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Nguyen TNP, Nguyen SH, Tran MT. Disposable impedance sensors based on novel hybrid MoS2 nanosheets and microparticles to detect Escherichia Coli DNA. PLoS One 2024; 19:e0299272. [PMID: 38422053 PMCID: PMC10903914 DOI: 10.1371/journal.pone.0299272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
The rapid and accurate detection of pathogenic bacteria is essential for food safety and public health. Conventional detection techniques, such as nucleic acid sequence-based amplification and polymerase chain reaction, are time-consuming and require specialized equipment and trained personnel. Here, we present quick, disposable impedance sensors based on the novel hybrid MoS2 nanomaterial for detecting Escherichia coli DNA. Our results indicate that the proposed sensors operate linearly between 10- 20 and 10-15 M concentrations, achieving an impressive detection limit of 10-20 M with the highest sensitivity observed at a 0.325 nM probe concentration sensor. Furthermore, the electrochemical impedance spectroscopy biosensors exhibited potential selectivity for Escherichia coli DNA over Bacillus subtilis and Vibrio proteolyticus DNA sequences. The findings offer a promising avenue for efficient and precise DNA detection, with potential implications for broader biotechnology and medical diagnostics applications.
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Affiliation(s)
- Tien Ngoc Phuc Nguyen
- College of Engineering and Computer Science, VinUniversity, Hanoi, Vietnam
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, Vietnam
| | - Son Hai Nguyen
- School of Mechanical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Mai Thi Tran
- College of Engineering and Computer Science, VinUniversity, Hanoi, Vietnam
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, Vietnam
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2
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Attoye B, Pou C, Blair E, Rinaldi C, Thomson F, Baker MJ, Corrigan DK. Developing a Low-Cost, Simple-to-Use Electrochemical Sensor for the Detection of Circulating Tumour DNA in Human Fluids. BIOSENSORS 2020; 10:E156. [PMID: 33126531 PMCID: PMC7692145 DOI: 10.3390/bios10110156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
It is well-known that two major issues, preventing improved outcomes from cancer are late diagnosis and the evolution of drug resistance during chemotherapy, therefore technologies that address these issues can have a transformative effect on healthcare workflows. In this work we present a simple, low-cost DNA biosensor that was developed specifically to detect mutations in a key oncogene (KRAS). The sensor employed was a screen-printed array of carbon electrodes, used to perform parallel measurements of DNA hybridisation. A DNA amplification reaction was developed with primers for mutant and wild type KRAS sequences which amplified target sequences from representative clinical samples to detectable levels in as few as twenty cycles. High levels of sensitivity were demonstrated alongside a clear exemplar of assay specificity by showing the mutant KRAS sequence was detectable against a significant background of wild type DNA following amplification and hybridisation on the sensor surface. The time to result was found to be 3.5 h with considerable potential for optimisation through assay integration. This quick and versatile biosensor has the potential to be deployed in a low-cost, point-of-care test where patients can be screened either for early diagnosis purposes or monitoring of response to therapy.
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Affiliation(s)
- Bukola Attoye
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (E.B.); (D.K.C.)
| | - Chantevy Pou
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK; (C.P.); (F.T.)
| | - Ewen Blair
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (E.B.); (D.K.C.)
| | - Christopher Rinaldi
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, 99 George street, Glasgow G1 1RD, UK; (C.R.); (M.J.B.)
| | - Fiona Thomson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK; (C.P.); (F.T.)
| | - Matthew J. Baker
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, 99 George street, Glasgow G1 1RD, UK; (C.R.); (M.J.B.)
| | - Damion K. Corrigan
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (E.B.); (D.K.C.)
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3
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Erdem A, Eksin E. Impedimetric Sensing of Factor V Leiden Mutation by Zip Nucleic Acid Probe and Electrochemical Array. BIOSENSORS-BASEL 2020; 10:bios10090116. [PMID: 32906640 PMCID: PMC7559847 DOI: 10.3390/bios10090116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 12/02/2022]
Abstract
A carbon nanofiber enriched 8-channel screen-printed electrochemical array was used for the impedimetric detection of SNP related to Factor V Leiden (FV Leiden) mutation, which is the most common inherited form of thrombophilia. FV Leiden mutation sensing was carried out in three steps: solution-phase nucleic acid hybridization between zip nucleic acid probe (Z-probe) and mutant type DNA target, followed by the immobilization of the hybrid on the working electrode area of array, and measurement by electrochemical impedance spectroscopy (EIS). The selectivity of the assay was tested against mutation-free DNA sequences and synthetic polymerase chain reaction (PCR) samples. The developed biosensor was a trustful assay for FV Leiden mutation diagnosis, which can effectively discriminate wild type and mutant type even in PCR samples.
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Bhai S, Ganguly B. Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study. J Mol Graph Model 2019; 93:107445. [PMID: 31494536 DOI: 10.1016/j.jmgm.2019.107445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 11/30/2022]
Abstract
Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg2+ (-49.6 kcal/mol), Zn2+ (-45.3 kcal/mol) and Cu2+ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg2+ and Cu2+ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn2+ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu2+ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg2+ and Zn2+ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu2+ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg2+, Zn2+, and Cu2+ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg2+ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn2+, Cu2+) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu2+ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.
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Affiliation(s)
- Surjit Bhai
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.
