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Ortiz M, Jauset-Rubio M, Trummer O, Foessl I, Kodr D, Acero JL, Botero ML, Biggs P, Lenartowicz D, Trajanoska K, Rivadeneira F, Hocek M, Obermayer-Pietsch B, O’Sullivan CK. Generic Platform for the Multiplexed Targeted Electrochemical Detection of Osteoporosis-Associated Single Nucleotide Polymorphisms Using Recombinase Polymerase Solid-Phase Primer Elongation and Ferrocene-Modified Nucleoside Triphosphates. ACS CENTRAL SCIENCE 2023; 9:1591-1602. [PMID: 37637735 PMCID: PMC10450878 DOI: 10.1021/acscentsci.3c00243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 08/29/2023]
Abstract
Osteoporosis is a multifactorial disease influenced by genetic and environmental factors, which contributes to an increased risk of bone fracture, but early diagnosis of this disease cannot be achieved using current techniques. We describe a generic platform for the targeted electrochemical genotyping of SNPs identified by genome-wide association studies to be associated with a genetic predisposition to osteoporosis. The platform exploits isothermal solid-phase primer elongation with ferrocene-labeled nucleoside triphosphates. Thiolated reverse primers designed for each SNP were immobilized on individual gold electrodes of an array. These primers are designed to hybridize to the SNP site at their 3'OH terminal, and primer elongation occurs only where there is 100% complementarity, facilitating the identification and heterozygosity of each SNP under interrogation. The platform was applied to real blood samples, which were thermally lysed and directly used without the need for DNA extraction or purification. The results were validated using Taqman SNP genotyping assays and Sanger sequencing. The assay is complete in just 15 min with a total cost of 0.3€ per electrode. The platform is completely generic and has immense potential for deployment at the point of need in an automated device for targeted SNP genotyping with the only required end-user intervention being sample addition.
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Affiliation(s)
- Mayreli Ortiz
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Olivia Trummer
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Ines Foessl
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - David Kodr
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo namesti 2, CZ 16610 Prague 6, Czech Republic
| | - Josep Lluís Acero
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Mary Luz Botero
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Phil Biggs
- Labman
Automation
Ltd., Seamer Hill, Stokesley, North Yorkshire, TS9 5NQ U.K.
| | - Daniel Lenartowicz
- Labman
Automation
Ltd., Seamer Hill, Stokesley, North Yorkshire, TS9 5NQ U.K.
| | - Katerina Trajanoska
- Department
of Internal Medicine, Erasmus MC, 40 3015 Rotterdam, The Netherlands
| | | | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo namesti 2, CZ 16610 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Barbara Obermayer-Pietsch
- Division
of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Ciara K. O’Sullivan
- INTERFIBIO
Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
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2
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Solid-phase recombinase polymerase amplification using ferrocene-labelled dNTPs for electrochemical detection of single nucleotide polymorphisms. Biosens Bioelectron 2022; 198:113825. [PMID: 34838372 DOI: 10.1016/j.bios.2021.113825] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/01/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022]
Abstract
Hypertrophic cardiomyopathies (HCM) are the principal cause of sudden cardiac death in young athletes and it is estimated that 1 in 500 people have HCM. The aim of this work was to develop an electrochemical platform for the detection of HCM-associated SNP in the Myosin Heavy Chain 7 (MYH7) gene, in fingerprick blood samples. The platform exploits isothermal solid-phase primer elongation using recombinase polymerase amplification with either individual or a combination of four ferrocene-labelled nucleoside triphosphates. Four thiolated reverse primers containing a variable base at their 3' end were immobilised on individual gold electrodes of an array. Following hybridisation with target DNA, solid phase recombinase polymerase amplification was carried out and primer elongation incorporating the ferrocene labelled oligonucleotides was only detected at one of the electrodes, thus facilitating identification of the SNP under interrogation. The assay was applied to the direct detection of the SNP in fingerprick blood samples from eight different individuals, with the results obtained corroborating with next generation sequencing. The ability to be able to robustly identify the SNP using a 10 μL fingerprick sample, demonstrates that SNP discrimination is achieved using low femtomolar (ca. 8 × 105 copies DNA) levels of DNA.
