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Wenck C, Leopoldt D, Habib M, Hegermann J, Stiesch M, Doll-Nikutta K, Heisterkamp A, Torres-Mapa ML. Colorimetric detection of oral bacteria using functionalized gold nanoparticles as a plasmonic biosensor array. NANOSCALE ADVANCES 2024; 6:1447-1459. [PMID: 38419865 PMCID: PMC10898432 DOI: 10.1039/d3na00477e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Early detection of specific oral bacterial species would enable timely treatment and prevention of certain oral diseases. In this work, we investigated the sensitivity and specificity of functionalized gold nanoparticles for plasmonic sensing of oral bacteria. This approach is based on the aggregation of positively charged gold nanoparticles on the negatively charged bacteria surface and the corresponding localized surface plasmon resonance (LSPR) shift. Gold nanoparticles were synthesized in different sizes, shapes and functionalization. A biosensor array was developed consisting of spherical- and anisotropic-shaped (1-hexadecyl) trimethylammonium bromide (CTAB) and spherical mercaptoethylamine (MEA) gold nanoparticles. It was used to detect four oral bacterial species (Aggregatibacter actinomycetemcomitans, Actinomyces naeslundii, Porphyromonas gingivalis and Streptococcus oralis). The plasmonic response was measured and analysed using RGB and UV-vis absorbance values. Both methods successfully detected the individual bacterial species based on their unique responses to the biosensor array. We present an in-depth study relating the bacteria zeta potential and AuNP aggregation to plasmonic response. The sensitivity depends on multiple parameters, such as bacterial species and concentration as well as gold nanoparticle shape, concentration and functionalization.
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Affiliation(s)
- Christina Wenck
- Institute of Quantum Optics, Leibniz University Hannover Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
| | - Dorthe Leopoldt
- Institute of Quantum Optics, Leibniz University Hannover Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
| | - Mosaieb Habib
- Institute of Inorganic Chemistry, Leibniz University Hannover Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
| | - Jan Hegermann
- Research Core Unit Electron Microscopy, Institute of Functional and Applied Anatomy, Hannover Medical School Germany
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
| | - Katharina Doll-Nikutta
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
| | - Alexander Heisterkamp
- Institute of Quantum Optics, Leibniz University Hannover Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
| | - Maria Leilani Torres-Mapa
- Institute of Quantum Optics, Leibniz University Hannover Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE) Germany
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2
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Confinement of defect-rich bimetallic In 2O 3/CeO 2 nanocrystals in mesoporous nitrogen-doped carbon as a sensitive platform for photoelectrochemical aptasensing of Escherichia coli. Anal Chim Acta 2023; 1248:340893. [PMID: 36813455 DOI: 10.1016/j.aca.2023.340893] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/14/2023] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
The sensitive determination of food-borne pathogens from food products is essential to ensure food safety and to protect people's health. Herein, a novel photoelectrochemical (PEC) aptasensor was manufactured based on defect-rich bimetallic cerium/indium oxide nanocrystals confined in mesoporous nitrogen-doped carbon (denoted as In2O3/CeO2@mNC) for sensitively detecting Escherichia coli (E. coli) from real samples. A new cerium-based polymer-metal-organic framework [polyMOF(Ce)] was synthesized using polyether polymer containing 1,4-benzenedicarboxylic acid unit (L8) as ligand, trimesic acid as co-ligand, and cerium ions as coordination centers. After adsorbing trace indium ions (In3+), the gained polyMOF(Ce)/In3+ complex was calcined at high temperature under nitrogen atmosphere, resulting in the production of a series of defect-rich In2O3/CeO2@mNC hybrids. Benefitting from the advantages of high specific surface area, large pore size, and multiple functionality of polyMOF(Ce), In2O3/CeO2@mNC hybrids showed enhanced visible light absorption ability, separation performance of the photo-generated electrons and holes, promoted electron transfer, as well as the strong bioaffinity toward E. coli-targeted aptamer. Accordingly, the constructed PEC aptasensor illustrated an ultralow detection limit of 1.12 CFU mL-1, remarkably lower than most of the reported E. coli biosensors, along with high stability and selectivity, excellent reproducibility, and expected regeneration ability. The present work provides insight into the construction of a general PEC biosensing strategy based on MOF-based derivatives for the sensitive analysis of food-borne pathogens.
