1
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Omar C, Freisa M, Man HM, Kechkeche D, Dinh THN, Haghiri-Gosnet AM, Le Potier I, Gamby J. Optimizing Tris(2-Carboxyethyl)phosphine and Mercaptohexanol Concentrations for Thiolated Oligonucleotide Immobilization on Platinum Electrodes in Microfluidic Platforms. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:26616-26625. [PMID: 39628051 DOI: 10.1021/acs.langmuir.4c03566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
In this study, we propose a strategy to explore the impact of the proportion of tris(2-carboxyethyl)phosphine (TCEP) and 6-mercaptohexanol (MCH) on the efficiency of oligonucleotide functionalization on PDMS microfluidic channels equipped with pairs of homemade microfabricated platinum microelectrodes. We identified an optimal concentration of these compounds that enables the effective orientation and distribution of probes, thereby facilitating subsequent target hybridization. The experiment included optimizing sample injection into microfluidic channels. We used TCEP as a reducing agent to help the DNA probes adhere to the channel electrode better. This stopped the formation of disulfide bonds during the probe immobilization step. We found the optimal TCEP/MCH mixture ratio (5 mM TCEP and 50 mM MCH), which led to a more uniform distribution and orientation of the DNA probes on the platinum electrode. These optimized conditions resulted in a more compact DNA monolayer and enhanced detection capabilities. The biosensor's performance was evaluated by the detection of the hybridization of complementary DNA sequences in the presence of equimolar Fe(CN)63-/Fe(CN)64-. The detection of the synthetic GP8 resistance gene is facilitated by a measurable decrease in the electron transfer rate, which is directly proportional to its concentration. Under the optimized conditions, the DNA biosensor showed excellent sensitivity (with a detection limit of 10-17 M) and high specificity when tested against noncomplementary DNA strands.
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Affiliation(s)
- Choayb Omar
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Martina Freisa
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Hiu Mun Man
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Djamila Kechkeche
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Thi Hong Nhung Dinh
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Anne-Marie Haghiri-Gosnet
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Isabelle Le Potier
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
| | - Jean Gamby
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies (C2N), 91120 Palaiseau, France
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2
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Chen P, Wang J, Xue Y, Wang C, Sun W, Yu J, Guo H. From challenge to opportunity: Revolutionizing the monitoring of emerging contaminants in water with advanced sensors. WATER RESEARCH 2024; 265:122297. [PMID: 39208686 DOI: 10.1016/j.watres.2024.122297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/23/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Emerging contaminants in water represent long-term and unpredictable threats to both environmental and human health due to their persistence and bioaccumulation. Current research predominantly focuses on their removal rather than sustained monitoring. This review comprehensively investigates advanced sensor technologies for detecting these contaminants in water, critically evaluating biosensors, optical sensors, electrochemical sensors, and nanomaterial sensors. Elucidating the operational principles, performance metrics such as detection thresholds, and the pros and cons of their practical applications, the review addresses a significant research gap in environmental monitoring. Moreover, it enhances understanding of sensor effectiveness, which in turn guides researchers in selecting the right sensor types for various environmental scenarios. Furthermore, by emphasizing the integration of nanotechnology and the standardization of evaluation protocols, it promotes the development of robust, deployable sensing solutions. Ultimately, this leads to the proposal of a strategic framework aimed at significantly improving the detection capabilities of emerging contaminants and supporting the preservation of environmental health.
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Affiliation(s)
- Peng Chen
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Jingquan Wang
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Yanei Xue
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chunmiao Wang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jianwei Yu
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hongguang Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, 610065, China.
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3
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Lucia-Tamudo J, Nogueira JJ, Díaz-Tendero S. Charge Transfer Mechanism in Guanine-Based Self-Assembled Monolayers on a Gold Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:15129-15139. [PMID: 38984413 PMCID: PMC11270990 DOI: 10.1021/acs.langmuir.4c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
In this work, we have theoretically determined the one-electron oxidation potentials and charge transfer mechanisms in complex systems based on a self-assembled monolayer of guanine molecules adsorbed on a gold surface through different organic linkers. Classical molecular dynamics simulations were carried out to sample the conformational space of both the neutral and the cationic species. Thus, the redox potentials were determined for the ensembles of geometries through multiscale quantum-mechanics/molecular-mechanics/continuum solvation model calculations in the framework of the Marcus theory and in combination with an additive scheme previously developed. In this context, conformational sampling, description of the environment, and effects caused by the linker have been considered. Applying this methodology, we unravel the phenomena of electric current transport by evaluating the different stages in which charge transfer could occur. The results revealed how the positive charge migrates from the organic layer to the gold surface. Specifically, the transport mechanism seems to take place mainly along a single ligand and driven with the help of the electrostatic interactions of the surrounding molecules. Aside, several self-assembled monolayers with different linkers have been analyzed to understand how the nature of that moiety can tune the redox properties and the efficiency of the transport. We have found that the conjugation between the guanine and the linker, at the same time conjugated to the gold surface, gives rise to a more efficient transport. In conclusion, the established computational protocol sheds light on the mechanism behind charge transport in electrochemical DNA-based biosensor nanodevices.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
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4
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches. J Chem Inf Model 2024; 64:4802-4810. [PMID: 38856665 PMCID: PMC11200263 DOI: 10.1021/acs.jcim.4c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The number of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge-transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes, and the Marcus theory. One-electron oxidation potential and hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by clustering analysis provides accurate results when compared with those obtained from sampling, reducing considerably the computational cost.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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5
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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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6
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Fattahi M, Maghsudlu M, Razipour M, Movahedpour A, Ghadami M, Alizadeh M, Khatami SH, Taheri-Anganeh M, Ghasemi E, Ghasemi H, Aiiashi S, Ghadami E. MicroRNA biosensors for detection of glioblastoma. Clin Chim Acta 2024; 556:117829. [PMID: 38355000 DOI: 10.1016/j.cca.2024.117829] [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: 12/10/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Glioblastoma (GBM) is the most common type of malignant brain tumor.The discovery of microRNAs and their unique properties have made them suitable tools as biomarkers for cancer diagnosis, prognosis, and evaluation of therapeutic response using different types of nanomaterials as sensitive and specific biosensors. In this review, we discuss microRNA-based electrochemical biosensing systems and the use of nanoparticles in the evolving development of microRNA-based biosensors in glioblastoma.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Mohadese Maghsudlu
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Razipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohsen Ghadami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Alizadeh
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | | | | | - Saleh Aiiashi
- Abadan University of Medical Sciences, Abadan, Iran.
| | - Elham Ghadami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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7
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Li R, Zeng X, Lv M, Zhang R, Zhang S, Zhang T, Yu X, Li C, Jin L, Zhao C. First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne. Phys Chem Chem Phys 2024; 26:5558-5568. [PMID: 38284214 DOI: 10.1039/d3cp04726a] [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: 01/30/2024]
Abstract
Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.
