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Qahwaji R, Ashankyty I, Sannan NS, Hazzazi MS, Basabrain AA, Mobashir M. Pharmacogenomics: A Genetic Approach to Drug Development and Therapy. Pharmaceuticals (Basel) 2024; 17:940. [PMID: 39065790 PMCID: PMC11279827 DOI: 10.3390/ph17070940] [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: 05/06/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The majority of the well-known pharmacogenomics research used in the medical sciences contributes to our understanding of medication interactions. It has a significant impact on treatment and drug development. The broad use of pharmacogenomics is required for the progress of therapy. The main focus is on how genes and an intricate gene system affect the body's reaction to medications. Novel biomarkers that help identify a patient group that is more or less likely to respond to a certain medication have been discovered as a result of recent developments in the field of clinical therapeutics. It aims to improve customized therapy by giving the appropriate drug at the right dose at the right time and making sure that the right prescriptions are issued. A combination of genetic, environmental, and patient variables that impact the pharmacokinetics and/or pharmacodynamics of medications results in interindividual variance in drug response. Drug development, illness susceptibility, and treatment efficacy are all impacted by pharmacogenomics. The purpose of this work is to give a review that might serve as a foundation for the creation of new pharmacogenomics applications, techniques, or strategies.
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Affiliation(s)
- Rowaid Qahwaji
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia; (R.Q.); (I.A.); (M.S.H.); (A.A.B.)
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ibraheem Ashankyty
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia; (R.Q.); (I.A.); (M.S.H.); (A.A.B.)
| | - Naif S. Sannan
- College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Ar Rimayah, Riyadh 14611, Saudi Arabia;
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia
| | - Mohannad S. Hazzazi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia; (R.Q.); (I.A.); (M.S.H.); (A.A.B.)
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ammar A. Basabrain
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia; (R.Q.); (I.A.); (M.S.H.); (A.A.B.)
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Mobashir
- Department of Biomedical Laboratory Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
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2
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Zhang Y, Xu S, Luo M, Chen J, Wang L, Yang F, Ye J, Liu J, He B, Weng L, Li S, Zhang D. Hairpin-Empowered Invasive Reaction Combined with Catalytic Hairpin Assembly Cascade Amplification for the Specific Detection of Single-Nucleotide Polymorphisms. Anal Chem 2024; 96:10283-10293. [PMID: 38864304 DOI: 10.1021/acs.analchem.4c01049] [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: 06/13/2024]
Abstract
Single-nucleotide polymorphism (SNP) is widely used in the study of disease-related genes and in the genetic study of animal and plant strains. Therefore, SNP detection is crucial for biomedical diagnosis and treatment as well as for molecular design breeding of animals and plants. In this regard, this article describes a novel technique for detecting SNP using flap endonuclease 1 (FEN 1) as a specific recognition element and catalytic hairpin assembly (CHA) cascade reaction as a signal amplification strategy. The mutant target (MT) was hybridized with a biotin-modified upstream probe and hairpin-type downstream probe (DP) to form a specific three-base overlapping structure. Then, FEN 1 was employed for three-base overlapping structure-specific recognition, namely, the precise SNP site identification and the 5' flap of DP dissociation. After dissociation, the hybridized probes were magnetically separated by a streptavidin-biotin complex. Especially, the ability to establish such a hairpin-type DP provided a powerful tool that could be used to hide the cut sequence (CS) and avoid false-positive signals. The cleaved CS initiated the CHA reaction and allowed superior fluorescence signal generation. Owing to the high specificity of FEN 1 for single base recognition, only the MT could be distinguished from the wild-type target and mismatched DNA. Owing to the dual signal amplification, as low as 0.36 fM MT and 1% mutation abundance from the mixtures could be detected, respectively. Furthermore, it could accurately identify SNPs from human cancer cells, as well as soybean leaf genome extracts. This strategy paves the way for the development of more precise and sensitive tools for diagnosing early onset diseases as well as molecular design breeding tools.
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Affiliation(s)
- Yunshan Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shijie Xu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Ma Luo
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Lanyue Wang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Fang Yang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Jing Ye
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jichong Liu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Bingxiao He
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Diming Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
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Xi G, Wu L, Meng H, Li F, Ge Q, Tu J. Discriminating Single Nucleotide Variations in Solid-State Nanopores by Evaluating the Combination Efficiency between DNA Polymerase and Its Substrate. J Phys Chem B 2023. [PMID: 37197998 DOI: 10.1021/acs.jpcb.3c01912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A single nucleotide variant present between two otherwise identical nucleic acids will have unexpected functional consequences frequently. Here, a neoteric single nucleotide variation (SNV) detection assay that integrates two complementary nanotechnology systems, nanoassembly technology and an ingenious nanopore biosensing platform, has been applied to this research. Specifically, we set up a detection system to reflect the binding efficiency of the polymerase and nanoprobe through the difference of nanopore signals and then explore the effect of base mutation at the binding site. In addition, machine learning based on support vector machines is used to automatically classify characteristic events mapped by nanopore signals. Our system reliably discriminates single nucleotide variants at binding sites, even possessing the recognition among transitions, transversions, and hypoxanthine (base I). Our results demonstrate the potential of solid-state nanopore detection for SNV and provide some ideas for expanding solid-state nanopore detection platforms.
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Affiliation(s)
- Guohao Xi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lingzhi Wu
- School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Hao Meng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Fuyao Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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Yu X, Bai S, Wang L. In situ reduction of gold nanoparticles-decorated MXenes-based electrochemical sensing platform for KRAS gene detection. Front Bioeng Biotechnol 2023; 11:1176046. [PMID: 37008032 PMCID: PMC10063977 DOI: 10.3389/fbioe.2023.1176046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
In this work, gold nanoparticles@Ti3C2 MXenes nanocomposites with excellent properties were combined with toehold-mediated DNA strand displacement reaction to construct an electrochemical circulating tumor DNA biosensor. The gold nanoparticles were synthesized in situ on the surface of Ti3C2 MXenes as a reducing and stabilizing agent. The good electrical conductivity of the gold nanoparticles@Ti3C2 MXenes composite and the nucleic acid amplification strategy of enzyme-free toehold-mediated DNA strand displacement reaction can be used to efficiently and specifically detect the non-small cell cancer biomarker circulating tumor DNA KRAS gene. The biosensor has a linear detection range of 10 fM −10 nM and a detection limit of 0.38 fM, and also efficiently distinguishes single base mismatched DNA sequences. The biosensor has been successfully used for the sensitive detection of KRAS gene G12D, which has excellent potential for clinical analysis and provides a new idea for the preparation of novel MXenes-based two-dimensional composites and their application in electrochemical DNA biosensors.
