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Kumar S, Mohan A, Sharma NR, Kumar A, Girdhar M, Malik T, Verma AK. Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review. ACS OMEGA 2024; 9:26838-26862. [PMID: 38947800 PMCID: PMC11209897 DOI: 10.1021/acsomega.4c02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.
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Affiliation(s)
- Shubham Kumar
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anand Mohan
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Neeta Raj Sharma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anil Kumar
- Gene
Regulation Laboratory, National Institute
of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Madhuri Girdhar
- Division
of Research and Development, Lovely Professional
University, Phagwara 144401, Punjab, India
| | - Tabarak Malik
- Department
of Biomedical Sciences, Institute of Health, Jimma University, MVJ4+R95 Jimma, Ethiopia
| | - Awadhesh Kumar Verma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
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2
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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: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/17/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
The growing use of aptamers as target recognition elements in label-free biosensing necessitates corresponding transducers that can be used in relevant environments. While popular in many fields, capacitive sensors have seen relatively little, but growing use in conjunction with aptamers for sensing diverse targets. Few reports have shown physiologically relevant sensitivity in laboratory conditions and a cohesive picture on how target capture modifies the measured capacitance has been lacking. In this review, we assess the current state of the field in three areas: small molecule, protein, and cell sensing. We critically analyze the proposed hypotheses on how aptamer-target capture modifies the capacitance, as many mechanistic postulations appear to conflict between published works. As the field matures, we encourage future works to investigate individual aptamer-target interactions and to interrogate the physical mechanisms leading to measured changes in capacitance. To this point, we provide recommendations on best practices for developing aptasensors with a particular focus on considerations for biosensing in clinical settings.
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3
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Wang T, Chen L, Chikkanna A, Chen S, Brusius I, Sbuh N, Veedu RN. Development of nucleic acid aptamer-based lateral flow assays: A robust platform for cost-effective point-of-care diagnosis. Theranostics 2021; 11:5174-5196. [PMID: 33859741 PMCID: PMC8039946 DOI: 10.7150/thno.56471] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Lateral flow assay (LFA) has made a paradigm shift in the in vitro diagnosis field due to its rapid turnaround time, ease of operation and exceptional affordability. Currently used LFAs predominantly use antibodies. However, the high inter-batch variations, error margin and storage requirements of the conventional antibody-based LFAs significantly impede its applications. The recent progress in aptamer technology provides an opportunity to combine the potential of aptamer and LFA towards building a promising platform for highly efficient point-of-care device development. Over the past decades, different forms of aptamer-based LFAs have been introduced for broad applications ranging from disease diagnosis, agricultural industry to environmental sciences, especially for the detection of antibody-inaccessible small molecules such as toxins and heavy metals. But commercial aptamer-based LFAs are still not used widely compared with antibodies. In this work, by analysing the key issues of aptamer-based LFA design, including immobilization strategies, signalling methods, and target capturing approaches, we provide a comprehensive overview about aptamer-based LFA design strategies to facilitate researchers to develop optimised aptamer-based LFAs.
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Affiliation(s)
- Tao Wang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth 6009, Australia
| | - Lanmei Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
- Guangdong Key Laboratory for Research and Development of Nature Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang 524023, China
| | - Arpitha Chikkanna
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Isabell Brusius
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Nabayet Sbuh
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth 6009, Australia
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4
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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: 47] [Impact Index Per Article: 15.7] [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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6
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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7
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Hughes ZE, Walsh TR. Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design. ACS Sens 2017; 2:1602-1611. [PMID: 29063764 DOI: 10.1021/acssensors.7b00435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.
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Affiliation(s)
- Zak E. Hughes
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
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8
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Ercan M, Ozalp VC, Tuna BG. Genotyping of single nucleotide polymorphism by probe-gated silica nanoparticles. Anal Biochem 2017; 537:78-83. [DOI: 10.1016/j.ab.2017.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/01/2017] [Accepted: 09/07/2017] [Indexed: 01/12/2023]
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9
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Rivilla I, de Cózar A, Schäfer T, Hernandez FJ, Bittner AM, Eleta-Lopez A, Aboudzadeh A, Santos JI, Miranda JI, Cossío FP. Catalysis of a 1,3-dipolar reaction by distorted DNA incorporating a heterobimetallic platinum(ii) and copper(ii) complex. Chem Sci 2017; 8:7038-7046. [PMID: 29147531 PMCID: PMC5637124 DOI: 10.1039/c7sc02311a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/11/2017] [Indexed: 12/28/2022] Open
Abstract
A novel catalytic system based on covalently modified DNA is described. This catalyst promotes 1,3-dipolar reactions between azomethine ylides and maleimides. The catalytic system is based on the distortion of the double helix of DNA by means of the formation of Pt(ii) adducts with guanine units. This distortion, similar to that generated in the interaction of DNA with platinum chemotherapeutic drugs, generates active sites that can accommodate N-metallated azomethine ylides. The proposed reaction mechanism, based on QM(DFT)/MM calculations, is compatible with thermally allowed concerted (but asynchronous) [π4s + π2s] mechanisms leading to the exclusive formation of racemic endo-cycloadducts.