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Affiliation(s)
- Ruirui Li
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Xia Zeng
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Mengdan Lv
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Ruiying Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Shengrui Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Tianlei Zhang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Xiaohu Yu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Chen Li
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
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8
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Lucia-Tamudo J, Alcamí M, Díaz-Tendero S, Nogueira JJ. One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA. Biochemistry 2023; 62:3312-3322. [PMID: 37923303 PMCID: PMC10666269 DOI: 10.1021/acs.biochem.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
| | - Manuel Alcamí
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Sergio Díaz-Tendero
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
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9
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Akbari Nakhjavani S, Tokyay BK, Soylemez C, Sarabi MR, Yetisen AK, Tasoglu S. Biosensors for prostate cancer detection. Trends Biotechnol 2023; 41:1248-1267. [PMID: 37147246 DOI: 10.1016/j.tibtech.2023.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/22/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023]
Abstract
Prostate cancer (PC) is one of the most common tumors and a leading cause of mortality among men, resulting in ~375 000 deaths annually worldwide. Various analytical methods have been designed for quantitative and rapid detection of PC biomarkers. Electrochemical (EC), optical, and magnetic biosensors have been developed to detect tumor biomarkers in clinical and point-of-care (POC) settings. Although POC biosensors have shown potential for detection of PC biomarkers, some limitations, such as the sample preparation, should be considered. To tackle such shortcomings, new technologies have been utilized for development of more practical biosensors. Here, biosensing platforms for the detection of PC biomarkers such as immunosensors, aptasensors, genosensors, paper-based devices, microfluidic systems, and multiplex high-throughput platforms, are discussed.
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Affiliation(s)
- Sattar Akbari Nakhjavani
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul 34450, Turkey; Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Begum K Tokyay
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey; Department of Biomedical Sciences and Engineering, Koç University, 34450 Istanbul, Turkey
| | - Cansu Soylemez
- Department of Biomedical Sciences and Engineering, Koç University, 34450 Istanbul, Turkey
| | - Misagh R Sarabi
- Department of Biomedical Sciences and Engineering, Koç University, 34450 Istanbul, Turkey; Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany 70569
| | - Ali K Yetisen
- Department of Chemical Engineering, Imperial College, London SW7 2AZ, UK
| | - Savas Tasoglu
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul 34450, Turkey; Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey; Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany 70569; Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Turkey; Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey.
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10
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA. Phys Chem Chem Phys 2023; 25:14578-14589. [PMID: 37191244 DOI: 10.1039/d3cp00884c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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11
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Eskiköy Bayraktepe D, Yıldız C, Yazan Z. The development of electrochemical DNA biosensor based on poly-l-methionine and bimetallic AuPt nanoparticles coating: Picomolar detection of Imatinib and Erlotinib. Talanta 2023; 257:124361. [PMID: 36801759 DOI: 10.1016/j.talanta.2023.124361] [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: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
We report on the preparation of a new and simple electrochemical DNA biosensor based on DNA/AuPt/p-L-Met coating on a screen-printed carbon electrode (SPE) and its use in the determination of the cancer therapy agents, Imatinib (IMA) and Erlotinib (ERL). Poly-l-methionine (p-L-Met), gold, and platinum nanoparticles (AuPt) were successfully coated by one-step electrodeposition onto the SPE from a solution containing L-Met, HAuCl4, and H2PtCl6. The immobilization of DNA was achieved by drop-casting on the surface of the modified electrode. Cyclic Voltammetry (CV), Electrochemical Impedance Spectroscopy (EIS), Field-Emission Scanning Electron Microscopy (FE-SEM), Energy-Dispersive X-ray Spectroscopy (EDX), and Atomic Force Microscopy (AFM) were used to investigate the morphology, the structure, and the electrochemical performance of the sensor. Experimental factors influencing the coating and DNA immobilization processes were optimized. The peak currents originating from guanine (G) and adenine (A) oxidation of ds-DNA were used as signals to quantify IMA and ERL in the concentration range 2.33-80 nM and 0.032-1.0 nM with the LODs of 0.18 nM and 0.009 nM, respectively. The biosensor developed was suitable for determining IMA and ERL in human serum and pharmaceutical samples.
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Affiliation(s)
| | - Ceren Yıldız
- Ankara University Faculty of Science Department of Chemistry, Ankara, 06560, Turkey
| | - Zehra Yazan
- Ankara University Faculty of Science Department of Chemistry, Ankara, 06560, Turkey.
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12
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Lucia-Tamudo J, Nogueira JJ, Díaz-Tendero S. An Efficient Multilayer Approach to Model DNA-Based Nanobiosensors. J Phys Chem B 2023; 127:1513-1525. [PMID: 36779932 PMCID: PMC9969517 DOI: 10.1021/acs.jpcb.2c07225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
In this work, we present a full computational protocol to successfully obtain the one-electron reduction potential of nanobiosensors based on a self-assembled monolayer of DNA nucleobases linked to a gold substrate. The model is able to account for conformational sampling and environmental effects at a quantum mechanical (QM) level efficiently, by combining molecular mechanics (MM) molecular dynamics and multilayer QM/MM/continuum calculations within the framework of Marcus theory. The theoretical model shows that a guanine-based biosensor is more prone to be oxidized than the isolated nucleobase in water due to the electrostatic interactions between the assembled guanine molecules. In addition, the redox properties of the biosensor can be tuned by modifying the nature of the linker that anchor the nucleobases to the metal support.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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13
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Liu L, Chang Y, Ji X, Chen J, Zhang M, Yang S. Surface-tethered electrochemical biosensor for telomerase detection by integration of homogeneous extension and hybridization reactions. Talanta 2023; 253:123597. [PMID: 35710468 DOI: 10.1016/j.talanta.2022.123597] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/02/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
The general electrochemical biosensors for telomerase detection require the immobilization of primers on the electrode surface for telomeric extension and hybridization reactions. However, immobilization of primers may suffer from the challenges of hindrance effect and configuration freedom, thus reducing the extension and hybridization efficiency. Herein, we developed a sensitive electrochemical biosensor for telomerase detection by integration of homogeneous extension and hybridization reactions and surface-tethered detection. In the presence of telomerase, the biotinylated primer (bio-primer) was efficiently elongated with telomeric repeats of (TTAGGG)n at the 3' end in solution. Then, the extension product (bio-DNA) was hybridized with the signal probe DNA modified on the surface of ferrocene (Fc)-capped gold nanoparticle (AuNP). The bio-DNA/DNA/Fc-AuNP hybrids were then tethered by streptavidin-modified electrodes through the specific avidin-biotin interactions, thus producing strong electrochemical signals from the oxidation of Fc tags. The biosensor was successfully used to determine telomerase in HeLa cells and monitor the inhibition efficiency of inhibitor. A wide linear range for the detection of telomerase extracted from HeLa cells was attained. This method has great potential in clinical diagnosis and anti-cancer drug development, and should be beneficial for the fabrication of novel biosensors by integration of homogeneous catalysis and hybridization reactions.
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Affiliation(s)
- Lin Liu
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China.
| | - Yong Chang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China; School of Chemistry and Materials Engineering, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xingyue Ji
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Jiayu Chen
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Mengyu Zhang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Suling Yang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan 455000, People's Republic of China.
