1
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Marangoni JM, Ng KKS, Emadi A. Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification. MICROMACHINES 2023; 14:472. [PMID: 36838172 PMCID: PMC9960872 DOI: 10.3390/mi14020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.
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Affiliation(s)
- Jesse M. Marangoni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Arezoo Emadi
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, ON N9B 3P4, Canada
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2
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Gao Q, Li Y, Li Q, Ma C, Shi C. Sensitive Dual Electrochemical-Colorimetric Point-of-Care (POC) Sensor for the Rapid Detection of Mycoplasma pneumoniae. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2134887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Qian Gao
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yang Li
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Qi Li
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chao Shi
- Department of Pathogenic Biology, School of Basic Medicine, College of Life Sciences, Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, the Clinical Laboratory Department of the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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3
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González-López A, Cima-Cabal MD, Rioboó-Legaspi P, Costa-Rama E, García-Suárez MDM, Fernández-Abedul MT. Electrochemical Detection for Isothermal Loop-Mediated Amplification of Pneumolysin Gene of Streptococcus pneumoniae Based on the Oxidation of Phenol Red Indicator. Anal Chem 2022; 94:13061-13067. [PMID: 36106671 PMCID: PMC9523611 DOI: 10.1021/acs.analchem.2c02127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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A highly sensitive electrochemical methodology for end-point detection
of loop-mediated isothermal nucleic acid amplification reactions was
developed. It is based on the oxidation process of phenol red (PR),
commonly used as a visual indicator. The dependence of its redox process
on pH, which changes during amplification, allows performing quantitative
measurements. Thus, the change in the oxidation potential of PR during
the amplification is used, for the first time, as the analytical signal
that correlates with the number of initial DNA copies. As a proof-of-concept,
the amplification of the pneumolysin gene from Streptococcus
pneumoniae, one of the main pathogens causing community-acquired
pneumonia, is performed. Combination of isothermal amplification with
electrochemical detection, performed on small-size flexible electrodes,
allows easy decentralization. Adaptation to the detection of other
pathogens causing infectious diseases would be very useful in the
prevention of future epidemics.
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Affiliation(s)
- Andrea González-López
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - María Dolores Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Avda. de La Paz 137, Logroño 26006, Spain
| | - Pablo Rioboó-Legaspi
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - Estefanía Costa-Rama
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | | | - M. Teresa Fernández-Abedul
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
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4
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Liao Y, Gao J, Huang W, Yuan R, Xu W. LAMP-H +-responsive electrochemical ratiometric biosensor with minimized background signal for highly sensitive assay of specific short-stranded DNA. Biosens Bioelectron 2022; 195:113662. [PMID: 34571484 DOI: 10.1016/j.bios.2021.113662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 11/02/2022]
Abstract
Herein, the sequence-specific short-stranded biomarker DNA (hDNA, 21-nt) is acted as targeting out-primer to implement the loop-mediated isothermal amplification for releasing hydrogen ions (LAMP-H+). Using LAMP-H+ as signaling transducer, we report a highly sensitive electrochemical ratiometric biosensor for hDNA with minimized background signal, which is achieved via magnetic separation using AuNPs-modified Fe3O4 (Au@Fe3O4) as micro-reactor. In Au@Fe3O4, a double-stranded complex of a pH-responsible strand (I*) and a substrate strand (S*) is bound via Au-N bonds, where the treatment with LAMP-H+ leads to I* folding into i-motif conformation and S* dehybridization. The S* further hybridizes a catalytic strand (C*) to assemble Mg2+-DNAzymes that are cleaved by Mg2+, releasing C* for repeated formation and robust nicking of Mg2+-DNAzymes. The resultant output fuel strands (F*) are introduced in a modified electrode to drive the strand displacement of two hairpins individually labeled with two electron mediators. Through F*-mediated recycled amplification, the ratio of their electrochemical currents changed in opposite is highly sensitive to the varied hDNA down to 2.1 fM. By integrating LAMP-H+-stimulated i-motif switching with Mg2+-DNAzyme cleavage, this logic transduction of LAMP-H+(i-motif/Mg2+-DNAzyme)F* efficiently minimizes the inherent background of traditional LAMP-based assays. Resultantly, our electrochemical ratiometric strategy would be applicable to diverse short-stranded DNAs or even RNAs as targeting primers of LAMP.
