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Goswami PP, Bonam S, Jeyaram K, Singh SG. Device-Physics Realization of ZnO-MWCNT Nanostructure-Based Field-Effect Biosensor for Ultrasensitive Simultaneous Genomic Detection of Foodborne Pathogens. Anal Chem 2023; 95:14695-14701. [PMID: 37727978 DOI: 10.1021/acs.analchem.3c02786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
The complex and versatile interactions among the wide variety of the nanostructures and the target analytes have primarily limited the detailed investigation of the transduction mechanism of nanomaterial-assisted electrical signal-based biosensors despite their high sensitivity, low-cost, portability, and ease of deployment. Hence, no common ground is formed detailing the principle of operation, demanding a strong need for systematic examination instead of hit and trial. Therefore, a maiden mechanistic investigation has been carried out in this paper for a field-effect-based biosensor device relying on the energy band diagram and the surface potential profile. To demonstrate the experimental evidence and appreciate the importance of food safety, three hazardous foodborne pathogens (Proteus mirabilis, Escherichia coli, and Clostridium botulinum) have been detected herein. The biosensor device, built on a hydrothermally synthesized zinc oxide and MWCNT (ZnO-MWCNT) composite nanostructure, simultaneously incorporates three fairly specific ss-DNA probes. Furthermore, the unmet challenge of biosensor device variability is addressed through the optimum selection of operating voltage of the device via a unique "voltage-selection-algorithm". We believe that the rigorous experimentation and the insightful device-physics realization demonstrated in this work will pave the way for a future decisive biosensor platform.
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Affiliation(s)
- Partha Pratim Goswami
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285, India
| | - Satish Bonam
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285, India
| | - Kumaraswamy Jeyaram
- Institute of Bioresources and Sustainable Development (IBSD), Regional Centre, Gangtok, Sikkim 737102, India
| | - Shiv Govind Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285, India
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Azeem MM, Shafa M, Aamir M, Zubair M, Souayeh B, Alam MW. Nucleotide detection mechanism and comparison based on low-dimensional materials: A review. Front Bioeng Biotechnol 2023; 11:1117871. [PMID: 36937765 PMCID: PMC10018150 DOI: 10.3389/fbioe.2023.1117871] [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: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.
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Affiliation(s)
- M. Mustafa Azeem
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO, United States
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Shafa
- Yunnan Key Laboratory of Metal-Organic Molecular Materials and Devices, Kunming University, Kunming, Yunnan, China
| | - Muhammad Aamir
- Department of Basic Science, Deanship of Preparatory Year, King Faisal University, Hofuf, Saudi Arabia
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Zubair
- Mechanical and Nuclear Engineering Department, University of Sharjah, Sharjah, United Arab Emirates
| | - Basma Souayeh
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
| | - Mir Waqas Alam
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
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Gangwar R, Rao KT, Khatun S, Rengan AK, Subrahmanyam C, Krishna Vanjari SR. Label-free miniaturized electrochemical nanobiosensor triaging platform for swift identification of the bacterial type. Anal Chim Acta 2022; 1233:340482. [DOI: 10.1016/j.aca.2022.340482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/21/2022] [Accepted: 10/02/2022] [Indexed: 11/01/2022]
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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies for the preparation of non-amplified and amplified genomic dengue gene samples for electrochemical DNA biosensing applications. RSC Adv 2021; 12:1-10. [PMID: 35424522 PMCID: PMC8978653 DOI: 10.1039/d1ra06753b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
The application of electrochemical DNA biosensors in real genomic sample detection is challenging due to the existence of complex structures and low genomic concentrations, resulting in inconsistent and low current signals. This work highlights strategies for the treatment of non-amplified and amplified genomic dengue virus gene samples based on real samples before they can be used directly in our DNA electrochemical sensing system, using methylene blue (MB) as a redox indicator. The main steps in this study for preparing non-amplified cDNA were cDNA conversion, heat denaturation, and sonication. To prepare amplified cDNA dengue virus genomic samples using an RT-PCR approach, we optimized a few parameters, such as the annealing temperature, sonication time, and reverse to forward (R/F) primer concentration ratio. We discovered that the generated methylene blue (MB) signals during the electrochemical sensing of non-amplified and amplified samples differ due to the different MB binding affinities based on the sequence length and base composition. The findings show that our developed electrochemical DNA biosensor successfully discriminates MB current signals in the presence and absence of the target genomic dengue virus, indicating that both samples were successfully treated. This work also provides interesting information about the critical factors in the preparation of genomic gene samples for developing miniaturized PCR-based electrochemical sensing applications in the future. We also discuss the limitations and provide suggestions related to using redox-indicator-based electrochemical biosensors to detect real genomic nucleic acid genes.