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Cheng L, He Y, Yang Y, Su C, He H, You M, Chen J, Lin Z, Hong G. Highly specific and sensitive sandwich-type electrochemiluminescence biosensor for HPV16 DNA detection based on the base-stacking effect and bovine serum albumin carrier platform. Biosens Bioelectron 2023; 241:115706. [PMID: 37757512 DOI: 10.1016/j.bios.2023.115706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
The detection of specific DNA sequences and the identification of single nucleotide polymorphisms are important for disease diagnosis. Herein, by combining the high specificity of the base-stacking effect with the high reproducibility of bovine serum albumin (BSA) modified electrodes and the high loading performance of DNA nanoclews (DNA NCs), a novel sandwich-type electrochemiluminescence (ECL) biosensor is reported for the highly specific detection of HPV16 (chosen as the model target). The capture probes are loaded by BSA carrier platforms modified on the gold electrode surface to improve reproducibility. DNA NCs loaded with a large amount of Ru(phen)32+ worked as signal probes. The template probe is composed of the complementary strand of the target and two free nucleic acid anchors at the head and tail. In the presence of the target DNA, the template probes can form stacked base pairs with target, generating high base-stacking energy. This results in the shorter free anchors of template probes being able to bind to the capture and signal probes. This eventually forms a sandwich structure that allows Ru(phen)32+ to be near the electrode surface, producing an ECL signal. There is a linear relationship between the signal and the target concentration range from 10 fM to 100 pM, with a detection limit of 5.03 fM (S/N=3). Moreover, the base-stacking effect has single base recognition ability for base pairs, effectively avoiding false positive signals. The results of this strategy for clinical samples are consistent with classical methods.
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Affiliation(s)
- Lingjun Cheng
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Yinghao He
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Yuanyuan Yang
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Canping Su
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Hongzhang He
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Mingming You
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Jiaming Chen
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, People's Republic of China.
| | - Guolin Hong
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361005, People's Republic of China.
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Deepa, Pundir S, Pundir C. Detection of tumor suppressor protein p53 with special emphasis on biosensors: A review. Anal Biochem 2020; 588:113473. [DOI: 10.1016/j.ab.2019.113473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/21/2023]
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Meza-Menchaca T, Williams J, Rodríguez-Estrada RB, García-Bravo A, Ramos-Ligonio Á, López-Monteon A, Zepeda RC. A low density microarray method for the identification of human papillomavirus type 18 variants. SENSORS 2013; 13:12975-93. [PMID: 24077317 PMCID: PMC3859045 DOI: 10.3390/s131012975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/08/2013] [Accepted: 08/30/2013] [Indexed: 12/01/2022]
Abstract
We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings.
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Affiliation(s)
- Thuluz Meza-Menchaca
- Laboratory of Molecular Biology, Health Services Studies Centre, University of Veracruz, 147 Carmen Serdan St., Centre, Veracruz-Llave, Veracruz 91700, Mexico; E-Mails: (R.B.R.-E.); (A.G.-B.)
- Biomedical Research Centre, University of Veracruz, Av. Luis Castelazo Ayala St. Xalapa-Enriquez, Veracruz 91120, Mexico; E-Mails: (Á.R.L.); (A.L.-M.); (R.C.Z.)
- LADISER Inmunology and Molecular Biology, Faculty of Chemical Sciences, University of Veracruz, Orizaba, Veracruz 94340, Mexico
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +52-229-932-49-78
| | - John Williams
- Department of Biochemistry, Biosciences Institute, University College Cork, College Road, Cork, Ireland; E-Mail:
| | - Rocío B. Rodríguez-Estrada
- Laboratory of Molecular Biology, Health Services Studies Centre, University of Veracruz, 147 Carmen Serdan St., Centre, Veracruz-Llave, Veracruz 91700, Mexico; E-Mails: (R.B.R.-E.); (A.G.-B.)
| | - Aracely García-Bravo
- Laboratory of Molecular Biology, Health Services Studies Centre, University of Veracruz, 147 Carmen Serdan St., Centre, Veracruz-Llave, Veracruz 91700, Mexico; E-Mails: (R.B.R.-E.); (A.G.-B.)
| | - Ángel Ramos-Ligonio
- Biomedical Research Centre, University of Veracruz, Av. Luis Castelazo Ayala St. Xalapa-Enriquez, Veracruz 91120, Mexico; E-Mails: (Á.R.L.); (A.L.-M.); (R.C.Z.)
