1
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Jamal RB, Bay Gosewinkel U, Ferapontova EE. Electrocatalytic aptasensor for bacterial detection exploiting ferricyanide reduction by methylene blue on mixed PEG/aptamer monolayers. Bioelectrochemistry 2024; 156:108620. [PMID: 38006817 DOI: 10.1016/j.bioelechem.2023.108620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Pathogen-triggered infections are the most severe global threat to human health, and to provide their timely treatment and prevention, robust methods for rapid and reliable identification of pathogenic microorganisms are required. Here, we have developed a fast and inexpensive electrocatalytic aptamer assay enabling specific and ultrasensitive detection of E. coli. E. coli, a biomarker of environmental contamination and infections, was captured on the mixed aptamer/thiolated PEG self-assembled monolayers formed on electrochemically pre-treated gold screen-printed electrodes (SPE). Signals from aptamer - E. coli binding were amplified by electrocatalytic reduction of ferricyanide mediated by methylene blue (MB) adsorbed on bacterial and aptamer surfaces. PEG operated as an antifouling agent and inhibited direct (not MB-mediated) discharge of ferricyanide. The assay allowed from 10 to 1000 CFU mL-1E. coli detection in 30 min, with no interference from B. subtilis, in buffer and artificial urine samples. This electrocatalytic approach is fast, specific, sensitive, and can be used directly in in-field and point-of-care applications for analysis of bacteria in human environment.
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Affiliation(s)
- Rimsha B Jamal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Ulrich Bay Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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2
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Díaz-Fernández A, Ferapontov A, Vendelbo MH, Ferapontova EE. Electrochemical Cellulase-Linked ELASA for Rapid Liquid Biopsy Testing of Serum HER-2/ neu. ACS Meas Sci Au 2023; 3:226-235. [PMID: 37360033 PMCID: PMC10288612 DOI: 10.1021/acsmeasuresciau.2c00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 06/28/2023]
Abstract
Non-invasive liquid biopsy assays for blood-circulating biomarkers of cancer allow both its early diagnosis and treatment monitoring. Here, we assessed serum levels of protein HER-2/neu, overexpressed in a number of aggressive cancers, by the cellulase-linked sandwich bioassay on magnetic beads. Instead of traditional antibodies we used inexpensive reporter and capture aptamer sequences, transforming the enzyme-linked immuno-sorbent assay (ELISA) into an enzyme-linked aptamer-sorbent assay (ELASA). The reporter aptamer was conjugated to cellulase, whose digestion of nitrocellulose film electrodes resulted in the electrochemical signal change. ELASA, optimized relative aptamer lengths (dimer vs monomer and trimer), and assay steps allowed 0.1 fM detection of HER-2/neu in the 10% human serum in 1.3 h. Urokinase plasminogen activator and thrombin as well as human serum albumin did not interfere, and liquid biopsy analysis of serum HER-2/neu was similarly robust but 4 times faster and 300 times cheaper than both electrochemical and optical ELISA. Simplicity and low cost of cellulase-linked ELASA makes it a perspective diagnostic tool for fast and accurate liquid biopsy detection of HER-2/neu and of other proteins for which aptamers are available.