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Yu X, Jiang B, Wang L. A signal-on electrochemical DNA biosensor based on exonuclease III-assisted recycling amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:5041-5046. [PMID: 36448304 DOI: 10.1039/d2ay01592g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA electrochemical detection technology has attracted tremendous interest in recent years. However, a facile and sensitive method for the detection of the disease indicators or genes is still waiting. Herein, we constructed a signal-on electrochemical platform for detecting the manganese superoxide dismutase (MnSOD) gene by incorporating a redox electrochemical signal probe (methylene blue) and exonuclease III-assisted target recycling signal amplification strategy. The sensor was prepared by self-assembly of a capture DNA probe of thiol-modified on GCE with gold electrodeposition. In the presence of target DNA, the exonuclease III can cleave the duplexes formed by the target DNA and the redox-labeled hairpin probes, release the target DNA and produce a residual sequence. The target DNA can continue to hybridize with the hairpin probe for the next cycle of amplification. The residual sequence hybridized with the surface-immobilized capture probes on AuNPs-modified GCE to generate a significantly amplified redox current. In particular, the redox current value of the resultant sensor showed a linear relationship with MnSOD gene concentration in the range of 1-104 pM with the detection limit as low as 0.3 pM. Furthermore, the sensor has excellent specificity and can distinguish single-base mismatch from perfectly matched target DNA. The sensor is fast in operation, and simple in design for detecting different DNA sequences or DNA identification by selecting the appropriate probe sequence, thus shedding light on a good promising application when encountering disease outbreaks or for the early clinical diagnosis of gene-related diseases.
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Affiliation(s)
- Xiongtao Yu
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Bowen Jiang
- College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Lishi Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, China.
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Madej-Kiełbik L, Gzyra-Jagieła K, Jóźwik-Pruska J, Dziuba R, Bednarowicz A. Biopolymer Composites with Sensors for Environmental and Medical Applications. MATERIALS (BASEL, SWITZERLAND) 2022; 15:7493. [PMID: 36363084 PMCID: PMC9659006 DOI: 10.3390/ma15217493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
One of the biggest economic and environmental sustainability problems is the over-reliance on petroleum chemicals in polymer production. This paper presents an overview of the current state of knowledge on biopolymers combined with biosensors in terms of properties, compounding methods and applications, with a focus on medical and environmental aspects. Therefore, this article is devoted to environmentally friendly polymer materials. The paper presents an overview of the current state of knowledge on biopolymers combined with biosensors in terms of properties, compounding methods and applications, with a special focus on medical and environmental aspects. The paper presents the current state of knowledge, as well as prospects. The article shows that biopolymers made from renewable raw materials are of great interest in various fields of science and industry. These materials not only replace existing polymers in many applications, but also provide new combinations of properties for new applications. Composite materials based on biopolymers are considered superior to traditional non-biodegradable materials due to their ability to degrade when exposed to environmental factors. The paper highlights the combination of polymers with nanomaterials which allows the preparation of chemical sensors, thus enabling their use in environmental or medical applications due to their biocompatibility and sensitivity. This review focuses on analyzing the state of research in the field of biopolymer-sensor composites.
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Affiliation(s)
- Longina Madej-Kiełbik
- Lukasiewicz Research Network—Lodz Institute of Technology, 19/27 M. Sklodowskiej-Curie Str., 90-570 Lodz, Poland
| | - Karolina Gzyra-Jagieła
- Lukasiewicz Research Network—Lodz Institute of Technology, 19/27 M. Sklodowskiej-Curie Str., 90-570 Lodz, Poland
- Faculty of Material Technologies and Textile Design, Lodz University of Technology, 116 Żeromskiego Street, 90-924 Lodz, Poland
| | - Jagoda Jóźwik-Pruska
- Lukasiewicz Research Network—Lodz Institute of Technology, 19/27 M. Sklodowskiej-Curie Str., 90-570 Lodz, Poland
| | - Radosław Dziuba
- Department of World Economy and European Integration, University of Lodz, 41/43 Rewolucji 1905 Str., 90-214 Lodz, Poland
| | - Anna Bednarowicz
- Lukasiewicz Research Network—Lodz Institute of Technology, 19/27 M. Sklodowskiej-Curie Str., 90-570 Lodz, Poland
- Faculty of Material Technologies and Textile Design, Lodz University of Technology, 116 Żeromskiego Street, 90-924 Lodz, Poland
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7
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Wang W, Chen T, Liu Y, Wang S, Yang N, Luo M. Predictive value of single-nucleotide polymorphisms in curve progression of adolescent idiopathic scoliosis. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2022; 31:2311-2325. [PMID: 35434775 DOI: 10.1007/s00586-022-07213-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 12/18/2022]
Abstract
PURPOSE Genetic diagnosis is a promising approach because several single-nucleotide polymorphisms (SNPs) associated with adolescent idiopathic scoliosis (AIS) progression have been reported. We review the predictive value of SNPs in curve progression of adolescent idiopathic scoliosis. METHODS We reviewed DNA-based prognostic testing to predict curve progression. Then, the multiple polymorphisms in loci related to AIS progression were also reviewed, and we elucidated the predictive value of SNPs from four functional perspectives, including endocrine metabolism, neuromuscular system, cartilage and extracellular matrix, enzymes, and cytokines. RESULTS The ScoliScores were less successful predictors than expected, and the weak power of predictive SNPs might account for its failure. Susceptibility loci in ESR1, ESR2, GPER, and IGF1, which related to endocrine metabolism, have been reported to predict AIS progression. Neuromuscular imbalance might be a potential mechanism of scoliosis, and SNPs in LBX1, NTF3, and SOCS3 have been reported to predict the curve progression of AIS. Susceptibility loci in SOX9, MATN1, AJAP1, MMP9, and TIMP2, which are related to cartilage and extracellular matrix, are also potentially related to AIS progression. Enzymes and cytokines play essential roles in regulating bone metabolism and embryonic development. SNPs in BNC2, SLC39A8, TGFB1, IL-6, IL-17RC, and CHD7 were suggested as predictive loci for AIS curve progression. CONCLUSIONS Many promising SNPs have been identified to predict the curve progression of AIS. However, conflicting results from replication studies and different ethnic groups hamper their reliability. Convincing SNPs from multiethnic populations and functional verification are needed.