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3
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Ortiz M, Jauset-Rubio M, Skouridou V, Machado D, Viveiros M, Clark TG, Simonova A, Kodr D, Hocek M, O’Sullivan CK. Electrochemical Detection of Single-Nucleotide Polymorphism Associated with Rifampicin Resistance in Mycobacterium tuberculosis Using Solid-Phase Primer Elongation with Ferrocene-Linked Redox-Labeled Nucleotides. ACS Sens 2021; 6:4398-4407. [PMID: 34797987 PMCID: PMC8715531 DOI: 10.1021/acssensors.1c01710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Here, we report the
electrochemical detection of single-point mutations
using solid-phase isothermal primer elongation with redox-labeled
oligonucleotides. A single-base mutation associated with resistance
to rifampicin, an antibiotic commonly used for the treatment of Mycobacterium tuberculosis, was used as a model system
to demonstrate a proof-of-concept of the approach. Four 5′-thiolated
primers, designed to be complementary with the same fragment of the
target sequence and differing only in the last base, addressing the
polymorphic site, were self-assembled via chemisorption on individual
gold electrodes of an array. Following hybridization with single-stranded
DNA, Klenow (exo-) DNA polymerase-mediated primer extension with ferrocene-labeled
2′-deoxyribonucleoside triphosphates (dNFcTPs) was
only observed to proceed at the electrode where there was full complementarity
between the surface-tethered probe and the target DNA being interrogated.
We tested all four ferrocenylethynyl-linked dNTPs and optimized the
ratio of labeled/natural nucleotides to achieve maximum sensitivity.
Following a 20 min hybridization step, Klenow (exo-) DNA polymerase-mediated
primer elongation at 37 °C for 5 min was optimal for the enzymatic
incorporation of a ferrocene-labeled nucleotide, achieving unequivocal
electrochemical detection of a single-point mutation in 14 samples
of genomic DNA extracted from Mycobacterium tuberculosis strains. The approach is rapid, cost-effective, facile, and can
be extended to multiplexed electrochemical single-point mutation genotyping.
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Affiliation(s)
- Mayreli Ortiz
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Vasso Skouridou
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
| | - Taane G. Clark
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, U.K
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic
| | - David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Ciara K. O’Sullivan
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain
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4
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Sun XC, Wang Y, Yang L, Zhang H. Detection of influenza A virus subtypes using a solid-phase PCR microplate chip assay. J Virol Methods 2014; 211:12-8. [PMID: 25447756 DOI: 10.1016/j.jviromet.2014.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
A rapid and sensitive microplate chip based on solid PCR was developed to identify influenza A subtypes. A simple ultraviolet cross-linking method was used to immobilize DNA probes on pretreated microplates. Solid-phase PCR was proven to be a convenient method for influenza A screening. The sensitivity of the microplate chip was 10(-3) μg/mL for the enzymatic colorimetric method and 10(-4) μg/mL for the fluorescence method. The 10 sets of primers and probes for the microplate chip were highly specific and did not interfere with each other. These results suggest that the microplate chip based on solid PCR can be used to rapidly detect universal influenza A and its subtypes. This platform can also be used to detect other pathogenic microorganisms.
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Affiliation(s)
- Xin-Cheng Sun
- Basic Medical School of Zhengzhou University, Zhengzhou, China; College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - YunLong Wang
- Basic Medical School of Zhengzhou University, Zhengzhou, China; Henan Biotechnology Research Centre, Zhengzhou, China
| | - Liping Yang
- Basic Medical School of Henan University of Traditional Chinese Medicine, Zhengzhou, China.
| | - HuiRu Zhang
- Bioengineering Research Center of Henan Province, Zhengzhou, China
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5
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Raj D, Ghosh E, Mukherjee AK, Nozaki T, Ganguly S. Differential gene expression in Giardia lamblia under oxidative stress: Significance in eukaryotic evolution. Gene 2014; 535:131-9. [DOI: 10.1016/j.gene.2013.11.048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/31/2013] [Accepted: 11/20/2013] [Indexed: 11/25/2022]
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6
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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7
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Andresen D, Nickisch-Rosenegk MV, Bier FF. Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics. Expert Rev Mol Diagn 2014; 9:645-50. [DOI: 10.1586/erm.09.46] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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9
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Profiling in situ microbial community structure with an amplification microarray. Appl Environ Microbiol 2012; 79:799-807. [PMID: 23160129 DOI: 10.1128/aem.02664-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO(3)(-)) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO(3), but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.
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10
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Chandler DP, Bryant L, Griesemer SB, Gu R, Knickerbocker C, Kukhtin A, Parker J, Zimmerman C, George KS, Cooney CG. Integrated Amplification Microarrays for Infectious Disease Diagnostics. MICROARRAYS 2012; 1:107-24. [PMID: 27605339 PMCID: PMC5003434 DOI: 10.3390/microarrays1030107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 10/31/2012] [Accepted: 11/07/2012] [Indexed: 11/17/2022]
Abstract
This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics.