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Affiliation(s)
- Iván Rivilla
- Department of Organic Chemistry I , Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) , Donostia International Physics Center (DIPC) , Po Manuel Lardizabal 3 , E-20018 Donostia/San Sebastián , Spain .
| | - Abel de Cózar
- Department of Organic Chemistry I , Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) , Donostia International Physics Center (DIPC) , Po Manuel Lardizabal 3 , E-20018 Donostia/San Sebastián , Spain .
- Ikerbasque, Basque Foundation for Science , Ma Díaz de Haro 3 , E-48013 Bilbao , Spain
| | - Thomas Schäfer
- Ikerbasque, Basque Foundation for Science , Ma Díaz de Haro 3 , E-48013 Bilbao , Spain
- NanoBioSeparations Group , POLYMAT University of the Basque Country (UPV/EHU) , Avda. Tolosa 72 , E-20018 Donostia/San Sebastián , Spain
| | - Frank J Hernandez
- NanoBioSeparations Group , POLYMAT University of the Basque Country (UPV/EHU) , Avda. Tolosa 72 , E-20018 Donostia/San Sebastián , Spain
| | - Alexander M Bittner
- NanoBioSeparations Group , POLYMAT University of the Basque Country (UPV/EHU) , Avda. Tolosa 72 , E-20018 Donostia/San Sebastián , Spain
- CIC NanoGUNE , Consolider. Tolosa Hiribidea, 76 , E-200018 Donostia/San Sebastián , Spain
| | - Aitziber Eleta-Lopez
- CIC NanoGUNE , Consolider. Tolosa Hiribidea, 76 , E-200018 Donostia/San Sebastián , Spain
| | - Ali Aboudzadeh
- NanoBioSeparations Group , POLYMAT University of the Basque Country (UPV/EHU) , Avda. Tolosa 72 , E-20018 Donostia/San Sebastián , Spain
| | - José I Santos
- SGIker NMR Facility , Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) , Avda. Tolosa 72 , E-20018 Donostia/San Sebastián , Spain
| | - José I Miranda
- SGIker NMR Facility , Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) , Avda. Tolosa 72 , E-20018 Donostia/San Sebastián , Spain
| | - Fernando P Cossío
- Department of Organic Chemistry I , Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) , Donostia International Physics Center (DIPC) , Po Manuel Lardizabal 3 , E-20018 Donostia/San Sebastián , Spain .
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10
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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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11
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Özalp VC, Çam D, Hernandez FJ, Hernandez LI, Schäfer T, Öktem HA. Small molecule detection by lateral flow strips via aptamer-gated silica nanoprobes. Analyst 2016; 141:2595-9. [PMID: 27041474 DOI: 10.1039/c6an00273k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A fast, sensitive and ratiometric biosensor strategy for small molecule detection was developed through nanopore actuation. The new platform engineers together, a highly selective molecular recognition element, aptamers, and a novel signal amplification mechanism, gated nanopores. As a proof of concept, aptamer gated silica nanoparticles have been successfully used as a sensing platform for the detection of ATP concentrations at a wide linear range from 100 μM up to 2 mM.
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Affiliation(s)
- V Cengiz Özalp
- School of Medicine, Istanbul Kemerburgaz University, Istanbul, 34217, Turkey.
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12
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Kavruk M, Celikbicak O, Ozalp VC, Borsa BA, Hernandez FJ, Bayramoglu G, Salih B, Arica MY. Antibiotic loaded nanocapsules functionalized with aptamer gates for targeted destruction of pathogens. Chem Commun (Camb) 2016; 51:8492-5. [PMID: 25891472 DOI: 10.1039/c5cc01869b] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this study, we designed aptamer-gated nanocapsules for the specific targeting of cargo to bacteria with controlled release of antibiotics based on aptamer-receptor interactions. Aptamer-gates caused a specific decrease in minimum inhibitory concentration (MIC) values of vancomycin for Staphylococcus aureus when mesoporous silica nanoparticles (MSNs) were used for bacteria-targeted delivery.
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Affiliation(s)
- M Kavruk
- Department of Biotechnology, Middle East Technical University, Turkey
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13
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Zhu X, Zhang B, Ye Z, Shi H, Shen Y, Li G. An ATP-responsive smart gate fabricated with a graphene oxide-aptamer-nanochannel architecture. Chem Commun (Camb) 2015; 51:640-3. [PMID: 25406894 DOI: 10.1039/c4cc07990f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Here, we report a graphene oxide-aptamer-nanochannel architecture for the fabrication of a novel stimuli-responsive gate. The gate is switched OFF in the absence of ATP, and is switched ON when ATP is present. The concept we proposed may contribute to a versatile platform for the development of stimuli-responsive gates.
