1
|
Naoumi N, Araya-Farias M, Megariti M, Alexandre L, Papadakis G, Descroix S, Gizeli E. Acoustic detection of a mutation-specific Ligase Chain Reaction based on liposome amplification. Analyst 2024; 149:3537-3546. [PMID: 38758167 DOI: 10.1039/d3an02142d] [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: 05/18/2024]
Abstract
Single nucleotide variants (SNVs) play a crucial role in understanding genetic diseases, cancer development, and personalized medicine. However, existing ligase-based amplification and detection techniques, such as Rolling Circle Amplification and Ligase Detection Reaction, suffer from low efficiency and difficulties in product detection. To address these limitations, we propose a novel approach that combines Ligase Chain Reaction (LCR) with acoustic detection using highly dissipative liposomes. In our study, we are using LCR combined with biotin- and cholesterol-tagged primers to produce amplicons also modified at each end with a biotin and cholesterol molecule. We then apply the LCR mix without any purification directly on a neutravidin modified QCM device Au-surface, where the produced amplicons can bind specifically through the biotin end. To improve sensitivity, we finally introduce liposomes as signal enhancers. For demonstration, we used the detection of the BRAF V600E point mutation versus the wild-type allele, achieving an impressive detection limit of 220 aM of the mutant target in the presence of the same amount of the wild type. Finally, we combined the assay with a microfluidic fluidized bed DNA extraction technology, offering the potential for semi-automated detection of SNVs in patients' crude samples. Overall, our LCR/acoustic method outperforms other LCR-based approaches and surface ligation biosensing techniques in terms of detection efficiency and time. It effectively overcomes challenges related to DNA detection, making it applicable in diverse fields, including genetic disease and pathogen detection.
Collapse
Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Monica Araya-Farias
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Maria Megariti
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Lucile Alexandre
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Stephanie Descroix
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| |
Collapse
|
2
|
Yang LY, Xu XW, Lin Y, Ye CL, Liu WQ, Liu ZJ, Zhong GX, Xu YF, Lin XH, Chen JY. Nucleic Acid Amplification by Template-Dominated Click Chemistry for Ultrasensitive DNA/RNA Detection on an Electrochemical Readout Platform. Anal Chem 2023; 95:5331-5339. [PMID: 36926822 DOI: 10.1021/acs.analchem.2c05421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
As an enzyme-free exponential nucleic acid amplification method, the click chemistry-mediated ligation chain reaction (ccLCR) has shown great prospects in the molecular diagnosis. However, the current optics-based ccLCR is challenged by remarkable nonspecific amplification, severely hindering its future application. This study demonstrated that the severe nonspecific amplification was generated probably due to high random collision in the high DNA probe concentration (μM level). To solve this hurdle, a nucleic acid template-dominated ccLCR was constructed using nM-level DNA probes and read on an electrochemical platform (cc-eLCR). Under the optimal conditions, the proposed cc-eLCR detected a low-level nucleic acid target (1 fM) with a single-base resolution. Furthermore, this assay was applied to detect the target of interest in cell extracts with a satisfactory result. The proposed cc-eLCR offers huge possibility for click chemistry-mediated enzyme-free exponential nucleic acid amplification in the application of medical diagnosis and biomedical research.
Collapse
Affiliation(s)
- Liang-Yong Yang
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.,Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Yan Lin
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmacy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan 364000, China
| | - Wei-Qiang Liu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Zhou-Jie Liu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Guang-Xian Zhong
- Department of Rehabilitation Medicine, School of Health, Fujian Medical University, Fuzhou 350122, China
| | - Yan-Fang Xu
- Department of Nephrology, the Central Laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| |
Collapse
|
3
|
Simultaneous quantification of multiple single nucleotide variants in PIK3CA ctDNA using mass-tagged LCR probe sets. Talanta 2023; 258:124426. [PMID: 36933295 DOI: 10.1016/j.talanta.2023.124426] [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: 01/06/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023]
Abstract
Circulating tumor DNA (ctDNA) in blood carries genetic variations associated with tumors. There is evidence indicating that the abundance of single nucleotide variant (SNV) in ctDNA is correlated well with cancer progression and metastasis. Thus, accurate and quantitative detection of SNVs in ctDNA may benefit clinical practice. However, most current methods are unsuitable for the quantification of SNV in ctDNA that usually differentiates from wild-type DNA (wtDNA) only by a single base. In this setting, ligase chain reaction (LCR) coupled with mass spectrometry (MS) was developed to simultaneously quantify multiple SNVs using PIK3CA ctDNA as a model. Mass-tagged LCR probe set for each SNV including mass-tagged probe and three DNA probes was firstly designed and prepared. Then, LCR was initiated to discriminate SNVs specifically and amplify the signal of SNVs in ctDNA selectively. Afterward, a biotin-streptavidin reaction system was used to separate the amplified products, and photolysis was initiated to release mass tags. Finally, mass tags were monitored and quantified by MS. After optimizing conditions and verifying performance, this quantitative system was applied for blood samples from breast cancer patients, and risk stratification for breast cancer metastasis was also performed. This study is among the first to quantify multiple SNVs in ctDNA in a signal amplification and conversion manner, and also highlights the potential of SNV in ctDNA as a liquid biopsy marker to monitor cancer progression and metastasis.