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Affiliation(s)
- Darrell P Chandler
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Lexi Bryant
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Sara B Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany, NY 12208, USA.
| | - Rui Gu
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany, NY 12208, USA.
| | | | - Alexander Kukhtin
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Jennifer Parker
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Cynthia Zimmerman
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany, NY 12208, USA.
| | - Christopher G Cooney
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick, MD 21701, USA.
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11
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Sun Y, Dhumpa R, Bang DD, Høgberg J, Handberg K, Wolff A. A lab-on-a-chip device for rapid identification of avian influenza viral RNA by solid-phase PCR. LAB ON A CHIP 2011; 11:1457-63. [PMID: 21369571 DOI: 10.1039/c0lc00528b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The endemic of Avian Influenza Virus (AIV) in Asia and epizootics in some European regions have caused serious economic losses. Multiplex reverse-transcriptase (RT) PCR has been developed to detect and subtype AIV. However, the number of targets that can be amplified in a single run is limited because of uncontrollable primer-primer interferences. In this paper, we describe a lab-on-a-chip device for fast AIV screening by integrating DNA microarray-based solid-phase PCR on a microfluidic chip. A simple UV cross-linking method was used to immobilize the DNA probes on unmodified glass surface, which makes it convenient to integrate microarray with microfluidics. This solid-phase RT-PCR method combined RT amplification of extracted RNA in the liquid phase and species-specific nested PCR on the solid phase. Using the developed approach, AIV viruses and their subtypes were unambiguously identified by the distinct patterns of amplification products. The whole process was reduced to less than 1 hour and the sample volume used in the microfluidic chip was at least 10 times less than in the literature. By spatially separating the primers, highly multiplexed amplification can be performed in solid-phase PCR. Moreover, multiplex PCR and sequence detection were done in one step, which greatly simplified the assay and reduced the processing time. Furthermore, by incorporating the microarray into a microchamber-based PCR chip, the sample and the reagent consumption were greatly reduced, and the problems of bubble formation and solution evaporation were effectively prevented. This microarray-based PCR microchip can be widely employed for virus detection and effective surveillance in wild avian and in poultry productions.
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Affiliation(s)
- Yi Sun
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark (DTU), Kgs Lyngby, Denmark
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12
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Sun Y, Dhumpa R, Bang DD, Handberg K, Wolff A. DNA microarray-based solid-phase RT-PCR for rapid detection and identification of influenza virus type A and subtypes H5 and H7. Diagn Microbiol Infect Dis 2011; 69:432-9. [DOI: 10.1016/j.diagmicrobio.2010.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/04/2010] [Accepted: 11/12/2010] [Indexed: 10/18/2022]
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Drobyshev AL, Nasedkina TV, Zakharova NV. The role of DNA diffusion in solid phase polymerase chain reaction with gel-immobilized primers in planar and capillary microarray format. BIOMICROFLUIDICS 2009; 3:44112. [PMID: 20216974 PMCID: PMC2835292 DOI: 10.1063/1.3271461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 11/13/2009] [Indexed: 05/11/2023]
Abstract
The solid phase polymerase chain reaction (PCR) on a gel-based microarray system was studied under various durations of individual stages of the PCR cycle and spatial restriction of the reaction volume. Combining the experimental study with numerical modeling, we demonstrated that the diffusion of the PCR product in and out of a microarray element during the annealing and melting stages, respectively, is the main factor responsible for distinctive features of the studied type of PCR. The restriction of reaction volume leads to faster PCR signal growth. Particularly, the capillary array, whereby gel-based microarray elements are located on a glass bar inserted into capillary chamber, was found to be a suitable format for the development of the platform.
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14
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An oligonucleotide microarray for multiplex real-time PCR identification of HIV-1, HBV, and HCV. Biotechniques 2008; 44:241-6, 248. [PMID: 18330353 DOI: 10.2144/000112628] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We describe a novel microarray-based approach for simultaneous identification and quantification of human immunodeficiency virus type 1 (HIV-1) and hepatitis B and C viruses (HBV and HCV) in donor plasma specimens. The method is based on multiplex real-time RT-PCR performed within the microarray hydrogel pads. Double-stranded amplification products are simultaneously detected using nonspecific SYBR Green I dye due to the reaction run in separate pads bearing 5'-immobilized specific primers. Both the sensitivity and specificity of the assay, based on 132 blood specimens analyzed, were 100% (56, 26, and 8 specimens were seropositive to HBV HCV and HIV-1, respectively; 22 were positive to both HIV-1 and HCV and 2 positive to all three viruses; 18 samples were pathogen-negative). The dynamic range of the quantitative analysis covered a six-order interval ranging from 100 to 106 genome equivalents per assay. The 95% detection limits were 14 gEq for HIV-1, 10 gEq (1.7 IU) for HBV, and 15 gEq (7.5 IU) for HCV per assay. The proposed approach is considered to be versatile and could be adapted for simultaneous identification and quantification of numerous genetic targets.