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A review of microfabricated electrochemical biosensors for DNA detection. Biosens Bioelectron 2019; 134:57-67. [DOI: 10.1016/j.bios.2019.03.055] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
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Guo X, Nejad MI, Gu LQ, Gates KS. Selective covalent capture of a DNA sequence corresponding to a cancer-driving C>G mutation in theKRASgene by a chemically reactive probe: optimizing a cross-linking reaction with non-canonical duplex structures. RSC Adv 2019; 9:32804-32810. [PMID: 35529740 PMCID: PMC9073178 DOI: 10.1039/c9ra08009k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022] Open
Abstract
A covalent cross-linking reaction used for selective capture of a disease-relevant DNA sequence.
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Affiliation(s)
- Xu Guo
- Department of Chemistry
- University of Missouri
- Columbia
- USA
| | | | - Li-Qun Gu
- Department of Bioengineering
- Dalton Cardiovascular Research Center
- University of Missouri
- Columbia
- USA
| | - Kent S. Gates
- Department of Chemistry
- University of Missouri
- Columbia
- USA
- Department of Biochemistry
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Nanoporous platinum electrode grown on anodic aluminum oxide membrane: Fabrication, characterization, electrocatalytic activity toward reactive oxygen and nitrogen species. Anal Chim Acta 2018; 1035:44-50. [PMID: 30224143 DOI: 10.1016/j.aca.2018.06.076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/14/2018] [Accepted: 06/29/2018] [Indexed: 11/20/2022]
Abstract
A new type of nanoelectrode, nanoporous platinum (NPt) electrode was prepared on aluminum oxide membrane by thermal evaporation deposition. The morphology, conductivity and electrocatalytic activity of NPt electrode were characterized and compared with those of nanofilm-Pt electrode through scanning electron microscopy (SEM), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) techniques, respectively. SEM images showed that "nanocavities" observed in NPt electrode were actually 2-dimensional enclosures by linked nanoparticles. It was different from the conventional arrays of "nanocavities" formed on homogeneous metal films. EIS data indicated that NPt electrode possesses higher conductivity. Compared with that on nanofilm-Pt electrode (14.05 Ω·cm2), the impedance spectrum on NPt electrode exhibits a semicircle portion with much smaller diameters (1.24 Ω·cm2 for NPt-100, 1.48 Ω·cm2 for NPt-200). Meanwhile, the response sensitivity of NPt electrode to O2 is 0.85 mA cm-2, which is larger than that of nanofilm-Pt electrode (0.54 mA cm-2). The largest catalytic current for nitric oxide (NO) was obtained in buffer with pH value of 9.4 while for Angeli's salt (AS) was obtained in buffer with pH value of 5.4. Additionally, electrocatalytic mechanisms of NPt electrode toward NO and AS were proposed, which indicating it depended on pH value of buffer solution.
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Quan Li P, Piper A, Schmueser I, Mount AR, Corrigan DK. Impedimetric measurement of DNA-DNA hybridisation using microelectrodes with different radii for detection of methicillin resistant Staphylococcus aureus (MRSA). Analyst 2018; 142:1946-1952. [PMID: 28492640 DOI: 10.1039/c7an00436b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to their electroanalytical advantages, microelectrodes are a very attractive technology for sensing and monitoring applications. One highly important application is measurement of DNA hybridisation to detect a wide range of clinically important phenomena, including single nucleotide polymorphisms (SNPs), mutations and drug resistance genes. The use of electrochemical impedance spectroscopy (EIS) for measurement of DNA hybridisation is well established for large electrodes but as yet remains relatively unexplored for microelectrodes due to difficulties associated with electrode functionalisation and impedimetric response interpretation. To shed light on this, microelectrodes were initially fabricated using photolithography and characterised electrochemically to ensure their responses matched established theory. Electrodes with different radii (50, 25, 15 and 5 μm) were then functionalised with a mixed film of 6-mercapto-1-hexanol and a thiolated single stranded DNA capture probe for a specific gene from the antibiotic resistant bacterium MRSA. The complementary oligonucleotide target from the mecA MRSA gene was hybridised with the surface tethered ssDNA probe. The EIS response was evaluated as a function of electrode radius and it was found that charge-transfer (RCT) was more significantly affected by hybridisation of the mecA gene than the non-linear resistance (RNL) which is associated with the steady state current. The discrimination of mecA hybridisation improved as electrode radius reduced with the RCT component of the response becoming increasingly dominant for smaller radii. It was possible to utilise these findings to produce a real time measurement of oligonucleotide binding where changes in RCT were evident one minute after nanomolar target addition. These data provide a systematic account of the effect of microelectrode radius on the measurement of hybridisation, providing insight into critical aspects of sensor design and implementation for the measurement of clinically important DNA sequences. The findings open up the possibility of developing rapid, sensitive DNA based measurements using microelectrodes.
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Nejad MI, Shi R, Zhang X, Gu LQ, Gates KS. Sequence-Specific Covalent Capture Coupled with High-Contrast Nanopore Detection of a Disease-Derived Nucleic Acid Sequence. Chembiochem 2017; 18:1383-1386. [PMID: 28422400 PMCID: PMC6139021 DOI: 10.1002/cbic.201700204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 01/12/2023]
Abstract
Hybridization-based methods for the detection of nucleic acid sequences are important in research and medicine. Short probes provide sequence specificity, but do not always provide a durable signal. Sequence-specific covalent crosslink formation can anchor probes to target DNA and might also provide an additional layer of target selectivity. Here, we developed a new crosslinking reaction for the covalent capture of specific nucleic acid sequences. This process involved reaction of an abasic (Ap) site in a probe strand with an adenine residue in the target strand and was used for the detection of a disease-relevant T→A mutation at position 1799 of the human BRAF kinase gene sequence. Ap-containing probes were easily prepared and displayed excellent specificity for the mutant sequence under isothermal assay conditions. It was further shown that nanopore technology provides a high contrast-in essence, digital-signal that enables sensitive, single-molecule sensing of the cross-linked duplexes.