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3
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Kongpreecha P, Phanchai W, Puangmali T, Siri S. Development of sensitive colorimetric aptasensor based on short DNA aptamer and its application to screening for paraquat residues in agricultural soil. Biotechnol Appl Biochem 2022; 70:857-869. [PMID: 36112641 DOI: 10.1002/bab.2405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/04/2022] [Indexed: 11/11/2022]
Abstract
Paraquat is a widely used herbicide for controlling weeds and grasses in agriculture, and its contaminated residues in agricultural areas are of increasing concern. This work reports the development of the sensitive and easy-to-use colorimetric aptasensor for screening paraquat residues in agricultural soil. The short DNA fragments derived from the original aptamer were analyzed for their capability to interact with paraquat by molecular dynamic simulation. The paraquat-aptasensor was developed using the selected DNA fragment and gold nanoparticles. Its limit of detection (LOD) for paraquat is 2.76 nM, which is more sensitive than the aptasensor with long-length aptamer (LOD = 12.98 nM). The developed aptasensor shows the selectivity to paraquat, but not to other tested herbicides; ametryn, atrazine, difenzoquat, 2,4-D-dimethyl ammonium, and glufosinate. The recovery rates of paraquat detection in the spiked soil samples were in a range of 99.5%-105.1%, with relative standard deviation values of <4%. The developed aptasensor was used to screen for paraquat residues in agricultural soils, and three out of 23 soil samples were tested positive for paraquat, which was confirmed by a high-performance liquid chromatography analysis. These results suggested the potential application of the developed aptasensor to detect paraquat residues in agricultural sites.
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Affiliation(s)
- Pakawat Kongpreecha
- School of Biology, Institute of Science Suranaree University of Technology, Ratchasima Nakhon 30000 Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science Khon Kaen University Khon Kaen 40002 Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science Khon Kaen University Khon Kaen 40002 Thailand
| | - Sineenat Siri
- School of Biology, Institute of Science Suranaree University of Technology, Ratchasima Nakhon 30000 Thailand
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4
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Margiana R, Hammid AT, Ahmad I, Alsaikhan F, Turki Jalil A, Tursunbaev F, Umar F, Romero Parra RM, Fakri Mustafa Y. Current Progress in Aptasensor for Ultra-Low Level Monitoring of Parkinson's Disease Biomarkers. Crit Rev Anal Chem 2022; 54:617-632. [PMID: 35754381 DOI: 10.1080/10408347.2022.2091920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In today's world, Parkinson's disease (PD) has been introduced as a long-term degenerative disorder of the central nervous system which mainly affects approximately more than ten million people worldwide. The vast majority of diagnostic methods for PD have operated based on conventional sensing platforms, while the traditional laboratory tests are not efficient for diagnosis of PD in the early stage due to symptoms of this common neurodegenerative syndrome starting slowly. The advent of the aptasensor has revolutionized the early-stage diagnosis of PD by measuring related biomarkers due to the myriad advantages of originating from aptamers which can be able to sensitive and selective capture various types of related biomarkers. The progress of numerous sensing platforms and methodologies in terms of biosensors based on aptamer application for PD diagnosis has revealed promising results. In this review, we present the latest developments in myriad types of aptasensors for the determination of related PD biomarkers. Working strategies, advantages and limitations of these sensing approaches are also mentioned, followed by prospects and challenges.