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15
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Abstract
Microarray technology provides new analytical devices that allow the parallel and simultaneous detection of several thousands of probes within one sample. Microarrays, sometimes called DNA chips, are widely used in gene-expression analysis, genotyping of individuals, analysis of point mutations and single nucleotide polymorphisms (SNP) as well as other genomic or transcriptomic variations. In this chapter we give a survey of common microarray manufacturing, the selection of support material, immobilisation and hybridisation and the detection with labelled complementary strands. However, DNA arrays may also serve as the basis for more complex analysis based on the action of enzymes on the immobilized templates. This property gives DNA microarrays the potential for being the template for whole PCR and transcription experiments with high parallelism, as will be discussed in the last section of this chapter.
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16
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Peltonen J, Welsh JA, Vähäkangas KH. Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Hum Exp Toxicol 2007; 26:9-18. [PMID: 17334176 DOI: 10.1177/0960327107071918] [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: 01/01/2023]
Abstract
Mutation analysis methods have increased in variety during the past years. High-throughput microarray methods have especially increased in popularity. However, new methods require reference points, and not all of the methods are equal in sensitivity and specificity. Furthermore, the detection of unknown missense mutations, such as unknown TP53 mutations in human tumors, for clinical purposes requires great accuracy, which may be difficult to acquire with the current high-throughput methods. For these reasons, the classical methods, such as PCR-manual sequencing and PCR-SSCP, are still valuable and necessary.
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Affiliation(s)
- J Peltonen
- Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
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17
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Kinoshita K, Fujimoto K, Yakabe T, Saito S, Hamaguchi Y, Kikuchi T, Nonaka K, Murata S, Masuda D, Takada W, Funaoka S, Arai S, Nakanishi H, Yokoyama K, Fujiwara K, Matsubara K. Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer. Nucleic Acids Res 2006; 35:e3. [PMID: 17135189 PMCID: PMC1747182 DOI: 10.1093/nar/gkl939] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 10/01/2006] [Accepted: 10/16/2006] [Indexed: 11/14/2022] Open
Abstract
DNA microarrays are routinely used to monitor gene expression profiling and single nucleotide polymorphisms (SNPs). However, for practically useful high performance, the detection sensitivity is still not adequate, leaving low expression genes undetected. To resolve this issue, we have developed a new plastic S-BIO PrimeSurface with a biocompatible polymer; its surface chemistry offers an extraordinarily stable thermal property for a lack of pre-activated glass slide surface. The oligonucleotides immobilized on this substrate are robust in boiling water and show no significant loss of hybridization activity during dissociation treatment. This allowed us to hybridize the templates, extend the 3' end of the immobilized DNA primers on the S-Bio by DNA polymerase using deoxynucleotidyl triphosphates (dNTP) as extender units, release the templates by denaturalization and use the same templates for a second round of reactions similar to that of the PCR method. By repeating this cycle, the picomolar concentration range of the template oligonucleotide can be detected as stable signals via the incorporation of labeled dUTP into primers. This method of Multiple Primer EXtension (MPEX) could be further extended as an alternative route for producing DNA microarrays for SNP analyses via simple template preparation such as reverse transcript cDNA or restriction enzyme treatment of genome DNA.
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Affiliation(s)
- Kenji Kinoshita
- Sumitomo Bakelite Co., Ltd. 1-1-5 Muroya, Nishi-ku, Kobe 651-2241, Japan.
