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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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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
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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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3
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Debela AM, Ortiz M, Beni V, Thorimbert S, Lesage D, Cole RB, O'Sullivan CK, Hasenknopf B. Biofunctionalization of Polyoxometalates with DNA Primers, Their Use in the Polymerase Chain Reaction (PCR) and Electrochemical Detection of PCR Products. Chemistry 2015; 21:17721-7. [PMID: 26490074 DOI: 10.1002/chem.201502247] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 12/18/2022]
Abstract
The bioconjugation of polyoxometalates (POMs), which are inorganic metal oxido clusters, to DNA strands to obtain functional labeled DNA primers and their potential use in electrochemical detection have been investigated. Activated monooxoacylated polyoxotungstates [SiW11 O39 {Sn(CH2 )2 CO}](8-) and [P2 W17 O61 {Sn(CH2 )2 CO}](6-) have been used to link to a 5'-NH2 terminated 21-mer DNA forward primer through amide coupling. The functionalized primer was characterized by using a battery of techniques, including electrophoresis, mass spectrometry, as well as IR and Raman spectroscopy. The functionality of the POM-labeled primers was demonstrated through hybridization with a surface-immobilized probe. Finally, the labeled primers were successfully used in the polymerase chain reaction (PCR) and the PCR products were characterized by using electrophoresis.
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Affiliation(s)
- Ahmed M Debela
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans, 26, 43007 Tarragona (Spain)
| | - Mayreli Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans, 26, 43007 Tarragona (Spain)
| | - Valerio Beni
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans, 26, 43007 Tarragona (Spain)
| | - Serge Thorimbert
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (UMR 8232), 4 place Jussieu, 75005 Paris (France)
| | - Denis Lesage
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (UMR 8232), 4 place Jussieu, 75005 Paris (France)
| | - Richard B Cole
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (UMR 8232), 4 place Jussieu, 75005 Paris (France)
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans, 26, 43007 Tarragona (Spain). .,ICREA, Passeig Lluis Companys 23, 08010 Barcelona (Spain).
| | - Bernold Hasenknopf
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (UMR 8232), 4 place Jussieu, 75005 Paris (France).
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4
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Iurlo M, Mengozzi L, Rapino S, Marcaccio M, Perone RC, Masiero S, Cozzi P, Paolucci F. New Approaches toward Ferrocene–Guanine Conjugates: Synthesis and Electrochemical Behavior. Organometallics 2014. [DOI: 10.1021/om5002809] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matteo Iurlo
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Luca Mengozzi
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Stefania Rapino
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Massimo Marcaccio
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Rosaria C. Perone
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Stefano Masiero
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Piergiorgio Cozzi
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Francesco Paolucci
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
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Huang Y, Zhu J, Li G, Chen Z, Jiang JH, Shen GL, Yu RQ. Electrochemical detection of point mutation based on surface hybridization assay conjugated allele-specific polymerase chainreaction. Biosens Bioelectron 2013; 42:526-31. [DOI: 10.1016/j.bios.2012.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/23/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]
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7
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Chen W, Wang L, Huang X, Wang M. Enhancing the Analytical Selectivity of Voltammetric Technique by the Combination of Harmonic Analysis and “Fingerprint” Phase Angle Lock-in Detection. Anal Chem 2012. [DOI: 10.1021/ac302947w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenting Chen
- College of Chemical Science and Engineering, South China University of Technology, Guangzhou 510641,
China
| | - Lishi Wang
- College of Chemical Science and Engineering, South China University of Technology, Guangzhou 510641,
China
| | - Xinjian Huang
- College of Chemical Science and Engineering, South China University of Technology, Guangzhou 510641,
China
| | - Min Wang
- College of Chemical Science and Engineering, South China University of Technology, Guangzhou 510641,
China
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Zhu M, Zeng C, Ye J. Graphene-Modified Carbon Fiber Microelectrode for the Detection of Dopamine in Mice Hippocampus Tissue. ELECTROANAL 2011. [DOI: 10.1002/elan.201000712] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Chan OTM, Westover KD, Dietz L, Zehnder JL, Schrijver I. Comprehensive and efficient HBB mutation analysis for detection of beta-hemoglobinopathies in a pan-ethnic population. Am J Clin Pathol 2010; 133:700-7. [PMID: 20395516 DOI: 10.1309/ajcp7hq2kwghecio] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Current methods that assay hemoglobin beta-globin chain variants can have limited clinical sensitivity when applied techniques identify only a predefined panel of mutations. Even sequence-based assays may be limited depending on which gene regions are investigated. We sought to develop a clinically practical yet inclusive molecular assay to identify beta-globin mutations in multicultural populations. We highlight the beta-globin mutation detection assay (beta-GMDA), an extensive gene sequencing assay. The polymerase chain reaction (PCR) primers are located to encompass virtually all hemoglobin beta locus (HBB) mutations. In addition, this assay is able to detect, by gap PCR, a common large deletion (Delta619 base pair), which would be missed by sequencing alone. We describe our 5-year experience with the beta-GMDA and indicate its capability for detecting homozygous, heterozygous, and compound heterozygous sequence changes, including previously unknown HBB variants. The beta-GMDA offers superior sensitivity and ease of use with comprehensive detection of HBB mutations that result in beta-globin chain variants.