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Affiliation(s)
- Wengang Wang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, People's Republic of China
| | - Tailong Chen
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, People's Republic of China
| | - Yibin Liu
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, People's Republic of China
| | - Songsong Wang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, People's Republic of China
| | - Ningning Yang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, People's Republic of China. .,Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, People's Republic of China.
| | - Ming Luo
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People's Republic of China.
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Lázaro A, Maquieira Á, Tortajada-Genaro LA. Discrimination of Single-Nucleotide Variants Based on an Allele-Specific Hybridization Chain Reaction and Smartphone Detection. ACS Sens 2022; 7:758-765. [PMID: 35188365 PMCID: PMC8961872 DOI: 10.1021/acssensors.1c02220] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Massive DNA testing
requires novel technologies to support a sustainable
health system. In recent years, DNA superstructures have emerged as
alternative probes and transducers. We, herein, report a multiplexed
and highly sensitive approach based on an allele-specific hybridization
chain reaction (AS-HCR) in the array format to detect single-nucleotide
variants. Fast isothermal amplification was developed before activating
the HCR process on a chip to work with genomic DNA. The assay principle
was demonstrated, and the variables for integrating the AS-HCR process
and smartphone-based detection were also studied. The results were
compared to a conventional polymerase reaction chain (PCR)-based test.
The developed multiplex method enabled higher selectivity against
single-base mismatch sequences at concentrations as low as 103 copies with a limit of detection of 0.7% of the mutant DNA
percentage and good reproducibility (relative error: 5% for intra-assay
and 17% for interassay). As proof of concept, the AS-HCR method was
applied to clinical samples, including human cell cultures and biopsied
tissues of cancer patients. Accurate identification of single-nucleotide
mutations in KRAS and NRAS genes
was validated, considering those obtained from the reference sequencing
method. To conclude, AS-HCR is a rapid, simple, accurate, and cost-effective
isothermal method that detects clinically relevant genetic variants
and has a high potential for point-of-care demands.
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Affiliation(s)
- Ana Lázaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Av. Fernando Abril Martorell, 46026 Valencia, Spain
| | - Luis A. Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Av. Fernando Abril Martorell, 46026 Valencia, Spain
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Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
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Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
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Jing L, Xie C, Li Q, Yang M, Li S, Li H, Xia F. Electrochemical Biosensors for the Analysis of Breast Cancer Biomarkers: From Design to Application. Anal Chem 2021; 94:269-296. [PMID: 34854296 DOI: 10.1021/acs.analchem.1c04475] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Le Jing
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Chongyu Xie
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Qianqian Li
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meiqing Yang
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shaoguang Li
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hui Li
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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11
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Hajialyani M, Hosseinzadeh L, Wu JJ. Microfluidics-Integrated Sensors toward Rapid Detection of Single Nucleotide Variations. ACS OMEGA 2021; 6:24297-24303. [PMID: 34604613 PMCID: PMC8482391 DOI: 10.1021/acsomega.1c02563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Indexed: 05/03/2023]
Abstract
Rapid detection of single nucleotide variations (SNVs) is of critical importance to early diagnosis of several diseases and the prediction of diverse responses to a specific treatment. Based on the information published in the literature, discrimination of SNVs is a developing area of study with great research enthusiasm and is also an area that can benefit from microfluidics-integrated designs. This review provides a brief overview of different microfluidics-based strategies for rapid detection of SNVs and mismatched bases. Sensors based on various microfluidic formats, such as paper-based microfluidic biosensors, droplet-based microfluidic systems, and magnetic bead-based microfluidic biosensors, have been discussed with respect to their specific pros and cons for SNV detection. These systems have shown promise for distributed on-site diagnostics in personalized medicine.
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Affiliation(s)
- Marziyeh Hajialyani
- Department
of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee 37996-4519, United States
| | - Leila Hosseinzadeh
- Pharmaceutical
Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, 6715847141 Kermanshah, Iran
| | - Jie Jayne Wu
- Department
of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee 37996-4519, United States
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12
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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: 2.8] [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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13
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Hu Y, Tan C, Lin X, Lai Z, Zhang X, Lu Q, Feng N, Yang D, Weng L. Exonuclease III-Regulated Target Cyclic Amplification-Based Single Nucleotide Polymorphism Detection Using Ultrathin Ternary Chalcogenide Nanosheets. Front Chem 2020; 7:844. [PMID: 31921768 PMCID: PMC6913186 DOI: 10.3389/fchem.2019.00844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
Herein, we report that the ternary chalcogenide nanosheet exhibits different affinity toward oligonucleotides with different lengths and efficiently quenches the fluorescence of dye-labeled DNA probes. Based on these findings, as a proof-of-concept application, the ternary chalcogenide nanosheet is used as a target cyclic amplification biosensor, showing high specificity in discriminating single-base mismatch. This simple strategy is fast and sensitive for the single nucleotide polymorphism detection. Ultralow detection limit of unlabeled target (250 fM) and high discrimination ratio (5%) in the mixture of perfect match (mutant-type) and single-base mismatch (wild-type) target are achieved. This sensing method is extensively compatible for the single nucleotide polymorphism detection in clinical samples, making it a promising tool for the mutation-based clinical diagnostic and genomic research.
