsteler J, Buckingham D, Momotenko D, Garoli D, Nakatsuka N. Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores. ACS NANO 2023; 17:19168-19179. [PMID: 37721359 PMCID: PMC10569099 DOI: 10.1021/acsnano.3c05377] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Ali Douaki
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Denis Buckingham
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Dmitry Momotenko
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, Oldenburg D-26129, Germany
| | - Denis Garoli
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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6
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Jakab K, Melios N, Tsekenis G, Shaban A, Horváth V, Keresztes Z. Comparative Analysis of pH and Target-Induced Conformational Changes of an Oxytetracycline Aptamer in Solution Phase and Surface-Immobilized Form. Biomolecules 2023; 13:1363. [PMID: 37759762 PMCID: PMC10526194 DOI: 10.3390/biom13091363] [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: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite the impact of these conformational rearrangements on sensor performance, the influence of the environment on the structural conformations of aptamers has rarely been investigated, so the link between parameters directly influencing aptamer folding and the ability of the aptamer to bind to the target analyte remains elusive. Herein, the effect a number of variables have on an aptamer's 3D structure was examined, including the pH of the buffering medium, as well as the anchoring of the aptamer on a solid support, with the use of two label-free techniques. Circular dichroism spectroscopy was utilized to study the conformation of an aptamer in solution along with any changes induced to it by the environment (analyte binding, pH, composition and ionic strength of the buffer solution), while quartz crystal microbalance with dissipation monitoring was employed to investigate the surface-bound aptamer's behavior and performance. Analysis was performed on an aptamer against oxytetracycline, serving as a model system, representative of aptamers selected against small molecule analytes. The obtained results highlight the influence of the environment on the folding and thus analyte-binding capacity of an aptamer and emphasize the need to deploy appropriate surface functionalization protocols in sensor development as a means to minimize the steric obstructions and undesirable interactions of an aptamer with a surface onto which it is tethered.
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Affiliation(s)
- Kristóf Jakab
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary;
| | - Nikitas Melios
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece; (N.M.); (G.T.)
| | - George Tsekenis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece; (N.M.); (G.T.)
| | - Abdul Shaban
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
| | - Viola Horváth
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary;
- ELKH-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Zsófia Keresztes
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
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7
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Aptamer-functionalized capacitive biosensors. Biosens Bioelectron 2023; 224:115014. [PMID: 36628826 DOI: 10.1016/j.bios.2022.115014] [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: 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.
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8
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Dutta S, Gagliardi M, Bellucci L, Agostini M, Corni S, Cecchini M, Brancolini G. Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study. Front Mol Biosci 2022; 9:1006525. [DOI: 10.3389/fmolb.2022.1006525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.
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9
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Li H, Long M, Su H, Tan L, Shi X, Du Y, Luo Y, Deng H. Carboxymethyl chitosan assembled piezoelectric biosensor for rapid and label-free quantification of immunoglobulin Y. Carbohydr Polym 2022; 290:119482. [DOI: 10.1016/j.carbpol.2022.119482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022]
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10
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Sinitsyna VV, Vetcher AA. Nucleic Acid Aptamers in Nanotechnology. Biomedicines 2022; 10:1079. [PMID: 35625815 PMCID: PMC9139068 DOI: 10.3390/biomedicines10051079] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 12/10/2022] Open
Abstract
Nucleic Acid (NA) aptamers are oligonucleotides. They are unique due to their secondary and tertiary structure; namely, the secondary structure defines the tertiary one by means of affinity and specificity. Our review is devoted only to DNA and RNA aptamers, since the majority of achievements in this direction were obtained with their application. NA aptamers can be used as macromolecular devices and consist of short single-stranded molecules, which adopt unique three-dimensional structures due to the interaction of complementary parts of the chain and stacking interactions. The review is devoted to the recent nanotechnological advances in NA aptamers application.
