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Ouedraogo SY, Zeye MMJ, Zhou X, Kiendrebeogo TI, Zoure AA, Chen H, Chen F, Ma C. Colorimetric detection of single-nucleotide mutations based on rolling circle amplification and G-quadruplex-based DNAzyme. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5785-5792. [PMID: 39140250 DOI: 10.1039/d4ay01080a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In this work, we proposed a sensitive and selective colorimetric assay for single nucleotide mutation (SNM) detection combining rolling circle amplification (RCA) and G-quadruplex/hemin DNAzyme complex formation. In the detection principle, the first step involves ssDNA hybridization with a padlock probe (PLP) DNA, which can discriminate a single base mismatch. The successful ligation is followed by an RCA event to generate an abundance of G-quadruplexes (GQ-RCA) which are then transformed into a DNAzyme (G-quadruplex/hemin complex) by the addition of hemin. The color change from colorless 3,3',5,5'-tetramethylbenzidine (TMB) into colored oxTMB when hydrogen peroxide (H2O2) is added indicated the presence of a mutation. The assay had a limit of detection (LOD) of 2.14 pM. Mutations in samples from breast cancer patients were successfully detected with an accuracy of 100% when compared to Sanger sequencing results. The method is easily applicable even in resource poor setting regions given that it doesn't require any sophisticated or expensive instruments, and the signal readout is detectable simply by the naked eye. Our assay might be a useful tool for genetic analysis and clinical molecular diagnosis for breast cancer risk assessment and early detection.
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Affiliation(s)
- Serge Yannick Ouedraogo
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410013, Hunan, China.
- Biomolecular Research Center Pietro Annigoni (CERBA), LABIOGENE, University of Ouaga 1 Pr Joseph KI ZERBO, UFR/SVT, Burkina Faso
| | - Moutanou Modeste Judes Zeye
- Department of Medical Parasitology, School of Basic Medicine, Central South University, Changsha 410013, Hunan, China
| | - Xi Zhou
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410013, Hunan, China.
| | | | - Abdou Azaque Zoure
- Biomolecular Research Center Pietro Annigoni (CERBA), LABIOGENE, University of Ouaga 1 Pr Joseph KI ZERBO, UFR/SVT, Burkina Faso
- Department of Biomedical and Public Health, Institute of Health Sciences Research (IRSS/CNRST), Burkina Faso
| | - Hanchun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Fangzhi Chen
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha 410007, Hunan, China.
| | - Changbei Ma
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410013, Hunan, China.
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Encinas-Gimenez M, Martin-Duque P, Martín-Pardillos A. Cellular Alterations Due to Direct and Indirect Interaction of Nanomaterials with Nucleic Acids. Int J Mol Sci 2024; 25:1983. [PMID: 38396662 PMCID: PMC10889090 DOI: 10.3390/ijms25041983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Deoxyribonucleic acid (DNA) represents the main reservoir of genetic information in the cells, which is why it is protected in the nucleus. Entry into the nucleus is, in general, difficult, as the nuclear membrane is a selective barrier to molecules longer than 40 kDa. However, in some cases, the size of certain nanoparticles (NPs) allows their internalization into the nucleus, thus causing a direct effect on the DNA structure. NPs can also induce indirect effects on DNA through reactive oxygen species (ROS) generation. In this context, nanomaterials are emerging as a disruptive tool for the development of novel therapies in a broad range of biomedical fields; although their effect on cell viability is commonly studied, further interactions with DNA or indirect alterations triggered by the internalization of these materials are not always clarified, since the small size of these materials makes them perfectly suitable for interaction with subcellular structures, such as the nucleus. In this context, and using as a reference the predicted interactions presented in a computational model, we describe and discuss the observed direct and indirect effects of the implicated nanomaterials on DNA.
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Affiliation(s)
- Miguel Encinas-Gimenez
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.E.-G.); (A.M.-P.)
- Department of Chemical Engineering and Environmental Technology (IQTMA), University of Zaragoza, 50018 Zaragoza, Spain
- Ciber Bioingeniería y Biomateriales (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pilar Martin-Duque
- Ciber Bioingeniería y Biomateriales (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Desarrollo de Medicamentos de Terapias Avanzadas (DDMTA), Centro de Terapias Avanzadas, Instituto de Salud Carlos lll, 28222 Madrid, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | - Ana Martín-Pardillos
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.E.-G.); (A.M.-P.)
