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Ávila Oliveira BD, Gomes RS, de Carvalho AM, Lima EMF, Pinto UM, da Cunha LR. Revolutionizing food safety with electrochemical biosensors for rapid and portable pathogen detection. Braz J Microbiol 2024:10.1007/s42770-024-01427-6. [PMID: 38922532 DOI: 10.1007/s42770-024-01427-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Foodborne diseases remain a worldwide concern, despite the advances made in sanitation, pathogen surveillance and food safety management systems. The methods routinely applied for detecting pathogens in foods are time consuming, labor intensive and usually require trained and qualified individuals. The objective of this review was to highlight the use of biosensors, with a focus on the electrochemical devices, as promising alternatives for detecting foodborne pathogens. These biosensors present high speed for obtaining results, with the possibility of evaluating foods in real time, at low cost, ease of use, in addition to being compact and portable. These aspects are considered advantageous and suitable for use in food safety management systems. This work also shows some limitations for the application of biosensors, and we present perspectives with the development and use of nanomaterials.
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Affiliation(s)
- Brígida D' Ávila Oliveira
- Health and Nutrition Graduate Program, Federal University of Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
| | - Raíssa Soares Gomes
- Health and Nutrition Graduate Program, Federal University of Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
| | - Alice Mendes de Carvalho
- Health and Nutrition Graduate Program, Federal University of Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
| | - Emília Maria França Lima
- Food Research Center (FoRC), Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Uelinton Manoel Pinto
- Food Research Center (FoRC), Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Luciana Rodrigues da Cunha
- Department of Foods, Health and Nutrition Graduate Program, Federal University of Ouro Preto, Federal University of Ouro Preto (UFOP), Ouro Preto, 35400-000, Minas Gerais, Brazil.
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2
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Gunasekaran BM, Srinivasan S, Ezhilan M, Nesakumar N. Nucleic acid-based electrochemical biosensors. Clin Chim Acta 2024; 559:119715. [PMID: 38735514 DOI: 10.1016/j.cca.2024.119715] [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: 04/09/2024] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024]
Abstract
Colorectal cancer, breast cancer, oxidative DNA damage, and viral infections are all significant and major health threats to human health, presenting substantial challenges in early diagnosis. In this regard, a wide range of nucleic acid-based electrochemical platforms have been widely employed as point-of-care diagnostics in health care and biosensing technologies. This review focuses on biosensor design strategies, underlying principles involved in the development of advanced electrochemical genosensing devices, approaches for immobilizing DNA on electrode surfaces, as well as their utility in early disease diagnosis, with a particular emphasis on cancer, leukaemia, oxidative DNA damage, and viral pathogen detection. Notably, the role of biorecognition elements and nanointerfaces employed in the design and development of advanced electrochemical genosensors for recognizing biomarkers related to colorectal cancer, breast cancer, leukaemia, oxidative DNA damage, and viral pathogens has been extensively reviewed. Finally, challenges associated with the fabrication of nucleic acid-based biosensors to achieve high sensitivity, selectivity, a wide detection range, and a low detection limit have been addressed. We believe that this review will provide valuable information for scientists and bioengineers interested in gaining a deeper understanding of the fabrication and functionality of nucleic acid-based electrochemical biosensors for biomedical diagnostic applications.
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Affiliation(s)
- Balu Mahendran Gunasekaran
- School of Chemical & Biotechnology (SCBT), SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India; Center for Nanotechnology & Advanced Biomaterials (CENTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India
| | - Soorya Srinivasan
- Department of Chemistry, A.V.V.M Sri Pushpam College (Autonomous), (Affiliated to Bharathidasan University, Tiruchirappalli), Poondi, Thanjavur, Tamil Nadu 613 503, India
| | - Madeshwari Ezhilan
- Department of biomedical engineering, Vel Tech Rangarajan Dr. Sagunthala R & D Institute of Science and Technology, Vel Nagar, Avadi, Chennai 600062, Tamil Nadu, India
| | - Noel Nesakumar
- School of Chemical & Biotechnology (SCBT), SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India; Center for Nanotechnology & Advanced Biomaterials (CENTAB), SASTRA Deemed University, Thanjavur 613401, Tamil Nadu, India.
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3
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Demir Gİ, Tekin A. NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond. J Chem Phys 2023; 159:244117. [PMID: 38153156 DOI: 10.1063/5.0176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.
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Affiliation(s)
- Gözde İniş Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), Kocaeli, Türkiye
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4
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Rousseau CR, Kumakli H, White RJ. Perspective-Assessing Electrochemical, Aptamer-Based Sensors for Dynamic Monitoring of Cellular Signaling. ECS SENSORS PLUS 2023; 2:042401. [PMID: 38152504 PMCID: PMC10750225 DOI: 10.1149/2754-2726/ad15a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/29/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Electrochemical, aptamer-based (E-AB) sensors provide a generalizable strategy to quantitatively detect a variety of targets including small molecules and proteins. The key signaling attributes of E-AB sensors (sensitivity, selectivity, specificity, and reagentless and dynamic sensing ability) make them well suited to monitor dynamic processes in complex environments. A key bioanalytical challenge that could benefit from the detection capabilities of E-AB sensors is that of cell signaling, which involves the release of molecular messengers into the extracellular space. Here, we provide a perspective on why E-AB sensors are suited for this measurement, sensor requirements, and pioneering examples of cellular signaling measurements.
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Affiliation(s)
- Celeste R. Rousseau
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
| | - Hope Kumakli
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
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5
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Teixeira C, Ipatov A, Carvalho J, Purwidyantri A, Fontes N, Prado M. Miniaturized Microscale Solid-Phase Extraction-Based Module for Highly Efficient DNA Extraction and Purification from Grapevine Samples. ACS OMEGA 2023; 8:31738-31746. [PMID: 37692237 PMCID: PMC10483517 DOI: 10.1021/acsomega.3c02717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
Several developments over the last few years are being directed toward improving DNA-based analysis to simplify, miniaturize, and reduce the time and cost of analysis, with the objective to allow its use in decentralized settings. One of the most interesting fields is DNA extraction and purification, a key step for ensuring good analytical performance. In this sense, microscale solid phase extraction (μSPE) offers paramount advantages for an improved DNA yield. In this work, we have developed a miniaturized module for DNA purification based on μSPE using a borosilicate glass microfiber filter as the solid phase. We also established a protocol for highly efficient DNA purification from vegetable samples, including leaves and grapes from four different varieties from the PDO Douro and two varieties from the Minho wine regions. The protocol demonstrated excellent performance when compared with a commercial kit with a DNA recovery yield of around 50%.
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Affiliation(s)
- Carla Teixeira
- International
Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, 4715-310 Braga, Portugal
- Department
of Biological Engineering, University of
Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Faculty
of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Andrey Ipatov
- International
Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, 4715-310 Braga, Portugal
| | - Joana Carvalho
- International
Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, 4715-310 Braga, Portugal
- Department
of Analytical Chemistry, Faculty of Veterinary Science, University of Santiago de Compostela, 27002 Lugo, Spain
| | - Agnes Purwidyantri
- International
Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, 4715-310 Braga, Portugal
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, David
Keir Building, Stranmillis Road, BT9
5AG Belfast, U.K.
| | - Natacha Fontes
- Sogrape, Rua 5 de outubro, 4527, 4430-809 Avintes, Portugal
| | - Marta Prado
- International
Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, 4715-310 Braga, Portugal
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6
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Jang Y, Jung J, Oh J. Bio-Microfabrication of 2D and 3D Biomimetic Gut-on-a-Chip. MICROMACHINES 2023; 14:1736. [PMID: 37763899 PMCID: PMC10537549 DOI: 10.3390/mi14091736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Traditional goal of microfabrication was to limitedly construct nano- and micro-geometries on silicon or quartz wafers using various semiconductor manufacturing technologies, such as photolithography, soft lithography, etching, deposition, and so on. However, recent integration with biotechnologies has led to a wide expansion of microfabrication. In particular, many researchers studying pharmacology and pathology are very interested in producing in vitro models that mimic the actual intestine to study the effectiveness of new drug testing and interactions between organs. Various bio-microfabrication techniques have been developed while solving inherent problems when developing in vitro micromodels that mimic the real large intestine. This intensive review introduces various bio-microfabrication techniques that have been used, until recently, to realize two-dimensional and three-dimensional biomimetic experimental models. Regarding the topic of gut chips, two major review subtopics and two-dimensional and three-dimensional gut chips were employed, focusing on the membrane-based manufacturing process for two-dimensional gut chips and the scaffold-based manufacturing process for three-dimensional gut chips, respectively.