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Affiliation(s)
- Ana Díaz-Fernández
- Interdisciplinary
Nanoscience Center (iNANO), Faculty of Natural Sciences, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Alexey Ferapontov
- Interdisciplinary
Nanoscience Center (iNANO), Faculty of Natural Sciences, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Mikkel Holm Vendelbo
- Department
of Nuclear Medicine & PET Centre, Aarhus
University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark
- Department
of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary
Nanoscience Center (iNANO), Faculty of Natural Sciences, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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3
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Jamal RB, Vitasovic T, Gosewinkel U, Ferapontova EE. Detection of E.coli 23S rRNA by electrocatalytic "off-on" DNA beacon assay with femtomolar sensitivity. Biosens Bioelectron 2023; 228:115214. [PMID: 36906990 DOI: 10.1016/j.bios.2023.115214] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Prevention of food spoilage, environmental bio-contamination, and pathogenic infections requires rapid and sensitive bacterial detection systems. Among microbial communities, the bacterial strain of Escherichia coli is most widespread, with pathogenic and non-pathogenic strains being biomarkers of bacterial contamination. Here, we have developed a fM-sensitive, simple, and robust electrocatalytically-amplified assay facilitating specific detection of E.coli 23S ribosomal rRNA, in the total RNA sample, after its site-specific cleavage by RNase H enzyme. Gold screen-printed electrodes (SPE) were electrochemically pre-treated to be productively modified with a methylene-blue (MB) - labelled hairpin DNA probes, which hybridization with the E. coli-specific DNA placed MB in the top region of the DNA duplex. The formed duplex acted as an electrical wire, mediating electron transfer from the gold electrode to the DNA-intercalated MB, and further to ferricyanide in solution, enabling its electrocatalytic reduction otherwise impeded on the hairpin-modified SPEs. The assay facilitated 20 min 1 fM detection of both synthetic E. coli DNA and 23S rRNA isolated from E.coli (equivalent to 15 CFU mL-1), and can be extended to fM analysis of nucleic acids isolated from any other bacteria.
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Affiliation(s)
- Rimsha B Jamal
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Toni Vitasovic
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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4
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Sosna M, Ferapontova EE. Electron Transfer in Binary Hemin-Modified Alkanethiol Self-Assembled Monolayers on Gold: Hemin's Lateral and Interfacial Interactions. Langmuir 2022; 38:11180-11190. [PMID: 36062334 DOI: 10.1021/acs.langmuir.2c01064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Orientated coupling of redox enzymes to electrodes by their reconstitution onto redox cofactors, such as hemin conjugated to self-assembled monolayers (SAMs) formed on the electrodes, poses the requirements for a SAM design enabling reconstitution. We show that the kinetics of electron transfer (ET) in binary SAMs of alkanethiols on gold composed of in situ hemin-conjugated 11-amino-1-undecanethiol (AUT) and diluting OH-terminated alkanethiols with 11, 6, and 2 methylene groups (MC11OH, MC6OH, and MC2OH) depends on both the SAM composition and surface density of hemin, Γheme. In AUT/MC11OH SAMs composed of equal linker/diluent lengths, the heterogeneous ET rate constant ks decreased with the Γheme and varied between 70 and 500 s-1. For shorter diluents, the ks of 245-330 s-1 (C6) and 300-340 s-1 (C2) showed a little (if any) Γheme dependence. In AUT/MC11OH SAMs, the increasing Γheme resulted in the steric crowding of hemin species and their neighboring lateral interactions in the plane of hemin localization, affecting the potential distribution at the SAM/electrode interface and inducing local electrostatic effects interfering with hemin oxidation. In AUT/MC6OH and AUT/MC2OH SAMs, hemin discharged at the plane of the closest approach to the gold surface, equal to the diluent length and permeable to electrolyte ions, which lessened those effects. All studied binary SAMs provided steric hindrance for protein reconstitution on the hemin cofactor conjugated to the extended AUT linker. Further use of SAM-modified electrodes with the covalently attached hemin as interfaces for heme proteins' reconstitution should consider SAMs with loosely dispersed redox centers terminating more rigid molecular wires. Such wires place hemin at fixed distances from the electrode surface and thus ensure the interfacial properties required for the effective on-surface reconstitution of proteins and enzymes.