- LADISER Inmunology and Molecular Biology, Faculty of Chemical Sciences, University of Veracruz, Orizaba, Veracruz 94340, Mexico
| | - Aracely López-Monteon
- Biomedical Research Centre, University of Veracruz, Av. Luis Castelazo Ayala St. Xalapa-Enriquez, Veracruz 91120, Mexico; E-Mails: (Á.R.L.); (A.L.-M.); (R.C.Z.)
- LADISER Inmunology and Molecular Biology, Faculty of Chemical Sciences, University of Veracruz, Orizaba, Veracruz 94340, Mexico
| | - Rossana C. Zepeda
- Biomedical Research Centre, University of Veracruz, Av. Luis Castelazo Ayala St. Xalapa-Enriquez, Veracruz 91120, Mexico; E-Mails: (Á.R.L.); (A.L.-M.); (R.C.Z.)
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Duan D, Zheng KX, Shen Y, Cao R, Jiang L, Lu Z, Yan X, Li J. Label-free high-throughput microRNA expression profiling from total RNA. Nucleic Acids Res 2011; 39:e154. [PMID: 21976734 PMCID: PMC3239174 DOI: 10.1093/nar/gkr774] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
MicroRNAs (miRNAs) are key biological regulators and promising disease markers whose detection technologies hold great potentials in advancing fundamental research and medical diagnostics. Currently, miRNAs in biological samples have to be labeled before being applied to most high-throughput assays. Although effective, these labeling-based approaches are usually labor-intensive, time-consuming and liable to bias. Besides, the cross-hybridization of co-existing miRNA precursors (pre-miRNAs) is not adequately addressed in most assays that use total RNA as input. Here, we present a hybridization-triggered fluorescence strategy for label-free, microarray-based high-throughput miRNA expression profiling. The total RNA is directly applied to the microarray with a short fluorophore-linked oligonucleotide Universal Tag which can be selectively captured by the target-bound probes via base-stacking effects. This Stacking-Hybridized Universal Tag (SHUT) assay has been successfully used to analyze as little as 100 ng total RNA from human tissues, and found to be highly specific to homogenous miRNAs. Superb discrimination toward single-base mismatch at the 5′ or 3′ end has been demonstrated. Importantly, the pre-miRNAs generated negligible signals, validating the direct use of total RNA.
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Affiliation(s)
- Demin Duan
- Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou, 215123, China
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Pacheco-Rivera RA, Hernández-Zamora E, González-Yebra B, Beattie K, Maldonado-Rodríguez R, Santiago-Hernández JC, Medrano-Ortiz de Zárate ME, Salcedo M. Single oligoarray-based detection of specific M918T mutation in RET oncogene in multiple endocrine neoplasia type 2B. Clin Exp Med 2011; 11:227-34. [PMID: 21253810 DOI: 10.1007/s10238-010-0128-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 12/22/2010] [Indexed: 11/25/2022]
Abstract
The most important mutation associated with Multiple Endocrine Neoplasia type 2B (MEN 2B) is the change of thymine to cytosine in codon 918 of exon 16 in the RET oncogene (ATG → ACG). The aim of this work was to develop a single oligoarray by using tandem hybridization to detect the T918C/RET mutation for MEN 2B patients. Two genetically non-related families were studied; each family had a member affected by MEN2B. Both patients presented the T918C/RET mutation in a heterozygous fashion. None of the relatives was positive for this mutation; thus, these cases arose de novo. The proper mutation was confirmed by with different tools, PCR-Fok I endonuclease, direct sequencing, and also using our oligoarray. In this case, it is suitable to use a DNA target smaller than 150 bases with single- or double-stranded DNA and short probes of 7-mer. It was also possible to detect the mutation by employing different sources of DNA, fresh or paraffin-embedded tissues. Therefore, the present oligoarray can identify the most common M918T mutation of RET oncogene from a variety of DNA sources with good specificity and be a good alternative in the molecular diagnosis for MEN 2B cases.