Collapse
|
4
|
Williamson P, Piskunen P, Ijäs H, Butterworth A, Linko V, Corrigan DK. Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles. ACS Sens 2023; 8:1471-1480. [PMID: 36914224 PMCID: PMC10152479 DOI: 10.1021/acssensors.2c02469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (RCT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.
Collapse
Affiliation(s)
- Paul Williamson
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1QE, United Kingdom
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.,Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Adrian Butterworth
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1QE, United Kingdom
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.,LIBER Center of Excellence, Aalto University, 00076 Aalto, Finland.,Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Damion K Corrigan
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1QE, United Kingdom.,Department of Pure & Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| |
Collapse
|
5
|
Electrochemical biosensors for analysis of DNA point mutations in cancer research. Anal Bioanal Chem 2023; 415:1065-1085. [PMID: 36289102 DOI: 10.1007/s00216-022-04388-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
Cancer is a genetic disease induced by mutations in DNA, in particular point mutations in important driver genes that lead to protein malfunctioning and ultimately to tumorigenesis. Screening for the most common DNA point mutations, especially in such genes as TP53, BRCA1 and BRCA2, EGFR, KRAS, or BRAF, is crucial to determine predisposition risk for cancer or to predict response to therapy. In this review, we briefly depict how these genes are involved in cancer, followed by a description of the most common techniques routinely applied for their analysis, including high-throughput next-generation sequencing technology and less expensive low-throughput options, such as real-time PCR, restriction fragment length polymorphism, or high resolution melting analysis. We then introduce benefits of electrochemical biosensors as interesting alternatives to the standard methods in terms of cost, speed, and simplicity. We describe most common strategies involved in electrochemical biosensing of point mutations, relying mostly on PCR or isothermal amplification techniques, and critically discuss major challenges and obstacles that, until now, prevented their more widespread application in clinical settings.
Collapse
|
6
|
Zakaria ND, Hamzah HH, Salih IL, Balakrishnan V, Abdul Razak K. A Review of Detection Methods for Vancomycin-Resistant Enterococci (VRE) Genes: From Conventional Approaches to Potentially Electrochemical DNA Biosensors. BIOSENSORS 2023; 13:294. [PMID: 36832060 PMCID: PMC9954664 DOI: 10.3390/bios13020294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Vancomycin-resistant Enterococci (VRE) genes are bacteria strains generated from Gram-positive bacteria and resistant to one of the glycopeptides antibiotics, commonly, vancomycin. VRE genes have been identified worldwide and exhibit considerable phenotypic and genotypic variations. There are six identified phenotypes of vancomycin-resistant genes: VanA, VanB, VanC, VanD, VanE, and VanG. The VanA and VanB strains are often found in the clinical laboratory because they are very resistant to vancomycin. VanA bacteria can pose significant issues for hospitalized patients due to their ability to spread to other Gram-positive infections, which changes their genetic material to increase their resistance to the antibiotics used during treatment. This review summarizes the established methods for detecting VRE strains utilizing traditional, immunoassay, and molecular approaches and then focuses on potential electrochemical DNA biosensors to be developed. However, from the literature search, no information was reported on developing electrochemical biosensors for detecting VRE genes; only the electrochemical detection of vancomycin-susceptible bacteria was reported. Thus, strategies to create robust, selective, and miniaturized electrochemical DNA biosensor platforms to detect VRE genes are also discussed.