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Tripathy S, Supraja P, Mohanty S, Sai VM, Agrawal T, Chowdary CG, Taranikanti M, Bandaru R, Mudunuru AK, Tadi LJ, Suravaram S, Siddiqui IA, Maddur S, Guntuka RK, Singh R, Singh V, Singh SG. Artificial Intelligence-Based Portable Bioelectronics Platform for SARS-CoV-2 Diagnosis with Multi-nucleotide Probe Assay for Clinical Decisions. Anal Chem 2021; 93:14955-14965. [PMID: 34694783 DOI: 10.1021/acs.analchem.1c01650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the context of the recent pandemic, the necessity of inexpensive and easily accessible rapid-test kits is well understood and need not be stressed further. In light of this, we report a multi-nucleotide probe-based diagnosis of SARS-CoV-2 using a bioelectronics platform, comprising low-cost chemiresistive biochips, a portable electronic readout, and an Android application for data acquisition with machine-learning-based decision making. The platform performs the desired diagnosis from standard nasopharyngeal and/or oral swabs (both on extracted and non-extracted RNA samples) without amplifying the viral load. Being a reverse transcription polymerase chain reaction-free hybridization assay, the proposed approach offers inexpensive, fast (time-to-result: ≤ 30 min), and early diagnosis, as opposed to most of the existing SARS-CoV-2 diagnosis protocols recommended by the WHO. For the extracted RNA samples, the assay accounts for 87 and 95.2% test accuracies, using a heuristic approach and a machine-learning-based classification method, respectively. In case of the non-extracted RNA samples, 95.6% decision accuracy is achieved using the heuristic approach, with the machine-learning-based best-fit model producing 100% accuracy. Furthermore, the availability of the handheld readout and the Android application-based simple user interface facilitates easy accessibility and portable applications. Besides, by eliminating viral RNA extraction from samples as a pre-requisite for specific detection, the proposed approach presents itself as an ideal candidate for point-of-care SARS-CoV-2 diagnosis.
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Affiliation(s)
- Suryasnata Tripathy
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Patta Supraja
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Swati Mohanty
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Vallepu Mohan Sai
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Tushant Agrawal
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | | | - Madhuri Taranikanti
- All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana 508126, India
| | - Rajiv Bandaru
- ESIC Medical College, S R Nagar, Hyderabad, Telangana 500038, India
| | | | - Lakshmi Jyothi Tadi
- All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana 508126, India.,ESIC Medical College, S R Nagar, Hyderabad, Telangana 500038, India
| | - Swathi Suravaram
- ESIC Medical College, S R Nagar, Hyderabad, Telangana 500038, India
| | | | - Srinivas Maddur
- ESIC Medical College, S R Nagar, Hyderabad, Telangana 500038, India
| | | | - Ranjana Singh
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Vikrant Singh
- School of Medicine, University of California, 1 Shields Avenue, Davis, California 95616, United States
| | - Shiv Govind Singh
- Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
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Gangwar R, Subrahmanyam C, Vanjari SRK. Facile, Label‐Free, Non‐Enzymatic Electrochemical Nanobiosensor Platform as a Significant Step towards Continuous Glucose Monitoring. ChemistrySelect 2021. [DOI: 10.1002/slct.202102727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Rahul Gangwar
- Department of Electrical Engineering Indian Institute of Technology Hyderabad India
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Zhang YY, Guillon FX, Griveau S, Bedioui F, Lazerges M, Slim C. Evolution of nucleic acids biosensors detection limit III. Anal Bioanal Chem 2021; 414:943-968. [PMID: 34668044 DOI: 10.1007/s00216-021-03722-9] [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: 04/06/2021] [Revised: 09/17/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022]
Abstract
This review is an update of two previous ones focusing on the limit of detection of electrochemical nucleic acid biosensors allowing direct detection of nucleic acid target (miRNA, mRNA, DNA) after hybridization event. A classification founded on the nature of the electrochemical transduction pathway is established. It provides an overall picture of the detection limit evolution of the various sensor architectures developed during the last three decades and a critical report of recent strategies.
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Affiliation(s)
- Yuan Yuan Zhang
- Institute of Chemistry for Life and Health Sciences (iCLeHS), Synthesis, Electrochemistry, Imaging and Analytical Systems for Diagnosis (SEISAD) Team, PSL Research University, CNRS, Chimie ParisTech, 75231, Paris, France
| | - François-Xavier Guillon
- Institute of Chemistry for Life and Health Sciences (iCLeHS), Synthesis, Electrochemistry, Imaging and Analytical Systems for Diagnosis (SEISAD) Team, PSL Research University, CNRS, Chimie ParisTech, 75231, Paris, France
| | - Sophie Griveau
- Institute of Chemistry for Life and Health Sciences (iCLeHS), Synthesis, Electrochemistry, Imaging and Analytical Systems for Diagnosis (SEISAD) Team, PSL Research University, CNRS, Chimie ParisTech, 75231, Paris, France
| | - Fethi Bedioui
- Institute of Chemistry for Life and Health Sciences (iCLeHS), Synthesis, Electrochemistry, Imaging and Analytical Systems for Diagnosis (SEISAD) Team, PSL Research University, CNRS, Chimie ParisTech, 75231, Paris, France.
| | - Mathieu Lazerges
- Faculté de Pharmacie de Paris, Faculté de Santé, Université de Paris, 4 avenue de l'Observatoire, 75006, Paris, France
| | - Cyrine Slim
- Institute of Chemistry for Life and Health Sciences (iCLeHS), Synthesis, Electrochemistry, Imaging and Analytical Systems for Diagnosis (SEISAD) Team, PSL Research University, CNRS, Chimie ParisTech, 75231, Paris, France.