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10
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Hüsken N, Gasser G, Köster SD, Metzler-Nolte N. "Four-potential" ferrocene labeling of PNA oligomers via click chemistry. Bioconjug Chem 2009; 20:1578-86. [PMID: 19586015 DOI: 10.1021/bc9001272] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The scope of the Cu(I)-catalyzed [2 + 3] azide/alkyne cycloaddition (CuAAC, click chemistry) as a key reaction for the conjugation of ferrocene derivatives to N-terminal functionalized PNA oligomers is explored herein (PNA: peptide nucleic acid). The facile solid-phase synthesis of N-terminal azide or alkyne-functionalized PNA oligomer precursors and their cycloaddition with azidoferrocene, ethynylferrocene, and N-(3-ethylpent-1-yn-3-yl)ferrocene-carboxamide (DEPA-ferrocene) on the solid phase are presented. While the click reaction with azidomethylferrocene worked equally well, the ferrocenylmethyl group is lost from the conjugate upon acid cleavage. However, the desired product was obtained via a post-SPPS conversion of the alkyne-PNA oligomer with azidomethylferrocene in solution. The synthesis of all ferrocene-PNA conjugates (trimer t(3)-PNA, 3, 4, 5, 6; 12mer PNA, 10 - t c t a c a a g a c t c, 11 - t c t a c c g t a c t c) succeeded with excellent yields and purities, as determined by mass spectrometry and HPLC. Electrochemical studies of the trimer Fc-PNA conjugates 3, 4, 5, and 6 with four different ferrocene moieties revealed quasi-reversible redox processes of the ferrocenyl redox couple Fc(0/+) and electrochemical half-wave potentials in a range of E(1/2) = -20 mV to +270 mV vs FcH(0/+) (Fc: ferrocenyl, C(10)H(9)Fe). The observed potential differences ΔE(1/2)(min) are always greater than 60 mV for any given pair of Fc-PNA conjugates, thus allowing a reliable differentiation with sensitive electrochemical methods like e.g. square wave voltammetry (SWV). This is the electrochemical equivalent of "four-color" detection and is hence denoted "four-potential" labeling. Preparation and electrochemical investigation of the set of four structurally different and electrochemically distinguishable ferrocenyl groups conjugated to PNA oligomers, as exemplified by the conjugates 3, 4, 5, and 6, demonstrates the scope of the azide/alkyne cycloaddition for the labeling of PNA with electrochemically active ferrocenyl groups. Furthermore, it provides a PNA-based system for the electrochemical detection of single-nucleotide polymorphism (SNP) in DNA/RNA.