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Affiliation(s)
- Yeongseok Jang
- Department of Mechanical Design Engineering, Jeonbuk National University, Jeonju-si 54896, Jeollabuk-do, Republic of Korea;
| | - Jinmu Jung
- Department of Nano-Bio Mechanical System Engineering, Jeonbuk National University, Jeonju-si 54896, Jeollabuk-do, Republic of Korea
| | - Jonghyun Oh
- Department of Nano-Bio Mechanical System Engineering, Jeonbuk National University, Jeonju-si 54896, Jeollabuk-do, Republic of Korea
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7
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Shrestha P, Kand D, Weinstain R, Winter AH. meso-Methyl BODIPY Photocages: Mechanisms, Photochemical Properties, and Applications. J Am Chem Soc 2023; 145:17497-17514. [PMID: 37535757 DOI: 10.1021/jacs.3c01682] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
meso-methyl BODIPY photocages have recently emerged as an exciting new class of photoremovable protecting groups (PPGs) that release leaving groups upon absorption of visible to near-infrared light. In this Perspective, we summarize the development of these PPGs and highlight their critical photochemical properties and applications. We discuss the absorption properties of the BODIPY PPGs, structure-photoreactivity studies, insights into the photoreaction mechanism, the scope of functional groups that can be caged, the chemical synthesis of these structures, and how substituents can alter the water solubility of the PPG and direct the PPG into specific subcellular compartments. Applications that exploit the unique optical and photochemical properties of BODIPY PPGs are also discussed, from wavelength-selective photoactivation to biological studies to photoresponsive organic materials and photomedicine.
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Affiliation(s)
- Pradeep Shrestha
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Dnyaneshwar Kand
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Roy Weinstain
- School of Plant Sciences and Food Security, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Arthur H Winter
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
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8
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Rana M, Yilmaz T, Cohen S, Beyhan S, Argun AA. A novel biosensor for ultrasensitive detection of fungal genes. Biosens Bioelectron 2023; 222:114986. [PMID: 36508932 PMCID: PMC10289176 DOI: 10.1016/j.bios.2022.114986] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022]
Abstract
Fungal infections are a rapidly increasing public health problem due to their high morbidity and mortality rates, especially in populations with compromised immune systems. Rapid and accurate diagnosis of these diseases is, therefore, necessary to improve the prognosis of afflicted patients. Unfortunately, current clinical chemistry practice relies on lengthy culturing methods that are insufficient to meet the fast turnaround requirements. Here we present a cost-effective and robust nucleic acid sensor that can identify the presence of histoplasmosis causing fungal genes, in whole blood or bronchoalveolar lavage (BAL) samples, far earlier than current methods. Our novel assay involves the hybridization of target gene sequences with immobilized nucleic acid probes, allowing direct, label-free detection of Hcp100, CBP1, and M antigen genes through electrochemical analysis. The resultant current is attributed to the presence of fungal targets in the sample solution. The assay provides ultra-sensitive detection of DNA molecules with a limit of detection (LOD) values down to 100 aM, sufficient to meet the clinical diagnostic need. In addition, the turnaround time for the sample to result is less than 90 min compared to the current clinical procedure's turnaround time of 3-4 weeks.
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Affiliation(s)
- Muhit Rana
- Giner Inc., 89 Rumford Avenue, Newton, MA, 02466, United States
| | - Tugba Yilmaz
- Giner Inc., 89 Rumford Avenue, Newton, MA, 02466, United States
| | - Shirli Cohen
- J. Craig Venter Institute (JCVI), 4120 Capricorn Lane La Jolla, CA, 92037, United States
| | - Sinem Beyhan
- J. Craig Venter Institute (JCVI), 4120 Capricorn Lane La Jolla, CA, 92037, United States; The University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA, 92093, United States
| | - Avni A Argun
- Giner Inc., 89 Rumford Avenue, Newton, MA, 02466, United States.
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9
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Shahabipour F, Satta S, Mahmoodi M, Sun A, de Barros NR, Li S, Hsiai T, Ashammakhi N. Engineering organ-on-a-chip systems to model viral infections. Biofabrication 2023; 15:10.1088/1758-5090/ac6538. [PMID: 35390777 PMCID: PMC9883621 DOI: 10.1088/1758-5090/ac6538] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
Abstract
Infectious diseases remain a public healthcare concern worldwide. Amidst the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 infection, increasing resources have been diverted to investigate therapeutics targeting the COVID-19 spike glycoprotein and to develop various classes of vaccines. Most of the current investigations employ two-dimensional (2D) cell culture and animal models. However, 2D culture negates the multicellular interactions and three-dimensional (3D) microenvironment, and animal models cannot mimic human physiology because of interspecies differences. On the other hand, organ-on-a-chip (OoC) devices introduce a game-changer to model viral infections in human tissues, facilitating high-throughput screening of antiviral therapeutics. In this context, this review provides an overview of thein vitroOoC-based modeling of viral infection, highlighting the strengths and challenges for the future.
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Affiliation(s)
- Fahimeh Shahabipour
- Skin Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Sandro Satta
- Department of Medicine, School of Medicine, University of California, Los Angeles, California, USA
| | - Mahboobeh Mahmoodi
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
- Department of Biomedical Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Argus Sun
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
| | - Natan Roberto de Barros
- Department of Medicine, School of Medicine, University of California, Los Angeles, California, USA
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
| | - Song Li
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
| | - Tzung Hsiai
- Division of Cardiology, Department of Medicine, School of Medicine, University of California, Los Angeles, California, USA
- Greater Los Angeles VA Healthcare System, Los Angeles, California, USA
| | - Nureddin Ashammakhi
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, Michigan, USA
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10
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Truong PL, Yin Y, Lee D, Ko SH. Advancement in COVID-19 detection using nanomaterial-based biosensors. EXPLORATION (BEIJING, CHINA) 2023; 3:20210232. [PMID: 37323622 PMCID: PMC10191025 DOI: 10.1002/exp.20210232] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/11/2022] [Indexed: 06/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has exemplified how viral growth and transmission are a significant threat to global biosecurity. The early detection and treatment of viral infections is the top priority to prevent fresh waves and control the pandemic. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified through several conventional molecular methodologies that are time-consuming and require high-skill labor, apparatus, and biochemical reagents but have a low detection accuracy. These bottlenecks hamper conventional methods from resolving the COVID-19 emergency. However, interdisciplinary advances in nanomaterials and biotechnology, such as nanomaterials-based biosensors, have opened new avenues for rapid and ultrasensitive detection of pathogens in the field of healthcare. Many updated nanomaterials-based biosensors, namely electrochemical, field-effect transistor, plasmonic, and colorimetric biosensors, employ nucleic acid and antigen-antibody interactions for SARS-CoV-2 detection in a highly efficient, reliable, sensitive, and rapid manner. This systematic review summarizes the mechanisms and characteristics of nanomaterials-based biosensors for SARS-CoV-2 detection. Moreover, continuing challenges and emerging trends in biosensor development are also discussed.
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Affiliation(s)
- Phuoc Loc Truong
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Yiming Yin
- New Materials InstituteDepartment of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingboChina
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
| | - Daeho Lee
- Laser and Thermal Engineering LabDepartment of Mechanical EngineeringGachon UniversitySeongnamKorea
| | - Seung Hwan Ko
- Applied Nano and Thermal Science LabDepartment of Mechanical EngineeringSeoul National UniversityGwanak‐guSeoulKorea
- Institute of Advanced Machinery and Design (SNU‐IAMD)/Institute of Engineering ResearchSeoul National UniversityGwanak‐guSeoulKorea
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11
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Eksin E, Erdem A. Recent Progress on Optical Biosensors Developed for Nucleic Acid Detection Related to Infectious Viral Diseases. MICROMACHINES 2023; 14:mi14020295. [PMID: 36837995 PMCID: PMC9966969 DOI: 10.3390/mi14020295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 05/28/2023]
Abstract
Optical biosensors have many advantages over traditional analytical methods. They enable the identification of several biological and chemical compounds directly, instantly, and without the need of labels. Their benefits include excellent specificity, sensitivity, compact size, and low cost. In this review, the main focus is placed on the nucleic acid-based optical biosensor technologies, including colorimetric, fluorescence, surface plasmon resonance (SPR), Evanescent-Wave Optical, Fiber optic and bioluminescent optical fibre. The fundamentals of each type of biosensor are briefly explained, and particular emphasis has been placed on the achievements which have been gained in the last decade on the field of diagnosis of infectious viral diseases. Concluding remarks concerning the perspectives of further developments are discussed.
