1
|
Hu F, Zhang W, Meng W, Ma Y, Zhang X, Xu Y, Wang P, Gu Y. Ferrocene-labeled and purification-free electrochemical biosensor based on ligase chain reaction for ultrasensitive single nucleotide polymorphism detection. Anal Chim Acta 2020; 1109:9-18. [PMID: 32252909 DOI: 10.1016/j.aca.2020.02.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 11/29/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are crucial during the early diagnosis of a given disease as well as in evaluating their response to certain drugs. Thus, this study sought the development of ferrocene (Fc)-labeled electrochemical biosensor for SNP detection. This proposed system involves the ligation of four short probes (e.g., A, B, A', and B', where B' is labeled with an Fc-tag) in the presence of target DNA via ligase chain reaction (LCR), resulting in the formation of Fc-tagged duplex AB-A'B' in 2n. Subsequently, immobilization of the Fc-tagged duplex AB-A'B' on a single-stranded DNA capture probe (SC-DNA)-carboxyl multi-wall carbon nanotube (MWCNT-COOH) modified glassy carbon electrode (GCE) was accomplished through hybridization. Owing to the specificity of hybridization, and the use of Fc as electrochemical probe for detection of duplex AB-A'B', such strategy realized directly analysis of LCR products without the need for purification. By taking advantage of the thermal stability and high-discrimination ability of HiFi Taq DNA ligase for single-base differences, the specificity of hybridization, the EGFR T790 M mutant DNA (MT-DNA) biosensor was developed to offer a low limit of detection (0.75 aM), a high discrimination of single-base mismatches [as low as 0.01% (molar fraction)], a wide linear range of more than 7 orders of magnitude (1 aM-10 pM), and the recovery rates (95.3%-107.8%) from human serum samples. Thus, the biosensor under development was found to be economical, highly-sensitive, and exceptionally selective for detection of SNPs, and as well as extending the versatile applications of LCR to offer great potential for diagnosis and individual clinical regimens.
Collapse
Affiliation(s)
- Fang Hu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, China; Key Laboratory of Biomedical Functional Materials, School of Science, China Pharmaceutical University, Nanjing, 211198, China
| | - Wancun Zhang
- Department of Pediatric Oncology Surgery, Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated of Zhengzhou University, Zhengzhou, 450018, China
| | - Wei Meng
- Key Laboratory of Biomedical Functional Materials, School of Science, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuxiang Ma
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, China
| | - Xianwei Zhang
- Department of Pediatric Oncology Surgery, Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated of Zhengzhou University, Zhengzhou, 450018, China
| | - Ying Xu
- Department of Pediatric Oncology Surgery, Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated of Zhengzhou University, Zhengzhou, 450018, China
| | - Peng Wang
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yueqing Gu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, China.
| |
Collapse
|
2
|
Ghorbanzadeh N, Peymani A, Ahmadpour-Yazdi H. Colorimetric-based detection of Ureaplasma urealyticum using gold nanoparticles. IET Nanobiotechnol 2020; 14:19-24. [PMID: 31935673 DOI: 10.1049/iet-nbt.2019.0088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ureaplasma urealyticum (uu) is one of the most common agents of urogenital infections and is associated with complications such as infertility, spontaneous abortion and other sexually transmitted diseases. Here, a DNA sensor based on oligonucleotide target-specific gold nanoparticles (AuNPs) was developed, in which the dispersed and aggregated states of oligonucleotide-functionalised AuNPs were optimised for the colorimetric detection of a polymerase chain reaction (PCR) amplicon of U. urealyticum DNA. A non-cross-linking approach utilising a single Au-nanoprobe specific of the urease gene was utilised and the effect of a PCR product concentration gradient evaluated. Results from both visual and spectral analyses showed that target-Au-nanoprobe hybrids were stable against aggregation after adding the inducer. Furthermore, when a non-target PCR product was used, the peak position shifted and salt-induced aggregation occurred. The assay's limit of detection of the assay was 10 ng with a dynamic range of 10-60 ng. This procedure provides a rapid, facile and low-cost detection format, compared to methods currently used for the identification of U. urealyticum.
Collapse
Affiliation(s)
- Nahid Ghorbanzadeh
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Peymani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | | |
Collapse
|
3
|
Farhangi A, Peymani A, Ahmadpour-Yazdi H. Design of a gold nanoprobe for the detection of Pseudomonas aeruginosa elastase gene (lasB). RSC Adv 2020; 10:11590-11597. [PMID: 35496606 PMCID: PMC9051652 DOI: 10.1039/d0ra00848f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/20/2020] [Indexed: 11/21/2022] Open
Abstract
In this study, a gold nanoparticle-based DNA diagnostic sensor that is sensitive to the aggregation states of gold nanoparticles was used to identify the amplified and non-amplified lasB gene.