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Affiliation(s)
- Nina Hüsken
- Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie, Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Bochum, Germany
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11
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Won BY, Shin SC, Chung WY, Shin S, Cho DY, Park HG. Mismatch DNA-specific enzymatic cleavage employed in a new method for the electrochemical detection of genetic mutations. Chem Commun (Camb) 2009:4230-2. [DOI: 10.1039/b907268c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Hung CC, Su YN, Lin CY, Chang YF, Chang CH, Cheng WF, Chen CA, Lee CN, Lin WL. Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations. BMC Biotechnol 2008; 8:62. [PMID: 18694524 PMCID: PMC2525636 DOI: 10.1186/1472-6750-8-62] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 08/12/2008] [Indexed: 11/24/2022] Open
Abstract
Background Beta-thalassemia is a common autosomal recessive hereditary disease in the Meditertanean, Asia and African areas. Over 600 mutations have been described in the beta-globin (HBB), of which more than 200 are associated with a beta-thalassemia phenotype. Results We used two highly-specific mutation screening methods, mismatch-specific endonuclease and denaturing high-performance liquid chromatography, to identify mutations in the HBB gene. The sensitivity and specificity of these two methods were compared. We successfully distinguished mutations in the HBB gene by the mismatch-specific endonuclease method without need for further assay. This technique had 100% sensitivity and specificity for the study sample. Conclusion Compared to the DHPLC approach, the mismatch-specific endonuclease method allows mutational screening of a large number of samples because of its speed, sensitivity and adaptability to semi-automated systems. These findings demonstrate the feasibility of using the mismatch-specific endonuclease method as a tool for mutation screening.
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Affiliation(s)
- Chia-Cheng Hung
- 1Institute of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan.
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13
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Enzyme-Linked Electrochemical Detection of PCR-Amplified Nucleotide Sequences Using Disposable Screen-Printed Sensors. Applications in Gene Expression Monitoring. SENSORS 2008; 8:193-210. [PMID: 27879703 PMCID: PMC3681127 DOI: 10.3390/s8010193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 01/07/2008] [Indexed: 11/17/2022]
Abstract
Electrochemical enzyme-linked techniques for sequence-specific DNA sensing are presented. These techniques are based on attachment of streptavidin-alkaline phosphatase conjugate to biotin tags tethered to DNA immobilized at the surface of disposable screen-printed carbon electrodes (SPCE), followed by production and electrochemical determination of an electroactive indicator, 1-naphthol. Via hybridization of SPCE surface-confined target DNAs with end-biotinylated probes, highly specific discrimination between complementary and non-complementary nucleotide sequences was achieved. The enzyme-linked DNA hybridization assay has been successfully applied in analysis of PCR-amplified real genomic DNA sequences, as well as in monitoring of plant tissue-specific gene expression. In addition, we present an alternative approach involving sequence-specific incorporation of biotin-labeled nucleotides into DNA by primer extension. Introduction of multiple biotin tags per probe primer resulted in considerable enhancement of the signal intensity and improvement of the specificity of detection.
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14
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Zhang P, Chu X, Xu X, Shen G, Yu R. Electrochemical detection of point mutation based on surface ligation reaction and biometallization. Biosens Bioelectron 2007; 23:1435-41. [PMID: 18242973 DOI: 10.1016/j.bios.2007.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 12/10/2007] [Accepted: 12/13/2007] [Indexed: 12/20/2022]
Abstract
A highly sensitive electrochemical method for point mutation detection based on surface enzymatic ligation reaction and biometallization is demonstrated. In this method the surface-immobilized allele-specific probe, complementary to the mutant target, undergoes allele-specific ligation with the 5'-phosphorylated ligation probe in the presence of the mutant oligonucleotide target and E. coli DNA ligase. If there is an allele mismatch, no ligation takes place. After thermal treatment at 90 degrees C, the formed duplex melts apart, which merely allows the ligation product to remain on the electrode surface. Then, biotinylated detection probes hybridize with the ligation product. With the binding of streptavidin-alkaline phosphatase (SA-ALP) to the biotinylated probes, a non-reductive substrate of alkaline phosphatase, ascorbic acid 2-phosphate (AA-P), can be converted into ascorbic acid (AA) at the electrode surface. Silver ions in solution are then reduced by AA, resulting in the deposition of silver metal onto the electrode surface. Linear sweep voltammetry (LSV) is used to detect the amount of deposited silver. The proposed approach has been successfully implemented for the identification of single base mutation in codon 12 of K-ras oncogene target with a detection limit of 80fM, demonstrating that this method provides a highly specific, sensitive and cost-efficient approach for point mutation detection.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Chemo/Bio-sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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15
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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16
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Seiwert B, Karst U. Ferrocene-based derivatization in analytical chemistry. Anal Bioanal Chem 2007; 390:181-200. [PMID: 17934723 DOI: 10.1007/s00216-007-1639-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 09/14/2007] [Accepted: 09/17/2007] [Indexed: 11/25/2022]
Abstract
Ferrocene-based derivatization has raised considerable interest in many fields of analytical chemistry. This is due to the well-established chemistry of ferrocenes, which allows rapid and easy access to a large number of reagents and derivatives. Furthermore, the electrochemical properties of ferrocenes are attractive with respect to their detection. This paper summarizes the available reagents, the reaction conditions and the different approaches for detection. While electrochemical detection is still most widely used to detect ferrocene derivatives, e.g., in the field of DNA analysis, the emerging combination of analytical separation methods with electrochemistry, mass spectrometry and atomic spectroscopy allows ferrocenes to be applied more universally and in novel applications where strongly improved selectivity and limits of detection are required.