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Affiliation(s)
- Ece Eksin
- Biomedical Device Technology Program, Vocational School of Health Services, Izmir Democracy University, 35290 Izmir, Turkey
| | - Arzum Erdem
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, 35100 Izmir, Turkey
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12
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Guo J, Feng S, Yu H, Ou B, Jiang D, Zhuang W, Ding C, Chen X, Zhang M, Ling Y, Zeng Y, Qiu H. Transcriptomic study of gastrointestinal stromal tumors with liver metastasis. Front Genet 2023; 14:1007135. [PMID: 36911388 PMCID: PMC9996342 DOI: 10.3389/fgene.2023.1007135] [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: 07/30/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: GIST (gastrointestinal stromal tumor) is the most prominent mesenchymal neoplasms of the gastrointestinal tract, and liver is the most common metastasis site for GIST. The molecular mechanism leading to liver metastasis of GIST is currently unclear. Methods: With the goal of revealing the underlying mechanism, we performed whole-genome gene expression profiling on 18 pairs of RNA samples comprised of GIST tissues (with liver metastasis) and corresponding non-tumor tissues. After identifying differentially expressed gene, functional annotation and signal pathway analyses were conducted. GSE13861, datasets that compare GIST (without liver metastasis) with adjacent tissues, served as a comparison. Results: A total of 492 up-regulated genes and 629 down-regulated genes were identified as differentially expressed genes between liver metastasis tissues and non-tumor tissues. We characterized expression patterns of DEGs identified from our cohort and GSE13861 that show signatures of enrichment for functionality. In subsequent gene set enrichment analysis, differentially expressed genes were mainly enriched in Epithelial Mesenchymal Transition in both datasets. 493 genes were overlapped among our whole-genome gene expression profiling results and GSE13861, consisting 188 up-regulated genes and 305 down-regulated genes. By using CytoHubba plugin of Cytoscape, CDH1, CD34, KIT, PROM1, SOX9, FGF2, CD24, ALDH1A1, JAG1 and NES were identified as top ten hub genes in tumorigenesis and liver metastasis of GIST. higher expression levels of FGF2, JAG1, CD34, ALDH1A1 and the lower expression level of CDH1 were respectively associated with unfavorable overall survival. Meanwhile higher expression levels of CD34, FGF2, KIT, JAG1, ALDH1A were correlated with worse disease-free survival. Discussion: The present study may help to provide candidate pathways and targets for treatment of GIST and prevention methods to liver metastasis.
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Affiliation(s)
- Jianrong Guo
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shoucheng Feng
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Hong Yu
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Biyi Ou
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dan Jiang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wei Zhuang
- Department of Pharmacy, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Chao Ding
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xiaojiang Chen
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Miaoquan Zhang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yudong Ling
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yi Zeng
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Haibo Qiu
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Guthula LS, Yeh KT, Huang WL, Chen CH, Chen YL, Huang CJ, Chau LK, Chan MWY, Lin SH. Quantitative and amplification-free detection of SOCS-1 CpG methylation percentage analyses in gastric cancer by fiber optic nanoplasmonic biosensor. Biosens Bioelectron 2022; 214:114540. [PMID: 35834975 DOI: 10.1016/j.bios.2022.114540] [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: 01/22/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 01/16/2023]
Abstract
A new innovative approach is essential for early and effective diagnosis of gastric cancer, using promoter hypermethylation of the tumor suppressor, SOCS-1, that is frequently inactivated in human cancers. We have developed an amplification-free fiber optic nanoplasmonic biosensor for detecting DNA methylation of the SOCS-1 human genome. The method is based on the fiber optic nanogold-linked sorbent assay of PCR-free DNA from human gastric tumor tissue and cell lines. We designed a specific DNA probe fabricated on the fiber core surface while the other probe is bioconjugated with gold nanoparticles in free form to allow percentage determination and differentiating the methylated and unmethylated cell lines, further demonstrating the SOCS-1 methylation occurs in cancer patients but not in normal cell lines. The observed detection limit is 0.81 fM for methylated DNA, and the detection time is within 15 min. In addition, our data were significantly correlated to the data obtained from PCR-based pyrosequencing, and yet with superior accuracy. Hence our results provide new insight to the quantitative evaluation of methylation status of the human genome and can act as an alternative to PCR with a great potential.
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Affiliation(s)
| | - Kun-Tu Yeh
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua, Taiwan; College of Medicine, National Chung Hsiung University, Taichung, Taiwan
| | - Wen-Long Huang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Chun-Hsien Chen
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Ling Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan; Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, NCU-Covestro Research Center, National Central University, Taoyuan, Taiwan; R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan; Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, Taiwan; Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chiayi, Taiwan.
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan; Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, Taiwan; Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chiayi, Taiwan; Epigenomics and Human Disease Research Center, National Chung Cheng University, Chiayi, Taiwan.
| | - Shu-Hui Lin
- Department of Surgical Pathology, Changhua Christian Hospital, Changhua, Taiwan; Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan.
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14
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Demir Gİ, Demir S, Tekin A. 2D‐FFCASP—A New Approach for 2D Structure Prediction Applied to Self‐Assemblies of DNA Bases. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gözde İniş Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
| | - Samet Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
| | - Adem Tekin
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
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15
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McLean C, Brown K, Windmill J, Dennany L. Innovations In Point-Of-Care Electrochemical Detection Of Pyocyanin. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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17
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Identification of immune-infiltrated hub genes as potential biomarkers of Moyamoya disease by bioinformatics analysis. Orphanet J Rare Dis 2022; 17:80. [PMID: 35197088 PMCID: PMC8867641 DOI: 10.1186/s13023-022-02238-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 02/06/2022] [Indexed: 12/21/2022] Open
Abstract
Background Moyamoya disease (MMD) is a rare chronic progressive cerebrovascular disease. Recent studies have shown that autoimmune inflammation may also be an important pathology in MMD but the molecular mechanisms of inflammation in this disease are still large unknown. This study was designed to identify key biomarkers and the immune infiltration in vessel tissue of MMD using bioinformatics analysis. Methods Raw gene expression profiles (GSE157628, GSE141024) were downloaded from the Gene Expression Omnibus (GEO) database, identified differentially expressed genes (DEGs) and performed functional enrichment analysis. The CIBERSORT deconvolution algorithm was used to analyze the proportion of immune cells between MMD and an MMD-negative control group. We screened for neutrophil-associated DEGs, constructed a protein–protein interaction network (PPI) using STRING, and clarified the gene cluster using the Cytoscape plugin MCODE analysis. The receiver operating characteristic (ROC) curve was applied to test and filter the best gene signature. Results A total of 570 DEGs were detected, including 212 downregulated and 358 up-regulated genes. Reactome and KEGG enrichment revealed that DEGs were involved in the cell cycle, molecular transport, and metabolic pathways. The immune infiltration profile demonstrated that MMD cerebrovascular tissues contained a higher proportion of neutrophils, monocytes, and natural killer cells in MMD than in controls. The PPI network and MCODE cluster identified nine DEGs (UNC13D, AZU1, PYCARD, ELANE, SDCBP, CCL11, CCL15, CCL20, and CXCL5) associated with neutrophil infiltration. ROC results showed that UNC13D has good specificity and sensitivity (AUC = 0.7846). Conclusions The characteristics of immune infiltration in the cerebrovascular tissues of MMD patients and abnormal expression of hub genes provide new insights for understanding MMD progression. UNC13D is shows promise as a candidate molecule to determine neutrophil infiltration characteristics in MMD. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02238-4.
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18
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Aledhari M, Razzak R, Qolomany B, Al-Fuqaha A, Saeed F. Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2022; 10:31306-31339. [PMID: 35441062 PMCID: PMC9015691 DOI: 10.1109/access.2022.3159235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This paper provides a comprehensive literature review of various technologies and protocols used for medical Internet of Things (IoT) with a thorough examination of current enabling technologies, use cases, applications, and challenges. Despite recent advances, medical IoT is still not considered a routine practice. Due to regulation, ethical, and technological challenges of biomedical hardware, the growth of medical IoT is inhibited. Medical IoT continues to advance in terms of biomedical hardware, and monitoring figures like vital signs, temperature, electrical signals, oxygen levels, cancer indicators, glucose levels, and other bodily levels. In the upcoming years, medical IoT is expected replace old healthcare systems. In comparison to other survey papers on this topic, our paper provides a thorough summary of the most relevant protocols and technologies specifically for medical IoT as well as the challenges. Our paper also contains several proposed frameworks and use cases of medical IoT in hospital settings as well as a comprehensive overview of previous architectures of IoT regarding the strengths and weaknesses. We hope to enable researchers of multiple disciplines, developers, and biomedical engineers to quickly become knowledgeable on how various technologies cooperate and how current frameworks can be modified for new use cases, thus inspiring more growth in medical IoT.