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Affiliation(s)
- Yanling Hu
- School of Electrical and Control Engineering, Nanjing Polytechnic Institute, Nanjing, China.,Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Chaoliang Tan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xin Lin
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhuangchai Lai
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiao Zhang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qipeng Lu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ning Feng
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Dongliang Yang
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China.,School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, China
| | - Lixing Weng
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
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14
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Wu F, Lin Q, Wang L, Zou Y, Chen M, Xia Y, Lan J, Chen J. A DNA electrochemical biosensor based on triplex DNA-templated Ag/Pt nanoclusters for the detection of single-nucleotide variant. Talanta 2019; 207:120257. [PMID: 31594620 DOI: 10.1016/j.talanta.2019.120257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 01/24/2023]
Abstract
A label-free electrochemical biosensor based on the triplex DNA-templated Ag/Pt bimetallic nanoclusters (triplex-Ag/PtNCs) and locked nucleic acid (LNA) modified X-shaped DNA probe was developed for the detection of single-nucleotide variant (SNV) related to β-thalassemia. Firstly, using triplex DNA as template, a site-specific and homogeneous Ag/PtNCs was prepared, which can effectively catalyze the 3,3,5,5-tetramethylbenzidine-H2O2 system and thus be employed as a signal reporter in the field of electrochemical biosensor. Secondly, the LNA modified X-shaped probes were assembled on gold electrode surface, which can only be dissociated in the presence of target, leading to the hybridization with triplex-Ag/PtNCs and significant increase of current signal. In this way, the detection limit for SNV of β-thalassemia was 0.8 fM with variant allele frequency (VAF) as low as 0.0001%.
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Affiliation(s)
- Fang Wu
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Qian Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Liangliang Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yulian Zou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Mei Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yaokun Xia
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jianming Lan
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China.
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15
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Chou WC, Hu WP, Yang YS, Chan HWH, Chen WY. Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor. Sci Rep 2019; 9:11056. [PMID: 31363139 PMCID: PMC6667443 DOI: 10.1038/s41598-019-47522-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022] Open
Abstract
Silicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.
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Affiliation(s)
- Wei-Cheng Chou
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, 32001, Taiwan
| | - Wen-Pin Hu
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, 41354, Taiwan
| | - Yuh-Shyong Yang
- Institute of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Hardy Wai-Hong Chan
- Helios Bioelectronics, Inc. 3F., No. 2, Sec. 2, Shengyi Rd., Zhubei City, Hsinchu County, 302, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Jhong-Li, 32001, Taiwan.
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16
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Erdem A, Eksin E. ZNA probe immobilized single-use electrodes for impedimetric detection of nucleic acid hybridization related to single nucleotide mutation. Anal Chim Acta 2019; 1071:78-85. [PMID: 31128758 DOI: 10.1016/j.aca.2019.04.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/14/2019] [Accepted: 04/16/2019] [Indexed: 12/16/2022]
Abstract
The development of a low-cost and disposable biosensing technologies has received a great interest of healthcare for the sensitive and reliable detection of single nucleotide mutation related to single nucleotide polymorphisms (SNPs). In the present study, an impedimetric biosensing platform based on zip nucleic acids (ZNA) was developed for the sensitive detection of Factor V Leiden (FV Leiden) mutation. After optimization of experimental parameters, the sequence selective hybridization between ZNA probe and target related to FV Leiden mutation was evaluated via electrochemical impedance spectroscopy technique (EIS) by measuring changes at the charge transfer resistance, Rct. Sensitive and selective impedimetric analysis was performed using carbon nanofiber (CNF) modified screen printed electrodes (SPE) and multi-channel screen printed array of electrodes (MULTIx8 CNF-SPE) resulting in a relatively shorter time in comparison to conventional methods. The selectivity of ZNA probe to mutation-free DNA sequences was also investigated. The applicability of single-use ZNA biosensor was also tested in synthetic PCR samples containing a single base mutation.
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Affiliation(s)
- Arzum Erdem
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir, 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir, 35100, Turkey.
| | - Ece Eksin
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir, 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir, 35100, Turkey
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17
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Dong B, Nie K, Shi H, Chao L, Ma M, Gao F, Liang B, Chen W, Long M, Liu Z. Film-Spotting chiral miniPEG-γPNA array for BRCA1 gene mutation detection. Biosens Bioelectron 2019; 136:1-7. [PMID: 31026759 DOI: 10.1016/j.bios.2019.04.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/01/2019] [Accepted: 04/14/2019] [Indexed: 12/24/2022]
Abstract
Peptide nucleic acids array technology is a method of greatly increasing the throughput of laboratory processes to efficiently perform large-scale genetic tests. Diethylene glycol-containing chiral γPNA (miniPEG-γPNA) is considered to be the best PNA derivative and one of the best candidates for gene detection, because it can hybridize DNA with greater affinity and sequence selectivity than DNA and ordinary aminoethylglycyl PNA (aegPNA). Herein, miniPEG-γPNA probes are synthesized by 9-fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS) in a mild condition, and a new biochip fabrication method "Film-Spotting" is invented, by which γPNA arrays with regular pattern, uniform luminance, and very low fluorescence background are obtained easily and cheaply. The miniPEG-γPNA array can effectively distinguish the full matched and mismatched targets in SSarc buffer, serum and urine, and the detection limit of complementary DNA is less than 5.97 nM. A miniPEG-γPNA array for BRCA1 gene mutation (3099delT) detection is also fabricated with a very good detection performance. This work provides an effective avenue for the diagnosis of breast cancer biomarker and expands the application of miniPEG-γPNA in the field of biochip.
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Affiliation(s)
- Bo Dong
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, PR China
| | - Kaixuan Nie
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, PR China
| | - Huanhuan Shi
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, PR China
| | - Lemeng Chao
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, PR China
| | - Mingyang Ma
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China
| | - Fengxiao Gao
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China
| | - Bo Liang
- State Engineering Laboratory of Highway Maintenance Technology, School of Traffic and Transportation Engineering, Changsha University of Science and Technology, Changsha, 410114, PR China
| | - Wei Chen
- (d)Xiangya Hospital Central South University, Changsha, 410008, PR China
| | - Mengqiu Long
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China
| | - Zhengchun Liu
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan, 410083, PR China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, PR China.