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14
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Sarwar S, Lin MC, Amezaga C, Wei Z, Iyayi E, Polk H, Wang R, Wang H, Zhang X. Ultrasensitive electrochemical biosensors based on zinc sulfide/graphene hybrid for rapid detection of SARS-CoV-2. ADVANCED COMPOSITES AND HYBRID MATERIALS 2023; 6:49. [PMID: 36718472 PMCID: PMC9879254 DOI: 10.1007/s42114-023-00630-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/07/2023] [Accepted: 01/15/2023] [Indexed: 05/12/2023]
Abstract
UNLABELLED The coronavirus disease 2019 (COVID-19) is a highly contagious and fatal disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In general, the diagnostic tests for COVID-19 are based on the detection of nucleic acid, antibodies, and protein. Among different analytes, the gold standard of the COVID-19 test is the viral nucleic acid detection performed by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. However, the gold standard test is time-consuming and requires expensive instrumentation, as well as trained personnel. Herein, we report an ultrasensitive electrochemical biosensor based on zinc sulfide/graphene (ZnS/graphene) nanocomposite for rapid and direct nucleic acid detection of SARS-CoV-2. We demonstrated a simple one-step route for manufacturing ZnS/graphene by employing an ultrafast (90 s) microwave-based non-equilibrium heating approach. The biosensor assay involves the hybridization of target DNA or RNA samples with probes that are immersed into a redox active electrolyte, which are detectable by electrochemical measurements. In this study, we have performed the tests for synthetic DNA samples and, SARS-CoV-2 standard samples. Experimental results revealed that the proposed biosensor could detect low concentrations of all different SARS-CoV-2 samples, using such as S, ORF 1a, and ORF 1b gene sequences as targets. This microwave-synthesized ZnS/graphene-based biosensor could be reliably used as an on-site, real-time, and rapid diagnostic test for COVID-19. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42114-023-00630-7.
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Affiliation(s)
- Shatila Sarwar
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849 USA
| | - Mao-Chia Lin
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849 USA
| | - Carolina Amezaga
- Department of Material Engineering, Auburn University, Auburn, AL 36849 USA
| | - Zhen Wei
- Department of Metallurgical and Materials Engineering, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Etinosa Iyayi
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088 USA
| | - Haseena Polk
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088 USA
| | - Ruigang Wang
- Department of Metallurgical and Materials Engineering, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Honghe Wang
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088 USA
| | - Xinyu Zhang
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849 USA
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15
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Bilge S, Dogan-Topal B, Taskin Tok T, Atici EB, Sınağ A, Ozkan SA. Investigation of the interaction between anticancer drug ibrutinib and double-stranded DNA by electrochemical and molecular docking techniques. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Mereuta L, Asandei A, Dragomir I, Park J, Park Y, Luchian T. A Nanopore Sensor for Multiplexed Detection of Short Polynucleotides Based on Length-Variable, Poly-Arginine-Conjugated Peptide Nucleic Acids. Anal Chem 2022; 94:8774-8782. [PMID: 35666169 DOI: 10.1021/acs.analchem.2c01587] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Real-time and easy-to-use detection of nucleic acids is crucial for many applications, including medical diagnostics, genetic screening, forensic science, or monitoring the onset and progression of various diseases. Herein, an exploratory single-molecule approach for multiplexed discrimination among similar-sized single-stranded DNAs (ssDNA) is presented. The underlying strategy combined (i) a method based on length-variable, short arginine (poly-Arg) tags appended to peptide nucleic acid (PNA) probes, designed to hybridize with selected regions from complementary ssDNA targets (cDNA) in solution and (ii) formation and subsequent detection with the α-hemolysin nanopore of (poly-Arg)-PNA-cDNA duplexes containing two overhangs associated with the poly-Arg tail and the non-hybridized segment from ssDNA. We discovered that the length-variable poly-Arg tail marked distinctly the molecular processes associated with the nanopore-mediated duplexes capture, trapping and unzipping. This enabled the detection of ssDNA targets via the signatures of (poly-Arg)-PNA-cDNA blockade events, rendered most efficient from the β-barrel entrance of the nanopore, and scaled proportional in efficacy with a larger poly-Arg moiety. We illustrate the approach by sensing synthetic ssDNAs designed to emulate fragments from two regions of SARS-CoV-2 nucleocapsid phosphoprotein N-gene.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Isabela Dragomir
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, 38065 Kongju, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, 61452 Gwangju, Republic of Korea
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
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17
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Wasiewska LA, Diaz FG, Shao H, Burgess CM, Duffy G, O'Riordan A. Highly sensitive electrochemical sensor for the detection of Shiga toxin-producing E. coli (STEC) using interdigitated micro-electrodes selectively modified with a chitosan-gold nanocomposite. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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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 2022. [PMID: 34851806 DOI: 10.1016/j.apsadv.2021.100064] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
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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19
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Du R, Yang X, Jin P, Guo Y, Cheng Y, Yu H, Xie Y, Qian H, Yao W. G-quadruplex based biosensors for the detection of food contaminants. Crit Rev Food Sci Nutr 2022; 63:8808-8822. [PMID: 35389275 DOI: 10.1080/10408398.2022.2059753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
G-quadruplex (G4) is a very interesting DNA structure, commonly associated with cancer and its treatment. With flexible binding ability, G4 has been extended as a significant component in biosensors. On account of its simple operation, high sensitivity and low cost, G4-based biosensors have attracted considerable interest for the detection of food contaminants. In this review, research published in recent 5 years is collated from a principle perspective, that is target recognition and signal transduction. Contaminants with G4 binding capacity are illustrated, emerging G4-based biosensors including colorimetric, electrochemical and fluorescent sensors are also elaborated. The current review indicates that G4 has provided an efficient and effective solution for the rapid detection of food contaminants. A distinctive feature of G4 as recognition unit is the simple composition, but the selectivity is still unsatisfactory. As signal reporter, G4/hemin DNAzyme has not only achieved amplified signals, but also enabled visualized detection, which offers great potential for on-site measurement. With improved selectivity and visualized signal, the combination of aptamer and G4 seems to be an ideal strategy. This promising combination should be developed for the real-time monitor of multiple contaminants in food matrix.
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Affiliation(s)
- Rong Du
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiebingqing Yang
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Ping Jin
- Suzhou Product Quality Supervision and Inspection Institute, Suzhou, China
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Engineering Research Center of Dairy Quality and Safety Control Technology (Ministry of Education), Inner Mongolia University, Inner Mongolia Autonomous Region, China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
- Engineering Research Center of Dairy Quality and Safety Control Technology (Ministry of Education), Inner Mongolia University, Inner Mongolia Autonomous Region, China
| | - He Qian
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China
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20
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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: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [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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21
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Xu L, Zhou B, Song Y, Cai X, Lu W. Electron-Transfer Study and Single Nucleotide Discrimination of a DNA Sequence on a Polymer Gold Electrode (PGE) by Differential Pulse Voltammetry (DPV). ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2035390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Long Xu
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Binyu Zhou
- Department of Interventional Oncology, the People's Hospital of China Medical University, Shenyang, China
| | - Yaling Song
- Zhejiang GeneX Precision Medicine Co., Ltd, Hangzhou, P.R. China
| | - Xu Cai
- Department of Songbei Respiratory Medicine, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Lu
- Zhejiang GeneX Precision Medicine Co., Ltd, Hangzhou, P.R. China
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22
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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: 18] [Impact Index Per Article: 4.5] [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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23
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Ning Z, Chen M, Wu G, Zhang Y, Shen Y. Recent advances of functional nucleic acids-based electrochemiluminescent sensing. Biosens Bioelectron 2021; 191:113462. [PMID: 34198172 DOI: 10.1016/j.bios.2021.113462] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/12/2021] [Accepted: 06/21/2021] [Indexed: 12/19/2022]
Abstract
Electroluminescence (ECL) has been used in extensive applications ranging from bioanalysis to clinical diagnosis owing to its simple device requirement, low background, high sensitivity, and wide dynamic range. Nucleic acid is a significant theme in ECL bioanalysis. The inherent versatile selective molecular recognition of nucleic acids and their programmable self-assembly make it desirable for the robust construction of nanostructures. Benefiting from their unique structures and physiochemical properties, ECL biosensing based on nucleic acids has experienced rapid growth. This review focuses on recent applications of nucleic acids in ECL sensing systems, particularly concerning the employment of nucleic acids as molecular recognition elements, signal amplification units, and sensing interface schemes. In the end, an outlook of nucleic acid-based ECL biosensing will be provided for future developments and directions. We envision that nucleic acids, which act as an essential component for both bioanalysis and clinical diagnosis, will provide a new thinking model and driving force for developing next-generation sensing systems.