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Affiliation(s)
- Mohammed Aledhari
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA
| | - Rehma Razzak
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA
| | - Basheer Qolomany
- College of Business and Technology, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Ala Al-Fuqaha
- College of Science and Engineering (CSE), Hamad Bin Khalifa University, Doha, Qatar
| | - Fahad Saeed
- School of Computing and Information Sciences, Florida International University, Miami, FL 33199, USA
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19
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Molecular Simulation Study of Gold Clusters for Transporting of Thioguanine Anticancer Drug in Aqueous Solution. J CLUST SCI 2022. [DOI: 10.1007/s10876-020-01974-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Hashem A, Hossain MAM, Marlinda AR, Mamun MA, Sagadevan S, Shahnavaz Z, Simarani K, Johan MR. Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: Advances, challenges, and opportunities. Crit Rev Clin Lab Sci 2021; 59:156-177. [PMID: 34851806 DOI: 10.1080/10408363.2021.1997898] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Clinical diagnostic tests should be quick, reliable, simple to perform, and affordable for diagnosis and treatment of diseases. In this regard, owing to their novel properties, biosensors have attracted the attention of scientists as well as end-users. They are efficient, stable, and relatively cheap. Biosensors have broad applications in medical diagnosis, including point-of-care (POC) monitoring, forensics, and biomedical research. The electrochemical nucleic acid (NA) biosensor, the latest invention in this field, combines the sensitivity of electroanalytical methods with the inherent bioselectivity of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The NA biosensor exploits the affinity of single-stranded DNA/RNA for its complementary strand and is used to detect complementary sequences of NA based on hybridization. After the NA component in the sensor detects the analyte, a catalytic reaction or binding event that generates an electrical signal in the transducer ensues. Since 2000, much progress has been made in this field, but there are still numerous challenges. This critical review describes the advances, challenges, and prospects of NA-based electrochemical biosensors for clinical diagnosis. It includes the basic principles, classification, sensing enhancement strategies, and applications of biosensors as well as their advantages, limitations, and future prospects, and thus it should be useful to academics as well as industry in the improvement and application of EC NA biosensors.
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Affiliation(s)
- Abu Hashem
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia.,Microbial Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - M A Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Ab Rahman Marlinda
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohammad Al Mamun
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia.,Department of Chemistry, Jagannath University, Dhaka, Bangladesh
| | - Suresh Sagadevan
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Zohreh Shahnavaz
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Khanom Simarani
- Department of Microbiology, Institute of Biological Sciences, Faculty of Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
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21
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Koklu A, Ohayon D, Wustoni S, Druet V, Saleh A, Inal S. Organic Bioelectronic Devices for Metabolite Sensing. Chem Rev 2021; 122:4581-4635. [PMID: 34610244 DOI: 10.1021/acs.chemrev.1c00395] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electrochemical detection of metabolites is essential for early diagnosis and continuous monitoring of a variety of health conditions. This review focuses on organic electronic material-based metabolite sensors and highlights their potential to tackle critical challenges associated with metabolite detection. We provide an overview of the distinct classes of organic electronic materials and biorecognition units used in metabolite sensors, explain the different detection strategies developed to date, and identify the advantages and drawbacks of each technology. We then benchmark state-of-the-art organic electronic metabolite sensors by categorizing them based on their application area (in vitro, body-interfaced, in vivo, and cell-interfaced). Finally, we share our perspective on using organic bioelectronic materials for metabolite sensing and address the current challenges for the devices and progress to come.
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Affiliation(s)
- Anil Koklu
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - David Ohayon
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Shofarul Wustoni
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Victor Druet
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Abdulelah Saleh
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Sahika Inal
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
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22
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Tian S, Chen S, Feng Y, Li Y. The Interactions of Small Proline-Rich Proteins with Late Cornified Envelope Proteins are Involved in the Pathogenesis of Psoriasis. Clin Cosmet Investig Dermatol 2021; 14:1355-1365. [PMID: 34594126 PMCID: PMC8478164 DOI: 10.2147/ccid.s336072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022]
Abstract
Purpose Psoriasis is a common cutaneous disease with multiple characteristics including inflammation and aberrant keratinocyte proliferation. However, the pathogenesis of psoriasis is not completely clear yet. The objective of this study is to perform an in-depth analysis of the association between SPRR and LCE in the pathogenesis of psoriasis. Methods In this study, we explore the differentially expressed genes (DEGs) in psoriasis by analyzing different gene expression profiles obtained from the Gene Expression Omnibus (GEO) database. The DEGs were examined using gene ontology (GO) functional enrichment analysis and protein–protein interactions (PPI) network. Correlation analysis in R studio software was used to analyze the association between SPRR and LCE genes. Further, potential direct protein–protein interactions between SPRR proteins and LCE3D were verified by co-localization observations and co-immunoprecipitation (CO-IP) assays in 293T cells. Also, the expression levels of SPRR and LCE genes were detected in lesional skin of the IMQ-induced psoriasiform dermatitis mice using RT-PCR. Results Interestingly, the small proline-rich (SPRR) and late cornified envelope (LCE) genes were identified as a module in the constructed PPI network. And the analysis of the gene expression profile GSE63684 showed that both SPRR family and LCE family genes were significantly upregulated in imiquimod (IMQ) induced psoriasiform dermatitis mice. Also, the correlation analysis in R studio software recognized the association of SPRR and LCE genes, which were further verified by co-localization and co-immunoprecipitation (CO-IP) assays in 293T cells, and the results show that the direct interactions between SPRR2 and LCE3D. Notably, we also found that the expression levels of SPRR and LCE genes were significantly increased in the IMQ-induced psoriasiform dermatitis mice, while specifically decreased under the tazarotene cream treatment, indicating that the SPRR and LCEs were regulated simultaneously in psoriasis. Conclusion In summary, our study found that interactions between SPRR proteins and LCE proteins may provide new insights into the pathogenesis of psoriasis.
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Affiliation(s)
- Siyu Tian
- School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Shuming Chen
- School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Yongyi Feng
- School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Yong Li
- School of Life Sciences, Xiamen University, Xiamen, People's Republic of China
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23
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Zaczek-Moczydlowska MA, Beizaei A, Dillon M, Campbell K. Current state-of-the-art diagnostics for Norovirus detection: Model approaches for point-of-care analysis. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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24
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Adampourezare M, Dehghan G, Hasanzadeh M, Hosseinpoure Feizi MA. Application of lateral flow and microfluidic bio-assay and biosensing towards identification of DNA-methylation and cancer detection: Recent progress and challenges in biomedicine. Biomed Pharmacother 2021; 141:111845. [PMID: 34175816 DOI: 10.1016/j.biopha.2021.111845] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an important epigenetic alteration that results from the covalent transfer of a methyl group to the fifth carbon of a cytosine residue in CpG dinucleotides by DNA methyltransferase. This modification mostly happens in the promoter region and the first exon of most genes and suppresses gene expression. Therefore, aberrant DNA methylation cause tumor progression, metastasis, and resistance to current anti-cancer therapies. So, the detection of DNA methylation is an important issue in diagnosis and therapy of most diseases. Conventional methods for the assay of DNA methylation and activity of DNA methyltransferases are time consuming. So, we need to multiplex operations and expensive instrumentation. To overcome the limitations of conventional methods, new methods such as microfluidic platforms and lateral flow tests have been developed to evaluate DNA methylation. The microfluidic tests are based on optical and electrical biosensing. These tests able us to can analyze DNA methylation with high efficiency and sensitivity without the need for expensive equipment and skilled people. Lateral flow strip tests are another type of rapid, simple, and sensitive test with advanced technology used to assess DNA methylation. Lateral flow strip tests are based on optical biosensors. This review attempts to evaluate new methods for assessing DNA extraction, DNA methylation and DNA methyltransferase activity as well as recent developments in microfluidic technology application for bisulfite treatment and restriction enzyme (bisulfite free), and lateral flow relying on their application in the field of recognition of DNA methylation in blood and body fluids. Also, the advantages and disadvantages of each test are reviewed. Finally, future prospects for the development of the microfluidics biodevices for the detection of DNA methylation is briefly discussed.