Collapse
Affiliation(s)
- Nor Dyana Zakaria
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Hairul Hisham Hamzah
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Ibrahim Luqman Salih
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Venugopal Balakrishnan
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Khairunisak Abdul Razak
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
- School of Materials and Mineral Resources Engineering, Universiti Sains Malaysia, Nibong Tebal 14300, Penang, Malaysia
| |
Collapse
|
7
|
Chen L, Yang W, Li D, Ma Y, Chen L, You S, Liu S. Poly cytosine (C)/poly adenine (A) modified probe for signal "on-off-on" assay of single-base mismatched dsDNA by a competitive mechanism. Anal Chim Acta 2023; 1239:340705. [PMID: 36628713 DOI: 10.1016/j.aca.2022.340705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Direct discrimination of single-base mismatched dsDNA by a simple method or strategy would provide enormous opportunities for applications in the fields of life sciences and disease diagnosis. Herein, the peroxidase-mimicking activity of a metal-organic framework nanoprobe (MOF) was well exploited for the direct discrimination of single-base mismatched dsDNA based on a competition-induced signal on-off-on mechanism. The single-base mismatched dsDNA related with FecB gene (usually guanine (G)/thymine (T) mismatch) and MIL-88B-NH2 were used as target and MOF model, respectively. Firstly, polyA/polyC were loosely adsorbed onto the MOFs via the weak interaction to block the peroxidase activity of MOF, inducing the signal transition from on to off. Unexpectedly, the single-base mismatched (GT) dsDNA could reverse the signal response of MOF probe from off to on. But it could not occur for other nonspecific mismatches, such as CT and TT-mismatched dsDNA. A synergistic interaction mechanism between multiple GT mismatches and polyA/polyC was attempted to explain the competitive dissociation of polyA/polyC from MOF for the recovery of peroxidase activity. With it, a wide linear detection ranges from 10-9 M-10-5 M of GT mismatched dsDNA and a low detection limit of 0.247 nM could be achieved, even in the real samples. The effect of mismatched base number or position was also studied. Such a simple, rapid, cost-effective, and one-step mixing and checking method for single-base mismatched dsDNA discrimination eliminates the complex sample pretreatment, special DNA probe design, exclusive amplification or signal readout means. It thus offers a simple and effective route for direct discrimination of mismatched dsDNA and might hold a huge potential for the applications in gene analysis, disease diagnosis, and elementary research in life sciences.
Collapse
Affiliation(s)
- Lihua Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Wenjie Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Dong Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Yunkang Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Lili Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Shuang You
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, PR China.
| |
Collapse
|
8
|
Advances in ligase-based nucleic acid amplification technology for detecting gene mutations: a review. Mol Cell Biochem 2022; 478:1621-1631. [DOI: 10.1007/s11010-022-04615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]
|
9
|
RPA-ligation-qPCR combined method for genotyping the SARS-CoV-2 key mutation E484Q. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1924-1927. [PMID: 36305725 PMCID: PMC10157626 DOI: 10.3724/abbs.2022152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
10
|
Zhang W, Zhang P, Liang Y, Cheng W, Li L, Wang H, Yu Z, Liu Y, Zhang X. Rapid electrochemical quantification of trace Hg 2+ using a hairpin DNA probe and quantum dot modified screen-printed gold electrodes. RSC Adv 2022; 12:13448-13455. [PMID: 35527727 PMCID: PMC9067431 DOI: 10.1039/d2ra01817a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/18/2022] [Indexed: 11/21/2022] Open
Abstract