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Affiliation(s)
- Zhenqiang Ning
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China
| | - Mengyuan Chen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China
| | - Guoqiu Wu
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China; Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, China
| | - Yuanjian Zhang
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China
| | - Yanfei Shen
- Medical School, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210009, China; Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, China.
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24
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Development of Electrochemical DNA Biosensor for Equine Hindgut Acidosis Detection. SENSORS 2021; 21:s21072319. [PMID: 33810389 PMCID: PMC8037926 DOI: 10.3390/s21072319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 12/20/2022]
Abstract
The pH drop in the hindgut of the horse is caused by lactic acid-producing bacteria which are abundant when a horse’s feeding regime is excessively carbohydrate rich. This drop in pH below six causes hindgut acidosis and may lead to laminitis. Lactic acid-producing bacteria Streptococcus equinus and Mitsuokella jalaludinii have been found to produce high amounts of L-lactate and D-lactate, respectively. Early detection of increased levels of these bacteria could allow the horse owner to tailor the horse’s diet to avoid hindgut acidosis and subsequent laminitis. Therefore, 16s ribosomal ribonucleic acid (rRNA) sequences were identified and modified to obtain target single stranded deoxyribonucleic acid (DNA) from these bacteria. Complementary single stranded DNAs were designed from the modified target sequences to form capture probes. Binding between capture probe and target single stranded deoxyribonucleic acid (ssDNA) in solution has been studied by gel electrophoresis. Among pairs of different capture probes and target single stranded DNA, hybridization of Streptococcus equinus capture probe 1 (SECP1) and Streptococcus equinus target 1 (SET1) was portrayed as gel electrophoresis. Adsorptive stripping voltammetry was utilized to study the binding of thiol modified SECP1 over gold on glass substrates and these studies showed a consistent binding signal of thiol modified SECP1 and their hybridization with SET1 over the gold working electrode. Cyclic voltammetry and electrochemical impedance spectroscopy were employed to examine the binding of thiol modified SECP1 on the gold working electrode and hybridization of thiol modified SECP1 with the target single stranded DNA. Both demonstrated the gold working electrode surface was modified with a capture probe layer and hybridization of the thiol bound ssDNA probe with target DNA was indicated. Therefore, the proposed electrochemical biosensor has the potential to be used for the detection of the non-synthetic bacterial DNA target responsible for equine hindgut acidosis.
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25
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Eksin E, Torul H, Yarali E, Tamer U, Papakonstantinou P, Erdem A. Paper-based electrode assemble for impedimetric detection of miRNA. Talanta 2020; 225:122043. [PMID: 33592766 DOI: 10.1016/j.talanta.2020.122043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
In the present work, a paper-based electrode assemble was developed and implemented to detect target microRNA 155 (miRNA 155) via electrochemical impedance spectroscopy (EIS) measurements. In this concept, gold nanoparticles (AuNPs) modified paper based electrode assemble system (AuNP-PE) was designed, and characterized by scanning electron microscopy (SEM), cyclic voltammetry (CV) and EIS measurements. The impedimetric detection of miRNA 155 was performed by measuring the fractional change at the charge transfer resistance (Rct). The detection limits were found as 33.8 nM in PBS and 93.4 nM in fetal bovine serum (FBS) medium, respectively. The selectivity of the proposed assay was tested against to non-complementary (NC) and mismatch (MM) miRNA sequences in the presence of mixture sample containing miRNA:NC (1:1) and miRNA:MM (1:1) in PBS (pH 7.40) or FBS. The analytical performance and the selectivity of impedimetric biosensor were also tested in FBS.
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Affiliation(s)
- Ece Eksin
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Bornova, 35100, İzmir, Turkey
| | - Hilal Torul
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06330, Ankara, Turkey
| | - Ece Yarali
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Bornova, 35100, İzmir, Turkey
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, 06330, Ankara, Turkey.
| | - Pagona Papakonstantinou
- School of Engineering, Engineering Research Institute, Ulster University, Newtownabbey BT37 0QB, United Kingdom
| | - Arzum Erdem
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, Bornova, 35100, İzmir, Turkey.
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Hai X, Li Y, Zhu C, Song W, Cao J, Bi S. DNA-based label-free electrochemical biosensors: From principles to applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116098] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Homogeneous electrochemical biosensor for microRNA based on enzyme-driven cascaded signal amplification strategy. Anal Bioanal Chem 2020; 413:4681-4688. [PMID: 33185746 DOI: 10.1007/s00216-020-03027-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
Infectious diseases are a long-standing and severe global public health problem. The rapid diagnosis of infectious diseases is an urgent need to solve this problem. MicroRNA (miRNA) plays an important role in the intervention of some infectious diseases and is expected to become a potential biomarker for the diagnosis and prognosis of infectious diseases. It is of great significance to develop rapid and sensitive methods for detecting miRNA for effective control of infectious diseases. In this study, a simple and highly sensitive homogeneous electrochemical method for microRNAs using enzyme-driven cascaded signal amplification has been developed. In the presence of target miRNA, the reaction system produced plenty of MB-labeled single-nucleotide fragments (MB-MF) containing a few negative charges, which can diffuse to the negative surface of the ITO electrode easily, so an obvious electrochemical signal enhancement was obtained. Without the target, MB-HP contains a relatively large amount of negative charges due to the phosphates on the DNA chain, which cannot be digested by the enzyme and cannot diffuse freely to the negatively charged ITO electrode, so only a small signal was detected. The enhanced electrochemical response has a linear relationship with the logarithm of miRNA concentration in the range of 10 fM to 10 nM and the limit of detection as low as 3.0 fM. Furthermore, the proposed strategy showed the capability of discriminating single-base mismatch and performed eligibly in the analysis of miRNA in cell lysates, exhibiting great potential for disease diagnosis and biomedical research. Graphical abstract.