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Affiliation(s)
- Maryam Imani Nejad
- Department of Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Ruicheng Shi
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Xinyue Zhang
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Li-Qun Gu
- Department of Bioengineering and, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Kent S Gates
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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Castellarnau M, Ramón-Azcón J, Gonzalez-Quinteiro Y, López JF, Grimalt JO, Marco MP, Nieuwenhuijsen M, Picado A. Assessment of analytical methods to determine pyrethroids content of bednets. Trop Med Int Health 2016; 22:41-51. [PMID: 27717143 DOI: 10.1111/tmi.12794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To present and evaluate simple, cost-effective tests to determine the amount of insecticide on treated materials. METHODS We developed and evaluated a competitive immunoassay on two different platforms: a label-free impedimetric biosensor (EIS biosensor) and a lateral flow. Both approaches were validated by gas chromatography (GC) and ELISA, gold standards for analytical methods and immunoassays, respectively. Finally, commercially available pyrethroid-treated ITN samples were analysed. Different extraction methods were evaluated. RESULTS Insecticide extraction by direct infusion of the ITN samples with dichloromethane and dioxane showed recovery efficiencies around 100% for insecticide-coated bednets, and >70% for insecticide-incorporated bednets. These results were comparable to those obtained with standard sonication methods. The competitive immunoassay characterisation with ELISA presented a dynamic range between 12 nm and 1.5 μm (coefficient of variation (CV) below 5%), with an IC50 at 138 nm, and a limit of detection (LOD) of 3.2 nm. EIS biosensor had a linear range between 1.7 nm and 61 nm (CV around 14%), with an IC50 at 10.4 nm, and a LOD of 0.6 nm. Finally, the lateral flow approach showed a dynamic range between 150 nm and 1.5 μm, an IC50 at 505 nm and a LOD of 67 nm. CONCLUSIONS ELISA can replace chromatography as an accurate laboratory technique to determine insecticide concentration in bednets. The lateral flow approach developed can be used to estimate ITN insecticide concentration in the field. This new technology, coupled to the new extraction methods, should provide reliable guidelines for ITN use and replacement in the field.
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Affiliation(s)
- Marc Castellarnau
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Javier Ramón-Azcón
- Nanobiotechnology for Diagnostics, Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research, Barcelona, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain
| | | | - Jordi F López
- Institute of Environmental Assessment and Water Research, Barcelona, Spain
| | - Joan O Grimalt
- Institute of Environmental Assessment and Water Research, Barcelona, Spain
| | - María-Pilar Marco
- Nanobiotechnology for Diagnostics, Institute for Advanced Chemistry of Catalonia of the Spanish Council for Scientific Research, Barcelona, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain
| | - Mark Nieuwenhuijsen
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Universitat Pompeu Fabra (UPF), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Albert Picado
- ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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Ribeiro WC, Gonçalves LM, Liébana S, Pividori MI, Bueno PR. Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy. NANOSCALE 2016; 8:8931-8938. [PMID: 27074378 DOI: 10.1039/c6nr01076h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate.
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Affiliation(s)
- W C Ribeiro
- Instituto de Química, Universidade Estadual Paulista, (Nanobionics Research Group), CP 355, 14800-900, Araraquara, SP, Brazil
| | - L M Gonçalves
- Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - S Liébana
- Grup de Sensors & Biosensors, Unitat de Química Analítica, Bloc de Ciencias e Biociencias, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M I Pividori
- Grup de Sensors & Biosensors, Unitat de Química Analítica, Bloc de Ciencias e Biociencias, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - P R Bueno
- Instituto de Química, Universidade Estadual Paulista, (Nanobionics Research Group), CP 355, 14800-900, Araraquara, SP, Brazil
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Michaels P, Alam MT, Ciampi S, Rouesnel W, Parker SG, Choudhury MH, Gooding JJ. A robust DNA interface on a silicon electrode. Chem Commun (Camb) 2014; 50:7878-80. [DOI: 10.1039/c4cc03418j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Schematic of a DNA sensing interface formed on oxide-free silicon electrodes that both resist nonspecific adsorption of DNA and maintains stable electrical properties in biological media.