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Affiliation(s)
- Yumeng Liao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Jiaxi Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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5
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He S, Li P, Tang L, Chen M, Yang Y, Zeng Z, Xiong W, Wu X, Huang J. Dual-stage amplified fluorescent DNA sensor based on polymerase-Mediated strand displacement reactions. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Gao J, Hua X, Yuan R, Li Q, Xu W. Amplified electrochemical biosensing based on bienzymatic cascade catalysis confined in a functional DNA structure. Talanta 2021; 234:122643. [PMID: 34364452 DOI: 10.1016/j.talanta.2021.122643] [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: 05/08/2021] [Revised: 06/12/2021] [Accepted: 06/20/2021] [Indexed: 10/20/2022]
Abstract
Herein, an amplified and renewable electrochemical biosensor was developed via bienzymatic cascade catalysis of glucose oxidase (GOx) and horseradish peroxidase (HRP), which were confined in a functional Y-shaped DNA nanostructure oriented by a dual-thiol-ended hairpin probe (dSH-HP) with a paired stem as a rigid scaffold and unpaired loop as enclosed binding platform. For proof-of-concept assay of sequence-specific biomarker DNA related to Alzheimer's disease (aDNA), GOx and redox ferrocene-modified HRP (Fc@HRP) were chemically conjugated in two enzyme strands (GOx-ES1 and Fc@HRP-ES2), respectively. The repeated recycling of aDNA was powered by the displacement of GOx-ES1 by aDNA and exonuclease III (ExoIII)-assisted cleavage reaction for amplified output of numerous GOx-ES1 as dependent transducers, together with Fc@HRP-ES2 which was simultaneously hybridized with dSH-HP to assemble this DNA structure. Rationally, the bienzymatic cascade catalysis was motivated through GOx-catalyzed glucose oxidization to in situ generate hydrogen peroxide (H2O2) and overlapped HRP-catalyzed H2O2 decomposition to promote the electron transfer, producing significantly enhanced electrochemical signal of Fc with an ultrahigh sensitivity down to 0.22 fM of aDNA. Benefited from the unique design of dSH-HP-oriented bienzymatic cascades, this one-step strategy without non-specific blockers passivation was simple and renewable, and would pave a promising avenue for sensitive electrochemical assay of biomolecules.
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Affiliation(s)
- Jiaxi Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Xiaoyu Hua
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Qiong Li
- College of Geophysics, Chengdu University of Technology, Chengdu, 610059, China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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7
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Shi K, Cao L, Liu F, Xie S, Wang S, Huang Y, Lei C, Nie Z. Amplified and label-free electrochemical detection of a protease biomarker by integrating proteolysis-triggered transcription. Biosens Bioelectron 2021; 190:113372. [PMID: 34116447 DOI: 10.1016/j.bios.2021.113372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 10/25/2022]
Abstract
Cell-free synthetic biology provides a promising strategy for developing high-performance biosensors by integrating with advanced testing technologies. However, the combination of synthetic biology with electrochemical testing techniques is still underdeveloped. Here, we proposed an electrochemical biosensor for the label-free and ultrasensitive detection of target protease biomarker by coupling a protease-responsive RNA polymerase (PR) for signal amplification. Taking tumor biomarker matrix metalloprotease-2 (MMP-2) as a model protease, we employed PR to transduce each proteolysis reaction mediated by MMP-2 into multiple programmable RNA outputs that can be captured by the DNA probes immobilized on a gold electrode. Moreover, the captured RNAs are designed to contain a guanine-rich sequence that can form G-quadruplex and bind to hemin in the presence of potassium ions. In this scenario, the activity of MMP-2 is converted and amplified into the electrochemical signals of hemin. Under the optimal conditions, this PR-based electrochemical biosensor enabled the sensitive detection of MMP-2 in a wide linear dynamic range from 10 fM to 1.0 nM, with a limit of detection of 7.1 fM. Moreover, the proposed biosensor was further applied in evaluating MMP-2 activities in different cell cultures and human tissue samples, demonstrating its potential in the analysis of protease biomarkers in complex clinical samples.