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Affiliation(s)
- Mina Adampourezare
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamreza Dehghan
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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25
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Saha U, Todi K, Malhotra BD. Emerging DNA-based multifunctional nano-biomaterials towards electrochemical sensing applications. NANOSCALE 2021; 13:10305-10319. [PMID: 34086027 DOI: 10.1039/d1nr02409d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA is known to be ubiquitous in nature as it is the controlling unit for genetic information storage in most living organisms. Lately, there has been a surge in studies relating to the use of DNA as a biomaterial for various biomedical applications such as biosensing, therapeutics, and drug delivery. The role of DNA as a bioreceptor in biosensors has been known for a long time. DNA-based biosensors are gradually evolving into highly sophisticated and sensitive molecular devices. The current realization of DNA-based biosensors embraces the unique structural and functional properties of DNA in the form of a biopolymer. The interesting properties of DNA, such as self-assembly, programmability, catalytic activity, dynamic behavior, and precise molecular recognition, have led to the emergence of innovative DNA assembly based electrochemical biosensors. This review article aims to cover the recent progress in the field of DNA-based electrochemical (EC) biosensors. It commences with an introduction to electrochemical biosensors and elucidates the advantages of integrating DNA-based materials into them. Besides this, we discuss the principles of EC biosensors based on different types of DNA-based materials. The article concludes by highlighting the outlook and importance of this interesting field for biomedical developments.
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Affiliation(s)
- Udiptya Saha
- Nanobioelectronics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India.
| | - Keshav Todi
- Nanobioelectronics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India.
| | - Bansi D Malhotra
- Nanobioelectronics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, New Delhi 110042, India.
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26
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Hasan MR, Sharma P, Anzar N, Pundir C, Pilloton R, Narang J, Shetti NP. Analytical methods for detection of human cytomegalovirus clinched biosensor a cutting-edge diagnostic tool. BIOMEDICAL ENGINEERING ADVANCES 2021. [DOI: 10.1016/j.bea.2021.100006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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27
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Qiu G, Gai Z, Saleh L, Tang J, Gui T, Kullak-Ublick GA, Wang J. Thermoplasmonic-Assisted Cyclic Cleavage Amplification for Self-Validating Plasmonic Detection of SARS-CoV-2. ACS NANO 2021; 15:7536-7546. [PMID: 33724796 PMCID: PMC8029440 DOI: 10.1021/acsnano.1c00957] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/10/2021] [Indexed: 05/23/2023]
Abstract
The coronavirus disease 2019 (COVID-19) has penetrated every populated patch of the globe and sows destruction in our daily life. Reliable and sensitive virus sensing systems are therefore of vital importance for timely infection detection and transmission prevention. Here we present a thermoplasmonic-assisted dual-mode transducing (TP-DMT) concept, where an amplification-free-based direct viral RNA detection and an amplification-based cyclic fluorescence probe cleavage (CFPC) detection collaborated to provide a sensitive and self-validating plasmonic nanoplatform for quantifying trace amounts of SARS-CoV-2 within 30 min. In the CFPC detection, endonuclease IV recognized the synthetic abasic site and cleaved the fluorescent probes in the hybridized duplex. The nanoscale thermoplasmonic heating dehybridized the shortened fluorescent probes and facilitated the cyclical binding-cleavage-dissociation (BCD) process, which could deliver a highly sensitive amplification-based response. This TP-DMT approach was successfully validated by testing clinical COVID-19 patient samples, which indicated its potential applications in fast clinical infection screening and real-time environmental monitoring.
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Affiliation(s)
- Guangyu Qiu
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
| | - Zhibo Gai
- Experimental Center, Shandong University of
Traditional Chinese Medicine, Jinan 250355, People’s
Republic of China
- Department of Clinical Pharmacology and Toxicology,
University Hospital Zurich, University of Zürich,
Zürich 8091, Switzerland
| | - Lanja Saleh
- Institute of Clinical Chemistry,
University Hospital Zurich, University of Zurich, Zurich
8091, Switzerland
| | - Jiukai Tang
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
| | - Ting Gui
- Experimental Center, Shandong University of
Traditional Chinese Medicine, Jinan 250355, People’s
Republic of China
| | - Gerd A. Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology,
University Hospital Zurich, University of Zürich,
Zürich 8091, Switzerland
- Mechanistic Safety, CMO & Patient Safety,
Global Drug Development, Novartis Pharma, Basel 4002,
Switzerland
| | - Jing Wang
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
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28
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Su W, Wei Y, Huang B, Ji J. Identification of Hub Genes and Immune Infiltration in Psoriasis by Bioinformatics Method. Front Genet 2021; 12:606065. [PMID: 33613635 PMCID: PMC7886814 DOI: 10.3389/fgene.2021.606065] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 01/11/2023] Open
Abstract
Background Psoriasis is a chronic, prolonged, and recurrent skin inflammatory disease. However, the pathogenesis of psoriasis is not completely clear, thus we aimed to explore potential molecular basis of it. Methods Two datasets were downloaded from the Gene Expression Omnibus database. After identifying the differentially expressed genes of psoriasis skin lesion samples and healthy controls, three kinds of analyses, namely functional annotation, protein-protein interaction (PPI) network, and immune infiltration analyses, were performed. Results A total of 152 up-regulated genes and 38 down-regulated genes were selected for subsequent analyses. Evaluation of the PPI network identified the most important module containing 13 hub genes. Gene ontology analysis showed that the hub genes have a significant enrichment effect on positive regulation of cell migration, defense response to the other organism and epithelial cell differentiation. KEGG signaling pathway analysis showed that the hub genes were significantly enriched in chemokine signaling, Toll-like receptor signaling pathway, and IL-17 signaling pathway. Compared with the normal control sample, naive B cells, CD8+ T cells, activated memory CD4+ T cells, follicular helper T cells, gamma delta T cells, resting NK cells, monocytes, M0 macrophages, M1 macrophages, activated dendritic cells and neutrophils infiltrated more, while memory B cells, naive CD4+ T cells, regulatory T cells (Tregs), activated NK cells, resting mast cells, and eosinophils infiltrated less. Conclusion To conclude, the hub genes and pathways identified from psoriasis lesions and normal controls along with the immune infiltration profile may provide new insights into the study of psoriasis.
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Affiliation(s)
- Wenxing Su
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Department of Medicine, Soochow University, Suzhou, China
| | - Yuqian Wei
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Department of Medicine, Soochow University, Suzhou, China
| | - Biao Huang
- Department of Medicine, Soochow University, Suzhou, China.,Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiang Ji
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Sharma A, Badea M, Tiwari S, Marty JL. Wearable Biosensors: An Alternative and Practical Approach in Healthcare and Disease Monitoring. Molecules 2021; 26:748. [PMID: 33535493 PMCID: PMC7867046 DOI: 10.3390/molecules26030748] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
With the increasing prevalence of growing population, aging and chronic diseases continuously rising healthcare costs, the healthcare system is undergoing a vital transformation from the traditional hospital-centered system to an individual-centered system. Since the 20th century, wearable sensors are becoming widespread in healthcare and biomedical monitoring systems, empowering continuous measurement of critical biomarkers for monitoring of the diseased condition and health, medical diagnostics and evaluation in biological fluids like saliva, blood, and sweat. Over the past few decades, the developments have been focused on electrochemical and optical biosensors, along with advances with the non-invasive monitoring of biomarkers, bacteria and hormones, etc. Wearable devices have evolved gradually with a mix of multiplexed biosensing, microfluidic sampling and transport systems integrated with flexible materials and body attachments for improved wearability and simplicity. These wearables hold promise and are capable of a higher understanding of the correlations between analyte concentrations within the blood or non-invasive biofluids and feedback to the patient, which is significantly important in timely diagnosis, treatment, and control of medical conditions. However, cohort validation studies and performance evaluation of wearable biosensors are needed to underpin their clinical acceptance. In the present review, we discuss the importance, features, types of wearables, challenges and applications of wearable devices for biological fluids for the prevention of diseased conditions and real-time monitoring of human health. Herein, we summarize the various wearable devices that are developed for healthcare monitoring and their future potential has been discussed in detail.