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Affiliation(s)
- Bettina Seiwert
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149, Münster, Germany
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17
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Li X, Huang Y, Guan Y, Zhao M, Li Y. A novel one cycle allele specific primer extension--molecular beacon displacement method for DNA point mutation detection with improved specificity. Anal Chim Acta 2006; 584:12-8. [PMID: 17386579 DOI: 10.1016/j.aca.2006.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Revised: 10/19/2006] [Accepted: 11/06/2006] [Indexed: 01/08/2023]
Abstract
We report here a new method for the real-time detection of DNA point mutations with molecular beacon as the fluorescence tracer and 3' (exo-) Bst DNA polymerase large fragment as the polymerase. The method is based on the mechanism of allele specific primer extension-strand displacement (ASPE-SD). To improve the specificity of the method only one cycle of the allele specific polymerase chain reaction (PCR) was used that could largely eliminate the non-specific reactions between the primers and template of the "wrong" genotype. At first, the primer and molecular beacon both hybridize to the DNA template, and the molecular beacon emits intensive fluorescence. The role of 3' exonuclease excision of Bst DNA polymerase large fragment is utilized for primer extension. When 3'-termini matches its corresponding template, the primer would efficiently extend and replace the molecular beacon that would simultaneously return to its closed form leading to the quenching of the fluorescence. However, when 3'-termini of the primer mismatches its corresponding template primer extension and molecular beacon displacement would not happen and fluorescence of the hybridized molecular beacon holds the line without fluorescence quenching. This approach was fully demonstrated in synthetic template systems and applied to detect point mutation at codon 259, a possible point mutation site in exon 7 of p53 gene, obtained from human genomic DNA samples with unambiguous differentiation power.
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Affiliation(s)
- Xiaomin Li
- The Key Laboratory of Bioorganic Chemistry & Molecular Engineering and the Research Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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18
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Pike AR, Ryder LC, Horrocks BR, Clegg W, Connolly BA, Houlton A. Ferrocenyl-modified DNA: synthesis, characterization and integration with semiconductor electrodes. Chemistry 2006; 11:344-53. [PMID: 15551318 DOI: 10.1002/chem.200400632] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The ferrocenyl-nucleoside, 5-ethynylferrocenyl-2'-deoxycytidine (1) has been prepared by Pd-catalyzed cross-coupling between ethynylferrocene and 5-iodo-2'-deoxycytidine and incorporated into oligonucleotides by using automated solid-phase synthesis at both silica supports (CPG) and modified single-crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl-nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl-modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12-mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid-phase methods were also used to synthesise 12-mer ferrocenyl-containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface-bound ferrocenyl-DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene-phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO(4), a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation-induced changes in ferrocene-phosphate distances.
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Affiliation(s)
- Andrew R Pike
- Chemistry Laboratories, School of Natural Sciences Bedson Building, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, UK
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Mukumoto K, Nojima T, Takenaka S. Synthesis of ferrocenylcarbodiimide as a convenient electrochemically active labeling reagent for nucleic acids. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.09.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Hung CC, Lee CN, Chen CP, Jong YJ, Chen CA, Cheng WF, Lin WL, Su YN. Quantification of Relative Gene Dosage by Single-Base Extension and High-Performance Liquid Chromatography: Application to the SMN1/SMN2 Gene. Anal Chem 2005; 77:6960-8. [PMID: 16255596 DOI: 10.1021/ac0512047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the most commonly used techniques for genotyping of single-nucleotide polymorphism (SNP) is detection of single-base extensions (SBEs). We present a new, rapid, simple, and highly reliable method for accurate quantification of SNP variants in a single reaction. Our approach is based on SBE detection coupled with high-performance liquid chromatography (HPLC) quantification. To demonstrate the utility of our approach, we report data to determine the gene dosage for relative amounts of alleles in a homologous gene, allowing detection of mutation causing exon skipping in human SMN genes to determine the ratio between the copy numbers of the SMN1/SMN2 gene. We successfully determined the relative ratio of the SMN1 and SMN2 genes and showed assay characteristics using the SBE reaction coupled with HPLC. This assay approach readily scaled to high parallelization with multiplex SBE reactions in a single sample screened in one analysis. By screening for particular SNP genotypes, this assay can be used to determine the relative gene dosage that correlates highly with the patient's disease state. The next challenge is to apply this novel methodology in a clinical screening and quantification setting for special gene regions within highly homologous genes.