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Farshchi F, Saadati A, Hasanzadeh M. Optimized DNA-based biosensor for monitoring Leishmania infantum in human plasma samples using biomacromolecular interaction: a novel platform for infectious disease diagnosis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4759-4768. [PMID: 32936128 DOI: 10.1039/d0ay01516d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Leishmania parasite identification is very important in clinical studies of leishmaniasis and its diagnosis. Though there are various clinical and epidemiological approaches to identifying Leishmania infantum, due to some limitations of the traditional methods, sensitive and specific techniques are needed and are in great demand. To achieve selective and rapid detection, a sensitive signal transducer with high surface area is necessary. In this work, a new paper sensor was fabricated using silver nanoprisms electrodeposited on the GQD conductive nano-ink (Ag NPr/GQDs nano-ink). A high surface area and suitable interface for anchoring biomolecules was achieved by electrodepositing gold nanoparticles (AuNPs) functionalized with cysteamine (AuNPs-CysA) on the surface of the paper sensor altered by Ag NPr/GQDs nano-ink. To prepare a sensitive and selective bio-device for the recognition of Leishmania in human plasma specimens, a DNA-thiol probe was stabilized on the surface of the platform. Hybridization of DNA was evaluated by chronoamperometry (ChA). The engineered DNA-based paper biosensor showed high sensitivity and selectivity for the identification of Leishmania genomic DNA. Under optimum circumstances, a linear range was obtained using photographic paper from 1 μM to 1 zM and an ivory sheet from 1 nM to 1 zM. The lower limits of quantitation (LLOQ) on the photographic paper and ivory sheet were 1 zM. In addition, the designed DNA-based biosensor revealed well-defined performance in the recognition of mismatched sequences (single base, two base and three base mismatches) and selectivity.
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Affiliation(s)
- Fatemeh Farshchi
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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29
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Lahcen AA, Rauf S, Beduk T, Durmus C, Aljedaibi A, Timur S, Alshareef HN, Amine A, Wolfbeis OS, Salama KN. Electrochemical sensors and biosensors using laser-derived graphene: A comprehensive review. Biosens Bioelectron 2020; 168:112565. [PMID: 32927277 DOI: 10.1016/j.bios.2020.112565] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
Laser-derived graphene (LDG) technology is gaining attention as a promising material for the development of novel electrochemical sensors and biosensors. Compared to established methods for graphene synthesis, LDG provides many advantages such as cost-effectiveness, fast electron mobility, mask-free, green synthesis, good electrical conductivity, porosity, mechanical stability, and large surface area. This review discusses, in a critical way, recent advancements in this field. First, we focused on the fabrication and doping of LDG platforms using different strategies. Next, the techniques for the modification of LDG sensors using nanomaterials, conducting polymers, biological and artificial receptors are presented. We then discussed the advances achieved for various LDG sensing and biosensing schemes and their applications in the fields of environmental monitoring, food safety, and clinical diagnosis. Finally, the drawbacks and limitations of LDG based electrochemical biosensors are addressed, and future trends are also highlighted.
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Affiliation(s)
- Abdellatif Ait Lahcen
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Sakandar Rauf
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tutku Beduk
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ceren Durmus
- Department of Biochemistry, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Abdulrahman Aljedaibi
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Suna Timur
- Department of Biochemistry, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Husam N Alshareef
- Materials Science and Engineering, Physical Science & Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Aziz Amine
- Chemical Analysis and Biosensors Group, Laboratory of Process Engineering and Environment, Faculty of Science and Techniques, Hassan II University of Casablanca, B.P. 146. Mohammedia, Morocco.
| | - Otto S Wolfbeis
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040, Regensburg, Germany.
| | - Khaled N Salama
- Sensors Lab, Advanced Membranes and Porous Materials Center (AMPMC), Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Zanut A, Cian A, Cefarin N, Pozzato A, Tormen M. Nanoelectrode Arrays Fabricated by Thermal Nanoimprint Lithography for Biosensing Application. BIOSENSORS 2020; 10:E90. [PMID: 32764306 PMCID: PMC7459808 DOI: 10.3390/bios10080090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Electrochemical sensors are devices capable of detecting molecules and biomolecules in solutions and determining the concentration through direct electrical measurements. These systems can be miniaturized to a size less than 1 µm through the creation of small-size arrays of nanoelectrodes (NEA), offering advantages in terms of increased sensitivity and compactness. In this work, we present the fabrication of an electrochemical platform based on an array of nanoelectrodes (NEA) and its possible use for the detection of antigens of interest. NEAs were fabricated by forming arrays of nanoholes on a thin film of polycarbonate (PC) deposited on boron-doped diamond (BDD) macroelectrodes by thermal nanoimprint lithography (TNIL), which demonstrated to be a highly reliable and reproducible process. As proof of principle, gliadin protein fragments were physisorbed on the polycarbonate surface of NEAs and detected by immuno-indirect assay using a secondary antibody labelled with horseradish peroxidase (HRP). This method allows a successful detection of gliadin, in the range of concentration of 0.5-10 μg/mL, by cyclic voltammetry taking advantage from the properties of NEAs to strongly suppress the capacitive background signal. We demonstrate that the characteristics of the TNIL technology in the fabrication of high-resolution nanostructures together with their low-cost production, may allow to scale up the production of NEAs-based electrochemical sensing platform to monitor biochemical molecules for both food and biomedical applications.
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Affiliation(s)
- Alessandra Zanut
- Department of Physics, University of Trieste, P.le Europa 1, 34100 Trieste, Italy;
- IOM-CNR, TASC Laboratory, Area Science Park—Basovizza, S.S 14 Km 163.5, I-34149 Trieste, Italy;
| | - Alessandro Cian
- ThunderNIL srl, via Foscolo 8, I-35131 Padova, Italy; (A.C.); (A.P.)
- Center for Materials and Microsystems, Fondazione Bruno Kessler, 38123 Trento, Italy
| | - Nicola Cefarin
- Department of Physics, University of Trieste, P.le Europa 1, 34100 Trieste, Italy;
- IOM-CNR, TASC Laboratory, Area Science Park—Basovizza, S.S 14 Km 163.5, I-34149 Trieste, Italy;
| | | | - Massimo Tormen
- IOM-CNR, TASC Laboratory, Area Science Park—Basovizza, S.S 14 Km 163.5, I-34149 Trieste, Italy;
- ThunderNIL srl, via Foscolo 8, I-35131 Padova, Italy; (A.C.); (A.P.)
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31
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Wu LR, Fang JZ, Khodakov D, Zhang DY. Nucleic Acid Quantitation with Log-Linear Response Hybridization Probe Sets. ACS Sens 2020; 5:1604-1614. [PMID: 32475109 DOI: 10.1021/acssensors.0c00052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Concentrations of different nucleic acid species in biological samples span many orders of magnitude. A real-time polymerase chain reaction maps the concentration of a target nucleic acid sequence log-linearly into cycle threshold to enable quantitation with a wide dynamic range but suffers from enzymatic biases. Here, we present a general design for constructing hybridization probe sets with highly log-linear response curves to enable accurate enzyme-free quantitation across large ranges (more than 6 logs) of target DNA concentrations. The sensitivity of each component probe is accurately adjusted via formulation stoichiometry to reduce the standard error of target quantitation down to 7%. As a proof of concept, we show multiplexed quantitation of three microRNA species in total RNA of the human brain and liver.