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Affiliation(s)
- Atul Sharma
- School of Chemistry, Monash University, Clayton, Melbourne, VIC 3800, Australia
- Department of Pharmaceutical Chemistry, SGT College of Pharmacy, SGT University, Budhera, Gurugram, Haryana 122505, India
| | - Mihaela Badea
- Fundamental, Prophylactic and Clinical Specialties Department, Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania;
| | - Swapnil Tiwari
- School of Studies in Chemistry, Pt Ravishankar Shukla University, Raipur, CHATTISGARH 492010, India;
| | - Jean Louis Marty
- University of Perpignan via Domitia, 52 Avenue Paul Alduy, CEDEX 9, 66860 Perpignan, France
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Tang M, Zhang M, Xia L, Wei D, Yang Z, Yan S, Du C, Cui HL. Detection of gene mutation responsible for Huntington's disease by terahertz attenuated total reflection microfluidic spectroscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000315. [PMID: 32981137 DOI: 10.1002/jbio.202000315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Terahertz absorption spectroscopy based on attenuated total reflection (ATR) from a microfluidic sample cell was designed and implemented to detect gene mutations leading to Huntington's disease (HD). The self-developed compact ATR microfluidic system was employed to detect two groups of base-repeated DNA molecules combined with a terahertz time-domain spectrometer in a marker-free manner. The first group featured different repetition patterns of oligonucleotide fragments, and the second group included the HD gene. For the oligonucleotides of different repetition patterns, there were significant differences among the three oligonucleotides with three repeats of the double bases, which could be unambiguously classified and identified; For the HD gene, it was found that the magnitude of the terahertz absorption coefficients of the four oligonucleotide solutions was, in ascending order, CAG-4 < CAG-16 < CAG-32 < CAG-40 (the numbers are the repeat times of the CAG base segment, with 40 repeats belonging to the HD gene), when the concentration of oligonucleotide was 1 mg/mL. Principal component analysis result indicated that the spectral differences of the four oligonucleotide solutions with different CAG repeat times were statistically significant and clearly distinguishable. These results demonstrate the potential of terahertz spectroscopy as a noninvasive, unmarked, fast and low-cost assay for gene diagnosis and clinical disease detection.
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Affiliation(s)
- Mingjie Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingkun Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Liangping Xia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Key Laboratory of Micro Nano Optoelectronic Devices and Intelligent Perception Systems, Yangtze Normal University, Chongqing, China
| | - Dongshan Wei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- School of Electronic Engineering, Dongguan University of Technology, Dongguan, China
| | - Zhongbo Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shihan Yan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Chunlei Du
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Hong-Liang Cui
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
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Bastos-Soares EA, Sousa RMO, Gómez AF, Alfonso J, Kayano AM, Zanchi FB, Funes-Huacca ME, Stábeli RG, Soares AM, Pereira SS, Fernandes CFC. Single domain antibodies in the development of immunosensors for diagnostics. Int J Biol Macromol 2020; 165:2244-2252. [DOI: 10.1016/j.ijbiomac.2020.10.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/26/2020] [Accepted: 10/04/2020] [Indexed: 12/16/2022]
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Sadighbayan D, Hasanzadeh M, Ghafar-Zadeh E. Biosensing based on field-effect transistors (FET): Recent progress and challenges. Trends Analyt Chem 2020; 133:116067. [PMID: 33052154 PMCID: PMC7545218 DOI: 10.1016/j.trac.2020.116067] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The use of field-Effect-Transistor (FET) type biosensing arrangements has been highlighted by researchers in the field of early biomarker detection and drug screening. Their non-metalized gate dielectrics that are exposed to an electrolyte solution cover the semiconductor material and actively transduce the biological changes on the surface. The efficiency of these novel devices in detecting different biomolecular analytes in a real-time, highly precise, specific, and label-free manner has been validated by numerous research studies. Considerable progress has been attained in designing FET devices, especially for biomedical diagnosis and cell-based assays in the past few decades. The exceptional electronic properties, compactness, and scalability of these novel tools are very desirable for designing rapid, label-free, and mass detection of biomolecules. With the incorporation of nanotechnology, the performance of biosensors based on FET boosts significantly, particularly, employment of nanomaterials such as graphene, metal nanoparticles, single and multi-walled carbon nanotubes, nanorods, and nanowires. Besides, their commercial availability, and high-quality production on a large-scale, turn them to be one of the most preferred sensing and screening platforms. This review presents the basic structural setup and working principle of different types of FET devices. We also focused on the latest progression regarding the use of FET biosensors for the recognition of viruses such as, recently emerged COVID-19, Influenza, Hepatitis B Virus, protein biomarkers, nucleic acids, bacteria, cells, and various ions. Additionally, an outline of the development of FET sensors for investigations related to drug development and the cellular investigation is also presented. Some technical strategies for enhancing the sensitivity and selectivity of detection in these devices are addressed as well. However, there are still certain challenges which are remained unaddressed concerning the performance and clinical use of transistor-based point-of-care (POC) instruments; accordingly, expectations about their future improvement for biosensing and cellular studies are argued at the end of this review.
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Affiliation(s)
- Deniz Sadighbayan
- Biologically Inspired Sensors and Actuators (BioSA), Faculty of Science, Dept. of Biology, York University, Toronto, Canada
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators (BioSA), Faculty of Science, Dept. of Biology, York University, Toronto, Canada
- Dept. of Elecrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, Canada
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Chalklen T, Jing Q, Kar-Narayan S. Biosensors Based on Mechanical and Electrical Detection Techniques. SENSORS (BASEL, SWITZERLAND) 2020; 20:E5605. [PMID: 33007906 PMCID: PMC7584018 DOI: 10.3390/s20195605] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/20/2022]
Abstract
Biosensors are powerful analytical tools for biology and biomedicine, with applications ranging from drug discovery to medical diagnostics, food safety, and agricultural and environmental monitoring. Typically, biological recognition receptors, such as enzymes, antibodies, and nucleic acids, are immobilized on a surface, and used to interact with one or more specific analytes to produce a physical or chemical change, which can be captured and converted to an optical or electrical signal by a transducer. However, many existing biosensing methods rely on chemical, electrochemical and optical methods of identification and detection of specific targets, and are often: complex, expensive, time consuming, suffer from a lack of portability, or may require centralised testing by qualified personnel. Given the general dependence of most optical and electrochemical techniques on labelling molecules, this review will instead focus on mechanical and electrical detection techniques that can provide information on a broad range of species without the requirement of labelling. These techniques are often able to provide data in real time, with good temporal sensitivity. This review will cover the advances in the development of mechanical and electrical biosensors, highlighting the challenges and opportunities therein.
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Affiliation(s)
| | - Qingshen Jing
- Department of Materials Science, University of Cambridge, Cambridge CB3 0FS, UK;
| | - Sohini Kar-Narayan
- Department of Materials Science, University of Cambridge, Cambridge CB3 0FS, UK;
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Su W, Guan Y, Huang B, Wang J, Wei Y, Zhao Y, Jiao Q, Ji J, Yu D, Xu L. Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis. BMC Cancer 2020; 20:863. [PMID: 32894090 PMCID: PMC7487637 DOI: 10.1186/s12885-020-07372-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/31/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. METHODS With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. RESULTS A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. CONCLUSIONS To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future.
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Affiliation(s)
- Wenxing Su
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu, 215000, People's Republic of China.,Department of Medicine, Soochow University, No. 199 Renai Street, Suzhou, Jiangsu, 215000, People's Republic of China
| | - Yi Guan
- School of Foreign Languages, Soochow University, No. 1 Shizi Street, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Biao Huang
- Department of Medicine, Soochow University, No. 199 Renai Street, Suzhou, Jiangsu, 215000, People's Republic of China.,Department of Burn and Plastic Surgery, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Suzhou, Jiangsu, 215000, People's Republic of China
| | - Juanjuan Wang
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu, 215000, People's Republic of China
| | - Yuqian Wei
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu, 215000, People's Republic of China
| | - Ying Zhao
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu, 215000, People's Republic of China
| | - Qingqing Jiao
- Department of Dermatology, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Suzhou, Jiangsu, 215000, People's Republic of China.
| | - Jiang Ji
- Department of Dermatology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu, 215000, People's Republic of China.
| | - Daojiang Yu
- Department of Plastic Surgery, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu, 215000, People's Republic of China.
| | - Longjiang Xu
- Department of Pathology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, 215000, Jiangsu, People's Republic of China
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Tang M, Zhang M, Xia L, Yang Z, Yan S, Wang H, Wei D, Du C, Cui HL. Detection of single-base mutation of DNA oligonucleotides with different lengths by terahertz attenuated total reflection microfluidic cell. BIOMEDICAL OPTICS EXPRESS 2020; 11:5362-5372. [PMID: 33014620 PMCID: PMC7510857 DOI: 10.1364/boe.400487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 05/15/2023]
Abstract
Many human genetic diseases are caused by single-base mutation in the gene sequence. Since DNA molecules with single-base mutation are extremely difficult to differentiate, existing detection methods are invariably complex and time-consuming. We propose a new label-free and fast terahertz (THz) spectroscopic technique based on a home-made terahertz attenuated total reflection (ATR) microfluidic cell and a terahertz time-domain spectroscopy (THz-TDS) system to detect single-base-mutated DNA molecules. The detected object DNA molecules are normal hemoglobin gene, sickle cell anemia gene (15 nt), JAK2 gene wild type and JAK2 V617F gene mutation (39 nt) from sickle cell anemia and thrombocytopenia, respectively. Results show that the oligonucleotide fragments with single-base mutation can be identified by THz spectroscopy combined with the ATR microfluidic cell, and the recognition effect of short oligonucleotide fragments with single-base mutation is better than that of long oligonucleotide fragments. The terahertz biosensor is shown to have high sensitivity and can be used to detect DNA molecules directly in the solution environment.