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Affiliation(s)
- Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Dr. Soetomo General Academic Hospital, Indonesia Surabaya
| | - Ali Thaeer Hammid
- Computer Engineering Techniques Department, Faculty of Information Technology, Imam Ja'afar Al-Sadiq University, Baghdad, Iraq
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, Iraq
| | - Farkhod Tursunbaev
- Independent Researcher, "Medcloud" Educational Centre, Tashkent, Uzbekistan
- Research Scholar, Department of Science and Innovation, Akfa University, Tashkent, Uzbekistan
| | - Fadilah Umar
- Department of Sports Science, Faculty of Sports, Sebelas Maret University, Surakarta, Indonesia
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq
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5
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Araujo-Rocha M, Piro B, Noël V, Barbault F. Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement. J Phys Chem B 2021; 125:9499-9506. [PMID: 34403245 DOI: 10.1021/acs.jpcb.1c05341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aptamers are a class of bioreceptors intensively used in current analytical tools dedicated to molecular diagnostics due to their ability to perform large structural reorganization upon target binding. However, there is a lack of methodologies allowing us to rationalize their structure in order to improve the transduction efficiency in aptamer sensors. We choose here, as a model system, a three-strand DNA structure as the probe, composed of two DNA strands anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to ampicillin (AMP). The DNA structure has been designed to show strong structural change upon AMP binding to its aptamer. Using a set of computational techniques including molecular dynamics simulations, we deeply investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses of ion distributions along the trajectories unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates the ability of computational investigations for the first time to drive, in silico, the design of aptasensors.
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Affiliation(s)
| | - Benoît Piro
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Vincent Noël
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
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Srikulwong U, Phanchai W, Srepusharawoot P, Sakonsinsiri C, Puangmali T. Computational Insights into Molecular Adsorption Characteristics of Methylated DNA on Graphene Oxide for Multicancer Early Detection. J Phys Chem B 2021; 125:6697-6708. [PMID: 34110832 DOI: 10.1021/acs.jpcb.1c02808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation is an epigenetic modification involving the transfer of a methyl group to cytosine residues of a DNA molecule. Altered DNA methylation of certain genes is associated with several diseases including cancer. Nanomaterials, such as graphene oxide (GO), offer great potential as sensing elements for methylated DNA (mDNA) detection due to their distinct properties. Understanding molecular interactions between mDNA and GO can make provision for developing a universal cancer screening test. Molecular dynamics (MD) simulation and density functional theory (DFT) calculation have been employed for investigating their detailed macro- and microscale interactions. Based upon the MD simulation, different adsorption levels of methylated and unmethylated DNAs on GO were represented by a contacting surface area (CSA), which depends on surrounding conditions (in water or a MgCl2 solution). In water, the CSAs of the methylated and unmethylated single-stranded DNA (ssDNA) were ≈13 and ≈5 nm2, respectively, representing more preferable adsorption on GO for the methylated ssDNA. In the presence of divalent ions (Mg2+), the CSAs of both methylated and unmethylated DNA molecules were ≈8 nm2, suggesting that there was no significant difference in adsorption in a saline solution. To reveal the electrical property of GO covered by either methylated or unmethylated DNA, its electronic structure was investigated by the DFT calculation. The energy gaps of pristine graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and 12.9 meV, respectively, while cytosine adsorption resulted in lower energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated DNA-covered GO with that covered with unmethylated DNA, remarkable differences in electrical conductivity, which were caused by the electronic structure of GO, were observed. These findings will provide a new route for an efficient detection method of DNA methylation, which can further be used to develop a universal cancer test.
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Affiliation(s)
- Unnop Srikulwong
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Pornjuk Srepusharawoot
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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7
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Pla L, Sancenón F, Martínez-Bisbal MC, Bañuls C, Estañ N, Botello-Marabotto M, Aznar E, Sáez G, Santiago-Felipe S, Martínez-Máñez R. A new 8-oxo-7,8-2'deoxyguanosine nanoporous anodic alumina aptasensor for colorectal cancer diagnosis in blood and urine. NANOSCALE 2021; 13:8648-8657. [PMID: 33942038 DOI: 10.1039/d0nr07948k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many important human diseases, and especially cancer, have been related to the overproduction of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG). This molecule is a product of oxidative stress processes over nucleophilic bases in DNA. In this work, an aptasensor for the rapid, selective and accurate detection of this oncomarker is presented. The aptasensor consists of a nanoporous anodic alumina material loaded with a dye and is functionalized with an aptamer-based "molecular gate". In the presence of target 8-oxo-dG, the capping aptamer displaces from the surface due to the high affinity of the analyte with the capping aptamer, thus inducing delivery of the preloaded fluorescent dye. In contrast, in the absence of 8-oxo-dG, a poor payload delivery is accomplished. This aptamer-based nanodevice has great sensitivity for 8-oxo-dG, resulting in a LOD of 1 nM and a detection time of ca. 60 min. Moreover, the aptasensor is able to accurately detect 8-oxo-dG in unmodified urine and serum without pre-concentration treatments. This diagnostic tool is validated in a set of 38 urine and serum samples from patients diagnosed of colorectal cancer and control patients. These samples are also analyzed using a standardized and specific ELISA kit. The aptasensor displays excellent sensitivity (95.83/100%) and specificity (80/100%) for 8-oxo-dG detection in serum and urine samples, respectively. Our results may serve as a basis for the development of generalized fluorogenic diagnostic platforms for the easy diagnosis of cancer in biofluids as well as for monitoring therapeutic treatments and detection of relapses without the use of expensive equipment or trained personnel.