Rapid, simple, sensitive and specific approaches for mercury(ii) (Hg2+) detection are essential for toxicology assessment, environmental protection, food analysis and human health. In this study, a ratiometric hairpin DNA probe based electrochemical biosensor, which relies on hairpin DNA probes conjugated with water-soluble and carboxyl functionalized quaternary Zn–Ag–In–S quantum dot (QD) on screen-printed gold electrodes (SPGE), referred to as the HP-QDs-SPGE electrochemical biosensor in this study, was developed for Hg2+ detection. Based on the “turn-off” reaction of a hairpin DNA probe binding with a mismatched target and Hg2+ through the formation of T–Hg2+–T coordination, the HP-QDs-SPGE electrochemical biosensor can rapidly quantify trace Hg2+ with high ultrasensitivity, specificity, repeatability and reproducibility. The conformational change of the hairpin DNA probe caused a significant decrease in electrochemical intensity, which could be used for the quantification of Hg2+. The linear dynamic range and high sensitivity of the HP-QDs-SPGE electrochemical biosensor for the detection of Hg2+ was studied in vitro, with a broad linear dynamic range of 10 pM to 1 μM and detection limits of 0.11 pM. In particular, this HP-QDs-SPGE electrochemical biosensor showed excellent selectivity toward Hg2+ ions in the presence of other metal ions. More importantly, this biosensor has been successfully used to detect Hg2+ in deionized water, tap water, groundwater and urine samples with good recovery rate and small relative standard deviations. In summary, the developed HP-QDs-SPGE electrochemical biosensor exhibited promising potential for further applications in on-site analysis. A ratiometric hairpin DNA probe based electrochemical biosensor, which relies on hairpin DNA probes conjugated with water-soluble and carboxyl functionalized quantum dot on screen-printed gold electrodes, was developed for Hg2+ detection.![]()
Collapse
Affiliation(s)
- Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Pin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Zhengzhou Key Laboratory of Precise Diagnosis and Treatment of Children's Malignant Tumors, Children's Hospital Affiliated to Zhengzhou University Zhengzhou 450018 China +86-373-63866536 +86-373-63866536
| | - Yan Liu
- Department of Medicine, The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Xianwei Zhang
- Department of Medicine, The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| |
Collapse
|
11
|
Hybridization chain reaction-mediated Fe2MoO4 bimetallic nanozyme for colorimetric risk prediction of bladder cancer. Biosens Bioelectron 2022; 210:114272. [DOI: 10.1016/j.bios.2022.114272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022]
|
12
|
Topkaya SN, Turunc E, Cetin AE. Multi‐walled Carbon Nanotubes and Gold Nanorod Decorated Biosensor for Detection of microRNA‐126. ELECTROANAL 2021. [DOI: 10.1002/elan.202100198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Seda Nur Topkaya
- Department of Analytical Chemistry, Faculty of Pharmacy Izmir Katip Celebi University Cigli 35620 Izmir Turkey
| | - Ezgi Turunc
- Department of Biochemistry, Faculty of Pharmacy Izmir Katip Celebi University Cigli 35620 Izmir Turkey
| | - Arif E. Cetin
- Izmir Biomedicine and Genome Center Balcova 35340 Izmir Turkey
| |
Collapse
|
13
|
Williamson P, Ijäs H, Shen B, Corrigan DK, Linko V. Probing the Conformational States of a pH-Sensitive DNA Origami Zipper via Label-Free Electrochemical Methods. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7801-7809. [PMID: 34128683 PMCID: PMC8280702 DOI: 10.1021/acs.langmuir.1c01110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/05/2021] [Indexed: 06/12/2023]
Abstract
DNA origami structures represent an exciting class of materials for use in a wide range of biotechnological applications. This study reports the design, production, and characterization of a DNA origami "zipper" structure, which contains nine pH-responsive DNA locks. Each lock consists of two parts that are attached to the zipper's opposite arms: a DNA hairpin and a single-stranded DNA that are able to form a DNA triplex through Hoogsteen base pairing. The sequences of the locks were selected in a way that the zipper adopted a closed configuration at pH 6.5 and an open state at pH 8.0 (transition pKa 7.6). By adding thiol groups, it was possible to immobilize the zipper structure onto gold surfaces. The immobilization process was characterized electrochemically to confirm successful adsorption of the zipper. The open and closed states were then probed using differential pulse voltammetry and electrochemical impedance spectroscopy with solution-based redox agents. It was found that after immobilization, the open or closed state of the zipper in different pH regimes could be determined by electrochemical interrogation. These findings pave the way for development of DNA origami-based pH monitoring and other pH-responsive sensing and release strategies for zipper-functionalized gold surfaces.