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Affiliation(s)
- Xiaoli Zhu
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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14
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Osypova A, Thakar D, Dejeu J, Bonnet H, Van der Heyden A, Dubacheva GV, Richter RP, Defrancq E, Spinelli N, Coche-Guérente L, Labbé P. Sensor Based on Aptamer Folding to Detect Low-Molecular Weight Analytes. Anal Chem 2015; 87:7566-74. [PMID: 26122480 DOI: 10.1021/acs.analchem.5b01736] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aptamers have emerged as promising biorecognition elements in the development of biosensors. The present work focuses on the application of quartz crystal microbalance with dissipation monitoring (QCM-D) for the enantioselective detection of a low molecular weight target molecule (less than 200 Da) by aptamer-based sensors. While QCM-D is a powerful technique for label-free, real-time characterization and quantification of molecular interactions at interfaces, the detection of small molecules interacting with immobilized receptors still remains a challenge. In the present study, we take advantage of the aptamer conformational changes upon the target binding that induces displacement of water acoustically coupled to the sensing layer. As a consequence, this phenomenon leads to a significant enhancement of the detection signal. The methodology is exemplified with the enantioselective recognition of a low molecular weight model compound, L-tyrosinamide (L-Tym). QCM-D monitoring of L-Tym interaction with the aptamer monolayer leads to an appreciable signal that can be further exploited for analytical purposes or thermodynamics studies. Furthermore, in situ combination of QCM-D with spectroscopic ellipsometry unambiguously demonstrates that the conformational change induces a nanometric decrease of the aptamer monolayer thickness. Since QCM-D is sensitive to the whole mass of the sensing layer including water that is acoustically coupled, a decrease in thickness of the highly hydrated aptamer layer induces a sizable release of water that can be easily detected by QCM-D.
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Affiliation(s)
- Alina Osypova
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Dhruv Thakar
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Jérôme Dejeu
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Hugues Bonnet
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Angéline Van der Heyden
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | | | - Ralf P Richter
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France.,§CIC biomaGUNE, 20009 Donostia-San Sebastian, Spain.,∥Max-Planck-Institute for Intelligent Systems, 70569 Stuttgart, Germany
| | - Eric Defrancq
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Nicolas Spinelli
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Liliane Coche-Guérente
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Pierre Labbé
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
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15
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Schäfer T, Özalp VC. DNA-aptamer gating membranes. Chem Commun (Camb) 2015; 51:5471-4. [PMID: 25633657 PMCID: PMC4840836 DOI: 10.1039/c4cc09660f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/14/2015] [Indexed: 11/21/2022]
Abstract
This report describes a membrane barrier whose permeability is modulated through the recognition of a small-molecule target, adenosine triphosphate (ATP), by a DNA-aptamer. The gating function of the DNA-aptamer in the stimulus-responsive membrane was shown to be specific, concentration dependent, and reversible.
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Affiliation(s)
- Thomas Schäfer
- POLYMAT, University of the Basque Country, Av. Tolosa 72, 20018 Donostia-San Sebastián, Spain.
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16
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Machado I, Özalp VC, Rezabal E, Schäfer T. DNA aptamers are functional molecular recognition sensors in protic ionic liquids. Chemistry 2014; 20:11820-5. [PMID: 25065686 DOI: 10.1002/chem.201403354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 12/14/2022]
Abstract
The function and structural changes of an AMP molecular aptamer beacon and its molecular recognition capacity for its target, adenosine monophosphate (AMP), was systematically explored in solution with a protic ionic liquid, ethylammonium nitrate (EAN). It could be proven that up to 2 M of EAN in TBS buffer, the AMP molecular aptamer beacon was still capable of recognizing AMP while also maintaining its specificity. The specificity was proven by using the guanosine monophosphate (GMP) as target; GMP is structurally similar to AMP but was not recognized by the aptamer. We also found that in highly concentrated EAN solutions the overall amount of double stranded DNA formed, as well as its respective thermal stability, diminished gradually, but surprisingly the hybridization rate (kh ) of single stranded DNA was significantly accelerated in the presence of EAN. The latter may have important implications in DNA technology for the design of biosensing and DNA-based nanodevices in nonconventional solvents, such as ionic liquids.
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Affiliation(s)
- Isabel Machado
- POLYMAT, University of the Basque Country UPV/EHU, Avda. Tolosa, 72, 20018 - Donostia - San Sebastián (Spain)
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17
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Study of the interactions of proteins with a solid surface using complementary acoustic and optical techniques. Biointerphases 2014; 9:029015. [DOI: 10.1116/1.4874736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hernandez FJ, Hernandez LI, Pinto A, Schäfer T, Özalp VC. Targeting cancer cells with controlled release nanocapsules based on a single aptamer. Chem Commun (Camb) 2013; 49:1285-7. [PMID: 23295617 DOI: 10.1039/c2cc37370j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular gates have received considerable attention as drug delivery systems. More recently, aptamer-based gates showed great potential in overcoming major challenges associated with drug delivery by means of nanocapsules. Based on a switchable aptamer nanovalves approach, we herein report the first demonstration of an engineered single molecular gate that directs nanoparticles to cancer cells and subsequently delivers the payload in a controllable fashion.
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Affiliation(s)
- Frank J Hernandez
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
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