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Affiliation(s)
- Pauline Michaels
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | | | - Simone Ciampi
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - William Rouesnel
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Stephen G. Parker
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
- Australian Centre for NanoMedicine
- The University of New South Wales
| | | | - J. Justin Gooding
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
- Australian Centre for NanoMedicine
- The University of New South Wales
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13
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Electrochemical impedance spectroscopy biosensor with interdigitated electrode for detection of human immunoglobulin A. Biosens Bioelectron 2013; 40:422-6. [DOI: 10.1016/j.bios.2012.07.052] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 11/22/2022]
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14
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Ripert M, Farre C, Chaix C. Selective functionalization of Au electrodes by electrochemical activation of the “click” reaction catalyst. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2012.12.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Martić S, Beheshti S, Kraatz HB, Litchfield DW. Electrochemical Investigations of Tau Protein Phosphorylations and Interactions with Pin1. Chem Biodivers 2012; 9:1693-702. [DOI: 10.1002/cbdv.201100418] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Wang J, Yi X, Tang H, Han H, Wu M, Zhou F. Direct quantification of microRNA at low picomolar level in sera of glioma patients using a competitive hybridization followed by amplified voltammetric detection. Anal Chem 2012; 84:6400-6. [PMID: 22788545 PMCID: PMC3418408 DOI: 10.1021/ac203368h] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs), acting as oncogenes or tumor suppressors in humans, play a key role in regulating gene expression and are believed to be important for developing novel therapeutic treatments and clinical prognoses. Due to their short lengths (17-25 nucleotides) and extremely low concentrations (typically < picomolar) in biological samples, quantification of miRNAs has been challenging to conventional biochemical methods, such as Northern blotting, microarray, and quantitative polymerase chain reaction (qPCR). In this work, a biotinylated miRNA (biotin-miRNA) whose sequence is the same as that of a miRNA target is introduced into samples of interest and allowed to compete with the miRNA target for the oligonucleotide (ODN) probe preimmobilized onto an electrode. Voltammetric quantification of the miRNA target was accomplished after complexation of the biotin-miRNA with ferrocene (Fc)-capped gold nanoparticle/streptavidin conjugates. The Fc oxidation current was found to be inversely proportional to the concentration of target miRNA between 10 fM and 2.0 pM. The method is highly reproducible (relative standard deviation (RSD) < 5%), regenerable (at least 8 regeneration/assay cycles without discernible signal decrease), and selective (with sequence specificity down to a single nucleotide mismatch). The low detection levels (10 fM or 0.1 attomoles of miRNA in a 10 μL solution) allow the direct quantification of miRNA-182, a marker correlated to the progression of glioma in patients, to be performed in serum samples without sample pretreatment and RNA extraction and enrichment. The concentration of miRNA-182 in glioma patients was found to be 3.1 times as high as that in healthy persons, a conclusion in excellent agreement with a separate qPCR measurement of the expression level. The obviations of the requirement of an internal reference in qPCR, simplicity, and cost-effectiveness are other additional advantages of this method for detection of nucleic acids in clinical samples.
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Affiliation(s)
- Jianxiu Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, People's Republic of China 410083
| | - Xinyao Yi
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, People's Republic of China 410083
| | - Hailin Tang
- Cancer Research Institute, Central South University, Changsha, Hunan, People's Republic of China 410013
| | - Hongxing Han
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, People's Republic of China 410083
| | - Minghua Wu
- Cancer Research Institute, Central South University, Changsha, Hunan, People's Republic of China 410013
| | - Feimeng Zhou
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, People's Republic of China 410083
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032
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Shamsi MH, Kraatz HB. Interactions of Metal Ions with DNA and Some Applications. J Inorg Organomet Polym Mater 2012. [DOI: 10.1007/s10904-012-9694-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Ahangar LE, Mehrgardi MA. Nanoporous gold electrode as a platform for the construction of an electrochemical DNA hybridization biosensor. Biosens Bioelectron 2012; 38:252-7. [PMID: 22727625 DOI: 10.1016/j.bios.2012.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/30/2022]
Abstract
The application of a nanoporous gold electrode (NPGE) in the fabrication of an electrochemical sensing system for the detection of single base mismatches (SBMs) using ferrocene-modified DNA probe has been investigated in the present manuscript. Ferrocene carboxylic acid is covalently attached to the amino-modified probe using EDC/NHS chemistry. By covalent attachment of the redox reporter molecules on the top of DNA, the direct oxidation of the ferrocene on the electrode surface is avoided. On the other hand, the electrochemical signals are amplified by anodizing the electrode surface and converting it to nanoporous form. By improving the sensitivity of the biosensor, the different SBMs including the thermodynamically stable G-A and G-T mismatches, can be easily distinguished. In this research, NPGE was prepared by anodization and chemical reduction of Au surface and used for signal amplification. Nanoporous electrode enhances the sensitivity of DNA biosensor and makes it capable to detect complementary target DNA in sub-nanomole scales.
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Affiliation(s)
- Laleh Enayati Ahangar
- Department of Chemistry, Faculty of Science, University of Isfahan, Isfahan 81746-73441, Iran
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19
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The effect of base-pair sequence on electrochemically driven denaturation. Bioelectrochemistry 2012; 85:7-13. [DOI: 10.1016/j.bioelechem.2011.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 11/18/2022]
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20
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Kaatz M, Schulze H, Ciani I, Lisdat F, Mount AR, Bachmann TT. Alkaline phosphatase enzymatic signal amplification for fast, sensitive impedimetric DNA detection. Analyst 2012; 137:59-63. [DOI: 10.1039/c1an15767a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Alam MN, Shamsi MH, Kraatz HB. Scanning positional variations in single-nucleotide polymorphism of DNA: an electrochemical study. Analyst 2012; 137:4220-5. [DOI: 10.1039/c2an35420a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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22
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Shamsi MH, Kraatz HB. Electrochemical identification of artificial oligonucleotides related to bovine species. Potential for identification of species based on mismatches in the mitochondrial cytochrome C1 oxidase gene. Analyst 2011; 136:4724-31. [PMID: 21847503 DOI: 10.1039/c1an15414a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our studies show that electrochemical impedance spectroscopy (EIS) and scanning electrochemical microscopy (SECM) of films of ds-DNA on gold allow us to distinguish between mitochondrial DNA fragments of the cytochrome c(1) oxidase (mt-Cox1) of three related species of the subfamily 'Bovinae' (Bos taurus, Bison bison, and Bison bonasus). In EIS, a perfectly matched DNA gives rise to a considerably larger charge transfer resistance R(ct) compared to mismatched pairings. Differences in charge transfer resistance, ΔR(ct), before and after the addition of Zn(2+) ions provide an additional tool for identification. In addition, all ds-DNA films were studied by SECM and their kinetic parameters were determined. Perfectly matched ds-DNAs are readily distinguished from mismatched duplexes by their lower rate constants. Our system can be used multiple times by dehybridization and rehybridization of capture strands up to the 250 pmole level.