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Affiliation(s)
- Chia-Cheng Hung
- Institute of Biomedical Engineering, National Taiwan University, Taipei 100, Taiwan
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21
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Nowicka AM, Donten M, Palys M, Stojek Z. Effect of Change in Angle between Microelectrode Surface and Jet Direction in Flow System on Current Response in Solutions of Different Ionic Strength. Anal Chem 2005; 77:5174-81. [PMID: 16097756 DOI: 10.1021/ac050498t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of stream orientation versus surface of microelectrode detector was examined in the range between vertical and parallel flow for various jet velocities and various levels of supporting electrolyte. The flow cell was equipped with a conical body Pt microdisk electrode, and the measurements involved voltammetry and chronoamperometry. Ferrocene, two its charged derivatives (sodium ferrocenylo sulfate and ferrocenylomethyltrimethylamino hexafluorophosphate) and sodium iodide were employed as the substrates in the experiments. The strongest convectional transport and the highest signal of the analytes was obtained for alpha = 60 degrees (alpha is the angle between the electrode surface and the stream direction). The measured current increased by up to 1.85 times versus the traditional setup, and therefore, this new geometry of the detector is analytically advantageous. The value of alpha corresponding to the highest signal tended to decrease to approximately 45 degrees in the absence of supporting electrolyte provided that either flow rate or analyte concentration was above a certain threshold value. The experiments indicated that the interplay of the convectional and migrational components in the analyte transport is different for the charge increase and the charge cancellation processes. These experimental facts were confirmed by digital simulation results.
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Affiliation(s)
- Anna Maria Nowicka
- Department of Chemistry, Warsaw University, ul. Pasteura 1, 02-093 Warsaw, Poland
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22
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Gibbs JM, Park SJ, Anderson DR, Watson KJ, Mirkin CA, Nguyen ST. Polymer-DNA hybrids as electrochemical probes for the detection of DNA. J Am Chem Soc 2005; 127:1170-8. [PMID: 15669856 DOI: 10.1021/ja046931i] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The syntheses of several norbornene block copolymers containing oligonucleotide and ferrocenyl side chains and their use in the electrochemical detection of DNA are described. Two kinds of DNA-containing block copolymers with either ferrocenyl or dibromoferrocenyl groups were prepared via ring-opening metathesis polymerization (ROMP). Based on these two distinct ferrocene derivatives, a triblock copolymer labeling strategy was developed. With this strategy, the identity of DNA target can be determined by the E1/2s of the ferrocenyl moieties and the ratio of peak currents. These polymers exhibit predictable and tailorable electrochemical properties, high DNA duplex stability, and unusually sharp melting transitions, which are highly desirable characteristics for DNA detection applications. Significantly, single-base mismatches could be easily detected using two distinct block copolymers as dual-channel detection probes in an electrochemical DNA detection format.
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Affiliation(s)
- Julianne M Gibbs
- Department of Chemistry and Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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23
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Di Giusto DA, Wlassoff WA, Gooding JJ, Messerle BA, King GC. Proximity extension of circular DNA aptamers with real-time protein detection. Nucleic Acids Res 2005; 33:e64. [PMID: 15817563 PMCID: PMC1074748 DOI: 10.1093/nar/gni063] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2005] [Revised: 03/16/2005] [Accepted: 03/16/2005] [Indexed: 01/08/2023] Open
Abstract
Multivalent circular aptamers or 'captamers' have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the 'proximity extension' assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer-thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier.