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18
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Devereux R, Rublee P, Paul JH, Field KG, Domingo JWS. Development and applications of microbial ecogenomic indicators for monitoring water quality: report of a workshop assessing the state of the science, research needs and future directions. ENVIRONMENTAL MONITORING AND ASSESSMENT 2006; 116:459-79. [PMID: 16779607 DOI: 10.1007/s10661-006-7665-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Accepted: 05/19/2005] [Indexed: 05/10/2023]
Abstract
This article brings forth recommendations from a workshop sponsored by the U.S. Environmental Protection Agency's Science to Achieve Results (STAR) and Environmental Monitoring and Assessment (EMAP) Programs and by the Council of State Governments, held during May 2002 in Kansas City, Kansas. The workshop assembled microbial ecologists and environmental scientists to determine what research and science is needed to bring existing molecular biological approaches and newer technologies arising from microbial genomic research into environmental monitoring and water quality assessments. Development of genomics and proteomics technologies for environmental science is a very new area having potential to improve environmental water quality assessments. The workshop participants noted that microbial ecologists are already using molecular biological methods well suited for monitoring and water quality assessments and anticipate that genomics-enabled technologies could be made available for monitoring within a decade. Recommendations arising from the workshop include needs for (i) identification of informative microbial gene sequences, (ii) improved understandings of linkages between indicator taxa, gene expression and environmental condition, (iii) technological advancements towards field application, and (iv) development of the appropriate databases.
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Affiliation(s)
- Richard Devereux
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Gulf Ecology Division, 1 Sabine Island Dr., Gulf Breeze, FL 32561, USA.
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Huber A, Keck CC, Hefler LA, Schneeberger C, Huber JC, Bentz EK, Tempfer CB. Ten estrogen-related polymorphisms and endometriosis: a study of multiple gene-gene interactions. Obstet Gynecol 2006; 106:1025-31. [PMID: 16260521 DOI: 10.1097/01.aog.0000185259.01648.41] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Genetic as well as hormonal factors are known to influence the development and clinical course of endometriosis. We aimed to investigate the association among 10 single nucleotide polymorphisms (SNPs) involved in the estrogen metabolism and endometriosis and to develop a multiple genetic model. METHODS In a case-control study, we investigated the genotype frequencies of 10 estrogen metabolizing SNPs in 32 patients with endometriosis and 790 healthy controls using sequencing-on-chip-technology with solid-phase polymerase chain reaction on oligonucleotide microarrays: catechol-O-methyltransferase, Val158Met G->A, 17-beta-hydroxysteroid dehydrogenase type 1 (HSD17), vlV A->C, cytochrome P450 (CYP), 17 A2 allele T->C, CYP1A1 MspI RFLP T->C, CYP1A1 Ile462Val A->G, CYP19 Arg264Cys C->T, CYP19 C1558T C->T, CYP 1B1 Leu432Val, CYP1B1 Asn453Ser, and estrogen receptor alpha IVS1 -401>C. Associations and 2-way interaction models between SNPs were calculated by stepwise logistic regression models. RESULTS In a univariate model, HSD17 vlV A->C was associated with a significantly increased risk of endometriosis (P = .004; odds ratio 3.9, 95% confidence interval 1.6-9.8). When all 2-way interactions of investigated SNPs were ascertained, no significant interactions among SNPs were observed. In a multivariate model, HSD17 vlV A->C was also significantly associated with endometriosis (P = .002). CONCLUSION We present data on multiple SNPs in patients with endometriosis indicating an association between HSD17 gene variation and the disease. Although not able to demonstrate interaction models of SNPs, we provide evidence of HSD17 vlV A->C as a low penetrance genetic marker of endometriosis. LEVEL OF EVIDENCE II-2.
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Affiliation(s)
- Ambros Huber
- Department of Obstetrics and Gynecology, Medical University Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
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20
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von Nickisch-Rosenegk M, Marschan X, Andresen D, Abraham A, Heise C, Bier FF. On-chip PCR amplification of very long templates using immobilized primers on glassy surfaces. Biosens Bioelectron 2005; 20:1491-8. [PMID: 15626602 DOI: 10.1016/j.bios.2004.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 06/28/2004] [Accepted: 07/08/2004] [Indexed: 11/19/2022]
Abstract
In this paper we describe a novel method for visualizing very long DNA fragments (for example >6 kb) which are difficult to spot with commonly used arrayers or capillary samplers with very small nanoliter volumes, using directly bound primers on "on-chip" polymerase chain reaction (PCR). We have used the genomes of the M13 bacteriophage (7.2 kb) the human mitochondrion (16.5 kb) as examples of long DNA templates to test the PCR and were able to elicit robust reactivity. Over 75% of the immobilized primers could be elongated to their fullest extent. In addition we were able to elicit the PCR reaction with double stranded templates in which one primer was immobilized and the other suspended in the reaction solution. These synthesized PCR products were visualized by either confocal microarray scanning or fluorescence microscopy using Cy5-dye fluorescence of the modified free primer, or the fluorescence of intercalating dyes.
