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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Detection of a SARS-CoV-2 sequence with genosensors using data analysis based on information visualization and machine learning techniques

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Soares, Juliana Coatrini [1] ; Soares, Andrey Coatrini [2] ; Rodrigues, Valquiria Cruz [1] ; Oiticica, Pedro Ramon Almeida [1] ; Raymundo-Pereira, Paulo Augusto [1] ; Bott-Neto, Jose Luiz [1] ; Buscaglia, Lorenzo A. [1] ; de Castro, Lucas Daniel Chiba [1] ; Ribas, Lucas C. [1, 3] ; Scabini, Leonardo [1] ; Brazaca, Lais C. [4, 5] ; Correa, Daniel S. [2] ; Mattoso, Luiz Henrique C. [2] ; de Oliveira, Maria Cristina Ferreira [3] ; de Carvalho, Andre Carlos Ponce Leon Ferreira [3] ; Carrilho, Emanuel [4, 5] ; Bruno, Odemir M. [1] ; Melendez, Matias Eliseo [6] ; Oliveira Jr, Osvaldo N.
Total Authors: 19
Affiliation:
[1] Univ Sao Paulo, Sao Carlos Inst Phys IFSC, BR-13566590 Sao Carlos, SP - Brazil
[2] Embrapa Instrumentacao, Nanotechnol Natl Lab Agr LNNA, BR-13560970 Sao Carlos, SP - Brazil
[3] Univ Sao Paulo, Inst Math & Comp Sci ICMC, BR-13566590 Sao Carlos, SP - Brazil
[4] Univ Sao Paulo, Sao Carlos Inst Chem IQSC, BR-13566590 Sao Carlos, SP - Brazil
[5] Natl Inst Sci & Technology Bioanalyt INCTBio, BR-13083970 Campinas, SP - Brazil
[6] Little Prince Coll, Pele Little Prince Res Inst, Little Prince Complex Curitiba, BR-80250060 Curitiba, PR - Brazil
Total Affiliations: 6
Document type: Journal article
Source: MATERIALS CHEMISTRY FRONTIERS; v. 5, n. 15, p. 5658-5670, AUG 7 2021.
Web of Science Citations: 0
Abstract

We report on genosensors to detect an ssDNA sequence from the SARS-CoV-2 genome, which mimics the GU280 gp10 gene (coding the viral nucleocapsid phosphoprotein), using four distinct principles of detection and treating the data with information visualization and machine learning techniques. Genosensors were fabricated on either gold (Au) interdigitated electrodes for electrical and electrochemical measurements or on Au nanoparticles on a glass slide for optical measurements. They contained a matrix of 11-mercaptoundecanoic acid (11-MUA) self-assembled monolayer (SAM) onto which a layer of capture probe (cpDNA) sequence was immobilized. Detection was performed using electrical and electrochemical impedance spectroscopies and localized surface plasmon resonance (LSPR). The highest sensitivity was reached with impedance spectroscopy, including using a low-cost (US\$ 100) homemade impedance analyzer. Complementary ssDNA sequences were detected with a detection limit of 0.5 aM (0.3 copy per mu L). This performance may be attributed to the high sensitivity of the electrical impedance technique combined with an appropriate arrangement of the sequences on the electrodes and hybridization between the complementary sequences, as inferred from polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). The selectivity of the genosensor was confirmed by plotting the impedance spectroscopy data with a multidimensional projection technique (interactive document mapping, IDMAP), where a clear separation was observed among the samples of the complementary DNA sequence at various concentrations and from buffer samples containing a non-complementary sequence and other DNA biomarkers. The diagnosis of SARS-CoV-2 mimicking sequences was also achieved with machine learning techniques applied to scanning electron microscope images taken from genosensors exposed to distinct concentrations of the complementary ssDNA sequences. In summary, the genosensors proposed here are promising for detecting SARS-CoV-2 genetic material (RNA) in biological fluids in point-of-care settings. (AU)

FAPESP's process: 16/23763-8 - Modeling and analysis of complex networks for computer vision
Grantee:Lucas Correia Ribas
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 16/01919-6 - Design and fabrication of nanostructured flexible devices for biomarkers detection
Grantee:Paulo Augusto Raymundo Pereira
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 20/02938-0 - Coloured patterns based on bioinspired photonic crystals for mechanocromic applications
Grantee:Lucas Daniel Chiba de Castro
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 14/50867-3 - INCT 2014: National Institute of Science and Technology in Bioanalysis
Grantee:Lauro Tatsuo Kubota
Support type: Research Projects - Thematic Grants
FAPESP's process: 18/18953-8 - Nanostructured films applied in microfluidic biosensors to mastitis detection
Grantee:Andrey Coatrini Soares
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 18/19750-3 - Exploring C4D detection for the development of innovative and low-cost microfluidic biosensors
Grantee:Laís Canniatti Brazaca
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 19/00101-8 - Development of a portable impedance analyzer
Grantee:Lorenzo Antonio Buscaglia
Support type: Scholarships in Brazil - Master
FAPESP's process: 19/13514-9 - Electrochemical sensors with a matrix containing graphene quantum dots or nanoribbons for the detection of biomarkers
Grantee:José Luiz Bott Neto
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 18/22214-6 - Toward a convergence of technologies: from sensing and biosensing to information visualization and machine learning for data analysis in clinical diagnosis
Grantee:Osvaldo Novais de Oliveira Junior
Support type: Research Projects - Thematic Grants
FAPESP's process: 19/07811-0 - Artificial neural networks and complex networks: an integrative study of topological properties and pattern recognition
Grantee:Leonardo Felipe dos Santos Scabini
Support type: Scholarships in Brazil - Doctorate