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Affiliation(s)
- Mingjie Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- These authors contributed equally to this work
| | - Mingkun Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- These authors contributed equally to this work
| | - Liangping Xia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Key Laboratory of Micro Nano Optoelectronic Devices and Intelligent Perception Systems, Yangtze Normal University, Chongqing, 408100, China
| | - Zhongbo Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shihan Yan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Huabin Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Dongshan Wei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Electronic Engineering, Dongguan University of Technology, Dongguan, Guangdong, 523808, China
| | - Chunlei Du
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Hong-Liang Cui
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
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Zhao J, Yang Z, Zhai Q, Wei D. Specific recognition of telomeric multimeric G-quadruplexes by a simple-structure quinoline derivative. Anal Chim Acta 2020; 1132:93-100. [PMID: 32980115 DOI: 10.1016/j.aca.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022]
Abstract
The development of highly sensitive fluorescence probes for telomeric multimeric G-quadruplexes has attracted extensive attention. However, few probes reported have exhibited selectivity for telomeric multimeric G-quadruplexes. Thus, it is challenging to design fluorescence probes with high specificity and selectivity for telomeric multimeric G-quadruplexes. This study employed a commercially available quinoline derivative BEPQ-1 as an effective switch-on sensor for telomeric multimeric G-quadruplexes. The fluorescence intensity enhanced more than 20 folds upon the addition of telomeric multimeric G-quadruplexes. This probe exhibited good selectivity and sensitivity for telomeric multimeric G-quadruplexes. And the detection limit of BEPQ-1 for the telomeric multimeric G-quadruplex TTA45 was calculated to be 0.11 μM. The distinctive feature of BEPQ-1 is the simple structure and small size. In the light of binding mode, BEPQ-1 could even simultaneously bind to the end two G-quartets of the two adjacent G-quadruplex units in telomeric multimeric G-quadruplex by π-π stacking. To our knowledge, this is the first simple-structure fluorescence probe for telomeric multimeric G-quadruplex. This finding might provide a strategy to design specific probes for telomeric multimeric G-quadruplexes and contribute to understand the structures and functions of G-quadruplexes in the telomere region.
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Affiliation(s)
- Jingfang Zhao
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ziyan Yang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianqian Zhai
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Dengguo Wei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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Abstract
DNA is now well-established as a nanoscale building material with applications in fields such as biosensing and molecular computation. Molecular processes such as logic gates, nucleic acid circuits, and multiplexed detection have used different readout strategies to measure the output signal. In biosensing, this output can be the diagnosis of a disease biomarker, whereas in molecular computation, the output can be the result of a mathematical operation carried out using DNA. Recent developments have shown that the output of such processes can be displayed graphically as a macroscopic symbol or an alphanumeric character on multiwell plates, microarray chips, gels, lateral flow devices, and DNA origami surfaces. This review discusses the concepts behind such graphical readouts of molecular events, available display platforms, and the advantages and challenges in adapting such methods for practical use. Graphical display systems have the potential to be used in the creation of intelligent computing and sensing devices by which nanoscale binding events are translated into macroscopic visual readouts.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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BEDNARIKOVA Z, GAZOVA Z, VALLE F, BYSTRENOVA E. Atomic force microscopy as an imaging tool to study the bio/nonbio complexes. J Microsc 2020; 280:241-251. [DOI: 10.1111/jmi.12936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Z. BEDNARIKOVA
- Slovak Academy of Science Institute of Experimental Physics Kosice Slovakia
| | - Z. GAZOVA
- Slovak Academy of Science Institute of Experimental Physics Kosice Slovakia
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Tseng YT, Li WY, Yu YW, Chiang CY, Liu SQ, Chau LK, Lai NS, Chou CC. Fiber Optic Particle Plasmon Resonance Biosensor for Label-Free Detection of Nucleic Acids and Its Application to HLA-B27 mRNA Detection in Patients with Ankylosing Spondylitis. SENSORS 2020; 20:s20113137. [PMID: 32492975 PMCID: PMC7309088 DOI: 10.3390/s20113137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 11/27/2022]
Abstract
We developed a label-free, real-time, and highly sensitive nucleic acid biosensor based on fiber optic particle plasmon resonance (FOPPR). The biosensor employs a single-strand deoxyoligonucleotides (ssDNA) probe, conjugated to immobilized gold nanoparticles on the core surface of an optical fiber. We explore the steric effects on hybridization affinity and limit of detection (LOD), by using different ssDNA probe designs and surface chemistries, including diluent molecules of different lengths in mixed self-assembled monolayers, ssDNA probes of different oligonucleotide lengths, ssDNA probes in different orientations to accommodate target oligonucleotides with a hybridization region located unevenly in the strand. Based on the optimized ssDNA probe design and surface chemistry, we achieved LOD at sub-nM level, which makes detection of target oligonucleotides as low as 1 fmol possible in the 10-μL sensor chip. Additionally, the FOPPR biosensor shows a good correlation in determining HLA-B27 mRNA, in extracted blood samples from patients with ankylosing spondylitis (AS), with the clinically accepted real-time reverse transcription-polymerase chain reaction (RT-PCR) method. The results from this fundamental study should guide the design of ssDNA probe for anti-sense sensing. Further results through application to HLA-B27 mRNA detection illustrate the feasibility in detecting various nucleic acids of chemical and biological relevance.
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Affiliation(s)
- Yen-Ta Tseng
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
| | - Wan-Yun Li
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
| | - Ya-Wen Yu
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
- Graduate School of Engineering Science and Technology, National Yunlin University of Science and Technology, Yunlin 64002, Taiwan
| | - Su-Qin Liu
- Immunology and Rheumatology, Department of Medicine, Buddhist Dalin Tzu Chi General Hospital, Chiayi 62247, Taiwan;
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
- Correspondence: (L.-K.C.); (N.-S.L.); (C.-C.C.); Tel.: +886-5-2729377 (L.-K.C.); +886-5-264-8000 (ext. 5003) (N.-S.L.); +886-5-2720411 (ext. 66506) (C.-C.C.)
| | - Ning-Sheng Lai
- Immunology and Rheumatology, Department of Medicine, Buddhist Dalin Tzu Chi General Hospital, Chiayi 62247, Taiwan;
- Correspondence: (L.-K.C.); (N.-S.L.); (C.-C.C.); Tel.: +886-5-2729377 (L.-K.C.); +886-5-264-8000 (ext. 5003) (N.-S.L.); +886-5-2720411 (ext. 66506) (C.-C.C.)
| | - Cheng-Chung Chou
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62102, Taiwan
- Correspondence: (L.-K.C.); (N.-S.L.); (C.-C.C.); Tel.: +886-5-2729377 (L.-K.C.); +886-5-264-8000 (ext. 5003) (N.-S.L.); +886-5-2720411 (ext. 66506) (C.-C.C.)
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Warner CN, Hunter ZD, Carte DD, Skidmore TJ, Vint ES, Day BS. Structure and Function Analysis of DNA Monolayers Created from Self-Assembling DNA-Dendron Conjugates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5428-5434. [PMID: 32336098 DOI: 10.1021/acs.langmuir.0c00340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Short sequences of DNA immobilized on gold surfaces can be used to capture an array of target molecules because of their high level of specificity. Depending on the nature of the target molecules, the proper density and distribution of the immobilized DNA molecules are fundamental to the quality of the sensor. With the aim to control the packing density and minimize the heterogeneity of the surfaces, DNA-dendron conjugate molecules were synthesized in solution and used to make self-assembled monolayers of single-stranded DNA surfaces on gold. The headgroups used were polyamido amine dendrons (cleaved cystamine core dendrimers) of generations two through five. The structural composition of these self-assembled monolayers was characterized using grazing angle Fourier-transform infrared and X-ray photoelectron spectroscopies. Surface plasmon resonance was used to measure surface densities of the probe monolayers and each monolayer's ability to capture fully complementary DNA strands from solution. The surface density of the probe monolayers was found to decrease with increasing dendron generation number, while the hybridization efficiency increased with increasing dendron generation number.