- Department of Chemical Engineering and Environmental Technology (IQTMA), University of Zaragoza, 50018 Zaragoza, Spain
- Ciber Bioingeniería y Biomateriales (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Jin Y, Huang Z, Xu B, Chen J. Localization of multiple DNAzymes as a branchedzyme-powered nanodevice for the immunoassay of tumor biomarkers. Anal Chim Acta 2023; 1274:341580. [PMID: 37455088 DOI: 10.1016/j.aca.2023.341580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Traditional immunoassay methods often face challenges due to the labeling procedure of protein enzymes, the use of multiple antibodies, and severe conditions. To address these limitations, we propose the concept of incorporating branchedzyme-powered nanodevices into immunoassays. In this strategy, multiple DNAzymes are localized onto gold nanoparticles (AuNPs) along with substrates. The localization format facilitates intramolecular reactions between DNAzymes and substrates, leading to accelerated kinetics of the nanodevice. Upon the formation of an immunocomplex with an antibody on a 96-well plate, the branchedzyme-powered nanodevice catalytically releases multiple fluorescent signals under ambient temperature, eliminating the need for secondary antibodies. The branched DNAzymes exhibit catalytic properties similar to those of protein enzymes, thus simplifying the assay procedure and achieving isothermal detection. Furthermore, the detection process can be controlled by the addition or deletion of cofactors. Additionally, the affinity ligand can be easily modified to construct nanodevices specific to different targets without requiring extensive redesign. This strategy has demonstrated successful quantification of tumor biomarkers such as alpha-fetoprotein (AFP) and prostate-specific antigen (PSA) at subpicomolar concentrations, showcasing its suitability for clinical applications. Consequently, the branchedzyme-powered nanodevice represents a valuable addition to the immunoassay toolbox, opening new possibilities for clinical diagnostics.
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Affiliation(s)
- Yanwen Jin
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan Universtity, Chengdu, Sichuan, 610064, China
| | - Zhuochun Huang
- Department of Laboratory Medicine, West China Hospital, Sichuan Universtity, Chengdu, Sichuan, 610064, China
| | - Bingyan Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan Universtity, Chengdu, Sichuan, 610064, China
| | - Junbo Chen
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan, 610064, China.
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Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
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Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Liang XX, Qian L, Huang RF. Label-free and ultrasensitive electrochemiluminescence detection of oxidative DNA damage using DNA repair enzyme. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Piao J, Zhou X, Wu X. Colorimetric human papillomavirus DNA assay based on the retardation of avidin-induced aggregation of gold nanoparticles. Mikrochim Acta 2018; 185:537. [PMID: 30413896 DOI: 10.1007/s00604-018-3065-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/20/2018] [Indexed: 01/08/2023]
Abstract
A colorimetric assay for human papillomavirus (HPV) DNA was developed based on the retardation of the avidin-induced aggregation of gold nanoparticles (AuNPs) by HPV DNA. Positively charged avidin acts as a coagulant for AuNP aggregation. In the presence of the target DNA, however, the aggregation of AuNPs is retarded owing to electrosteric stabilization as a result of the hybridization of the target and probe DNA. In the absence of HPV DNA, the stabilization effect caused by the biotinylated probe DNA is weak, resulting in NP aggregation and a color change from red to purple. Aggregation may be easily observed with bare eyes or spectrophotometrically at about 560 nm. The visual detection limit is 1 nM. The assay was used for the determination of HPV DNA after polymerase chain reaction (PCR) amplification without any further purification. Graphical abstract Schematic presentation of the avidin-induced aggregation of unmodified gold nanoparticles (AuNPs) which leads to a color change from red to purple. In the presence of dsDNA, however, the aggregation is remarkably retarded.
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Affiliation(s)
- Jingyu Piao
- Department of Chemistry, College of Science, Yanbian University, Yanji, Jilin, 133002, China.,Education Department of the Teachers College, Yanbian University, Yanji, Jilin, 133002, China
| | - Xin Zhou
- Department of Chemistry, College of Science, Yanbian University, Yanji, Jilin, 133002, China
| | - Xue Wu
- Department of Chemistry, College of Science, Yanbian University, Yanji, Jilin, 133002, China.
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