Collapse
Affiliation(s)
- Alireza Farhangi
- Student Research Committee
- Qazvin University of Medical Sciences
- Qazvin
- Iran
| | - Amir Peymani
- Medical Microbiology Research Center
- Qazvin University of Medical Sciences
- Qazvin
- Iran
| | - Hossien Ahmadpour-Yazdi
- Medical Biotechnology Department
- Faculty of Paramedical Sciences
- Qazvin University of Medical Sciences
- Qazvin
- Iran
| |
Collapse
|
4
|
Zhang Y, McKelvie ID, Cattrall RW, Kolev SD. Colorimetric detection based on localised surface plasmon resonance of gold nanoparticles: Merits, inherent shortcomings and future prospects. Talanta 2016; 152:410-22. [PMID: 26992537 DOI: 10.1016/j.talanta.2016.02.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Abstract
Localised surface plasmon resonance (LSPR) of gold nanoparticles (AuNPs) has been exploited for two decades in analytical science and has proven to be a powerful tool for the detection of various kinds of substances including small molecules, ions, macro biomolecules and microbes. Detection can be performed by visual colour change observations, photometry or resonance light scattering. A wide range of applications have been studied in the areas of environmental, pharmaceutical and biological analysis and clinical diagnosis. In this article, some fundamental aspects and important applications involving LSPR of AuNPs are reviewed. Several inherent shortcomings of these techniques and possible strategies to circumvent them are discussed.
Collapse
Affiliation(s)
- Yanlin Zhang
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Ian D McKelvie
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia; School of Geography, Earth and Environmental Sciences, Plymouth University, Plymouth PL4 8AA, United Kingdom.
| | - Robert W Cattrall
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Spas D Kolev
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia; Centre for Aquatic Pollution Identification and Management (CAPIM), The University of Melbourne, Victoria 3010, Australia.
| |
Collapse
|
5
|
Seow N, Tan YN, Yung LYL, Su X. DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection. Sci Rep 2015; 5:18293. [PMID: 26678946 PMCID: PMC4683372 DOI: 10.1038/srep18293] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/13/2015] [Indexed: 12/16/2022] Open
Abstract
We have developed a unique DNA-assembled gold nanoparticles (AuNPs) dimer for dynamic light scattering (DLS) sensing of transcription factors, exemplified by estrogen receptor (ER) that binds specifically to a double-stranded (ds) DNA sequence containing estrogen response element (ERE). Here, ERE sequence is incorporated into the DNA linkers to bridge the AuNPs dimer for ER binding. Coupled with DLS, this AuNP dimer-based DLS detection system gave distinct readout of a single ‘complex peak’ in the presence of the target molecule (i.e., ER). This unique signature marked the first time that such nanostructures can be used to study transcription factor-DNA interactions, which DLS alone cannot do. This was also unlike previously reported AuNP-DLS assays that gave random and broad distribution of particles size upon target binding. In addition, the ERE-containing AuNP dimers could also suppress the light-scattering signal from the unbound proteins and other interfering factors (e.g., buffer background), and has potential for sensitive detection of target proteins in complex biological samples such as cell lysates. In short, the as-developed AuNP dimer probe coupled with DLS is a simple (mix and test), rapid (readout in ~5 min) and sensitive (low nM levels of ER) platform to detect sequence-specific protein-DNA binding event.
Collapse
Affiliation(s)
- Nianjia Seow
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore 119260, Singapore
| | - Yen Nee Tan
- Institute of Material Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| | - Lin-Yue Lanry Yung
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore 119260, Singapore
| | - Xiaodi Su
- Institute of Material Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
| |
Collapse
|
6
|
Ahmadpour-Yazdi H, Hormozi-Nezhad M, Abadi A, Sanati MH, Kazemi B. Colorimetric Assay for Exon 7 SMN1/SMN2 Single Nucleotide Polymorphism Using Gold Nanoprobes. BIOIMPACTS : BI 2013; 3:185-94. [PMID: 24455482 DOI: 10.5681/bi.2013.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 11/29/2013] [Accepted: 12/15/2013] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Proximal spinal muscular atrophy (SMA) is one of the most significant neurodegenerative diseases amongst the autosomal-recessive genetic disorders which is caused by the absence of protein survival of motor neuron (SMN). A critical nucleotide difference in SMN2 compared to SMN1 gene leads to an inefficient protein. Hence, homozygous lack of SMN1 provides a progressive disease. Due to the high prevalence, up to now, several molecular diagnostic methods have been used which most of them are lengthy, expensive, and laborious. METHODS In the present study, we exploited a gold nanoprobe-based method for semi-quantitative SMN1 gene dosage analysis compared to SMN2. The assay was done under hybridization process between Au nanoprobes and different ratios of SMN1/SMN2 amplicons. RESULTS UV-vis spectra indicated that after the salt addition, nanoprobes aggregated gradually and their peak shifted to longer wavelengths except in the stable target-nanoprobes hybridization. The results revealed that the homozygous genotype of SMN2 gene is distinguished from the heterozygous genotypes of SMN genes by the naked eye, whereas different ratio of heterozygous genotypes (SMN1/SMN2) are differentiated better from each other using peak analysis ratios. CONCLUSION The presented strategy is an alternative simple method for discrimination of homozygous deletion of SMN1 in less than 30 min. However, further evaluation of the assay using clinical samples is recommended prior to real-world use.