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Affiliation(s)
- Lucia R. Wu
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - John Z. Fang
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Dmitriy Khodakov
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
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32
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Can F, Ökten HE, Ergön-Can T, Ergenekon P, Özkan M, Erhan E. Thermodynamically designed target-specific DNA probe as an electrochemical hybridization biosensor. Bioelectrochemistry 2020; 135:107553. [PMID: 32442773 DOI: 10.1016/j.bioelechem.2020.107553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 01/28/2023]
Abstract
Applications of molecular techniques to elucidate identity or function using biomarkers still remain highly empirical and biosensors are no exception. In the present study, target-specific oligonucleotide probes for E. coli K12 were designed thermodynamically and applied in an electrochemical DNA biosensor setup. Biosensor was prepared by immobilization of a stem-loop structured probe, modified with a thiol functional group at its 5' end and a biotin molecule at its 3' end, on a gold electrode through self-assembly. Mercaptopropionic acid (MPA) was used to optimize the surface probe density of the electrode. Hybridization between the immobilized probe and the target DNA was detected via the electrochemical response of streptavidin-horseradish peroxidase in the presence of the substrate. The amperometric response showed a linear relationship with the target DNA concentration, ranging from 10 and 400 nM, with a correlation coefficient of 0.989. High selectivity and good repeatability of the biosensor showed that the thermodynamic approach to oligonucleotide probe design can be used in development of electrochemical DNA biosensors.
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Affiliation(s)
- Faruk Can
- Gebze Technical University, Department of Environmental Engineering, 41400 Gebze, Kocaeli, Turkey
| | - Hatice Eser Ökten
- Izmir Institute of Technology, Department of Environmental Engineering, 35430 Urla, İzmir, Turkey
| | - Tülay Ergön-Can
- Atatürk University, Department of Biology, Faculty of Science, 25240 Erzurum, Turkey
| | - Pınar Ergenekon
- Gebze Technical University, Department of Environmental Engineering, 41400 Gebze, Kocaeli, Turkey
| | - Melek Özkan
- Gebze Technical University, Department of Environmental Engineering, 41400 Gebze, Kocaeli, Turkey
| | - Elif Erhan
- Uskudar University, Department of Bioengineering, 34662 Uskudar, Istanbul, Turkey.
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33
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Goodchild SA, Gao R, Shenton DP, McIntosh AJS, Brown T, Bartlett PN. Direct Detection and Discrimination of Nucleotide Polymorphisms Using Anthraquinone Labeled DNA Probes. Front Chem 2020; 8:381. [PMID: 32478035 PMCID: PMC7235368 DOI: 10.3389/fchem.2020.00381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023] Open
Abstract
A novel electrochemical detection approach using DNA probes labeled with Anthraquinone (AQ) as a reporter moiety has been successfully exploited as a method for the direct detection of DNA targets. This assay uses simple voltammetry techniques (Differential Pulse Voltammetry) to exploit the unique responsiveness of AQ to its chemical environments within oxygenated aqueous buffers, providing a specific detection mechanism as a result of DNA hybridization. This measurement is based on a cathodic shift of the reduction potential of the AQ tag and the concurrent reduction in peak current upon DNA binding. The further utility of this approach for discrimination of closely related DNA targets is demonstrated using DNA strands specific to B. anthracis and closely related bacillus species. DNA targets were designed to the rpoB gene incorporating nucleotide polymorphisms associated with different bacillus species. This assay was used to demonstrate that the shift in reduction potential is directly related to the homology of the target DNA. The discriminatory mechanism is dependent on the presence of oxygen in the measurement buffer and is strongly linked to the position of the nucleotide polymorphisms; with homology at the terminus carrying the AQ functionalised nucleotide critical to achieving accurate discrimination. This understanding of assay design was used to demonstrate an optimized assay capable of discriminating between Yersinia pestis (the causative agent of plague) and closely related species based on the groEL gene. This method is attractive as it can not only detect DNA binding, but can also discriminate between multiple Single Nucleotide Polymorphisms (SNPs) within that DNA without the need for any additional reagents, reporters, or processes such as melting of DNA strands. This indicates that this approach may have great potential to be exploited within novel biosensors for detection and diagnosis of infectious disease in future Point of Care (PoC) devices.
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Affiliation(s)
- Sarah A Goodchild
- Defence Science and Technology Laboratory, Salisbury, United Kingdom.,University of Southampton, Southampton, United Kingdom
| | - Rachel Gao
- University of Southampton, Southampton, United Kingdom
| | - Daniel P Shenton
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | | | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Philip N Bartlett
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
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34
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Binding of pDNA with cDNA using hybridization strategy towards monitoring of Haemophilus influenza genome in human plasma samples. Int J Biol Macromol 2020; 150:218-227. [DOI: 10.1016/j.ijbiomac.2020.02.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/01/2020] [Accepted: 02/07/2020] [Indexed: 11/24/2022]
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35
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Wang T, Peng Q, Guo B, Zhang D, Zhao M, Que H, Wu H, Yan Y. An integrated electrochemical biosensor based on target-triggered strand displacement amplification and "four-way" DNA junction towards ultrasensitive detection of PIK3CA gene mutation. Biosens Bioelectron 2020; 150:111954. [PMID: 31929087 DOI: 10.1016/j.bios.2019.111954] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/16/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022]
Abstract
A novel electrochemical biosensor was constructed for specific and ultrasensitive detection of PIK3CAH1047R gene mutation based on NsbI restriction enzyme-mediated strand displacement amplification (NsbI-SDA) and four-way DNA junction for the first time. In this biosensor, the NsbI restriction enzyme combined with strand displacement amplification (SDA) was able to specifically distinguish PIK3CAH1047R gene mutation and increase the number of DNA copies to improve electrochemical response. In the presence of target mutation gene, DNA fragments produced by the cleavage event of NsbI restriction enzyme could trigger the SDA reaction to generate massive linker chains. When the linker chains were captured on the electrode, the four-way DNA junction was then attached at the end of linker chain. By integrating electroactive molecules of methylene blue (MB) into four-way DNA junction, this sandwich-like electrochemical biosensor was able to determine the specific distinction of target mutation gene with a low detection limit of 0.001%. Finally, this strategy could be used to analyze mutation gene spiked into human serum samples, indicating the potential application in genetic analysis and clinical disease diagnosis.
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Affiliation(s)
- Tong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Qiling Peng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China; Basic Medical College, Chongqing Medical University, Chongqing, 400016, China
| | - Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Decai Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Haiying Que
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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36
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Wang CF, Sun XY, Su M, Wang YP, Lv YK. Electrochemical biosensors based on antibody, nucleic acid and enzyme functionalized graphene for the detection of disease-related biomolecules. Analyst 2020; 145:1550-1562. [DOI: 10.1039/c9an02047k] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The application of biomacromolecule functionalized graphene electrochemical biosensors in the detection of pathogens and disease markers was reviewed.