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Khristunova E, Dorozhko E, Korotkova E, Kratochvil B, Vyskocil V, Barek J. Label-Free Electrochemical Biosensors for the Determination of Flaviviruses: Dengue, Zika, and Japanese Encephalitis. SENSORS (BASEL, SWITZERLAND) 2020; 20:E4600. [PMID: 32824351 PMCID: PMC7472106 DOI: 10.3390/s20164600] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
A highly effective way to improve prognosis of viral infectious diseases and to determine the outcome of infection is early, fast, simple, and efficient diagnosis of viral pathogens in biological fluids. Among a wide range of viral pathogens, Flaviviruses attract a special attention. Flavivirus genus includes more than 70 viruses, the most familiar being dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV). Haemorrhagic and encephalitis diseases are the most common severe consequences of flaviviral infection. Currently, increasing attention is being paid to the development of electrochemical immunological methods for the determination of Flaviviruses. This review critically compares and evaluates recent research progress in electrochemical biosensing of DENV, ZIKV, and JEV without labelling. Specific attention is paid to comparison of detection strategies, electrode materials, and analytical characteristics. The potential of so far developed biosensors is discussed together with an outlook for further development in this field.
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Affiliation(s)
- Ekaterina Khristunova
- School of Earth Sciences and Engineering, Department of Chemical Engineering, National Research Tomsk Polytechnic University, Lenin Avenue 30, 634050 Tomsk, Russia; (E.K.); (E.D.); (E.K.); (B.K.)
- UNESCO Laboratory of Environmental Electrochemistry, Department of Analytical Chemistry, Faculty of Science, Charles University, Albertov 6, 12843 Prague 2, Czech Republic;
- Department of Solid State Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Elena Dorozhko
- School of Earth Sciences and Engineering, Department of Chemical Engineering, National Research Tomsk Polytechnic University, Lenin Avenue 30, 634050 Tomsk, Russia; (E.K.); (E.D.); (E.K.); (B.K.)
| | - Elena Korotkova
- School of Earth Sciences and Engineering, Department of Chemical Engineering, National Research Tomsk Polytechnic University, Lenin Avenue 30, 634050 Tomsk, Russia; (E.K.); (E.D.); (E.K.); (B.K.)
| | - Bohumil Kratochvil
- School of Earth Sciences and Engineering, Department of Chemical Engineering, National Research Tomsk Polytechnic University, Lenin Avenue 30, 634050 Tomsk, Russia; (E.K.); (E.D.); (E.K.); (B.K.)
- Department of Solid State Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Vlastimil Vyskocil
- UNESCO Laboratory of Environmental Electrochemistry, Department of Analytical Chemistry, Faculty of Science, Charles University, Albertov 6, 12843 Prague 2, Czech Republic;
| | - Jiri Barek
- School of Earth Sciences and Engineering, Department of Chemical Engineering, National Research Tomsk Polytechnic University, Lenin Avenue 30, 634050 Tomsk, Russia; (E.K.); (E.D.); (E.K.); (B.K.)
- UNESCO Laboratory of Environmental Electrochemistry, Department of Analytical Chemistry, Faculty of Science, Charles University, Albertov 6, 12843 Prague 2, Czech Republic;
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Tripathy S, Singh SG. Label-Free Electrochemical Detection of DNA Hybridization: A Method for COVID-19 Diagnosis. TRANSACTIONS OF THE INDIAN NATIONAL ACADEMY OF ENGINEERING : AN INTERNATIONAL JOURNAL OF ENGINEERING AND TECHNOLOGY 2020; 5:205-209. [PMID: 38624377 PMCID: PMC7247285 DOI: 10.1007/s41403-020-00103-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023]
Abstract
This paper presents label-free electrochemical transduction as a suitable scheme for COVID-19-specific viral RNA/c-DNA detection, with an aim to facilitate point of care diagnosis. In lieu of this, we discuss the proposed electrochemical biosensing scheme, based on electrodeposited gold nanoparticles as the transducing elements. Specific to this approach, here, the protocols associated with the immobilization of the single-stranded probe nucleotide on to the biosensor, have also been laid out. This paper also discusses the methods of electrochemical analysis, to be used for data acquisition and subsequent calibration, in relation to target analyte detection. Towards facilitating portable diagnosis, development of miniaturized sensors and their integration with readout units have also been discussed.
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Affiliation(s)
- Suryasnata Tripathy
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285 India
| | - Shiv Govind Singh
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, Telangana 502285 India
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