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18
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Sigolaeva LV, Bulko TV, Kozin MS, Zhang W, Köhler M, Romanenko I, Yuan J, Schacher FH, Pergushov DV, Shumyantseva VV. Long-term stable poly(ionic liquid)/MWCNTs inks enable enhanced surface modification for electrooxidative detection and quantification of dsDNA. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Wolfe MG, Ali MM, Brennan JD. Enzymatic Litmus Test for Selective Colorimetric Detection of C-C Single Nucleotide Polymorphisms. Anal Chem 2019; 91:4735-4740. [PMID: 30869875 DOI: 10.1021/acs.analchem.9b00235] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A paper based litmus test has been developed using modulation of urease enzyme activity for detection of C-C mismatch single nucleotide polymorphisms (SNPs) by the naked eye. Urease is first inactivated with silver ions and printed onto paper microzones. Addition of DNA containing C-C mismatches reactivates urease via binding of Ag(I), allowing restoration of urease activity, hydrolysis of urea to produce ammonia, and an increase in pH, which is monitored colorimetrically using a pH indicator with a limit of detection of 11 nM DNA in 40 min. The assay system is easy to use, portable, and stable for at least 30 days at ambient temperature. To assess the versatility and practical application of the paper sensor, we used it to identify a G > C transversion present in human genomic DNA from a ductal carcinoma cell line, a mutation commonly found in breast cancer. We believe this new assay system has the potential to be a low-cost method for rapidly identifying DNA with the C-C mismatch SNP as a means of cancer screening in resource-limited areas.
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Affiliation(s)
- Michael G Wolfe
- Biointerfaces Institute , McMaster University , 1280 Main Street West , Hamilton , ON L8S 4O3 , Canada
| | - M Monsur Ali
- Biointerfaces Institute , McMaster University , 1280 Main Street West , Hamilton , ON L8S 4O3 , Canada
| | - John D Brennan
- Biointerfaces Institute , McMaster University , 1280 Main Street West , Hamilton , ON L8S 4O3 , Canada
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20
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Borghei YS, Hosseini M, Ganjali MR, Ju H. A unique FRET approach toward detection of single-base mismatch DNA in BRCA1 gene. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 97:406-411. [PMID: 30678926 DOI: 10.1016/j.msec.2018.12.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 10/10/2018] [Accepted: 12/15/2018] [Indexed: 12/17/2022]
Abstract
Early detection of mutation carriers in predisposing genes such as BRCA1 plays an important role in disease prevention. This work developed a quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) technique for the detection of single-base mismatch DNA in BRCA1 gene. The FRET between QDs as the donor and silver nanocluster (AgNCs) as the acceptor was designed by the strong interaction between CdTe QDs with appropriate size and dsDNA through binding to its major groove. The dsDNA was formed by the hybridization of ssDNA labeled to AgNCs with target DNA, which introduced CdTe QDs into the major grooves to place the AgNCs in close proximity to the QDs. The complementary and single-base mismatch DNA led to obviously different FRET signals. The FRET signal linearly correlated to the concentration of single-base mismatch DNA in the range of 1.5 × 10-10-1.0 × 10-6 mol L-1. The proposed method showed a detection limit of 80 pmol L-1 and the sensitivity comparable to the previously reported assays, indicating promising potential for single nucleotide polymorphisms diagnosis in clinical application.
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Affiliation(s)
- Yasaman-Sadat Borghei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology & Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210023, China.
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21
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Erdem A, Eksin E. Magnetic beads assay based on Zip nucleic acid for electrochemical detection of Factor V Leiden mutation. Int J Biol Macromol 2018; 125:839-846. [PMID: 30552928 DOI: 10.1016/j.ijbiomac.2018.12.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 01/11/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among people. Development of reliable methods for the detection of SNP is crucial in aspects of molecular diagnosis and personalized medicine. In our study, a genomagnetic assay in combination with zip nucleic acid (ZNA) for electrochemical detection of SNP related to Factor V Leiden mutation. For the first time in the literature, a new generation nucleic acid; ZNA was applied herein for electrochemical monitoring of nucleic acid hybridization. Streptavidin coated magnetic beads (MBs) were used for preparation of samples containing ZNA-DNA hybrid and accordingly, the guanine signal was measured as a response of hybridization related to Factor V Leiden mutation by carbon nanofibers (CNF) modified screen printed electrodes (SPE) and multi-channel screen printed array of electrodes (CNF-MULTI SPEx8). The detection limit (DL) was found to be 3.79 μg/mL (376 nM) and, 11.63 μg/mL (1.624 μM), respectively by CNF-SPE and CNF-MULTI SPEx8. The selectivity of ZNA probe to mutation-free DNA sequences was also investigated in contrast to DNA probe. The applicability of ZNA based magnetic beads assay to sequence selective hybridization related to Factor V Leiden was also tested in synthetic PCR samples.
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Affiliation(s)
- Arzum Erdem
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey.
| | - Ece Eksin
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey
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22
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Soler M, Huertas CS, Lechuga LM. Label-free plasmonic biosensors for point-of-care diagnostics: a review. Expert Rev Mol Diagn 2018; 19:71-81. [PMID: 30513011 DOI: 10.1080/14737159.2019.1554435] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Introduction: Optical biosensors, particularly those based on nanoplasmonics technology, have emerged in recent decades as a potential solution for disease diagnostics and therapy follow-up at the point-of-care (POC). These biosensor platforms could overcome some of the challenges faced in conventional diagnosis techniques offering label-free assays with immediate results and employing small and user-friendly devices. Areas covered: In this review, we will provide a critical overview of the recent advances in the development of nanoplasmonic biosensors for the POC diagnostics. We focus on those systems with demonstrated capabilities for integration in portable platforms, highlighting some of the most relevant diagnostics applications targeting proteins, nucleic acids, and cells as disease biomarkers. Expert commentary: Despite the attractive features of label-free nanoplasmonic sensors in terms of miniaturization and analytical robustness, the route toward an effective clinical implementation involves the integration of fully automated microfluidic systems for sample processing and analysis, and the optimization of surface biofunctionalization procedures. Additionally, the development of multiplexed sensors for high-throughput analysis and including specific neoantigens and novel biomarkers in detection panels will provide the means for delivering a powerful analytical technology for an accurate and improved medical diagnosis.