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Affiliation(s)
- Daniel A. Di Giusto
- School of Biotechnology and Biomolecular Sciences, The University of New South WalesSydney NSW 2052, Australia
- School of Chemistry, The University of New South WalesSydney NSW 2052, Australia
| | - Wjatschesslaw A. Wlassoff
- School of Biotechnology and Biomolecular Sciences, The University of New South WalesSydney NSW 2052, Australia
- School of Chemistry, The University of New South WalesSydney NSW 2052, Australia
| | - J. Justin Gooding
- School of Chemistry, The University of New South WalesSydney NSW 2052, Australia
| | - Barbara A. Messerle
- School of Chemistry, The University of New South WalesSydney NSW 2052, Australia
| | - Garry C. King
- To whom correspondence should be addressed. Tel: +61 2 9385 2021; Fax: +61 2 9385 1483;
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24
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Affiliation(s)
- Dave R van Staveren
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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Di Giusto DA, Wlassoff WA, Giesebrecht S, Gooding JJ, King GC. Multipotential electrochemical detection of primer extension reactions on DNA self-assembled monolayers. J Am Chem Soc 2004; 126:4120-1. [PMID: 15053597 DOI: 10.1021/ja0319036] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electroactive nucleoside triphosphates ("electrotides") have been incorporated into primers by DNA polymerase and detected on oligonucleotide surface-assembled monolayers. Four electrotides bearing three different electroactive moieties-ferrocene, vinylferrocene, and anthraquinone-are detected in four alternative formats.
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Affiliation(s)
- Daniel A Di Giusto
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia
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26
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Ertl P, Emrich CA, Singhal P, Mathies RA. Capillary Electrophoresis Chips with a Sheath-Flow Supported Electrochemical Detection System. Anal Chem 2004; 76:3749-55. [PMID: 15228350 DOI: 10.1021/ac035282a] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microfabricated capillary electrophoresis chips containing an integrated sheath-flow electrochemical detector are developed with the goal of minimizing the influence of separation voltages on end-column detection while maintaining optimum performance. The microdevice consists of an upper glass wafer carrying the etched separation, injection, and sheath-flow channels and a lower glass wafer on which gold- and silver-plated electrodes have been fabricated. The sheath-flow channels join the end of the separation channel from each side, and gravity-driven flow carries the analytes to the electrochemical detector placed at working distances of 100, 150, 200, and 250 microm from the separation channel exit. The performance of this detector is evaluated using catechol and a detection limit of 4.1 microM obtained at a working distance of 250 microm. Detection of DNA restriction fragments and PCR product sizing is demonstrated using the electroactive intercalating dye, iron phenanthroline. Additionally, an allele-specific, PCR-based single-nucleotide polymorphism typing assay for the C282Y substitution diagnostic for hereditary hemochromatosis is developed and evaluated using ferrocene-labeled primers. This study advances the feasibility of high-speed, high-throughput chemical and genetic analysis using microchip electrochemical detection.
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Affiliation(s)
- Peter Ertl
- Department of Chemistry and Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
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Hebert NE, Snyder B, McCreery RL, Kuhr WG, Brazill SA. Performance of Pyrolyzed Photoresist Carbon Films in a Microchip Capillary Electrophoresis Device with Sinusoidal Voltammetric Detection. Anal Chem 2003; 75:4265-71. [PMID: 14632145 DOI: 10.1021/ac026425g] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrolyzed photoresist films (PPF) are introduced as planar carbon electrodes in a PDMS-quartz hybrid microchip device. The utility of PPF in electroanalytical applications is demonstrated by the separation and detection of various neurotransmitters. PPF is found to form a stable, low-capacitance, durable layer on quartz, which can then be used in conjunction with a microchip capillary electrophoretic device. Sinusoidal voltammetric detection at PPF electrodes is shown to be very sensitive, with a detection limit (S/N = 3) of 100 nM for dopamine, corresponding to a mass detection limit (S/N = 3) of 2 amol. The selectivity of analysis in the frequency domain is demonstrated by isolating each individual signal in a pair of analytes that are chromatographically unresolved. Effectively decoupling the electrophoresis and electrochemical systems allows the electrodes to be placed just inside the separation channel, which results in efficient separations (80 000-100 000 plates/m).