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Affiliation(s)
- Valentina V. Sinitsyna
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia
- Shirshov Institute of Oceanology, Russian Academy of Sciences 36, Nahimovskiy Prospect, Moscow 117997, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin 5, Yasnogorskaya St., Moscow 117588, Russia
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11
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Evaluation of the interactions between oligonucleotides and small molecules by partial filling-nonequilibrium affinity capillary electrophoresis. ANAL SCI 2022; 38:851-859. [PMID: 35314967 DOI: 10.1007/s44211-022-00101-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/01/2022] [Indexed: 11/01/2022]
Abstract
Recently, high-throughput analysis with minimal reagent consumption has been desired to assess interactions between drug candidates and disease-related oligonucleotides. To realize an ideal assay for drug screening, a rapid assay based on affinity capillary electrophoresis was generated to reduce the consumption of samples/reagents by a partial-filling technique under nonequilibrium conditions. In the proposed method, the first sample, oligonucleotide as a ligand, and second sample zones were injected into a capillary with spacers of background solution between the samples and oligonucleotide zones. After applying voltages, only the second sample zone passed through the partially filled oligonucleotide zone, resulting in variations in the peak parameters owing to this interaction. The electropherograms obtained were analyzed using equilibrium, reaction kinetics, and moment theories. In the interaction analyses between small molecules and DNA aptamers, only the small molecules binding to the aptamer showed significant changes in their peak heights and shapes. The estimated kinetic parameters were in good agreement with the reported values, indicating the applicability of the proposed method for drug screening. When interactions between drug candidates and disease-related RNAs were analyzed, one of the candidates showed remarkable variation in the peak parameters upon the addition of potassium ions. Consequently, the proposed method could be one of the ideal assays for drug screening.
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12
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Pons M, Perenon M, Bonnet H, Gillon E, Vallée C, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude. Analyst 2022; 147:4197-4205. [DOI: 10.1039/d2an00824f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The spacer length and immobilization mode impact the Surface plasmon resonance (SPR) signal and affinity measured for small target/aptamer recognition. The signal could be positive, negative or null explained by refractive index increment deviation.
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Affiliation(s)
- Marina Pons
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Marine Perenon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Hugues Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Emilie Gillon
- Univ. Grenoble Alpes, CERMAV-CNRS, 601 rue de la chimie, F-38610 Gières, France
| | - Celio Vallée
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Nicolas Spinelli
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
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13
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Hamming PH, Huskens J. Streptavidin Coverage on Biotinylated Surfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:58114-58123. [PMID: 34813287 PMCID: PMC8662640 DOI: 10.1021/acsami.1c16446] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Biosensors and other biological platform technologies require the functionalization of their surface with receptors to enhance affinity and selectivity. Control over the functionalization density is required to tune the platform's properties. Streptavidin (SAv) monolayers are widely used to immobilize biotinylated proteins, receptors, and DNA. The SAv density on a surface can be varied easily, but the predictability is dependent on the method by which the SAv is immobilized. In this study we show a method to quantitatively predict the SAv coverage on biotinylated surfaces. The method is validated by measuring the SAv coverage on supported lipid bilayers with a range of biotin contents and two different main phase lipids and by using quartz crystal microbalance and localized surface plasmon resonance. We explore a predictive model of the biotin-dependent SAv coverage without any fit parameters. Model and data allow to predict the SAv coverage based on the biotin coverage, in both the low- and high-density regimes. This is of special importance in applications with multivalent binding where control over surface receptor density is required, but a direct measurement is not possible.
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14
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Mehdipour G, Shabani Shayeh J, Omidi M, Pour Madadi M, Yazdian F, Tayebi L. An electrochemical aptasensor for detection of prostate-specific antigen using reduced graphene gold nanocomposite and Cu/carbon quantum dots. Biotechnol Appl Biochem 2021; 69:2102-2111. [PMID: 34632622 DOI: 10.1002/bab.2271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023]
Abstract
We report a label-free electrochemical aptamer-based biosensor for the detection of human prostate-specific antigen (PSA). The thiolate DNA aptamer against PSA was conjugated to the reduced graphene oxide/Au (RGO-Au) nanocomposite through the self-assembly of Au-S groups. Owing to the large volume to surface ratio, the RGO-Au nanocomposite provides a large surface for aptamer loading. The RGO-Au/aptamer was combined with a Nafion polymer and immobilized on a glassy carbon electrode. The interaction of aptamer with PSA was studied by cyclic voltammetry, square wave voltammetry, and electrochemical impedance spectroscopy. The detection of limit for prepared electrode was obtained about 50 pg/mL at the potential of 0.4 V in potassium hexacyanoferrate [K4 Fe(CN)6 ] medium. To decrease the limit of detection (LOD) and applied potential of the prepared nanoprobe Cu/carbon quantum dots (CuCQD) is introduced as a new redox. The results show that this new electrochemical medium provides better conditions for the detection of PSA. LOD of a nanoprobe in CuCQD media was obtained as 40 pg/mL at the potential of -0.2 V. Under optimal conditions, the aptasensor exhibits a linear response to PSA with a LOD as small as 3 pg/mL. The present aptasensor is highly selective and sensitive and shows satisfactory stability and repeatability.