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Affiliation(s)
- Markus von Nickisch-Rosenegk
- Department of Molecular Bioanalysis and Bioelectronics, Fraunhofer Institute for Biomedical Engineering, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany.
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21
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Mitterer G, Bodamer O, Harwanegg C, Maurer W, Mueller MW, Schmidt WM. Microarray-based Detection of Mannose-binding Lectin 2 (MBL2) Polymorphisms in a Routine Clinical Setting. ACTA ACUST UNITED AC 2005; 9:6-13. [PMID: 15857180 DOI: 10.1089/gte.2005.9.6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The assessment of allelic variants in the human mannose-binding lectin 2 (MBL2) gene is of great clinical importance in newborns or immune-suppressed patients at high risk for a variety of infections. Here, we present a study on the genotyping accuracy of a DNA microarray-based on-chip PCR method suited for the detection of five different polymorphisms in the MBL2 gene. We tested 153 genomic DNA samples, prepared from archival blood spots on Guthrie cards, for the presence of allelic variants in the human MBL2 gene by the on-chip PCR method and compared the obtained results of three variants to standard DNA capillary sequencing. The genotyping power of the described assay was readily comparable to DNA sequencing (453/459 correct genotype calls in 153 DNA samples; 98.7% accuracy), mainly due to intrinsic technical benefits of microarrays such as high number of test replicates and automated data analysis. This study demonstrates, for the first time, the accuracy and reliability of a microarray-based on-chip PCR genotyping assay for measuring allelic variants in a routine clinical setting.
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Affiliation(s)
- Georg Mitterer
- VBC-GENOMICS Bioscience Research GmbH, A-1030 Vienna, Austria
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22
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Abstract
We have developed a highly sensitive method for DNA analysis on 3D gel element microarrays, a technique we call multiplex microarray-enhanced PCR (MME-PCR). Two amplification strategies are carried out simultaneously in the reaction chamber: on or within gel elements, and in bulk solution over the gel element array. MME-PCR is initiated by multiple complex primers containing gene-specific, forward and reverse, sequences appended to the 3′ end of a universal amplification primer. The complex primer pair is covalently tethered through its 5′ end to the polyacryl- amide backbone. In the bulk solution above the gel element array, a single pair of unattached universal primers simultaneously directs pseudo-monoplex PCR of all targets according to normal solution-phase PCR. The presence of a single universal PCR primer pair in solution accelerates amplification within gel elements and eliminates the problem of primer interference that is common to conventional multiplex PCR. We show 106-fold amplification of targeted DNA after 50 cycles with average amplification efficiency 1.34 per cycle, and demonstrate specific on-chip amplification of six genes in Bacillus subtilis. All six genes were detected at 4.5 pg of bacterial genomic DNA (equivalent to 103 genomes) in 60 independent amplification reactions performed simultaneously in single reaction chamber.
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Affiliation(s)
| | | | | | - S. Bavykin
- To whom correspondence should be addressed. Tel: +1 630 252 3980; Fax: +1 630 252 9155;
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23
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Deng JY, Zhang XE, Mang Y, Zhang ZP, Zhou YF, Liu Q, Lu HB, Fu ZJ. Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism. Biosens Bioelectron 2004; 19:1277-83. [PMID: 15046760 DOI: 10.1016/j.bios.2003.11.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2003] [Revised: 10/24/2003] [Accepted: 11/26/2003] [Indexed: 10/26/2022]
Abstract
An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates.
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Affiliation(s)
- Jiao-Yu Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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24
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Mitterer G, Huber M, Leidinger E, Kirisits C, Lubitz W, Mueller MW, Schmidt WM. Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J Clin Microbiol 2004; 42:1048-57. [PMID: 15004052 PMCID: PMC356827 DOI: 10.1128/jcm.42.3.1048-1057.2004] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. We describe a DNA microarray-based PCR approach for the quick detection and identification of bacteria from cervical swab specimens from mares. This on-chip PCR method combines the amplification of a variable region of bacterial 23S ribosomal DNA and the simultaneous sequence-specific detection on a solid phase. The solid phase contains bacterial species-specific primers covalently bound to a glass support. During the solid-phase amplification reaction the polymerase elongates perfectly matched primers and incorporates biotin-labeled nucleotides. The reaction products are visualized by streptavidin-cyanine 5 staining, followed by fluorescence scanning. This procedure successfully identified from pure cultures 22 bacteria that are common causes of abortion and sterility in mares. Using the on-chip PCR method, we also tested 21 cervical swab specimens from mares for the presence of pathogenic bacteria and compared the results with those of conventional bacteriological culture methods. Our method correctly identified the bacteria in 12 cervical swab samples, 8 of which contained more than one bacterial species. Due to the higher sensitivity of the on-chip PCR, this method identified bacteria in five cervical swab samples which were not detected by the conventional identification procedure. Our results show that this method will have great potential to be incorporated into the routine microbiology laboratory.