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Affiliation(s)
- Kai Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Lei Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Fang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Shuo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
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8
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Zhang X, Zhou Y, Chai Y, Yuan R. Double Hairpin DNAs Recognition Induced a Novel Cascade Amplification for Highly Specific and Ultrasensitive Electrochemiluminescence Detection of DNA. Anal Chem 2021; 93:7987-7992. [PMID: 34029048 DOI: 10.1021/acs.analchem.1c01012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Herein, a novel DNA cascade amplification, including double hairpin DNAs recognition-triggered single-target recycling (D-STR) and concatenated DNA structure-controlled rolling circle amplification (C-RCA), was developed as a signal amplifier to construct a highly specific and ultrasensitive electrochemiluminescence (ECL) biosensor for human immunodeficiency virus (HIV) DNA fragments detection, which not only revealed tremendous potential in avoiding false positive signals but also obviously promoted the amplification efficiency simultaneously compared to conventional single recognition of the target. Once the target DNA triggered the rolling circle amplification (RCA), the obtained RCA products could be anchored on the Pt-modified glassy carbon electrode (GCE) via the Pt-N bond, capturing massive ruthenium (Ru)-labeled ssDNA as the ECL signal tag to generate remarkable ECL emission. As a result, the proposed biosensor showed highly specific and ultrasensitive detection of the target with the detection limit down to 27.0 aM, which gives great impetus to the development of a novel specific biosensor for practical bioanalysis and diagnostic technologies.
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Affiliation(s)
- Xiaoli Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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9
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Minasyan AS, Chakravarthy S, Vardelly S, Joseph M, Nesterov EE, Nesterova IV. Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes. NANOSCALE 2021; 13:8875-8883. [PMID: 33949568 PMCID: PMC8210535 DOI: 10.1039/d1nr00611h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.
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Affiliation(s)
- Alexander S Minasyan
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | | | - Suchitra Vardelly
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Mark Joseph
- Department of Natural Science, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Evgueni E Nesterov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
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10
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Figueredo F, Stolowicz F, Vojnov A, Coltro WKT, Larocca L, Carrillo C, Cortón E. Towards a versatile and economic Chagas Disease point-of-care testing system, by integrating loop-mediated isothermal amplification and contactless/label-free conductivity detection. PLoS Negl Trop Dis 2021; 15:e0009406. [PMID: 33989282 PMCID: PMC8153438 DOI: 10.1371/journal.pntd.0009406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/26/2021] [Accepted: 04/25/2021] [Indexed: 01/17/2023] Open
Abstract
Rapid diagnosis by using small, simple, and portable devices could represent one of the best strategies to limit the damage and contain the spread of viral, bacterial or protozoa diseases, principally when they can be transmitted by air and are highly contagious, as some respiratory viruses are. The presence of antibodies in blood or serum samples is not the best option for deciding when a person must be quarantined to stop transmission of disease, given that cured patients have antibodies, so the best diagnosis methods rely on the use of nucleic acid amplification procedures. Here we present a very simple device and detection principle, based on paper discs coupled to contactless conductivity (C4D) sensors, can provide fast and easy diagnostics that are needed when an epidemic outbreak develops. The paper device presented here solves one of the main drawbacks that nucleic acid amplification tests have when they are performed outside of central laboratories. As the device is sealed before amplification and integrally disposed in this way, amplimers release cannot occur, allowing repetitive testing in the physician’s practice, ambulances, or other places that are not prepared to avoid cross-contamination of new samples. The use of very low volume samples allows efficient reagent use and the development of low cost, simple, and disposable point-of-care diagnostic systems. In 2005, the World Health Organization (WHO) recognized Chagas Disease as a neglected tropical disease. Meanwhile the serological tests, recommended by WHO, can be performed for chronic disease diagnosis, the nucleic acid amplification tests must be performed for the detection of the acute phase of the disease. Although the existing laboratory diagnosis tests for Chagas Disease are sensitive and highly reproducible, they cannot be performed in rural, low infrastructure environments, where this disease prevails. In this sense, the use of simple and portable analytical devices may be able to offer an affordable solution to this problem, allowing fast sampling, diagnosis and treatment prescription in one simple and fast intervention, as the performed by short term medical missions. In this study we show for the first time a diagnosis test comprising low cost materials and employing a contactless and label-free conductivity detection system that is used to read the result of a nucleic acid amplification reaction. The test showed high sensitivity for Chagas Disease diagnosis showing the potential to be used in rural and low income places.