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Shamsi MH, Kraatz HB. The effects of oligonucleotide overhangs on the surface hybridization in DNA films: an impedance study. Analyst 2011; 136:3107-12. [PMID: 21701715 DOI: 10.1039/c1an15253j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While oligonucleotide hybridization and effects of nucleobase mismatches have been the intense focus of a number of electrochemical studies, the effects of the target strand length on the electrochemical response of oligonucleotide films have not been addressed yet. In this report, we have studied the electrochemical impedance of the oligonucleotide films having overhangs on either the target or the surface bound capture strand. Each system gives different impedance responses, which were interpreted with the help of modified Randles' equivalent. Results indicate that comparable sizes of target and capture strands ensure the higher hybridization efficiency and film order. The presence of nucleobase overhangs at the bottom of the film causes lower changes in charge transfer resistance (ΔR(CT)) after hybridization due to lower hybridization efficiency and presumably non-uniformity in the film. Nucleobase overhangs at the top of the film result in higher ΔR(CT) due to higher film order and accumulation of negative charges but appear not to cause any steric congestion.
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Affiliation(s)
- Mohtashim Hassan Shamsi
- Department of Chemistry, University of Western Ontario, 1151 Richmond, Street, London, Ontario, Canada N6A 5B7
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24
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Samanta D, Sarkar A. Immobilization of bio-macromolecules on self-assembled monolayers: methods and sensor applications. Chem Soc Rev 2011; 40:2567-92. [DOI: 10.1039/c0cs00056f] [Citation(s) in RCA: 313] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Shamsi MH, Kraatz HB. Probing nucleobase mismatch variations by electrochemical techniques: exploring the effects of position and nature of the single-nucleotide mismatch. Analyst 2010; 135:2280-5. [PMID: 20672148 DOI: 10.1039/c0an00184h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical impedance spectroscopy (EIS) has been used as an ultrasensitive tool for label-free detection of single-nucleotide mismatches in double-stranded DNA (ds-DNA) films. In this study, we have explored the effects of the position and of the type of single-nucleotide mismatch in ds-DNA on gold surfaces and were able to distinguish mismatch positions and mismatch pairs. The single-nucleotide mismatches A-C, A-A and A-G were introduced at three positions within the sequence in bottom, middle and top positions of ds-DNA, the films were studied by EIS, and the impedance results were interpreted with the help of equivalent circuits. The DeltaR(ct), the difference in charge transfer resistance before and after the addition of Zn(2+), was used to distinguish single-nucleotide mismatch within the DNA sequences. Importantly, the mismatch pair is easily distinguishable at the middle position. A purine-pyrimidine mismatch can be distinguished from purine-purine mismatch by its lower DeltaR(ct) value. In addition, all ds-DNA films were studied by scanning electrochemical microscopy in the absence and presence of Zn(2+), allowing us to distinguish a range of mismatched films from matched ds-DNA film.
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Affiliation(s)
- Mohtashim H Shamsi
- Department of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
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26
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Slinker JD, Muren NB, Gorodetsky AA, Barton JK. Multiplexed DNA-modified electrodes. J Am Chem Soc 2010; 132:2769-74. [PMID: 20131780 DOI: 10.1021/ja909915m] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 microm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format.
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Affiliation(s)
- Jason D Slinker
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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27
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Li C, Li X, Liu X, Kraatz HB. Exploiting the interaction of metal ions and peptide nucleic acids-DNA duplexes for the detection of a single nucleotide mismatch by electrochemical impedance spectroscopy. Anal Chem 2010; 82:1166-9. [PMID: 20055458 DOI: 10.1021/ac902813y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with DNA-peptide nucleic acid (PNA) films on a gold surface is studied by electrochemical impedance spectroscopy in the presence of [Fe(CN)(6)](3-/4-) as the redox probe. Impedance data were analyzed with the help of a modified Randles' equivalent circuit. Changes in the charge-transfer resistance, R(CT), decreases in the order of Ni(2+) > Co(2+) > Zn(2+) > Mg(2+). We interpret these results in terms of stronger interactions for Ni(2+) with the DNA-PNA film compared to the other metal ions, potentially involving interactions with the nucleobases, presumably with the N7 of purines or the N3 of pyrimidines. On the basis of these observations, Ni(2+) was chosen to probe the detection of a C-T mismatch in 15-mer PNA-DNA films. Using Ni(2+), it is possible to detect a single C-T mismatch. The resulting DeltaR(CT) is larger for the PNA-DNA hybrid compared to that for the identical 15-mer DNA-DNA hybrid.
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Affiliation(s)
- Congjuan Li
- Department of Chemistry, School of Environment, Beijing Normal University, Beijing, 100875, China
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28
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Zhang S, Wu ZS, Qiu L, Zhou H, Shen G, Yu R. G-quadruplex signaling probe for highly sensitive DNA detection. Chem Commun (Camb) 2010; 46:3381-3. [PMID: 20442907 DOI: 10.1039/b926646a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ferrocene-conjugated oligonucleotides that can form intermolecular guanine (G)-quadruplexes are prepared and used as signaling probes for detecting target DNA, improving substantially assay characteristics (e.g. a considerably wider linear dynamic range and lower detection limit).