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Affiliation(s)
- Maria Soler
- a Nanobiosensors and Bioanalytical Applications Group , Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and CIBER-BBN , Bellaterra , Barcelona , Spain
| | - Cesar S Huertas
- a Nanobiosensors and Bioanalytical Applications Group , Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and CIBER-BBN , Bellaterra , Barcelona , Spain.,b School of Engineering , RMIT University , Melbourne , Australia
| | - Laura M Lechuga
- a Nanobiosensors and Bioanalytical Applications Group , Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and CIBER-BBN , Bellaterra , Barcelona , Spain
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23
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Severins I, Szczepaniak M, Joo C. Multiplex Single-Molecule DNA Barcoding Using an Oligonucleotide Ligation Assay. Biophys J 2018; 115:957-967. [PMID: 30195940 DOI: 10.1016/j.bpj.2018.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/10/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
Detection of specific nucleic acid sequences is invaluable in biological studies such as genetic disease diagnostics and genome profiling. Here, we developed a highly sensitive and specific detection method that combines an advanced oligonucleotide ligation assay with multicolor single-molecule fluorescence. We demonstrated that under our experimental conditions, 7-nucleotide long DNA barcodes have the optimal short length to ascertain specificity while being long enough for sufficient ligation. Using four spectrally separated fluorophores to label DNA barcodes, we simultaneously distinguished four DNA target sequences differing by only a single nucleotide. Our single-molecule approach will allow for accurate identification of low-abundance molecules without the need for target DNA preamplification.
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Affiliation(s)
- Ivo Severins
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
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24
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A target-triggered biosensing platform for detection of HBV DNA based on DNA walker and CHA. Anal Biochem 2018; 554:16-22. [DOI: 10.1016/j.ab.2018.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 01/06/2023]
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25
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Ma Q, Gao Z. A simple and ultrasensitive fluorescence assay for single-nucleotide polymorphism. Anal Bioanal Chem 2018; 410:3093-3100. [PMID: 29644378 DOI: 10.1007/s00216-018-0874-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/11/2017] [Accepted: 01/12/2018] [Indexed: 11/30/2022]
Abstract
In this report, a simple, label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single-nucleotide polymorphism (SNP). Briefly, a designed padlock probe is first circularized by a DNA ligase when it perfectly complements to a mutant gene. Then, the mutant gene functions as a primer to initiate branched rolling circle amplification reaction (BRCA), generating a large number of branched DNA strands and a lot of pyrophosphate molecules which is equivalent to the number of nucleotides consumed. With the addition of a terpyridine-Zn(II) complex, pyrophosphate molecules can be sensitively detected owing to the formation of a fluorescent terpyridine-Zn(II)-pyrophosphate complex. The fluorescence intensity is directly associated with the content of the mutant gene in a sample solution. On the other hand, the circulation of the padlock probe is prohibited when it hybridizes with the wild-type gene. In this assay, the accumulative nature of the BRCA process produces a detection limit of 0.1 pM and an excellent selectivity factor of 1000 toward SNP. As little as 0.1% mutant in the wild-type gene can be successfully detected. The simple procedure, high sensitivity, and high selectivity of this assay offer a potentially viable alternative for routine SNP analysis. Graphical abstract A simple and label-free fluorescence assay for SNP detection by coupling BRCA with selective fluorescence detection of pyrophosphate using the terpyridine-Zn(II) complex.
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Affiliation(s)
- Qian Ma
- Department of Chemistry, National University of Singapore, 3 Science Drive 2, Singapore, 117543, Singapore
| | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, 3 Science Drive 2, Singapore, 117543, Singapore.
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26
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Alternative SNP detection platforms, HRM and biosensors, for varietal identification in Vitis vinifera L. using F3H and LDOX genes. Sci Rep 2018; 8:5850. [PMID: 29643453 PMCID: PMC5895793 DOI: 10.1038/s41598-018-24158-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 03/07/2018] [Indexed: 01/07/2023] Open
Abstract
The wine sector requires quick and reliable methods for Vitis vinifera L. varietal identification. The number of V. vinifera varieties is estimated in about 5,000 worldwide. Single Nucleotide Polymorphisms (SNPs) represent the most basic and abundant form of genetic sequence variation, being adequate for varietal discrimination. The aim of this work was to develop DNA-based assays suitable to detect SNP variation in V. vinifera, allowing varietal discrimination. Genotyping by sequencing allowed the detection of eleven SNPs on two genes of the anthocyanin pathway, the flavanone 3-hydroxylase (F3H, EC: 1.14.11.9), and the leucoanthocyanidin dioxygenase (LDOX, EC 1.14.11.19; synonym anthocyanidin synthase, ANS) in twenty V. vinifera varieties. Three High Resolution Melting (HRM) assays were designed based on the sequencing information, discriminating five of the 20 varieties: Alicante Bouschet, Donzelinho Tinto, Merlot, Moscatel Galego and Tinta Roriz. Sanger sequencing of the HRM assay products confirmed the HRM profiles. Three probes, with different lengths and sequences, were used as bio-recognition elements in an optical biosensor platform based on a long period grating (LPG) fiber optic sensor. The label free platform detected a difference of a single SNP using genomic DNA samples. The two different platforms were successfully applied for grapevine varietal identification.
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27
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Bao B, Pan Y, Gu B, Chen J, Xu Y, Su P, Liu Y, Tong L, Wang L. Highly sensitive detection of nucleic acids using a cascade amplification strategy based on exonuclease III-assisted target recycling and conjugated polyelectrolytes. Analyst 2018; 143:4267-4272. [DOI: 10.1039/c8an01024b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A ratiometric and cascade amplification strategy that combines the signal amplification and effecitive FRET property of CPEs with the Exo III-assisted target recycling method has been developed for DNA detection.
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Affiliation(s)
- Biqing Bao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yanrui Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Bingbing Gu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Jia Chen
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yu Xu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Peng Su
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yunfei Liu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Li Tong
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
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28
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Evtugyn GA, Porfireva AV, Stoikov II. Electrochemical DNA sensors based on spatially distributed redox mediators: challenges and promises. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-1124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
AbstractDNA and aptasensors are widely used for fast and reliable detection of disease biomarkers, pharmaceuticals, toxins, metabolites and other species necessary for biomedical diagnostics. In the overview, the concept of spatially distributed redox mediators is considered with particular emphasis to the signal generation and biospecific layer assembling. The application of non-conductive polymers bearing redox labels, supramolecular carriers with attached DNA aptamers and redox active dyes and E-sensor concept are considered as examples of the approach announced.