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Affiliation(s)
- Federico Figueredo
- Biological Chemistry Department, Science School and IQUIBICEN (FCEN–UBA-CONICET), Argentine
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Fabiana Stolowicz
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Adrián Vojnov
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Wendell K. T. Coltro
- Chemistry Institute, Federal University of Goiás, Campus Samambaia, Goiânia, Brazil
- National Institute of Science and Technology in Bioanalytics, Campinas, Brazil
| | - Luciana Larocca
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Carolina Carrillo
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Eduardo Cortón
- Biological Chemistry Department, Science School and IQUIBICEN (FCEN–UBA-CONICET), Argentine
- * E-mail:
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11
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Ren M, Zeng W, Li Z, Cao S, Liu C, Ouyang S, Zhang T, Cui Y, Yuan H. CoAl-layered double hydroxide nanosheet-based fluorescence assay for fast DNA detection. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 240:118618. [PMID: 32599482 DOI: 10.1016/j.saa.2020.118618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
In the study, CoAl-layered double hydroxide (CoAl-LDH) was prepared as a fluorescence quenching agent to detect DNA molecules. Because of its simple preparation for a large scale, excellent surface effect, good biocompatibility and high fluorescence quenching capability, the effective, rapid, and sensitive DNA detection was realized. The fluorescence quenching efficiency of LDH to 5(6)-carboxyfluorescein attached to single stranded DNA (FAM-ssDNA) was as high as 88%, and after FAM-ssDNA hybridized with the complementary DNA oligonucleotide, that to FAM-dsDNA was about 33%. The quenching mechanisms of LDH for ssDNA and dsDNA were discussed. Phosphate exposed of ssDNA played an important role in quenching effect. Compared to dsDNA, more exposed phosphate groups in ssDNA resulted in the stronger electrostatic interaction between ssDNA and LDH, and thus the higher quenching efficiency. Under optimal conditions, the linear equation was y = 38.26 + 3.37x in a linear relationship of 1-50 nM, and the correlation coefficient R2 corresponded to 0.999, and the limit of detection was calculated to be 0.79 nM (3σ). Cytotoxicity studies have shown that LDH has good biocompatibility. The study provides an effective, sensitive and safe approach for DNA detection and gives an insight for the design of LDH-based biosensing materials.
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Affiliation(s)
- Mengli Ren
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Weili Zeng
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zhenhua Li
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Shiqin Cao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Chunrong Liu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Shuxin Ouyang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Tierui Zhang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yanfang Cui
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.
| | - Hong Yuan
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China; Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing, Southwest University, Chongqing 400715, PR China.