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Affiliation(s)
- Nicole E Hebert
- Department of Chemistry, University of California, Riverside, California 92521, USA
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Hebert NE, Kuhr WG, Brazill SA. A Microchip Electrophoresis Device with Integrated Electrochemical Detection: A Direct Comparison of Constant Potential Amperometry and Sinusoidal Voltammetry. Anal Chem 2003; 75:3301-7. [PMID: 14570177 DOI: 10.1021/ac0262457] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A microchip electrophoresis system with integrated electrochemical detection is described in this work. The hybrid device utilizes poly(dimethylsiloxane) as the electrophoresis channel substrate and a planar gold electrode lithographically fabricated onto a glass slide for electrochemical detection. The system is characterized by the separation and detection of various neurotransmitters. The gold working electrode is placed just inside the separation channel without adverse effects on the detection sensitivity, due to the electrical decoupling of the detection and electrophoresis systems. The close proximity of the working electrode to the exit of the separation channel results in symmetric peak shapes and efficient separations (50,000-100,000 plates/m). A direct comparison between the frequency-based electrochemical technique, sinusoidal voltammetry, and the more commonly used constant potential (DC) amperometry is made. Sinusoidal voltammetry is found to be roughly an order of magnitude more sensitive than DC amperometry, with calculated mass detection limits (S/N = 3) of 12 amol and 15 amol for dopamine and isoproterenol, respectively.
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Affiliation(s)
- Nicole E Hebert
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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29
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Rucker VC, Foister S, Melander C, Dervan PB. Sequence specific fluorescence detection of double strand DNA. J Am Chem Soc 2003; 125:1195-202. [PMID: 12553822 DOI: 10.1021/ja021011q] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods for the fluorescent detection of specific sequences of double strand DNA in homogeneous solution may be useful in the field of human genetics. A series of hairpin polyamides with tetramethyl rhodamine (TMR) attached to an internal pyrrole ring were synthesized, and the fluorescence properties of the polyamide-fluorophore conjugates in the presence and absence of duplex DNA were examined. We observe weak TMR fluorescence in the absence of DNA. Addition of >/=1:1 match DNA affords a significant fluorescence increase over equimolar mismatch DNA for each polyamide-TMR conjugate. Polyamide-fluorophore conjugates offer a new class of sensors for the detection of specific DNA sequences without the need for denaturation. The polyamide-dye fluorescence-based method can be used to screen in parallel the interactions between aromatic ring pairs and the minor groove of DNA even when the binding site contains a non-Watson-Crick DNA base pair. A ranking of the specificity of three polyamide ring pairs-Py/Py, Im/Py, and Im/Im-was established for all 16 possible base pairs of A, T, G, and C in the minor groove. We find that Im/Im is an energetically favorable ring pair for minor groove recognition of the T.G base pair.
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Affiliation(s)
- Victor C Rucker
- The Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Di Giusto D, King GC. Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: improved fidelity in single-substrate assays. Nucleic Acids Res 2003; 31:e7. [PMID: 12560510 PMCID: PMC149219 DOI: 10.1093/nar/gng007] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Model single base extension (SBE) genotyping reactions with individual deoxy-, dideoxy- and acyclonucleoside triphosphates are monitored by MALDI-TOF mass spectrometry. Three non-proofreading DNA polymerases display remarkably high misincorporation (up to 64% of correct incorporation) when extending primers with single substrates at saturating concentrations. Introduction of one phosphorothioate (PS) linkage into the primer 3' terminus reduces misincorporation by these enzymes an average 1.4-fold (range 0- to 3.5-fold) versus correct incorporation. Combined use of 3'-PS primers with strongly proofreading DNA polymerases yields order of magnitude improvements in SBE fidelity over those produced by the equivalent non-proofreading enzymes. Errors are reduced to below MALDI-TOF detectable levels in almost all cases. The Sp diastereomer of the 3'-PS primer, which can be prepared in situ by incubation with proofreading polymerase, is stable to 3'-exonuclease activity over periods longer than 16 h. Products of correct extension by T7 DNAP are retained over 30-60 min during idling turnover at a dNTP concentration of 2.5 micro M, indicating that the assay can be applied over a broad range of substrate concentrations. These results suggest that the use of PS primers and proofreading polymerases will offer a simple and cost-effective means to improve fidelity in a range of single-substrate SBE assay formats.
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Affiliation(s)
- Daniel Di Giusto
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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