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Affiliation(s)
- Golnaz Mehdipour
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Meysam Omidi
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, Wisconsin, USA
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15
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Nakatsuka N, Faillétaz A, Eggemann D, Forró C, Vörös J, Momotenko D. Aptamer Conformational Change Enables Serotonin Biosensing with Nanopipettes. Anal Chem 2021; 93:4033-4041. [PMID: 33596063 DOI: 10.1021/acs.analchem.0c05038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report artificial nanopores in the form of quartz nanopipettes with ca. 10 nm orifices functionalized with molecular recognition elements termed aptamers that reversibly recognize serotonin with high specificity and selectivity. Nanoscale confinement of ion fluxes, analyte-specific aptamer conformational changes, and related surface charge variations enable serotonin sensing. We demonstrate detection of physiologically relevant serotonin amounts in complex environments such as neurobasal media, in which neurons are cultured in vitro. In addition to sensing in physiologically relevant matrices with high sensitivity (picomolar detection limits), we interrogate the detection mechanism via complementary techniques such as quartz crystal microbalance with dissipation monitoring and electrochemical impedance spectroscopy. Moreover, we provide a novel theoretical model for structure-switching aptamer-modified nanopipette systems that supports experimental findings. Validation of specific and selective small-molecule detection, in parallel with mechanistic investigations, demonstrates the potential of conformationally changing aptamer-modified nanopipettes as rapid, label-free, and translatable nanotools for diverse biological systems.
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Affiliation(s)
- Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Alix Faillétaz
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Dominic Eggemann
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Csaba Forró
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
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16
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Bonnet H, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Negative SPR Signals during Low Molecular Weight Analyte Recognition. Anal Chem 2021; 93:4134-4140. [PMID: 33577288 DOI: 10.1021/acs.analchem.1c00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface plasmon resonance (SPR) is a powerful technique for studying biomolecular interactions mainly due to its sensitivity and real-time and label free advantages. While SPR signals are usually positive, only a few studies have reported sensorgrams with negative signals. The aim of the present work is to investigate and to explain the observation of negative SPR signals with the hypothesis that it reflects major changes in ligand conformation resulting from target binding. We demonstrated that these negative unconventional signals were due to the negative complex (ligand/analyte) refractive index increment (RII) deviation from the sum of the RII of the individual entities which counterbalanced the theoretical increase of the signal triggered by the target recognition and the ligand folding. We also found that the conformation change of biomolecules can induce a negative or a positive complex RII deviation depending on its sequence and immobilization mode.
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Affiliation(s)
- H Bonnet
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - L Coche-Guérente
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - E Defrancq
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - N Spinelli
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - A Van der Heyden
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - J Dejeu
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
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17
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Template Stripping Method-Based Au Nanoarray for Surface-Enhanced Raman Scattering Detection of Antiepileptic Drug. MICROMACHINES 2020; 11:mi11100936. [PMID: 33066672 PMCID: PMC7602448 DOI: 10.3390/mi11100936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/03/2022]
Abstract
Surface-enhanced Raman scattering (SERS) is a potential candidate for highly sensitive detection of target molecules. A SERS active substrate with a noble metal nanostructure is required for this. However, a SERS active substrate requires complicated fabrication procedures. This in turn makes it difficult to fabricate highly sensitive SERS active substrates with high reproducibility. To overcome this difficulty, a plasmonic crystal (PC) with periodic noble metal nanostructures was fabricated via the template-stripping method using a polymer-based template. Using SERS active substrates, SERS was successfully achieved using the PC by detecting low concentrations of phenobarbital which is an antiepileptic drug using a commercially available portable Raman module. The PC can be fabricated by demolding the deposited gold layer from a polymer-based template. This method is rapid, economic, and has high reproducibility. SERS can be achieved easily using this PC for a wide variety of applications such as medical, pharmaceutical, and environmental protection.