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12
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Peng Y, Li R, Yu M, Yi X, Zhu H, Li Z, Yang Y. Electrochemical biosensor for detection of MON89788 gene fragments with spiny trisoctahedron gold nanocrystal and target DNA recycling amplification. Mikrochim Acta 2020; 187:494. [PMID: 32778963 DOI: 10.1007/s00604-020-04467-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/27/2020] [Indexed: 12/26/2022]
Abstract
The shape-controlled synthesis of gold nanocrystals via shape induction of hexadecyltrimethylammonium chloride, potassium bromide, and potassium iodide and enantioselective direction of L-cysteine is reported. The resulting gold nanocrystals (STO-Au) offer spiny trisoctahedron nanostructures with good monodispersity and enhanced exposed high-index facets and high catalytic activity. Construction of the electrochemical sensing platform for MON89788 gene involves the modification of STO-Au, thionine (Thi), and labeled bipedal DNA probe 1 or 2 (P1 or P2) for target DNA-induced recycling amplification. In the detection, two surface DNA probes were immobilized on gold electrode via the Au-S bond. Then, hairpin DNA 1 (H1), Thi-STO-Au-P1, and Thi-STO-Au-P2 self-assemble into two-dimensional DNA nanopores (DNPs) on the electrode surface. Target DNA hybridizes with hairpin DNA 2 (H2) to open hairpin structure of H2. The opened H2 binds with H1 in the DNPs to release Thi-STO-Au-P1, Thi-STO-Au-P2, and target DNA by toehold-mediated strand-displacement. The utilization of target DNA-induced recycling allows one target DNA to release 2N STO-Au-labeled DNA strands, promoting significant signal amplification. The detection signal is further enhanced by the catalyzed redox reaction of Thi with STO-Au. The differential pulse voltammetric signal, best measured at - 0.18 V vs. Ag/AgCl, decreases linearly with increasing concentration of MON89788 in the range 0.02-8 × 104 fM, and the detection limit is 0.0048 fM (S/N = 3). The proposed method was successfully applied for electrochemical detection of MON89788 gene fragments in the PCR products from genetically modified soybean. Graphical Abstract We develop l-cysteine controlled synthesis of spiny trisoctahedron gold nanocrystals with good monodispersity and highly exposed high-index facets. The architecture achieves to ultrahigh catalytic activity. The electrochemical biosensor based on gold nanocrystals and target DNA recycling amplification provides advantage of sensitivity, repeatability, and regeneration-free.
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Affiliation(s)
- Yuanfeng Peng
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Ruiyi Li
- , Lihu Road 1800, Wuxi, 214122, Jiangsu, China
| | - Minyi Yu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiaowen Yi
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Haiyan Zhu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zaijun Li
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, China.
| | - Yongqiang Yang
- National Graphene Product Quality Supervision and Inspection Center, Jiangsu Province Special Equipment Safety Supervision and Inspection Institute Branch, Wuxi, 214071, China.
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Highly sensitive detection of lipopolysaccharide based on collaborative amplification of dual enzymes. Anal Chim Acta 2020; 1126:31-37. [DOI: 10.1016/j.aca.2020.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
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14
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Identification of programmed death ligand-1 positive exosomes in breast cancer based on DNA amplification-responsive metal-organic frameworks. Biosens Bioelectron 2020; 166:112452. [PMID: 32738648 DOI: 10.1016/j.bios.2020.112452] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Cancer-derived exosomes have recently emerged as potent candidates for diagnosis and prognosis of breast cancer. As an example, programmed death ligand-1 positive (PD-L1+) exosomes are found to be correlated with the progression and immunotherapy response of breast cancer, and therefore show great potential in liquid biopsy. Herein, we propose an electrochemical biosensing method for accurate identification of PD-L1+ exosomes by using DNA amplification-responsive metal-organic frameworks, PVP@HRP@ZIF-8. Specially, PD-L1+ exosomes are captured by anti-CD63 functionalized magnetic beads and bound with anti-PD-L1-linked capture probe. Then, in situ hyperbranched rolling circle amplification, a typical DNA amplification reaction, is conducted using the surface-attached capture probes as primers, which lows environmental pH. As a result, disassembly of PVP@HRP@ZIF-8 takes place, leading to the release of enzymes, which can arouse amplified electrochemical responses for the identification of target exosomes. Experimental results reveal that the biosensing method displays a linear range for PD-L1+ exosomes identification from 1 × 103 to 1 × 1010 particles/mL and the detection limit reaches 334 particles/mL. What is more, by using the method, elevated level of circulating PD-L1+ exosomes is found in the undiluted serum samples from patients with breast cancer, particularly for metastatic breast cancer, revealing a positive correlation of the PD-L1+ exosome level with the tumor staging and disease progression of breast cancer. Therefore, the biosensing method may be valuable for not only exosome identification but also providing reference information for diagnosis and real-time monitoring of breast cancer in the future.