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MESH Headings
- Abortion, Veterinary/microbiology
- Animals
- Bacteria/genetics
- Bacteria/isolation & purification
- Base Sequence
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Female
- Horses
- Oligonucleotide Array Sequence Analysis
- Polymerase Chain Reaction/methods
- Pregnancy
- Pregnancy Complications, Infectious/microbiology
- Pregnancy Complications, Infectious/veterinary
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
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Affiliation(s)
- Georg Mitterer
- Institute of Microbiology & Genetics, University of Vienna, 1030 Vienna, Austria
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25
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Wu X, Zhou Y, Xu S. Chemiluminescent detection of genetic polymorphisms based on mismatch hybridization: application to cytochrome P4501A1. Mol Cell Probes 2004; 18:17-22. [PMID: 15036365 DOI: 10.1016/j.mcp.2003.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2002] [Accepted: 07/11/2003] [Indexed: 11/23/2022]
Abstract
An assay that makes use of differences in thermal stability between perfectly and imperfectly matched hybrids in combination with a sensitive chemiluminescence detection system was developed and applied to the identification of CYP1A1 polymorphisms. In this assay, two oligonucleotide probes for each polymorphic site were designed: one perfectly matching the wild type allele, the other perfectly matching the mutant allele. The genotypes were determined by calculating the ratio of signals obtained from the two probes. The method described here allows for the rapid, simple and cost-effective detection of DNA polymorphisms. Compared with fluorescence- and microarray-based assays, this method provides an alternative for genotyping where costly equipment or specialized reagents are not available.
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Affiliation(s)
- Xiaoming Wu
- Institute of Environmental Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
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26
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Wen JK, Zhang XE, Cheng Z, Liu H, Zhou YF, Zhang ZP, Yang JH, Deng JY. A visual DNA chip for simultaneous detection of hepatitis B virus, hepatitis C virus and human immunodeficiency virus type-1. Biosens Bioelectron 2004; 19:685-92. [PMID: 14709386 DOI: 10.1016/s0956-5663(03)00264-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
For the simultaneously visual detection of hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus type-1 (HIV-1), a qualitative DNA chip method, combining multiplex and nested polymerase chain reaction (PCR) with arrayed anchored primer PCR and a biotin-avidin alkaline phosphatase (Av-AP) indicator system, was developed. After pretreatment of infected blood samples and reverse transcription of the RNA virus genome, PCR was performed in a single tube by using the outer primer pairs. Second round nested multiplex PCR was performed on the DNA chip, on which the primers array had already been prepared. During the arrayed anchored multiplex PCR, 5[N-(N-biotinylaminocaproyl)-epsilon-3-aminoallyl]-2-deoxy-uridine-5-triphosphate (biotin-11-dUTP) was incorporated into the extended DNA chains in order to bind avidin alkaline phosphatase via avidin and biotin. To produce purple precipitates on the chips, the enzyme substrate 5-bromo-4-chloro-3-indolyl phosphate (BCIP) was used in conjunction with the enhancer, nitro blue tetrazolium (NBT). Blood samples containing the three viruses were tested using this DNA chip and about 1 pg of specific viral DNA fragments were detected on the chip wells after nested PCR.
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Affiliation(s)
- Ji-Kai Wen
- Wuhan Institution of Virology, Chinese Academy of Science, Wuhan 430071, China
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27
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Ketomäki K, Hakala H, Kuronen O, Lönnberg H. Hybridization properties of support-bound oligonucleotides: the effect of the site of immobilization on the stability and selectivity of duplex formation. Bioconjug Chem 2003; 14:811-6. [PMID: 12862435 DOI: 10.1021/bc0340058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four 12-mer oligodeoxyribonucleotide sequences were immobilized to uniformly sized (50 microm) polymer particles through C5-tethered thymine and N(4)-tethered cytosine bases at four different sites in each sequence. The effect of the site of immobilization on the efficiency and selectivity of hybridization of the particle-bound probes was quantified by a sandwich-type assay based on a time-resolved fluorometric measurement of an oligonucleotide probe labeled with a photoluminescent europium(III) chelate directly from the surface of a single particle. Immobilization through a base in the central part of the sequence was observed to destablize the duplex more markedly than tethering through a terminal base. The effect of a one-base mismatch on the duplex stability increased with the increasing distance from the site of immobilization.