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Affiliation(s)
- Songbai Zhang
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
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29
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Zhang K, Zhang Y. Lable-Free Electrochemical DNA Sensor Based on Gold Nanoparticles/Poly(neutral red) Modified Electrode. ELECTROANAL 2010. [DOI: 10.1002/elan.200900453] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Komarova E, Reber K, Aldissi M, Bogomolova A. New multispecific array as a tool for electrochemical impedance spectroscopy-based biosensing. Biosens Bioelectron 2010; 25:1389-94. [DOI: 10.1016/j.bios.2009.10.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 10/01/2009] [Accepted: 10/22/2009] [Indexed: 11/16/2022]
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31
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Gong H, Zhong T, Gao L, Li X, Bi L, Kraatz HB. Unlabeled hairpin DNA probe for electrochemical detection of single-nucleotide mismatches based on MutS-DNA interactions. Anal Chem 2010; 81:8639-43. [PMID: 19769379 DOI: 10.1021/ac901371n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paper described a label-free assay for the detection of single-nucleotide mismatches in which an unlabeled hairpin DNA probe and a MutS protein conjugate (His6-MutS-linker peptide-streptavidin binding peptide (HMLS)) are exploited for the detection of mismatches by electrochemical impedance spectroscopy (EIS). We demonstrate this method for eight single-nucleotide mismatches. Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened forming a duplex DNA. In duplexes containing a single nucleotide mismatch, the mismatch is present at the solvent exposed side, enabling more effective HMLS recognition and binding. The binding event is evaluated by EIS and analyzed with the help of Randles' equivalent circuits. The differences in the charge transfer resistance DeltaR(CT) before and after protein binding to the duplex DNA allows the unequivocal detection of all eight single-nucleotide mismatches. DeltaR(CT) allows the discrimination of a C-A mismatch with the concentration of the target strand as low as 100 pM.
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Affiliation(s)
- He Gong
- Department of Chemistry, Beijing Normal University, Beijing, China 100875
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32
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Chang BY, Park SM. Electrochemical impedance spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:207-29. [PMID: 20636040 DOI: 10.1146/annurev.anchem.012809.102211] [Citation(s) in RCA: 413] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This review describes recent advances in electrochemical impedance spectroscopy (EIS) with an emphasis on its novel applications to various electrochemistry-related problems. Section 1 discusses the development of new EIS techniques to reduce measurement time. For this purpose, various forms of multisine EIS techniques were first developed via a noise signal synthesized by mixing ac waves of various frequencies, followed by fast Fourier transform of the signal and the resulting current. Subsequently, an entirely new concept was introduced in which true white noise was used as an excitation source, followed by Fourier transform of both excitation and response signals. Section 2 describes novel applications of the newly developed techniques to time-resolved impedance measurements as well as to impedance imaging. Section 3 is devoted to recent applications of EIS techniques, specifically traditional measurements in various fields with a special emphasis on biosensor detections.
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Affiliation(s)
- Byoung-Yong Chang
- Department of Chemistry, Pohang University of Science and Technology, Korea.
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33
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Park JY, Park SM. DNA hybridization sensors based on electrochemical impedance spectroscopy as a detection tool. SENSORS (BASEL, SWITZERLAND) 2009; 9:9513-32. [PMID: 22303136 PMCID: PMC3267184 DOI: 10.3390/s91209513] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/28/2009] [Accepted: 11/11/2009] [Indexed: 12/18/2022]
Abstract
Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS) as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e., target DNA. The probe DNA is immobilized on a self-assembled monolayer, a conducting polymer film, or a layer of nanostructures on the electrode such that desired probe DNA would selectively hybridize with target DNA. The rate of charge transfer from the electrode thus modified to a redox indicator, e.g., [Fe(CN)(6)](3-/4-), which is measured by EIS in the form of charge transfer resistance (R(ct)), is modulated by whether or not, as well as how much, the intended target DNA is selectively hybridized. Efforts made to enhance the selectivity as well as the sensitivity of DNA sensors and to reduce the EIS measurement time are briefly described along with brief future perspectives in developing DNA sensors.
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Affiliation(s)
- Jin-Young Park
- Department of Chemistry, Pohang University of Science & Technology, Pohang 790-784, Korea; E-Mail:
| | - Su-Moon Park
- Interdisciplinary School of Green Energy Engineering, Ulsan National Institute of Science & Technology, Ulsan 689-805, Korea
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34
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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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Qavi AJ, Washburn AL, Byeon JY, Bailey RC. Label-free technologies for quantitative multiparameter biological analysis. Anal Bioanal Chem 2009; 394:121-35. [PMID: 19221722 PMCID: PMC2667559 DOI: 10.1007/s00216-009-2637-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/12/2009] [Accepted: 01/20/2009] [Indexed: 11/26/2022]
Abstract
In the postgenomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We describe the fundamental principles of these different methods and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.