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Han Y, An F, Liu J, Kong J, Zhang X. Highly sensitive determination of DNA via a new type of electrochemical zirconium signaling probe. NEW J CHEM 2020. [DOI: 10.1039/d0nj04405a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Exploiting Zr(iv) as a redox probe for the detection of DNA has great potential in clinical analysis.
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Affiliation(s)
- Yan Han
- School of Environmental and Biological Engineering
- Nanjing University of Science and Technology
- Nanjing
- P. R. China
| | - Fengxia An
- State Power Protection Research Institute Co., Ltd
- Nanjing
- P. R. China
| | - Jingliang Liu
- School of Environmental Science
- Nanjing XiaoZhuang University
- Nanjing
- P. R. China
| | - Jinming Kong
- School of Environmental and Biological Engineering
- Nanjing University of Science and Technology
- Nanjing
- P. R. China
| | - Xueji Zhang
- School of Biomedical Engineering
- Shenzhen University Health Science Center
- Shenzhen
- P. R. China
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Chaudhary S, Kaushik M, Ahmed S, Kukreti S. Exploring potential of i-motif DNA formed in the promoter region of GRIN1 gene for nanotechnological applications. RESULTS IN CHEMISTRY 2020. [DOI: 10.1016/j.rechem.2020.100086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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17
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Xu S, Chang Y, Wu Z, Li Y, Yuan R, Chai Y. One DNA circle capture probe with multiple target recognition domains for simultaneous electrochemical detection of miRNA-21 and miRNA-155. Biosens Bioelectron 2019; 149:111848. [PMID: 31726271 DOI: 10.1016/j.bios.2019.111848] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/23/2019] [Accepted: 11/02/2019] [Indexed: 12/18/2022]
Abstract
In this work, a novel DNA circle capture probe with multiple target recognition domains was designed to develop an electrochemical biosensor for ultrasensitive detection of microRNA-21 (miRNA-21) and miRNA-155 simultaneously. The DNA circle capture probe was anchored at the top of the tetrahedron DNA nanostructure (TDN) to simultaneously recognize miRNA-21 and miRNA-155 through multiple target recognition domains under the assistance of Helper strands, which could trigger mimetic proximity ligation assay (mPLA) for capturing the beacons ferrocene (Fc)-A1 and methylene blue (MB)-A2 to achieve multiple miRNAs detection. In this way, the local reaction concentration could be enhanced and avoid the interference of various capture probes compared with the traditional multiplexed electrochemical biosensor with the use of different capture probes, resulting in the significantly improvement of detection sensitivity. As a result, this proposed biosensor showed wide linearity ranging from 0.1 fM to 10 nM with detection limits of miRNA-21 and miRNA-155 as 18.9 aM and 39.6 aM respectively, which also could be applied in the simultaneously detection of miRNA-21 and miRNA-155 from cancer cell lysates. The present strategy paved a new path in the design of capture probes for achieving more efficient and sensitive multiple biomarkers detections and possessed the potential applications in clinical diagnostic of diseases.
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Affiliation(s)
- Sai Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yuanyuan Chang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Zhongyu Wu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yunrui Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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