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18
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Vignon A, Flaget A, Michelas M, Djeghdir M, Defrancq E, Coche-Guerente L, Spinelli N, Van der Heyden A, Dejeu J. Direct Detection of Low-Molecular-Weight Compounds in 2D and 3D Aptasensors by Biolayer Interferometry. ACS Sens 2020; 5:2326-2330. [PMID: 32786219 DOI: 10.1021/acssensors.0c00925] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The direct biolayer interferometry (BLI) measurement of low-molecular-weight (LMW) analytes (<200 Da) still represents a challenge, in particular, when low receptor densities are used. BLI is a powerful optical technique for the label-free, real-time characterization and quantification of biomolecular interactions at interfaces. We demonstrate herein that the quantification of biomolecular recognition is possible by BLI using either 2D-like or 3D platforms for aptamer ligand immobilization. The influence of the aptamer density on the interaction was evaluated and compared for the two sensor architectures. Despite the LMW of the analyte, BLI monitoring led to signals that are exploitable for affinity and kinetic studies, even at low aptamer density. We demonstrate that the immobilization format as well as the aptamer density has a crucial influence on the determination of the recognition parameters.
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Affiliation(s)
- Anthony Vignon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Arthur Flaget
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Maxime Michelas
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Mehdi Djeghdir
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Nicolas Spinelli
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
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19
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Milioni D, Mateos-Gil P, Papadakis G, Tsortos A, Sarlidou O, Gizeli E. Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection. Anal Chem 2020; 92:8186-8193. [PMID: 32449355 DOI: 10.1021/acs.analchem.0c00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.
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Affiliation(s)
- Dimitra Milioni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Pablo Mateos-Gil
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Olga Sarlidou
- Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece.,Department of Biology, University of Crete, Heraklion, Crete 71110, Greece
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20
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Electrochemical quartz crystal microbalance with dissipation investigation of fibronectin adsorption dynamics driven by electrical stimulation onto a conducting and partially biodegradable copolymer. Biointerphases 2020; 15:021003. [PMID: 32197572 DOI: 10.1116/1.5144983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Functional surface coatings are a key option for biomedical applications, from polymeric supports for tissue engineering to smart matrices for controlled drug delivery. Therefore, the synthesis of new materials for biological applications and developments is promising. Hence, biocompatible and stimuli-responsive polymers are interesting materials, especially when they present conductive properties. PEDOT-co-PDLLA graft copolymer exhibits physicochemical and mechanical characteristics required for biomedical purposes, associated with electroactive, biocompatible, and partially biodegradable properties. Herein, the study of fibronectin (FN) adsorption onto PEDOT-co-PDLLA carried out by an electrochemical quartz crystal microbalance with dissipation is reported. The amount of FN adsorbed onto PEDOT-co-PDLLA was higher than that adsorbed onto the Au surface, with a significant increase when electrical stimulation was applied (either at +0.5 or -0.125 V). Additionally, FN binds to the copolymer interface in an unfolded conformation, which can promote better NIH-3T3 fibroblast cell adhesion and later cell development.