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Affiliation(s)
- Luis Pla
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain and Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Félix Sancenón
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain and Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain and Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina. Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain and Departamento de Química, Universitat Politècnica de València, Valencia, Spain
| | - M Carmen Martínez-Bisbal
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain and Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain and Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina. Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain and Departamento de Química Física. Universitat de València, Burjasot, Valencia, Spain
| | - Celia Bañuls
- Servicio de Endocrinología y Nutrición. Hospital Universitario Dr Peset-FISABIO, Valencia, Spain
| | - Nuria Estañ
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología-INCLIVA, Universitat de València, Valencia, Spain and Servicio de Análisis Clínicos, Hospital Universitario Dr Peset-FISABIO, Valencia, Spain
| | - Marina Botello-Marabotto
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Elena Aznar
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain and Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain and Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina. Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain and Departamento de Química, Universitat Politècnica de València, Valencia, Spain
| | - Guillermo Sáez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Odontología-INCLIVA, Universitat de València, Valencia, Spain and Servicio de Análisis Clínicos, Hospital Universitario Dr Peset-FISABIO, Valencia, Spain
| | - Sara Santiago-Felipe
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain and Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Ramón Martínez-Máñez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain and Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València - Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. and Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València - Instituto de Investigación Sanitaria La Fe, Valencia, Spain and Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina. Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain and Departamento de Química, Universitat Politècnica de València, Valencia, Spain
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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9
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Matulakul P, Vongpramate D, Kulchat S, Chompoosor A, Thanan R, Sithithaworn P, Sakonsinsiri C, Puangmali T. Development of Low-Cost AuNP-Based Aptasensors with Truncated Aptamer for Highly Sensitive Detection of 8-Oxo-dG in Urine. ACS OMEGA 2020; 5:17423-17430. [PMID: 32715227 PMCID: PMC7377066 DOI: 10.1021/acsomega.0c01834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG), an oxidized form of guanosine residues, is a critical biomarker for various cancers. Herein, a sensitive citrate-capped gold nanoparticle-based aptasensor device has been developed for the detection of 8-oxo-dG in urine. We previously designed a 38-nt anti-8-oxo-dG-aptamer by a computer simulation and the experimental validation has been performed in the present work. The analytical performance of the 38-nt aptamer from the in silico design was compared with the parent 66-nt aptamer. This assay is based on the principle of salt-induced aggregation of citrate-capped gold nanoparticles. Based on this sensing mechanism, the difference between the absorbance in the presence and absence of 8-oxo-dG at λ = 525 nm (ΔA525) increased linearly as a function of 8-oxo-dG concentrations in the ranges of 10-100 and 15-100 nM for 38-nt and 66-nt aptasensors, respectively. This method can provide detection limits of 6.4 nM for 8-oxo-dG in the 38-nt aptasensor and 13.2 nM in the 66-nt aptasensor. Similar to the 66-nt aptamer, the shortened aptamer, 38-nt long, can provide high sensitivity and selectivity with rapid detection time. In addition, using the 38-nt aptamer as a recognition component in the developed portable low-cost device showed high sensitivity in the detection range of 15-100 nM with a detection limit of 12.9 nM, which is much lower than the threshold value (280 nM) for normal human urine. This easy-to-use device could effectively and economically be utilized for monitoring 8-oxo-dG in real urine samples and potentially serve as a prototype for a commercial device.