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Affiliation(s)
- Abraham J. Qavi
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Adam L. Washburn
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ji-Yeon Byeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
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Ito T, Kondo A, Kamashita T, Tanabe K, Yamada H, Nishimoto SI. Pathways of excess electron transfer in phenothiazine-tethered DNA containing single-base mismatches. Org Biomol Chem 2009; 7:2077-81. [PMID: 19421445 DOI: 10.1039/b820311c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of local structural disorder on excess electron transfer (EET) in DNA were investigated by evaluating photoinduced electron transfer in phenothiazine (PTZ)-modified oligodeoxynucleotides bearing single-base mismatches. Unexpectedly, more efficient electron transfer was observed for the mismatched duplexes than for the complementary DNA, suggesting that distraction of hydrogen bond interaction at the mismatch site enables electron injection or hopping beyond the mismatch sites. It was also anticipated that water accessibility of the mismatched nucleobases could affect EET because protonation of the electron-captured pyrimidine intermediates became competitive to EET, especially at the mismatch sites.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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Ito T, Hayashi A, Kondo A, Uchida T, Tanabe K, Yamada H, Nishimoto SI. DNA hairpins containing a diaminostilbene derivative as a photoinduced electron donor for probing the effects of single-base mismatches on excess electron transfer in DNA. Org Lett 2009; 11:927-30. [PMID: 19170616 DOI: 10.1021/ol802896y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To investigate the effects of local structural disorder induced by a single-base mismatch on excess electron transfer (EET) in DNA, a novel hairpin DNA containing diaminostilbene (DAS) as a photoinducible electron donor has been developed. It was clearly demonstrated that EET efficiency depends on the electron injection modes from the electron donors and redox properties of the mismatched bases.
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Affiliation(s)
- Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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38
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Bin X, Kraatz HB. Interaction of metal ions and DNA films on gold surfaces: an electrochemical impedance study. Analyst 2009; 134:1309-13. [PMID: 19562195 DOI: 10.1039/b821670c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical impedance spectroscopy (EIS) has been used to investigate the effects of a number of metal ions with DNA films on gold surfaces exploiting [Fe(CN)6](3-/4-) as a solution-based redox probe. Alkaline earth metal ions Mg2+, Ca2+, trivalent Al3+, La3+ and divalent transition metal ions Ni2+, Cu2+, Cd2+ and Hg2+ have been selected in this study and the results are compared with previous studies on the effects of Zn2+ on the EIS of DNA films. All experimental results were evaluated with the help of equivalent circuits which allowed the extraction of resistive and capacitive components. For all metal ions studied here, addition of the metal ions causes a decrease in the charge transfer resistance. The difference of charge transfer resistance (DeltaR(ct)) of ds-DNA films in the presence and absence of the various metal ions is different and particular to any given metal ion. In addition, we studied the EIS of ds-DNA films containing a single A-C mismatch in the presence and absence of Ca2+, Zn2+, Cd2+ and Hg2+. DeltaR(ct) values for ds-DNA films with a single A-C mismatch is smaller than those of fully matched ds-DNA films.
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Affiliation(s)
- Xiaomin Bin
- Department of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
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Zhu N, Gao H, Gu Y, Xu Q, He P, Fang Y. PAMAM dendrimer-enhanced DNA biosensors based on electrochemical impedance spectroscopy. Analyst 2009; 134:860-6. [PMID: 19381376 DOI: 10.1039/b815488k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel, simple and sensitive DNA biosensor based on DNA-poly(amidoamine) (PAMAM) dendrimer nanoconjugates was developed by using the electrochemical impedance spectroscopy (EIS) technique. In this context, the assay relies on the hybridization of the single-stranded DNA (ssDNA) probe covalently conjugated on a mercaptoacetic acid self-assembled monolayer on gold electrodes, with the generation 4.5 (G-4.5) PAMAM-target DNA complex in solution. Once the double-stranded DNA (dsDNA) formed on the gold electrodes, G-4.5 PAMAM bearing carboxyls on the periphery was anchored on the hybrids; the changes of interfacial electron-transfer resistance (R(et)) of the electrodes were measured using an Fe(CN)(6)(3-/4-) redox probe by electrochemical impedance spectroscopy. The results showed that only a complementary sequence could form a dsDNA-PAMAM with the DNA-PAMAM probe and give an obviously enlarged R(et) value. The non-complementary and three-base mismatched sequence exhibited negligible impedance change compared with the blank measurement (the blank measurement means: ssDNA probe-modified gold electrode was directly measured by EIS). The unique spherical structure combining with more negative charges on the G-4.5 PAMAM periphery anchored on the hybrids could significantly amplify the hybridization signal (R(et) value), and the detection limit for measuring the full complementary sequence is down to pM level.
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Affiliation(s)
- Ningning Zhu
- Department of Chemistry, Shanghai Normal University, Shanghai 200234, China.
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40
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Diakowski PM, Kraatz HB. Detection of single-nucleotide mismatches using scanning electrochemical microscopy. Chem Commun (Camb) 2009:1189-91. [PMID: 19240869 DOI: 10.1039/b819876d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probing ds-DNA films in the presence of Zn(2+) ions by scanning electrochemical microscopy (SECM) allows the unequivocal detection of a single-nucleotide mismatch and provides information about its position within the duplex.
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Affiliation(s)
- Piotr Michal Diakowski
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario, CanadaN6A 5B7
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41
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Kerman K, Vestergaard M, Tamiya E. Electrochemical DNA biosensors: protocols for intercalator-based detection of hybridization in solution and at the surface. Methods Mol Biol 2009; 504:99-113. [PMID: 19159093 DOI: 10.1007/978-1-60327-569-9_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An electrochemical DNA biosensor is a device that utilizes the inherent ability of two complementary strands of nucleic acids to form a double helix. The specificity of this reaction, namely hybridization, is used in the detection of target DNA sequences with a view toward developing point-of-care devices. Since the early 1990s, great progress has been made in this field, but there are still numerous challenges to overcome. This chapter describes the components of an electrochemical DNA biosensor for researchers new to the field, paying particular attention to intercalator-based DNA biosensors. We will use a well-defined electro-active DNA intercalator Hoechst 33258, as our running example. Two of the most classic DNA sensing methods: solution-based and surface-immobilized methods are discussed, along with guiding notes that would help identify and overcome possible problems in a typical electrochemical DNA biosensor experiment.