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Affiliation(s)
- Gennady A. Evtugyn
- A.M.Butlerov’ Chemistry Institute of Kazan Federal University, 420008 Kazan, Russian Federation
| | - Anna V. Porfireva
- A.M.Butlerov’ Chemistry Institute of Kazan Federal University, 420008 Kazan, Russian Federation
| | - Ivan I. Stoikov
- A.M.Butlerov’ Chemistry Institute of Kazan Federal University, 420008 Kazan, Russian Federation
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29
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Electrogenerated chemiluminescence biosensing method for highly sensitive detection of DNA hydroxymethylation: Combining glycosylation with Ru(phen) 3 2+ -assembled graphene oxide. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.04.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Park JH, Jang H, Jung YK, Jung YL, Shin I, Cho DY, Park HG. A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification. Biosens Bioelectron 2017; 91:122-127. [DOI: 10.1016/j.bios.2016.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 01/21/2023]
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31
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Bao B, Zhu J, Gong L, Chen J, Pan Y, Wang L. Sensitive DNA detection using cascade amplification strategy based on conjugated polyelectrolytes and hybridization chain reaction. RSC Adv 2017. [DOI: 10.1039/c6ra25882d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel cascade amplification strategy that combines the molecular wire effects of CPEs with the signal amplification capability of the HCR has been developed for sensitive DNA detection.
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Affiliation(s)
- Biqing Bao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Jin Zhu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Lina Gong
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Jia Chen
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Yanrui Pan
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID)
- Institute of Advanced Materials (IAM)
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts and Telecommunications (NUPT)
- Nanjing 210023
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32
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Kuzin Y, Ivanov A, Evtugyn G, Hianik T. Voltammetric Detection of Oxidative DNA Damage Based on Interactions between Polymeric Dyes and DNA. ELECTROANAL 2016. [DOI: 10.1002/elan.201600297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yury Kuzin
- A. M. Butlerov' Chemistry Institute of Kazan Federal University; 18 Kremlevskaya Street Kazan 420008 Russian Federation
- Department of Nuclear Physics and Biophysics; Comenius University; Mlynska dolina F1 842 48 Bratislava Slovakia
| | - Alexey Ivanov
- A. M. Butlerov' Chemistry Institute of Kazan Federal University; 18 Kremlevskaya Street Kazan 420008 Russian Federation
| | - Gennady Evtugyn
- A. M. Butlerov' Chemistry Institute of Kazan Federal University; 18 Kremlevskaya Street Kazan 420008 Russian Federation
- Department of Nuclear Physics and Biophysics; Comenius University; Mlynska dolina F1 842 48 Bratislava Slovakia
| | - Tibor Hianik
- A. M. Butlerov' Chemistry Institute of Kazan Federal University; 18 Kremlevskaya Street Kazan 420008 Russian Federation
- OpenLab “DNA-Sensors” of Kazan Federal University; 18 Kremlevskaya Street Kazan 420008 Russian Federation
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33
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Hernández-Ainsa S, Ricci M, Hilton L, Aviñó A, Eritja R, Keyser UF. Controlling the Reversible Assembly of Liposomes through a Multistimuli Responsive Anchored DNA. NANO LETTERS 2016; 16:4462-6. [PMID: 27367802 PMCID: PMC4956241 DOI: 10.1021/acs.nanolett.6b01618] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/23/2016] [Indexed: 05/21/2023]
Abstract
We present a novel approach to reversibly control the assembly of liposomes through an anchored multistimuli responsive DNA oligonucleotide decorated with an azobenzene moiety (AZO-ON1). We show that liposomes assembly can be simultaneously controlled by three external stimuli: light, Mg(2+), and temperature. (i) Light alters the interaction of AZO-ON1 with liposomes, which influences DNA coating and consequently liposomes assembly. (ii) Mg(2+) induces the assembly, hence variation in its concentration enables for reversibility. (iii) Double-stranded AZO-ON1 is more efficient than single-stranded AZO-ON1 in triggering the assembly of liposomes and temperature has been used for controllable assembly through DNA thermal denaturation. Our multiresponsive AZO-ON1 represents a unique example in which multiple stimuli can be simultaneously applied to regulate the reversible assembly of liposomes.
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Affiliation(s)
- Silvia Hernández-Ainsa
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Maria Ricci
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Lloyd Hilton
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Anna Aviñó
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Eritja
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ulrich F. Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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34
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Li Q, Yu C, Gao R, Xia C, Yuan G, Li Y, Zhao Y, Chen Q, He J. A novel DNA biosensor integrated with Polypyrrole/streptavidin and Au-PAMAM-CP bionanocomposite probes to detect the rs4839469 locus of the vangl1 gene for dysontogenesis prediction. Biosens Bioelectron 2016; 80:674-681. [DOI: 10.1016/j.bios.2016.02.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/31/2016] [Accepted: 02/09/2016] [Indexed: 10/22/2022]
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35
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Li F, Xu Y, Yu X, Yu Z, He X, Ji H, Dong J, Song Y, Yan H, Zhang G. A "signal on" protection-displacement-hybridization-based electrochemical hepatitis B virus gene sequence sensor with high sensitivity and peculiar adjustable specificity. Biosens Bioelectron 2016; 82:212-6. [PMID: 27085953 DOI: 10.1016/j.bios.2016.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022]
Abstract
One "signal on" electrochemical sensing strategy was constructed for the detection of a specific hepatitis B virus (HBV) gene sequence based on the protection-displacement-hybridization-based (PDHB) signaling mechanism. This sensing system is composed of three probes, one capturing probe (CP) and one assistant probe (AP) which are co-immobilized on the Au electrode surface, and one 3-methylene blue (MB) modified signaling probe (SP) free in the detection solution. One duplex are formed between AP and SP with the target, a specific HBV gene sequence, hybridizing with CP. This structure can drive the MB labels close to the electrode surface, thereby producing a large detection current. Two electrochemical testing techniques, alternating current voltammetry (ACV) and cyclic voltammetry (CV), were used for characterizing the sensor. Under the optimized conditions, the proposed sensor exhibits a high sensitivity with the detection limit of ∼5fM for the target. When used for the discrimination of point mutation, the sensor also features an outstanding ability and its peculiar high adjustability.