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Affiliation(s)
- Kaisa Ketomäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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28
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Horiike S, Kita-Sasai Y, Nakao M, Taniwaki M. Configuration of the TP53 gene as an independent prognostic parameter of myelodysplastic syndrome. Leuk Lymphoma 2003; 44:915-22. [PMID: 12854888 DOI: 10.1080/1042819031000067620] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Myelodysplastic syndrome (MDS) consists of a heterogeneous group of acquired hematopoietic stem cell disorders, characterized by bone marrow failure and leukemic transformation. Since hematological manifestations and clinical outcomes vary widely among MDS patients, a considerable number of studies have tried to identify the prognostic parameters for the stratification of patients into different risk groups. Based on reported risk-based studies, the International Prognostic Scoring System (IPSS) was proposed as a reliable risk assessment method for primary MDS patients, and several validating studies have clarified its usefulness. Critical prognostic parameters of the IPSS consist of chromosome findings, the percentage of marrow blasts, and the number of peripheral blood cytopenias. Although other laboratory findings, including several molecular alterations, have been identified as convincing prognostic factors in MDS, these molecular configurations were not selected as prognostic parameters in the IPSS, because analysis for these alterations were not routinely available for the management of patients with MDS. Because recent advances in molecular genetics may make it available as a routine work-up of MDS in the future, we discuss potential improvement of the IPSS by the addition of molecular analysis to the system, with particular reference to the configuration of the TP53 gene.
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Affiliation(s)
- Shigeo Horiike
- Third Department of Medicine, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan.
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29
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Brazill SA, Kuhr WG. A single base extension technique for the analysis of known mutations utilizing capillary gel electrophoreisis with electrochemical detection. Anal Chem 2002; 74:3421-8. [PMID: 12139049 DOI: 10.1021/ac025569s] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel single nucleotide polymorphism (SNP) detection system is described in which the accuracy of DNA polymerase and advantages of electrochemical detection are demonstrated. A model SNP system is presented to illustrate the potential advantages in coupling the single base extension (SBE) technique to capillary gel electrophoresis (CGE) with electrochemical detection. An electrochemically labeled primer, with a ferrocene acetate covalently attached to its 5' end, is used in the extension reaction. When the Watson-Crick complementary ddNTP is added to the SBE reaction, the primer is extended by a single nucleotide. The reaction mixture is subsequently separated by CGE, and the ferrocene-tagged fragments are detected at the separation anode with sinusoidal voltammetry. This work demonstrates the first single base resolution separation of DNA coupled with electrochemical detection. The unextended primer (20-mer) and the 21-mer extension product are separated with a resolution of 0.8.
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Affiliation(s)
- Sara A Brazill
- Department of Chemistry, University of California, Riverside 92521, USA
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30
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Huber M, Mündlein A, Dornstauder E, Schneeberger C, Tempfer CB, Mueller MW, Schmidt WM. Accessing single nucleotide polymorphisms in genomic DNA by direct multiplex polymerase chain reaction amplification on oligonucleotide microarrays. Anal Biochem 2002; 303:25-33. [PMID: 11906147 DOI: 10.1006/abio.2001.5565] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This study introduces a DNA microarray-based genotyping system for accessing single nucleotide polymorphisms (SNPs) directly from a genomic DNA sample. The described one-step approach combines multiplex amplification and allele-specific solid-phase PCR into an on-chip reaction platform. The multiplex amplification of genomic DNA and the genotyping reaction are both performed directly on the microarray in a single reaction. Oligonucleotides that interrogate single nucleotide positions within multiple genomic regions of interest are covalently tethered to a glass chip, allowing quick analysis of reaction products by fluorescence scanning. Due to a fourfold SNP detection approach employing simultaneous probing of sense and antisense strand information, genotypes can be automatically assigned and validated using a simple computer algorithm. We used the described procedure for parallel genotyping of 10 different polymorphisms in a single reaction and successfully analyzed more than 100 human DNA samples. More than 99% of genotype data were in agreement with data obtained in control experiments with allele-specific oligonucleotide hybridization and capillary sequencing. Our results suggest that this approach might constitute a powerful tool for the analysis of genetic variation.
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Affiliation(s)
- Martin Huber
- VBC-GENOMICS Bioscience Research GmbH, Rennweg 95b/5, A-1030 Vienna, Austria
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31
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447281 DOI: 10.1002/cfg.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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