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Affiliation(s)
- Piyaporn Matulakul
- Materials
Science and Nanotechnology Program, Department of Physics, Faculty
of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Drusawin Vongpramate
- Department
of Information Technology, Faculty of Science, Buriram Rajabhat University, Buriram 31000, Thailand
| | - Sirinan Kulchat
- Department
of Chemistry, Faculty of Science, Khon Kaen
University, Khon Kaen 40002, Thailand
| | - Apiwat Chompoosor
- Department
of Chemistry, Faculty of Science, Ramkhamhaeng
University, Bangkok 10240, Thailand
| | - Raynoo Thanan
- Department
of Biochemistry, Faculty of Medicine, Khon
Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma
Research Institute (CARI), Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma
Screening and Care Program (CASCAP), Khon
Kaen University, Khon Kaen 40002, Thailand
| | - Paiboon Sithithaworn
- Cholangiocarcinoma
Research Institute (CARI), Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma
Screening and Care Program (CASCAP), Khon
Kaen University, Khon Kaen 40002, Thailand
- Department
of Parasitology, Faculty of Medicine, Khon
Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department
of Biochemistry, Faculty of Medicine, Khon
Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma
Research Institute (CARI), Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma
Screening and Care Program (CASCAP), Khon
Kaen University, Khon Kaen 40002, Thailand
| | - Theerapong Puangmali
- Materials
Science and Nanotechnology Program, Department of Physics, Faculty
of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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10
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McConnell EM, Nguyen J, Li Y. Aptamer-Based Biosensors for Environmental Monitoring. Front Chem 2020; 8:434. [PMID: 32548090 PMCID: PMC7272472 DOI: 10.3389/fchem.2020.00434] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.
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Affiliation(s)
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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McConnell EM, Cozma I, Morrison D, Li Y. Biosensors Made of Synthetic Functional Nucleic Acids Toward Better Human Health. Anal Chem 2019; 92:327-344. [PMID: 31656066 DOI: 10.1021/acs.analchem.9b04868] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Ioana Cozma
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1.,Department of Surgery, Division of General Surgery , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Devon Morrison
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , Ontario , Canada , L8S 4K1
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Choodet C, Toomjeen P, Phanchai W, Matulakul P, Thanan R, Sakonsinsiri C, Puangmali T. Combinedin silicoandin vitrostudy of an aptasensor based on citrate-capped AuNPs for naked-eye detection of a critical biomarker of oxidative stress. RSC Adv 2019; 9:17592-17600. [PMID: 35520541 PMCID: PMC9064585 DOI: 10.1039/c9ra01497g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/10/2019] [Indexed: 11/27/2022] Open
Abstract
An elevated level of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) in biosamples has been found to correlate to oxidative stress, and it has been assigned as a critical biomarker of various diseases. Herein, insights into the mechanisms of an aptasensor, based on citrate-capped gold nanoparticles (AuNPs), for 8-oxo-dG detection were elucidated using molecular dynamics (MD) simulations and validated experimentally. We found that the binding mechanism for binding between the anti-8-oxo-dG aptamer and 8-oxo-dG has the following characteristic stages: (i) adsorption stage, (ii) binding stage, and (iii) complex stabilization stage. Our simulations also reveal the binding sites between the anti-8-oxo-dG aptamer and 8-oxo-dG formed through hydrogen bonding during complex formation. A shortened anti-8-oxo-dG-aptamer was also engineered using in silico design, which was expected to improve the analytical performance of the colorimetric aptasensor. The mechanisms of the colorimetric aptasensor in the presence and absence of 8-oxo-dG were also investigated, and found to be in good agreement with the experiments. Complete understanding of the mechanism of the colorimetric aptasensor would open the door for development of novel naked-eye aptasensors. A visual strategy for 8-oxo-dG monitoring based upon the dispersion of citrate-capped gold nanoparticles has been developed.![]()
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Affiliation(s)
- Cherdpong Choodet
- Department of Physics
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Pakawat Toomjeen
- Department of Physics
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Witthawat Phanchai
- Department of Physics
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Piyaporn Matulakul
- Department of Physics
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Raynoo Thanan
- Department of Biochemistry
- Faculty of Medicine
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry
- Faculty of Medicine
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Theerapong Puangmali
- Department of Physics
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
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