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Affiliation(s)
- Maciej Sosna
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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5
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Gómez-Arconada L, Díaz-Fernández A, Ferapontova EE. Ultrasensitive disposable apatasensor for reagentless electrocatalytic detection of thrombin: An O2-Dependent hemin-G4-aptamer assay on gold screen-printed electrodes. Talanta 2022; 245:123456. [DOI: 10.1016/j.talanta.2022.123456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/25/2022]
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6
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Malecka K, Ferapontova EE. Femtomolar Detection of Thrombin in Serum and Cerebrospinal Fluid via Direct Electrocatalysis of Oxygen Reduction by the Covalent G4-Hemin-Aptamer Complex. ACS Appl Mater Interfaces 2021; 13:37979-37988. [PMID: 33878266 DOI: 10.1021/acsami.1c03784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Thrombin, a serine protease playing a central role in the coagulation cascade reactions and a potent neurotoxin produced by injured brain endothelial cells, is a recognized cardiac biomarker and a critical biomarker for Alzheimer's disease development. Both in vivo and in vitro, its low physiological concentrations and nonspecific binding of other components of physiological fluids complicate electroanalysis of thrombin. Here, femtomolar levels of thrombin in serum and an artificial cerebrospinal fluid (CSF) were detected by the indicator-free electrochemical methodology exploiting the O2 reduction reaction directly, with no electron transfer mediators, electrocatalyzed by the covalent G4-hemin DNAzyme complex naturally self-assembling upon thrombin binding to the hemin-modified 29-mer DNA aptamer sequence tethered to gold via an alkanethiol linker. Coadsorbed PEG inhibited nonspecific protein binding and allowed the sought signal resolution. The proposed assay exploiting the "oxidase" activity of G4-hemin DNAzyme does not require any coreactants necessary for the traditional peroxidase activity-based assays with this DNAzyme, such as H2O2 and redox mediators, or solution deaeration and allows fast, overall 30 min analysis of thrombin in aerated buffer, CSF, and 1% human serum solutions. This pioneer approach exploiting the oxidase activity G4-hemin DNAzyme is simple, sensitive, and selective and represents a new tool for ultrasensitive electrocatalytic assays based on simple and efficient O2-dependent DNAzyme labels.
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Affiliation(s)
- Kamila Malecka
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn 10-748, Poland
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
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7
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Mirbagheri N, Campos R, Ferapontova EE. Electrocatalytic Oxidation of Water by OH
−
‐ and H
2
O‐Capped IrO
x
Nanoparticles Electrophoretically Deposited on Graphite and Basal Plane HOPG: Effect of the Substrate Electrode**. ChemElectroChem 2021. [DOI: 10.1002/celc.202100317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Naghmehalsadat Mirbagheri
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
- Department of Microsystems Engineering – IMTEK University of Freiburg Georges-Koehler-Allee 103 79110 Freiburg Germany
| | - Rui Campos
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
- AXES research group and NANOlab Center of Excellence University of Antwerp Groenenborgerlaan 171 2020 Antwerpen Belgium
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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8
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Malecka K, Mikuła E, Ferapontova EE. Design Strategies for Electrochemical Aptasensors for Cancer Diagnostic Devices. Sensors (Basel) 2021; 21:s21030736. [PMID: 33499136 PMCID: PMC7866130 DOI: 10.3390/s21030736] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
Improved outcomes for many types of cancer achieved during recent years is due, among other factors, to the earlier detection of tumours and the greater availability of screening tests. With this, non-invasive, fast and accurate diagnostic devices for cancer diagnosis strongly improve the quality of healthcare by delivering screening results in the most cost-effective and safe way. Biosensors for cancer diagnostics exploiting aptamers offer several important advantages over traditional antibodies-based assays, such as the in-vitro aptamer production, their inexpensive and easy chemical synthesis and modification, and excellent thermal stability. On the other hand, electrochemical biosensing approaches allow sensitive, accurate and inexpensive way of sensing, due to the rapid detection with lower costs, smaller equipment size and lower power requirements. This review presents an up-to-date assessment of the recent design strategies and analytical performance of the electrochemical aptamer-based biosensors for cancer diagnosis and their future perspectives in cancer diagnostics.
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Affiliation(s)
- Kamila Malecka
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima Str. 10, 10-748 Olsztyn, Poland; (K.M.); (E.M.)
| | - Edyta Mikuła
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima Str. 10, 10-748 Olsztyn, Poland; (K.M.); (E.M.)
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- Correspondence: ; Tel.: +45-87156703
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9
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Jamal RB, Shipovskov S, Ferapontova EE. Electrochemical Immuno- and Aptamer-Based Assays for Bacteria: Pros and Cons over Traditional Detection Schemes. Sensors (Basel) 2020; 20:E5561. [PMID: 32998409 PMCID: PMC7582323 DOI: 10.3390/s20195561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 01/20/2023]
Abstract
Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria quantification at a single cell level. Here, we discuss the existing electrochemical approaches for bacterial analysis that are based on the biospecific recognition of whole bacterial cells. Perspectives of such assays applications as emergency-use biosensors for quick analysis of trace levels of bacteria by minimally trained personnel are argued.