Collapse
Affiliation(s)
- Hossein Ahmadpour-Yazdi
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hormozi-Nezhad
- Department of Chemistry, Sharif University of Technology, Tehran, Iran ; Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Ali Abadi
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e- Pajoohesh, 15th Km, Tehran -Karaj Highway, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran ; Department of Biotechnology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
7
|
Fong KE, Yung LYL. Head-to-tail: hybridization and single-mismatch discrimination in metallic nanoparticle–DNA assembly. RSC Adv 2013. [DOI: 10.1039/c3ra23162c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
|
8
|
Ang YS, Yung LYL. Rapid and label-free single-nucleotide discrimination via an integrative nanoparticle-nanopore approach. ACS NANO 2012; 6:8815-8823. [PMID: 22994459 DOI: 10.1021/nn302636z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-nucleotide polymorphism (SNP) is an important biomarker for disease diagnosis, treatment monitoring, and development of personalized medicine. Recent works focused primarily on ultrasensitive detection, while the need for rapid and label-free single-nucleotide discrimination techniques, which are crucial criteria for translation into clinical applications, remains relatively unexplored. In this work, we developed a novel SNP detection assay that integrates two complementary nanotechnology systems, namely, a highly selective nanoparticle-DNA detection system and a single-particle sensitive nanopore readout platform, for rapid detection of single-site mutations. Discrete nanoparticle-DNA structures formed in the presence of perfectly matched (PM) or single-mismatched (SM) targets exhibited distinct size differences, which were resolved on a size-tunable nanopore platform to generate corresponding "yes/no" readout signals. Leveraging the in situ reaction monitoring capability of the nanopore platform, we demonstrated that real-time single-nucleotide discrimination of a model G487A mutation, responsible for glucose-6-phosphate dehydrogenase deficiency, can be achieved within 30 min with no false positives. Semiquantification of DNA samples down to picomolar concentration was carried out using a simple parameter of particle count without the need for sample labeling or signal amplification. The unique combination of nanoparticle-based detection and nanopore readout presented in this work brings forth a rapid, specific, yet simple biosensing strategy that can potentially be developed for point-of-care application.
Collapse
Affiliation(s)
- Yan Shan Ang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
| | | |
Collapse
|
9
|
A resonance light scattering sensor based on methylene blue–sodium dodecyl benzene sulfonate for ultrasensitive detection of guanine base associated mutations. Anal Bioanal Chem 2012; 404:1673-9. [DOI: 10.1007/s00216-012-6289-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/09/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
|
10
|
Abstract
Recently, controlling assembly process in a precise manner has attracted increasing attentions in nanofabrication. Gold nanoparticles (AuNPs) modified with countable number of DNA strands, i.e., DNA discrete modified AuNPs, which bring AuNPs much more controllable manipulating possibilities have been playing an important role in this field. In this feature article, we will summarize recent progress on their preparation strategies and application in positioning assembly, which could benefit to the improvement of preparation methods of DNA discrete modified AuNPs and even other nanoparticles.
Collapse
Affiliation(s)
- Tao Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | | | | |
Collapse
|
11
|
Simultaneous detection of dual single-base mutations by capillary electrophoresis using quantum dot-molecular beacon probe. Biosens Bioelectron 2010; 26:2317-22. [PMID: 21115340 DOI: 10.1016/j.bios.2010.10.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 09/15/2010] [Accepted: 10/02/2010] [Indexed: 01/14/2023]
Abstract
Here a novel capillary electrophoresis (CE) for simultaneous detection of dual single-base mutations using quantum dot-molecular beacon (QD-MB) probe is described. Two QD-MB probes were designed using 585 and 650-nm emitting CdTe QDs which were covalently conjugated to MBs with different DNA oligonucleotide sequences by amide linkage and streptavidin-biotin binding, respectively. The hybridizations of QD-MB probes with different DNA targets were then monitored by CE, and results indicated that the two QD-MB probes specifically hybridized with their complementary DNA sequences, respectively. Target DNA identification was observed to have a high sensitivity of 16.2 pg in CE. Furthermore, the simultaneous detection of dual single-base mutations in a given DNA oligonucleotide was successfully achieved in CE using above two QD-MB probes. This novel CE-assisted QD-MB biosensor offers a promising approach for simultaneous detection of multiple single-base mutations, and exhibits potential capability in the single nucleotide polymorphism (SNP) analysis and high-sensitivity DNA detection.
Collapse
|
12
|
Kang J, Loew M, Arbuzova A, Andreou I, Dähne L. Nucleic acid diagnostic FRET particles based on layer-by-layer technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:3548-3552. [PMID: 20665568 DOI: 10.1002/adma.201000794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Jing Kang
- Surflay Nanotec GmbH, Berlin, Schwarzschildstr. 8, 12489 Berlin, Germany
| | | | | | | | | |
Collapse
|