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21
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Papadakis G, Pantazis AK, Ntogka M, Parasyris K, Theodosi GI, Kaprou G, Gizeli E. 3D-printed Point-of-Care Platform for Genetic Testing of Infectious Diseases Directly in Human Samples Using Acoustic Sensors and a Smartphone. ACS Sens 2019; 4:1329-1336. [PMID: 30964650 DOI: 10.1021/acssensors.9b00264] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The objective of this work is to develop a methodology and associated platform for nucleic acid detection at the point-of-care (POC) that is sensitive, user-friendly, affordable, rapid, and robust. The heart of this system is an acoustic wave sensor, based on a Surface Acoustic Wave (SAW) or Quartz Crystal Microbalance (QCM) device, which is employed for the label-free detection of isothermally amplified target DNA. Nucleic acids amplification and detection is demonstrated inside three crude human samples, i.e., whole blood, saliva, and nasal swab, spiked in with 10-100 Salmonella cells. To qualify for POC applications, a portable platform was developed based on 3D printing, integrating inside a single box: (i) simple fluidics based on plastic tubing and a mini peristaltic pump, (ii) a heating plate combined with disposable reaction tubes for isothermal amplification; (iii) a mini antenna analyzer operated through a tablet; and (iv) an acoustic wave device housing unit. The simplicity of the method combined with smartphone operation and detection, rapid sample-to-answer analysis time (30 min), and high performance (detection limit 4 × 103 CFU/ml) in three of the most important human samples in diagnostics suggest that the methodology could become a tool of choice for nucleic acid detection at the POC. In addition, the low cost of the platform and assay holds promise for its adoption in resource limited areas. The acoustic detection method is shown to give similar results with a standard colorimetric assay carried out in saliva and nasal swab but can also be used to detect nucleic acids inside whole blood, where a colorimetric assay failed to perform.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Alexandros K. Pantazis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Maria Ntogka
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
| | | | - Gesthimani-Ioanna Theodosi
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
| | - Georgia Kaprou
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
- Institute of Nanoscience and Nanotechnology, NCSR-Demokritos, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Attiki, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
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22
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Piezoelectric arsenite aptasensor based on the use of a self-assembled mercaptoethylamine monolayer and gold nanoparticles. Mikrochim Acta 2019; 186:268. [PMID: 30953172 DOI: 10.1007/s00604-019-3373-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
Abstract
The authors describe a piezoelectric aptasensor for arsenite. A self assembeled monolayer (SAM) of mercaptoethylamine was prepared to immobilize arsenite on the surface of a quartz crystal microbalance. Gold nanoparticles were modified with arsenite aptamer to amplify the response frequency of the biosensor. Arsenite first binds to the SAM on the gold surface of the QCM. On addition of gold nanoparticles with aptamer (DNA-AuNp), the SAM-As(III)-aptamer sandwich is formed. This increases the resonance frequency of the sensor and allows trace concentration of arsenite to be determined. The aptasensor can detect arsenite in the 8 to 1000 nmol·L-1 concentration range with a 4.4 nmol·L-1 lower detection limit (at S/N = 3). The sandwich structure improves the specificity of the aptasensor without considering the conformational transition of the aptamer. The strategy described here conceivably has a large potential as it shows that small molecules can be sensed by using aptamers with unknown working mechanism. Graphical abstract Schematic presentation of a piezoelectric biosensor for arsenite detection by using a mercaptoethylamine monolayer and gold nanoparticles with respect to Arsenite first binds to the SAM on the gold surface of the QCM. Next, gold nanoparticles with aptamer (DNA-AuNp) are added to form a SAM-As(III)-aptamer sandwich which affects the resonance frequency.
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23
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Battu S, Itagi M, Manzoor Bhat Z, Khaire S, Kottaichamy AR, Sannegowda LK, Thimmappa R, Thotiyl MO. Metal Coordination Polymer Framework Governed by Heat of Hydration for Noninvasive Differentiation of Alkali Metal Series. Anal Chem 2018; 90:12917-12922. [PMID: 30289243 DOI: 10.1021/acs.analchem.8b03541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We illustrate that the extent of hydration and consequently the heat of hydration of alkali metal ions can be utilized to control their insertion/deinsertion chemistry in a redox active metal coordination polymer framework (CPF) electrode. The formal redox potential of CPF electrode for cation intercalation is inversely correlated to hydrated ionic radii, with clear distinction between the intercalation of ions across alkali metal series. This leads to noninvasive identification and differentiation of cations in the alkali metal series by utilizing a single sensing platform.