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Affiliation(s)
- Chen-Feng Wang
- College of Chemistry and Environmental Science
- Hebei University
- Key Laboratory of Analytical Science and Technology of Hebei Province
- Baoding 071002
- China
| | - Xin-Yue Sun
- College of Chemistry and Environmental Science
- Hebei University
- Key Laboratory of Analytical Science and Technology of Hebei Province
- Baoding 071002
- China
| | - Ming Su
- College of Chemistry and Environmental Science
- Hebei University
- Key Laboratory of Analytical Science and Technology of Hebei Province
- Baoding 071002
- China
| | - Yi-Peng Wang
- College of Chemistry and Environmental Science
- Hebei University
- Key Laboratory of Analytical Science and Technology of Hebei Province
- Baoding 071002
- China
| | - Yun-Kai Lv
- College of Chemistry and Environmental Science
- Hebei University
- Key Laboratory of Analytical Science and Technology of Hebei Province
- Baoding 071002
- China
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37
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Mobed A, Hasanzadeh M, Shadjou N, Hassanpour S, Saadati A, Agazadeh M. Immobilization of ssDNA on the surface of silver nanoparticles-graphene quantum dots modified by gold nanoparticles towards biosensing of microorganism. Microchem J 2020; 152:104286. [DOI: 10.1016/j.microc.2019.104286] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Rani A, Donovan N, Mantri N. Review: The future of plant pathogen diagnostics in a nursery production system. Biosens Bioelectron 2019; 145:111631. [DOI: 10.1016/j.bios.2019.111631] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022]
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Zhao Y, Zhou H, Zhang S, Xu J. The synthesis of metal nanoclusters and their applications in bio-sensing and imaging. Methods Appl Fluoresc 2019; 8:012001. [PMID: 31726445 DOI: 10.1088/2050-6120/ab57e7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Noble metal nanomaterials have been studied by many researchers for their ultra-small size, excellent photophysical properties and good biocompatibility. Metal nanoclusters are a kind of nanoscale ultrafine particle, which have completely different properties from macroscopic metals. In the visible region, they do not usually show the characteristic surface plasmon resonance absorption but instead show fluorescence in the visible to near infrared region. In particular, the noble metallic (Au, Ag, Cu, etc) nanoclusters (NMNCs) have broad application prospects in the field of biomedicine as probes for fluorescence sensing. Their strong photoluminescence, living cell compatibility, and easy availability make up for the shortcomings of traditional fluorescent probes such as organic fluorescent dyes, fluorescent proteins, and fluorescent quantum dots. In this review, we summarize the synthetic method and application of metal nanoclusters as fluorescent probes in bio-sensing and imaging, especially in the early diagnosis of cancer cells.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, People's Republic of China
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40
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Mobed A, Nami F, Hasanzadeh M, Hassanpour S, Saadati A, Mokhtarzadeh A. A novel nucleic acid based bio-assay toward recognition of Haemophilus influenza using bioconjugation and DNA hybridization method. Int J Biol Macromol 2019; 139:1239-1251. [PMID: 31400417 DOI: 10.1016/j.ijbiomac.2019.08.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 01/17/2023]
Abstract
Haemophilus influenza (H. influenza) is a gram negative coccobacillus pathogenic microorganism. H. influenza produces beta-lactamases, and it is also able to modify its penicillin-binding proteins, so it has gained resistance to the penicillin family of antibiotics. In this work, a novel sensitive approach was established for the monitoring of H. influenza using DNA based bio-assay. For the first time, specific sequence of thiolated probe of Haemophilus influenza (SH-5'-AAT TTT CCA ACT TTT TCA CCT GCA T-3') was immobilized on the surface of gold (Au) electrode. Square wave voltammetry (SWV) was carried out in toluidine blue (TB) solution for DNA hybridization and targeting of cDNA sequence of Haemophilus influenza. Field scanning electron microscope (FE-SEM) was applied to investigation of the electrode morphology and estimate of particle size. In the optimal conditions, the planned strategy could detect target DNA (5'-ATG CAG GTG AAA AAG TTG GAA AAT T-3') down to 1 ZM with a linear range from 1 μM to 1 ZM. Moreover, engineered geno-assay selectively differentiates the complementary sequence from target sequences with one, double and three base mismatch sequences.
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Affiliation(s)
- Ahmad Mobed
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Iran
| | - Fatemeh Nami
- Department of Biochemistry, Higher Education Institute of Rab-Rashid, Tabriz 51664, Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Soodabeh Hassanpour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arezoo Saadati
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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41
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Electrochemical DNA Biosensors Based on Labeling with Nanoparticles. NANOMATERIALS 2019; 9:nano9101361. [PMID: 31547500 PMCID: PMC6836269 DOI: 10.3390/nano9101361] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023]
Abstract
This work reviews the field of DNA biosensors based on electrochemical determination of nanoparticle labels. These labeling platforms contain the attachment of metal nanoparticles (NPs) or quantum dots (QDs) on the target DNA or on a biorecognition reporting probe. Following the development of DNA bioassay, the nanotags are oxidized to ions, which are determined by voltammetric methods, such as pulse voltammetry (PV) and stripping voltammetry (SV). The synergistic effects of NPs amplification (as each nanoprobe releases a large number of detectable ions) and the inherent sensitivity of voltammetric techniques (e.g., thanks to the preconcentration step of SV) leads to the construction of ultrasensitive, low cost, miniaturized, and integrated biodevices. This review focuses on accomplishments in DNA sensing using voltammetric determination of nanotags (such as gold and silver NPs, and Cd- and Pb-based QDs), includes published works on integrated three electrode biodevices and paper-based biosystems, and discusses strategies for multiplex DNA assays and signal enhancement procedures. Besides, this review mentions the electroactive NP synthesis procedures and their conjugation protocols with biomolecules that enable their function as labels in DNA electrochemical biosensors.
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Bilkiss M, Shiddiky MJA, Ford R. Advanced Diagnostic Approaches for Necrotrophic Fungal Pathogens of Temperate Legumes With a Focus on Botrytis spp. Front Microbiol 2019; 10:1889. [PMID: 31474966 PMCID: PMC6702891 DOI: 10.3389/fmicb.2019.01889] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Plant pathogens reduce global crop productivity by up to 40% per annum, causing enormous economic loss and potential environmental effects from chemical management practices. Thus, early diagnosis and quantitation of the causal pathogen species for accurate and timely disease control is crucial. Botrytis Gray Mold (BGM), caused by Botrytis cinerea and B. fabae, can seriously impact production of temperate grain legumes separately or within a complex. Accordingly, several immunogenic and molecular probe-type protocols have been developed for their diagnosis, but these have varying levels of species-specificity, sensitivity and consequent usefulness within the paddock. To substantially improve speed, accuracy and sensitivity, advanced nanoparticle-based biosensor approaches have been developed. These novel methods have made enormous impact toward disease diagnosis in the medical sciences and offer potential for transformational change within the field of plant pathology and disease management, with early and accurate diagnosis at the point-of-care in the field. Here we review several recently developed diagnostic tools that build on traditional approaches and are available for pathogen diagnosis, specifically for Botrytis spp. diagnostic applications. We then identify the specific gaps in knowledge and current limitations to these existing tools.
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Affiliation(s)
- Marzia Bilkiss
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia.,Queensland Micro- and Nanotechnology Centre (QMNC), Nathan, QLD, Australia
| | - Rebecca Ford
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
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43
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Mohammadniaei M, Park C, Min J, Sohn H, Lee T. Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1064:263-296. [PMID: 30471039 PMCID: PMC7120487 DOI: 10.1007/978-981-13-0445-3_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.