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Affiliation(s)
- Kagan Kerman
- Department of Chemistry, University of Western Ontario, London, ON, Canada
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Bratov A, Ramón-Azcón J, Abramova N, Merlos A, Adrian J, Sánchez-Baeza F, Marco MP, Domínguez C. Three-dimensional interdigitated electrode array as a transducer for label-free biosensors. Biosens Bioelectron 2008; 24:729-35. [DOI: 10.1016/j.bios.2008.06.057] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 06/17/2008] [Accepted: 06/23/2008] [Indexed: 11/15/2022]
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43
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Mahajan S, Richardson J, Brown T, Bartlett PN. SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences. J Am Chem Soc 2008; 130:15589-601. [DOI: 10.1021/ja805517q] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumeet Mahajan
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - James Richardson
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Tom Brown
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Philip N. Bartlett
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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44
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Characterisation of the interdigitated electrode array with tantalum silicide electrodes separated by insulating barriers. Electrochem commun 2008. [DOI: 10.1016/j.elecom.2008.07.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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45
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Zhang K, Ma H, Zhang L, Zhang Y. Fabrication of a Sensitive Impedance Biosensor of DNA Hybridization Based on Gold Nanoparticles Modified Gold Electrode. ELECTROANAL 2008. [DOI: 10.1002/elan.200804290] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays. Biotechniques 2008; 44:913-20. [PMID: 18533901 DOI: 10.2144/000112758] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Despite the great popularity and potential of microarrays, their use for research and clinical applications is still hampered by lengthy and costly design and optimization processes, mainly because the technology relies on the end point measurement of hybridization. Thus, the ability to monitor many hybridization events on a standard microarray slide in real time would greatly expand the use and benefit of this technology, as it would give access to better prediction of probe performance and improved optimization of hybridization parameters. Although real-time hybridization and thermal denaturation measurements have been reported, a complete walk-away system compatible with the standard format of microarrays is still unavailable. To address this issue, we have designed a biochip tool that combines a hybridization station with active mixing capability and temperature control together with a fluorescence reader in a single compact benchtop instrument. This integrated live hybridization machine (LHM) allows measuring in real time the hybridization of target DNA to thousands of probes simultaneously and provides excellent levels of detection and superior sequence discrimination. Here we show on an environmental single nucleotide polymorphism (SNP) model system that the LHM enables a variety of experiments unachievable with conventional biochip tools.
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47
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Characteristic differences in the X-ray photoelectron spectrum between B-DNA and M-DNA monolayers on gold. J Inorg Biochem 2008; 102:1599-606. [DOI: 10.1016/j.jinorgbio.2008.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 01/30/2008] [Accepted: 02/20/2008] [Indexed: 11/15/2022]
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48
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Affiliation(s)
- Benjamin J Privett
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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49
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Liu G, Wan Y, Gau V, Zhang J, Wang L, Song S, Fan C. An enzyme-based E-DNA sensor for sequence-specific detection of femtomolar DNA targets. J Am Chem Soc 2008; 130:6820-5. [PMID: 18459781 DOI: 10.1021/ja800554t] [Citation(s) in RCA: 370] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report an enzyme-based E-DNA sensor for the sequence-specific detection of nucleic acids. This DNA sensor employs a "stem-loop" DNA probe dually labeled with biotin and digoxigenin (DIG). The probe is immobilized at an avidin-modified electrode surface via the biotin-avidin bridge, and the DIG serves as an affinity tag for the enzyme binding. In the initial state of the sensor, the probe adopts the stem-loop structure, which shields DIG from being approached by a bulky horseradish peroxidase-linked-anti-DIG antibody (anti-DIG-HRP) due to the steric effect. After hybridization, the probe undergoes a significant conformational change, forcing DIG away from the electrode. As a result, the DIG label becomes accessible by the anti-DIG-HRP, and the target hybridization event can be sensitively transduced via the enzymatically amplified electrochemical current signal. By using this new strategy, we demonstrate that the prototype E-DNA sensor has been able to detect as low as femtomolar DNA targets with excellent differentiation ability for even single mismatches.
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Affiliation(s)
- Gang Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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50
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Wang Y, Li C, Li X, Li Y, Kraatz HB. Unlabeled hairpin-DNA probe for the detection of single-nucleotide mismatches by electrochemical impedance spectroscopy. Anal Chem 2008; 80:2255-60. [PMID: 18290674 DOI: 10.1021/ac7024688] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An unlabeled hairpin-DNA probe was used for the detection of eight single-nucleotide mismatches by electrochemical impedance spectroscopy (EIS). Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened and forms a duplex DNA. Accordingly, the film thickness is increased, which causes differences in the electrical properties of the film before and after hybridization. Randles equivalent circuits were employed to evaluate the EIS result. The differences in the charge-transfer resistance DeltaR(CT) between hairpin DNA (before hybridization) and duplex DNA (after hybridization) shows the consequence of a large structural rearrangement from hairpin to duplex. If a single-nucleotide mismatch is present in the center of the duplex, the difference in charge-transfer resistance DeltaR(CT) between B-DNA in the absence and presence of Zn(2+) allows the unequivocal detection of all eight single-nucleotide mismatches. The detection limit was measured, and DeltaR(CT) allows the discrimination of a single-nucleotide mismatch with the concentration of the target strand as low as 10 pM.
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Affiliation(s)
- Ying Wang
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
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