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Affiliation(s)
- Fengqin Li
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Yanmei Xu
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Xiang Yu
- College of Chemical and Environmental Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China
| | - Zhigang Yu
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China.
| | - Xunjun He
- Department of Electronic Science and Technology, Harbin University of Science and Technology, Harbin 150080, China
| | - Hongrui Ji
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Jinghao Dong
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Yongbin Song
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Hong Yan
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China
| | - Guiling Zhang
- College of Chemical and Environmental Engineering, Harbin University of Science and Technology, Harbin 150040, China.
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36
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Ngavouka MDN, Capaldo P, Ambrosetti E, Scoles G, Casalis L, Parisse P. Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:220-227. [PMID: 26977379 PMCID: PMC4778512 DOI: 10.3762/bjnano.7.20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/25/2016] [Indexed: 01/10/2023]
Abstract
Background: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA base-pairing that guarantee a high grade of selectivity. Nonetheless the presence of single base mismatches or not perfectly matched sequences can affect the response of the devices and the major challenge is, nowadays, to distinguish a mismatch of a single base and, at the same time, unequivocally differentiate devices read-out of fully and partially matching sequences. Results: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self-assembled monolayers we followed in real-time the variation of capacitance, being able to distinguish, through the difference in hybridization kinetics, not only the presence of single, double or triple mismatches in the complementary sequence, but also the position of the mismatched base pair with respect to the electrode surface. Conclusion: We demonstrate here two platforms based on different sensing strategies as sensitive and selective tools to discriminate mismatches. Our assays are ready for parallelization and can be used in the detection and quantification of single nucleotide mismatches in microRNAs or in genomic DNA.
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Affiliation(s)
- Maryse D Nkoua Ngavouka
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Pietro Capaldo
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Elena Ambrosetti
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,University of Trieste, Via Valerio 9, Trieste, Italy
| | - Giacinto Scoles
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.,INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy
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37
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Gavvala K, Barthes NPF, Bonhomme D, Dabert-Gay AS, Debayle D, Michel BY, Burger A, Mély Y. A turn-on dual emissive nucleobase sensitive to mismatches and duplex conformational changes. RSC Adv 2016. [DOI: 10.1039/c6ra19061h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein, we demonstrate the on–off dual emissive behaviour of a fluorescent nucleoside sensitive towards DNA hybridization and conformational changes as well as detection of single nucleotide polymorphisms.
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Affiliation(s)
- Krishna Gavvala
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
| | - Nicolas P. F. Barthes
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Dominique Bonhomme
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Anne Sophie Dabert-Gay
- Institut de Pharmacologie Moléculaire et Cellulaire
- UMR 6097
- Université de Nice Sophia Antipolis
- 660 Route des Lucioles
- 06560 Valbonne
| | - Delphine Debayle
- Institut de Pharmacologie Moléculaire et Cellulaire
- UMR 6097
- Université de Nice Sophia Antipolis
- 660 Route des Lucioles
- 06560 Valbonne
| | - Benoît Y. Michel
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Alain Burger
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- Parc Valrose
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
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38
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Moradi N, Noori A, Mehrgardi MA, Mousavi MF. Scanning Electrochemical Microscopy for Electrochemical Detection of Single-base Mismatches by Tagging Ferrocenecarboxylic Acid as a Redox Probe to DNA. ELECTROANAL 2015. [DOI: 10.1002/elan.201500598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Lu M, Xu L, Zhang X, Xiao R, Wang Y. Ag(I)-coordinated hairpin DNA for homogenous electronic monitoring of hepatitis C virus accompanying isothermal cycling signal amplification strategy. Biosens Bioelectron 2015; 73:195-201. [DOI: 10.1016/j.bios.2015.05.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/07/2015] [Accepted: 05/26/2015] [Indexed: 12/18/2022]
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40
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Huang Y, Yang HY, Ai Y. DNA Single-Base Mismatch Study Using Graphene Oxide Nanosheets-Based Fluorometric Biosensors. Anal Chem 2015; 87:9132-6. [DOI: 10.1021/acs.analchem.5b03037] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yinxi Huang
- Pillar of Engineering Product
Development, Singapore University of Technology and Design, Singapore 487372
| | - Hui Ying Yang
- Pillar of Engineering Product
Development, Singapore University of Technology and Design, Singapore 487372
| | - Ye Ai
- Pillar of Engineering Product
Development, Singapore University of Technology and Design, Singapore 487372
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41
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Liu X, Wang JY, Mao XB, Ning Y, Zhang GJ. Single-Shot Analytical Assay Based on Graphene-Oxide-Modified Surface Acoustic Wave Biosensor for Detection of Single-Nucleotide Polymorphisms. Anal Chem 2015; 87:9352-9. [PMID: 26316457 DOI: 10.1021/acs.analchem.5b02121] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Xiang Liu
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Jia-Ying Wang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Department
of Clinical Laboratory, Taihe Hospital, Hubei University of Medicine, 32 South Renmin Road, Shiyan 442000, China
| | - Xiao-Bing Mao
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- School
of Life Sciences, Southwest University, 2 Tian Sheng Road, Beibei, Chongqing 400715, China
| | - Yong Ning
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Guo-Jun Zhang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
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42
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Sun AL, Zhang YF, Wang XN. Sensitive voltammetric determination of DNA via a target-induced strand-displacement reaction using quantum dot-labeled probe DNA. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1467-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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43
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Chen J, Cai J, Hu H, Huang X, Yi T, Wang K, Pan S. A dielectric loss angle based portable biosensor system for bacterial concentration detection. RSC Adv 2015. [DOI: 10.1039/c5ra13055g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new type of portable sensor is proposed to detect bacterial concentration based on the change in dielectric loss angleδ.
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Affiliation(s)
- Jingyao Chen
- College of Food Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Jie Cai
- College of Food Science and Engineering
- Wuhan Polytechnic University
- Wuhan 430023
- China
| | - Hao Hu
- College of Food Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Xingjian Huang
- College of Food Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Tian Yi
- Hubei Academy of Agricultural Sciences
- Wuhan 430064
- China
| | - Kexing Wang
- College of Food Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
| | - Siyi Pan
- College of Food Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- China
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