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Affiliation(s)
- Mohsen Mohammadniaei
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, South Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea
| | - Junhong Min
- School of Integrative Engineering Chung-Ang University, Seoul, South Korea
| | - Hiesang Sohn
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
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44
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Mobed A, Hasanzadeh M, Hassanpour S, Saadati A, Agazadeh M, Mokhtarzadeh A. An innovative nucleic acid based biosensor toward detection of Legionella pneumophila using DNA immobilization and hybridization: A novel genosensor. Microchem J 2019; 148:708-716. [DOI: 10.1016/j.microc.2019.05.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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45
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Cesme M, Polat D, Senel P, Golcu A. Anodic Voltammetric Determination of an Atypical Antipsychotic Drug Amisulphide in Pharmaceutical Dosage Forms Using Electrochemical fsDNA Biosensor. RUSS J ELECTROCHEM+ 2019. [DOI: 10.1134/s1023193519030042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Nguyet NT, Yen LTH, Doan VY, Hoang NL, Van Thu V, Lan H, Trung T, Pham VH, Tam PD. A label-free and highly sensitive DNA biosensor based on the core-shell structured CeO 2-NR@Ppy nanocomposite for Salmonella detection. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019. [PMID: 30606592 DOI: 10.1007/s11664-019-07414-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A core-shell cerium oxide nanorod@polypyrrole (CeO2-NR@Ppy) nanocomposite-based electrochemical DNA biosensor was studied for Salmonella detection. The core-shell CeO2-NR@Ppy nanocomposite was prepared by in situ chemical oxidative polymerization of pyrrole monomer on CeO2-NRs, which provided a suitable platform for electrochemical DNA biosensor fabrication. The immobilization of ss-DNA sequences onto nanocomposite-coated microelectrode was performed via covalent attachment method. DNA biosensor electrochemical responses were studied by cyclic voltammetry and electrochemical impedance spectroscopy with [Fe (CN)6]3-/4- as redox probe. Under optimal conditions, DNA biosensor response showed good linearity in the range of 0.01-0.4 nM with sensitivity of 593.7 Ω·nM-1·cm-2. The low limit of detection and limit of quantification for the DNA biosensor were 0.084 and 0.28 nM, respectively. The proposed DNA biosensor also showed good results when used in detecting actual Salmonella samples.
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Affiliation(s)
- Nguyen Thi Nguyet
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam; Hung Yen University of Technology and Education, Viet Nam
| | - Le Thi Hai Yen
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam
| | - Vu Y Doan
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam
| | - Nguyen Luong Hoang
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam
| | - Vu Van Thu
- Faculty of Occupational Safety and Health (OSH), Trade Union University (TUU), Hanoi, Viet Nam
| | - Hoang Lan
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam
| | - Tran Trung
- Hung Yen University of Technology and Education, Viet Nam
| | - Vuong-Hung Pham
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam.
| | - Phuong Dinh Tam
- Advanced Institute for Science and Technology (AIST), Hanoi University of Science and Technology, Viet Nam; Faculty of Material Science and Engineering, Phenikaa University, Yen Nghia, Ha-Dong District, Hanoi 1000, Viet Nam.
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47
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León-Ordóñez K, Abad-Sojos S. Prevention of cervical cancer development through early detection of HPV using novelty molecular applications. BIONATURA 2019. [DOI: 10.21931/rb/cs/2019.02.01.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Human Papillomavirus (HPV) is the predominant cause of cervical cancer worldwide. The infections with HPVs 16 and 18 have a high oncogenic risk for cancer development. Besides, the genes E6 and E7 encode viral oncoproteins associated with infection. New molecular techniques for HPV detection, show important advantages such as high sensitivity, recognition capacity, reliability, among others. These techniques allow the standardization of new protocols associated with the detection in a variety of substances and samples. The stretch relationship between the virus and the disease open a new field to study early detection of the HPV infection. Additionally, less concentration of the sample is needed. Considering the significance of the detection, the present paper explains five novelty molecular applications for the prevention cervical cancer and early detection of HPV such as RNA in situ Hybridization for the detection of HPV E6/E7, genosensors, electrochemical DNA biosensor, PCR-based urine assay and a semen assay for detection of HPV. All the methods related to DNA samples could be used for both genders, there are more acceptable and easy to collect.
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48
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Dai S, Lu W, Wang Y, Yao B. Universal DNA biosensing based on instantaneously electrostatic attraction between hexaammineruthenium (III) and DNA molecules. Biosens Bioelectron 2019; 127:101-107. [PMID: 30594074 DOI: 10.1016/j.bios.2018.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Despite rapid progress in DNA biosensors by employing various materials as well as techniques, most of the reported sensors are based on specific recognition of a DNA fragment, however can not perform universal measurement of DNA molecules (i.e. genomic DNA). In this work, we proposed a novel DNA biosensing method based on instantaneously electrostatic attraction (IEA) between hexaammineruthenium (III) and DNA molecules. The current variation of freely diffused Ru(NH3)63+ caused by its quick and strong static interaction with phosphate backbones was employed as a universal probe to detect DNA molecules in solution, with no need for immobilization of capture probes on the electrode. After optimization, 30 μL of 300 μM Ru(NH3)63+ solution was added onto the gold electrode with a working electrode diameter of 2 mm, and a detection limit of 3.8 ng/μL was achieved, which is equivalent to NanoDrop™ One spectrometer, the commonly used instrument for DNA quantification. Using reusable and inexpensive gold electrode, the approach provided an easy-operated sequence-independent DNA detection method, and was proved to be able to detect genomic and plasmid DNA directly.
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Affiliation(s)
- Siya Dai
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Wei Lu
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yusheng Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Bo Yao
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
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Yang J, Gao L, Peng C, Zhang W. Construction of self-signal DNA electrochemical biosensor employing WS2 nanosheets combined with PIn6COOH. RSC Adv 2019; 9:9613-9619. [PMID: 35520724 PMCID: PMC9062153 DOI: 10.1039/c8ra10266j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/03/2019] [Indexed: 12/27/2022] Open
Abstract
In this work, a novel self-signal DNA electrochemical biosensor was constructed based on tungsten disulfide (WS2) nanosheets combined with poly(indole-6-carboxylic acid) (PIn6COOH) as the sensing interface. The WS2 nanosheets were synthesized via a simple solvent exfoliation method from bulk WS2, and then PIn6COOH was electropolymerized on the WS2 nanosheet-modified carbon paste electrode to obtain a unique nanocomposite. The electropolymerization efficiency was remarkably improved, ascribed to the physical adsorption between WS2 nanosheets and aromatic In6COOH monomers, resulting in an increase of the electrochemical response of PIn6COOH. Owing to the presence of π–π interactions between the conjugated PIn6COOH/WS2 nanocomposite and DNA bases, the probe ssDNA was noncovalently assembled on the nanocomposite substrate. After the hybridization of the probe ssDNA with the target DNA, the formation of the double-helix structure induced the resulting dsDNA to be released from the surface of the conjugated nanocomposite, accompanied with the self-signal regeneration of the nanocomposite (“signal-on”). The constructed PIn6COOH/WS2 nanocomposite was not only employed as an interface for DNA immobilization but also reflected the signal transduction stemming from DNA immobilization and hybridization without any external indicators or complex labeling processes. A detection limit of 2.3 × 10−18 mol L−1 has been estimated and a dynamic range of 1.0 × 10−17 mol L−1 to 1.0 × 10−11 mol L−1 has been shown for the detection of a PIK3CA gene related to lung cancer. Selectivity of the biosensor has been researched in the presence of noncomplementary and base mismatched DNA sequences. A self-signal DNA electrochemical biosensor was constructed employing WS2 nanosheets combined with PIn6COOH.![]()
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Affiliation(s)
- Jimin Yang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Lei Gao
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Cheng Peng
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
| | - Wei Zhang
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276005
- China
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50
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Amperometric DNA biosensor for Mycobacterium tuberculosis detection using flower-like carbon nanotubes-polyaniline nanohybrid and enzyme-assisted signal amplification strategy. Biosens Bioelectron 2018; 119:215-220. [DOI: 10.1016/j.bios.2018.08.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/02/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
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