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Affiliation(s)
- Shateesh Battu
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008
| | - Mahesh Itagi
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008.,Department of Chemistry , VSK University , Bellary , Karnataka 583104 , India
| | - Zahid Manzoor Bhat
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008
| | - Siddhi Khaire
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008
| | - Alagar Raja Kottaichamy
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008
| | | | - Ravikumar Thimmappa
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008
| | - Musthafa Ottakam Thotiyl
- Department of Chemistry , Indian Institute of Science Education and Research , Dr. Homibhaba Road , Pune , India , 411008
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24
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Jia Y, Li F. Studies of Functional Nucleic Acids Modified Light Addressable Potentiometric Sensors: X-ray Photoelectron Spectroscopy, Biochemical Assay, and Simulation. Anal Chem 2018; 90:5153-5161. [DOI: 10.1021/acs.analchem.7b05261] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yunfang Jia
- College of Electronic Information and Optic Engineering, Nankai University, Weijin Road, Tianjin, Nankai District, 300071, China
| | - Fang Li
- College of Electronic Information and Optic Engineering, Nankai University, Weijin Road, Tianjin, Nankai District, 300071, China
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25
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Gaikwad P, Kadlag K, Nambiar M, Devendrachari MC, Aralekallu S, Kottaichamy AR, Manzoor Bhat Z, Thimmappa R, Shafi SP, Thotiyl MO. Redox Active Binary Logic Gate Circuit for Homeland Security. Anal Chem 2017; 89:7893-7899. [PMID: 28670898 DOI: 10.1021/acs.analchem.7b00823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bipolar junction transistors are at the frontiers of modern electronics owing to their discrete voltage regulated operational levels. Here we report a redox active binary logic gate (RLG) which can store a "0" and "1" with distinct operational levels, albeit without an external voltage stimuli. In the RLG, a shorted configuration of half-cell electrodes provided the logic low level and decoupled configuration relaxed the system to the logic high level due to self-charge injection into the redox active polymeric system. Galvanostatic intermittent titration and electrochemical quartz crystal microbalance studies indicate the kinetics of self-charge injection are quite faster and sustainable in polypyrrole based RLG, recovering more than 70% signal in just 14 s with minor signal reduction at the end of 10000 cycles. These remarkable properties of RLGs are extended to design a security sensor which can detect and count intruders in a locality with decent precision and switching speed.
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Affiliation(s)
- Pramod Gaikwad
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kavita Kadlag
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Manasa Nambiar
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | | | - Shambhulinga Aralekallu
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Alagar Raja Kottaichamy
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Zahid Manzoor Bhat
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ravikumar Thimmappa
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Shahid Pottachola Shafi
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Musthafa Ottakam Thotiyl
- Department of Chemistry and Center for Energy Science, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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26
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Milioni D, Tsortos A, Velez M, Gizeli E. Extracting the Shape and Size of Biomolecules Attached to a Surface as Suspended Discrete Nanoparticles. Anal Chem 2017; 89:4198-4203. [DOI: 10.1021/acs.analchem.7b00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitra Milioni
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Achilleas Tsortos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Madrid, Spain
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department
of Biology, University of Crete, Heraklion 71110, Greece
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Dubacheva GV, Araya-Callis C, Geert Volbeda A, Fairhead M, Codée J, Howarth M, Richter RP. Controlling Multivalent Binding through Surface Chemistry: Model Study on Streptavidin. J Am Chem Soc 2017; 139:4157-4167. [PMID: 28234007 PMCID: PMC5364436 DOI: 10.1021/jacs.7b00540] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Although multivalent binding to surfaces is an important tool in nanotechnology, quantitative information about the residual valency and orientation of surface-bound molecules is missing. To address these questions, we study streptavidin (SAv) binding to commonly used biotinylated surfaces such as supported lipid bilayers (SLBs) and self-assembled monolayers (SAMs). Stability and kinetics of SAv binding are characterized by quartz crystal microbalance with dissipation monitoring, while the residual valency of immobilized SAv is quantified using spectroscopic ellipsometry by monitoring binding of biotinylated probes. Purpose-designed SAv constructs having controlled valencies (mono-, di-, trivalent in terms of biotin-binding sites) are studied to rationalize the results obtained on regular (tetravalent) SAv. We find that divalent interaction of SAv with biotinylated surfaces is a strict requirement for stable immobilization, while monovalent attachment is reversible and, in the case of SLBs, leads to the extraction of biotinylated lipids from the bilayer. The surface density and lateral mobility of biotin, and the SAv surface coverage are all found to influence the average orientation and residual valency of SAv on a biotinylated surface. We demonstrate how the residual valency can be adjusted to one or two biotin binding sites per immobilized SAv by choosing appropriate surface chemistry. The obtained results provide means for the rational design of surface-confined supramolecular architectures involving specific biointeractions at tunable valency. This knowledge can be used for the development of well-defined bioactive coatings, biosensors and biomimetic model systems.