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Affiliation(s)
- Christian N Warner
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Zachary D Hunter
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Destiny D Carte
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Tyler J Skidmore
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - Erik S Vint
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - B Scott Day
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
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Çelikbıçak Ö, Hamaloğlu KÖ, Salih B, Pişkin E. Following hybridization on sensor/array platforms by using SPR, elipsometer and MALDI-MS. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1057-1072. [PMID: 32397925 DOI: 10.1080/15257770.2020.1750635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The aim of this study is to develop a methodology in which Surface Plasmon Resonance (SPR), Ellipsometer (EM) and Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry (MALDI-MS) will be used together for detection of single-strand oligodeoxynucleotides (ssODNs) targets. A selected target-ssODNs, and its complementary, the probe-ssODNs carrying a -SH end group, a spacer arm (HS-(CH2)6-(T)15, and a non-complementary ssODNs were used. Silicone based stamps with 16 regions were prepared and used for micro-contact printing (µCP) of the probe-ssODNs on the gold coated surfaces homogeneously. A modulator-spacer molecule (6-mercapto-1-hexanol) was co-immobilized to control surface probe density, to orientate the probe-ssODNs, and to eliminate the nonspecific interactions. SPR was used successfully to follow the hybridization of the target-ssODNs with the immobilized probe-ssODNs on the platform surfaces. Complete hybridizations were achieved in 100 min. It was obtained that there was a linear relationship between relative change in delta and target concentration below 1 µm. Using imaging version of ellipsometer (IEM) allowed imaging of the surfaces and supported extra datum for the SPR results. After a very simple dehybridization protocol, MALDI-MS analysis allowed detection of the target-ssODNs hybridized on the sensor/array platforms.
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Affiliation(s)
- Ömür Çelikbıçak
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| | | | - Bekir Salih
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Erhan Pişkin
- Nanobiyomedtek, Cyberpark, Bilkent, Ankara, Turkey
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Tandon S, George SM, McIntyre R, Kandasubramanian B. Polymeric immunosensors for tumor detection. Biomed Phys Eng Express 2020; 6:032001. [PMID: 33438645 DOI: 10.1088/2057-1976/ab8a75] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer is a broad-spectrum disease which is spread globally, having high mortality rates. This results from genetic, epigenetic and molecular abnormalities caused by various mutations. The main reason behind this critical problem lies in its diagnostics, the late detection of the disease is the root cause of all this. This can be managed well by the timely diagnosis of cancer by means of the tumor biomarkers present in the body fluids such as serum, blood, and urine. These tumor biomarkers are present in normal conditions as well, but their concentrations are altered in the presence of a malignant tumor. Prolonged studies have reported that immunosensors can be used to detect the minimal amount of biomarkers present in the sample and also provides point-of-care detection. The recent investigations demonstrated the use of polymers along with immunosensors for enhancing their selectivity and sensitivity towards the biomarkers and making them even more efficient. This review focuses on the variety of tumor biomarkers, different types of immunosensors and polymeric immunosensors using different polymers like polypyrrole, polyaniline, PHEMA, etc.
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Affiliation(s)
- Saloni Tandon
- Biotechnology Lab, Center for Converging Technologies, University of Rajasthan, JLN Marg, Jaipur-302004, Rajasthan, India
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DNA Microsystems for Biodiagnosis. MICROMACHINES 2020; 11:mi11040445. [PMID: 32340280 PMCID: PMC7231314 DOI: 10.3390/mi11040445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
Researchers are continuously making progress towards diagnosis and treatment of numerous diseases. However, there are still major issues that are presenting many challenges for current medical diagnosis. On the other hand, DNA nanotechnology has evolved significantly over the last three decades and is highly interdisciplinary. With many potential technologies derived from the field, it is natural to begin exploring and incorporating its knowledge to develop DNA microsystems for biodiagnosis in order to help address current obstacles, such as disease detection and drug resistance. Here, current challenges in disease detection are presented along with standard methods for diagnosis. Then, a brief overview of DNA nanotechnology is introduced along with its main attractive features for constructing biodiagnostic microsystems. Lastly, suggested DNA-based microsystems are discussed through proof-of-concept demonstrations with improvement strategies for standard diagnostic approaches.
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45
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Early detection of cancer: Focus on antibody coated metal and magnetic nanoparticle-based biosensors. SENSORS INTERNATIONAL 2020. [DOI: 10.1016/j.sintl.2020.100050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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46
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Weisenstein C, Schaar D, Katharina Wigger A, Schäfer-Eberwein H, Bosserhoff AK, Haring Bolívar P. Ultrasensitive THz biosensor for PCR-free cDNA detection based on frequency selective surfaces. BIOMEDICAL OPTICS EXPRESS 2020; 11:448-460. [PMID: 32010527 PMCID: PMC6968760 DOI: 10.1364/boe.380818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 05/31/2023]
Abstract
THz technologies are a powerful tool for label-free detection of biomolecules. However, significant reduction of the lower detection limit is required to apply THz-sensors in biomedical diagnosis. This paper reports an ultrasensitive THz-biosensor based on asymmetric double split ring resonators (aDSRR) for the direct label- and PCR-free detection of DNA at physiologically relevant concentrations. We introduce selective functionalization and localized electric field concentration to enhance aDSRR sensitivity and specificity. The sensor characteristics are demonstrated using the human tumor marker MIA in cDNA samples produced from total RNA without PCR-amplification. Measurements of DNA samples with concentrations as low as 1.55 × 10-12 mol/l are presented.
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Affiliation(s)
- Christian Weisenstein
- Institute of High Frequency and Quantum Electronics HQE, University of Siegen, Germany
| | - Dominik Schaar
- Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Anna Katharina Wigger
- Institute of High Frequency and Quantum Electronics HQE, University of Siegen, Germany
| | | | - Anja K. Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Germany
| | - Peter Haring Bolívar
- Institute of High Frequency and Quantum Electronics HQE, University of Siegen, Germany
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Raoof JB, Bagheryan Z, Hashkavayi AB. Development of a DNA biosensor based on MCM41 modified screen-printed graphite electrode for the study of the short sequence of the p53 tumor suppressor gene in hybridization and its interaction with the flutamide drug using hemin as the electrochemical label. NEW J CHEM 2020. [DOI: 10.1039/c9nj04569d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical DNA biosensors are particularly attractive because of their high sensitivity, suitability and compatibility with miniaturization in nucleic acid technology.
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Affiliation(s)
- Jahan Bakhsh Raoof
- Electroanalytical Chemistry Research Laboratory
- Department of Analytical Chemistry
- Faculty of Chemistry
- University of Mazandaran
- Babolsar
| | - Zahra Bagheryan
- Electroanalytical Chemistry Research Laboratory
- Department of Analytical Chemistry
- Faculty of Chemistry
- University of Mazandaran
- Babolsar
| | - Ayemeh Bagheri Hashkavayi
- Electroanalytical Chemistry Research Laboratory
- Department of Analytical Chemistry
- Faculty of Chemistry
- University of Mazandaran
- Babolsar
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Teo RD, Smithwick ER, Migliore A. 2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport. Phys Chem Chem Phys 2019; 21:22869-22878. [PMID: 31599901 PMCID: PMC7050622 DOI: 10.1039/c9cp04805g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2'F-ANA. Moreover, we find that 2'F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2'F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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Osman DI, El-Sheikh SM, Sheta SM, Ali OI, Salem AM, Shousha WG, EL-Khamisy SF, Shawky SM. Nucleic acids biosensors based on metal-organic framework (MOF): Paving the way to clinical laboratory diagnosis. Biosens Bioelectron 2019; 141:111451. [DOI: 10.1016/j.bios.2019.111451] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
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50
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Katsarou K, Bardani E, Kallemi P, Kalantidis K. Viral Detection: Past, Present, and Future. Bioessays 2019; 41:e1900049. [PMID: 31441081 DOI: 10.1002/bies.201900049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/04/2019] [Indexed: 12/26/2022]
Abstract
Viruses are essentially composed of a nucleic acid (segmented or not, DNA, or RNA) and a protein coat. Despite their simplicity, these small pathogens are responsible for significant economic and humanitarian losses that have had dramatic consequences in the course of human history. Since their discovery, scientists have developed different strategies to efficiently detect viruses, using all possible viral features. Viruses shape, proteins, and nucleic acid are used in viral detection. In this review, the development of these techniques, especially for plant and mammalian viruses, their strengths and weaknesses as well as the latest cutting-edge technologies that may be playing important roles in the years to come are described.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, GR-70013, Greece.,Department of Biology, University of Crete, Heraklion, GR-70013, Greece
| | - Eirini Bardani
- Department of Biology, University of Crete, Heraklion, GR-70013, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, GR-70013, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, GR-70013, Greece.,Department of Biology, University of Crete, Heraklion, GR-70013, Greece
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