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Rangel-López A, Méndez-Tenorio A, Beattie KL, Maldonado R, Mendoza P, Vázquez G, Pérez-Plasencia C, Sánchez M, Navarro G, Salcedo M. Specific mutation screening of TP53 gene by low-density DNA microarray. Nanotechnol Sci Appl 2009; 2:1-12. [PMID: 24198462 PMCID: PMC3781765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
TP53 is the most commonly mutated gene in human cancers. Approximately 90% of mutations in this gene are localized between domains encoding exons 5 to 8. The aim of this investigation was to examine the ability of the low density DNA microarray with the assistance of double tandem hybridization platform to characterize TP53 mutational hotspots in exons 5, 7, and 8 of the TP53. Nineteen capture probes specific to each potential mutation site were designed to hybridize to specific site. Virtual hybridization was used to predict the stability of hybridization of each capture probe with the target. Thirty-three DNA samples from different sources were analyzed for mutants in these exons. A total of 32 codon substitutions were found by DNA sequencing. 24 of them a showed a perfect correlation with the hybridization pattern system and DNA sequencing analysis of the regions scanned. Although in this work we directed our attention to some of the most representative mutations of the TP53 gene, the results suggest that this microarray system proved to be a rapid, reliable, and effective method for screening all the mutations in TP53 gene.
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Affiliation(s)
- Angélica Rangel-López
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
- Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades, CMN Siglo XXI-IMSS, Mexico City; Mexico
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico
| | | | - Rogelio Maldonado
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico
| | - Patricia Mendoza
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
| | - Guelaguetza Vázquez
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
| | - Carlos Pérez-Plasencia
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, Instituto Nacional de Cancerología INCAN, Mexico City, Mexico
| | - Martha Sánchez
- Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades, CMN Siglo XXI-IMSS, Mexico City; Mexico
| | | | - Mauricio Salcedo
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
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Lucarelli F, Capponcelli S, Marrazza G, Sangiorgi L, Mascini M. Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms. Analyst 2008; 134:52-9. [PMID: 19082174 DOI: 10.1039/b806514d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.
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Affiliation(s)
- Fausto Lucarelli
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto F.no, Florence, Italy
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Channel Glass-based Detection of Human Short Insertion/Deletion Polymorphisms by Tandem Hybridization. Mol Biotechnol 2007; 38:145-53. [DOI: 10.1007/s12033-007-9004-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 09/05/2007] [Indexed: 10/23/2022]
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Mendoza-Lorenzo P, Maldonado R, Pacheco R, Méndez A, Piña-Sánchez P, Rangel A, Vazquez-Ortíz G, Salcedo M. An oligoarray for the detection of human papillomavirus type 16 variants. Int J Gynecol Cancer 2007; 17:1083-91. [PMID: 17877642 DOI: 10.1111/j.1525-1438.2007.00832.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
On the basis of human papillomavirus (HPV) E6 gene mutations, there are more than five variants of HPV 16. We applied a sensitive and specific stacking hybridization assay using an oligoarray for the detection of Asian–American (AA) and European (E) (E350G) HPV 16 variants. A simple glass slide was coated with capture probes consisting of short oligonucleotide DNA sequences (7–9 mers) specific for AA and E variants. Two different regions of the E6 HPV 16 gene were amplified with a set of two primers, which were used as target DNA. These targets were preannealed with auxiliary labeled oligonucleotides and hybridized to the oligoarray in the presence of specific and complementary capture probes. Our designed array based on shorter capture probes successfully discriminated between HPV 16 AA and E variants. The present DNA oligoarray system could be useful as a reliable technique for HPV 16 detection and does not require specialized equipment; nevertheless, further intra- and interlaboratory studies are needed.
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Affiliation(s)
- P Mendoza-Lorenzo
- Oncogenomics Laboratory, Oncology Diseases Research Unit, National Medical Center Siglo XXI-IMSS, Av. Mexico D.F., Mexico
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