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Affiliation(s)
- Galina V. Dubacheva
- Biosurfaces
Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 Donostia − San Sebastian, Spain
- PPSM
CNRS UMR8531, ENS Cachan, Université
Paris-Saclay, 61 Avenue du Président Wilson, 94235 Cachan, France
| | - Carolina Araya-Callis
- Biosurfaces
Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 Donostia − San Sebastian, Spain
| | - Anne Geert Volbeda
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Michael Fairhead
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jeroen Codée
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Mark Howarth
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ralf P. Richter
- Biosurfaces
Lab, CIC biomaGUNE, Paseo Miramon 182, 20014 Donostia − San Sebastian, Spain
- School
of Biomedical Sciences and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
- Laboratory
of Interdisciplinary Physics, University
Grenoble Alpes − CNRS, 140 Rue de la Physique, 38402 Saint Martin d’Hères, France
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28
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Aralekallu S, Thimmappa R, Gaikwad P, Devendrachari MC, Kottaichamy AR, Shafi SP, Lokesh KS, Sánchez J, Thotiyl MO. Tuning the Interfacial Chemistry of Redox-Active Polymer for Bifunctional Probing. ChemElectroChem 2017. [DOI: 10.1002/celc.201600775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shambhulinga Aralekallu
- Department of Chemistry; Dr. Homibaba Road IISER Pune 411008 India
- Department of Chemistry; VSK University; Bellary, Karnataka- 583104 India
| | | | - Pramod Gaikwad
- Department of Chemistry; Dr. Homibaba Road IISER Pune 411008 India
| | | | | | | | | | - Julio Sánchez
- Departamento de Ciencias del Ambient Universidad de Santiago de Chile; USACH, Casilla 40, Correo 33 Santiago Chile
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29
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Song W, Niu Q, Qiang W, Li H, Xu D. Enzyme-free electrochemical aptasensor by using silver nanoparticles aggregates coupling with carbon nanotube inducing signal amplification through electrodeposition. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.07.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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30
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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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Affiliation(s)
- Achilleas Tsortos
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - George Papadakis
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
| | - Electra Gizeli
- Institute of Molecular Biology & Biotechnology, FO.R.T.H, Vassilika Vouton, 70013, Heraklion, Greece
- Department
of Biology, University of Crete, Vassilika Vouton, 71409, Heraklion, Greece
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32
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Ruscito A, DeRosa MC. Small-Molecule Binding Aptamers: Selection Strategies, Characterization, and Applications. Front Chem 2016; 4:14. [PMID: 27242994 PMCID: PMC4861895 DOI: 10.3389/fchem.2016.00014] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/23/2016] [Indexed: 11/13/2022] Open
Abstract
Aptamers are single-stranded, synthetic oligonucleotides that fold into 3-dimensional shapes capable of binding non-covalently with high affinity and specificity to a target molecule. They are generated via an in vitro process known as the Systematic Evolution of Ligands by EXponential enrichment, from which candidates are screened and characterized, and then used in various applications. These applications range from therapeutic uses to biosensors for target detection. Aptamers for small molecule targets such as toxins, antibiotics, molecular markers, drugs, and heavy metals will be the focus of this review. Their accurate detection is needed for the protection and wellbeing of humans and animals. However, the small molecular weights of these targets, including the drastic size difference between the target and the oligonucleotides, make it challenging to select, characterize, and apply aptamers for their detection. Thus, recent (since 2012) notable advances in small molecule aptamers, which have overcome some of these challenges, are presented here, while defining challenges that still exist are discussed.
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Affiliation(s)
| | - Maria C DeRosa
- Department of Chemistry, Carleton University Ottawa, ON, Canada
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33
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Takahashi S. Development and Biosensor Applications of Novel Functional Electrodes. YAKUGAKU ZASSHI 2016; 136:1585-1590. [DOI: 10.1248/yakushi.16-00194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Aptamers as Synthetic Receptors for Food Quality and Safety Control. BIOSENSORS FOR SUSTAINABLE FOOD - NEW OPPORTUNITIES AND TECHNICAL CHALLENGES 2016. [DOI: 10.1016/bs.coac.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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