Collapse
Affiliation(s)
- Paul Williamson
- Department
of Biomedical Engineering, University of
Strathclyde, 40 George Street, Glasgow G1 1QE, United Kingdom
| | - Heini Ijäs
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Nanoscience
Center, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Damion K. Corrigan
- Department
of Biomedical Engineering, University of
Strathclyde, 40 George Street, Glasgow G1 1QE, United Kingdom
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, P.O. Box 15100, 00076 Aalto, Finland
| |
Collapse
|
14
|
Liu J, Xie G, Xiong Q, Liang T, Xu H. Sensitive dual readout assays based on rolling circle amplification for fluorescent and colorimetric detection of Cronobacter spp. in powdered infant formula. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
15
|
Chen J, Wei H, Fang X, Cai Y, Zhang Z, Wang Y, Lin J, Zhang W, Zhong G. A pragmatic eLCR for an ultrasensitive detection of methicillin-resistant Staphylococcus aureus in joint synovial fluid: superior to qPCR. Analyst 2021; 146:3500-3509. [PMID: 33885074 DOI: 10.1039/d1an00350j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
For periprosthetic joint infection (PJI) patients, an early and rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) in joint synovial fluid is of great significance for receiving timely treatment and avoiding side effects. In clinical practice, the methods for detecting MRSA include the culture-based method and the PCR-based mecA gene detection method with fluorescent readout. However, the culture-based method requires up to 3-7 days for incubation and elaborative screening. The PCR-based molecular diagnosis, due to its high sensitivity, improves the detection time but sacrifices cost and gives false-positive results. Herein, a ligation chain reaction (LCR)-based electrochemical biosensor was developed to detect the mecA of MRSA with the advantages of rapidity, accuracy and low cost. In this system, an integrated dsDNA labeled with thiol and biotin at both terminals is generated only in the presence of the target DNA after LCR, followed by immobilization of the integrated dsDNAs on the bovine serum albumin (BSA)-coated gold electrode, and then the streptavidin horseradish peroxidase (SA-HRPs) is specifically bound to the biotin labels via biotin-streptavidin interaction, generating the catalytic amperometric readout. Impressively, the developed method achieved the detection of rare mecA in the joint synovial fluid of PJI patients (417-666 copies as quantified by qPCR). The proposed electrochemistry-based method is highly convenient for the point-of-care testing and was comparable with PCR in sensitivity, but superior in selectivity (single-base differentiation) and cost (nanomolar DNA probe consumption and simple device), demonstrating its huge potential in clinical applications for MRSA diagnosis.
Collapse
Affiliation(s)
- Jinyuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China and Key Laboratory of Radiation Biology of Fujian higher education institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Hongxiang Wei
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| | - Xinyu Fang
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| | - Yuanqing Cai
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| | - Zhenzhen Zhang
- Department of Phthology, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Yunqing Wang
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| | - Jianhua Lin
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| | - Wenming Zhang
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| | - Guangxian Zhong
- Department of Orthopaedics, Fujian Provincial Institute of Orthopaedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China.
| |
Collapse
|
16
|
Zhang W, Liu K, Zhang P, Cheng W, Zhang Y, Li L, Yu Z, Chen M, Chen L, Li L, Zhang X. All-in-one approaches for rapid and highly specific quantifcation of single nucleotide polymorphisms based on ligase detection reaction using molecular beacons as turn-on probes. Talanta 2020; 224:121717. [PMID: 33378999 DOI: 10.1016/j.talanta.2020.121717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022]
Abstract
Rapid, simple, specific and sensitive approaches for single nucleotide polymorphisms (SNPs) detection are essential for clinical diagnosis. In this study, all-in-one approaches, consisting of the whole detection process including ligase detection reaction (LDR) and real time quantitative polymerase chain reaction performed in one PCR tube by a one-step operation on a real-time PCR system using molecular beacon (MB) as turn-on probe, were developed for rapid, simple, specific and sensitive quantifcation of SNPs. High specificity of the all-in-one approach was achieved by using the LDR, which employs a thermostable and single-base discerning Hifi Taq DNA ligase to ligate adjacently hybridized LDR-specific probes. In addition, a highly specific probe, MB, was used to detect the products of all-in-one approach, which doubly enhances the specificity of the all-in-one approach. The linear dynamic range and high sensitivity of mutant DNA (MutDNA) and wild-type DNA (WtDNA) all-in-one approaches for the detection of MutDNA and WtDNA were studied in vitro, with a broad linear dynamic range of 0.1 fM to 1 pM and detection limits of 65.3 aM and 31.2 aM, respectively. In addition, the MutDNA and WtDNA all-in-one approaches were able to accurately detect allele frequency changes as low as 0.1%. In particular, the epidermal growth factor receptor T790M MutDNA frequency in the tissue of five patients with non-small cell lung cancer detected by all-in-one approaches were in agreement with clinical detection results, indicating the excellent practicability of the developed approaches for the quantification of SNPs in real samples. In summary, the developed all-in-one approaches exhibited promising potential for further applications in clinical diagnosis.
Collapse
Affiliation(s)
- Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Kangbo Liu
- Biological Testing Room, Henan Medical Equipment Inspection Institute, Henan Medical Equipment Inspection and Testing Engineering Technology Research Center, Henan Medical Equipment Biotechnology and Application Engineering Research Center, Zhengzhou, 450000, China
| | - Pin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Linfei Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Mengmeng Chen
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
| | - Lin Chen
- Henan Joint International Research Laboratory of Drug Discovery of Small Molecules, Zhengzhou Key Laboratory of Synthetic Biology of Natural Products, Huanghe Science and Technology College, 450063, Zhengzhou, China.
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; Departments of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Xianwei Zhang
- Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
| |
Collapse
|