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Affiliation(s)
| | | | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark; (R.B.J.); (S.S.)
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10
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Pankratov D, Bendixen M, Shipovskov S, Gosewinkel U, Ferapontova EE. Cellulase-Linked Immunomagnetic Microbial Assay on Electrodes: Specific and Sensitive Detection of a Single Bacterial Cell. Anal Chem 2020; 92:12451-12459. [PMID: 32799451 DOI: 10.1021/acs.analchem.0c02262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathogen-associated infections represent one of the major threats to human health and require reliable methods for immediate and robust identification of pathogenic microorganisms. Here, an inexpensive cellulase-linked immunomagnetic methodology was developed for the specific and ultrasensitive analysis of bacteria at their single-cell levels within a 3 h procedure. Detection of a model bacterium, Escherichia coli, was performed in a sandwich reaction with E. coli-specific either aptamer or antibody (Ab)-modified magnetic beads (MBs) and Ab/aptamer reporter molecules linked to cellulase. The cellulase-labeled immuno-aptamer sandwich applied onto nitrocellulose-film-modified electrodes digested the film and changed its electrical conductivity. Electrode's chronocoulometric responses at 0.3 V, in the absence of any redox indicators, allowed a single E. coli cell detection and from 1 to 4 × 104 CFU mL-1 E. coli quantification. No interference/cross-reactivity from Salmonella enteritidis, Enterobacter agglomerans, Pseudomonas putida, Staphylococcus aureus, and Bacillus subtilis was observed when the assay was performed on Ab-modified MBs, and E. coli could be quantified in tap water and milk. This electrochemically label-free methodology is sufficiently fast, highly specific, and sensitive to be used in direct in-field applications. The assay can be adapted for specific detection of other bacterial strains of either the same or different species and offers new analytical tools for fast, specific, and reliable analysis of bacteria in the clinic, food, and environment.
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Affiliation(s)
- Dmitrii Pankratov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| | - Mads Bendixen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| | - Stepan Shipovskov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C DK-8000, Denmark
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11
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Sosna M, Leiva‐Eriksson N, Bülow L, Ferapontova EE. Electrochemical Characterization and Bioelectrocatalytic H2O2Sensing of Non‐Symbiotic Hexa‐Coordinated Sugar Beet Hemoglobins. ChemElectroChem 2020. [DOI: 10.1002/celc.202000358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Maciej Sosna
- Interdisciplinary Nanoscience Center (iNANO) Science and TechnologyAarhus University Gustav Wieds Vej 1590-14 8000 Aarhus C Denmark
| | | | - Leif Bülow
- Lund University P.O. Box 124 221 00 Lund Sweden
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) Science and TechnologyAarhus University Gustav Wieds Vej 1590-14 8000 Aarhus C Denmark
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12
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Abstract
The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, 8000, Aarhus C, Denmark
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13
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Jensen UB, Mohammad‐Beigi H, Shipovskov S, Sutherland DS, Ferapontova EE. Activation of Cellobiose Dehydrogenase Bioelectrocatalysis by Carbon Nanoparticles. ChemElectroChem 2019. [DOI: 10.1002/celc.201901066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Uffe Bjørnholt Jensen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Hossein Mohammad‐Beigi
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Stepan Shipovskov
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Duncan S. Sutherland
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
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14
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Lopes P, Koschorreck K, Nedergaard Pedersen J, Ferapontov A, Lörcher S, Skov Pedersen J, Urlacher VB, Ferapontova EE. Bacillus Licheniformis
CotA Laccase Mutant: ElectrocatalyticReduction of O
2
from 0.6 V (SHE) at pH 8 and in Seawater. ChemElectroChem 2019. [DOI: 10.1002/celc.201900363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paula Lopes
- Interdisciplinary Nanoscience Center, iNANOAarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
- Current address: Gent University Zwijnaard 126 9052 Belgium
| | - Katja Koschorreck
- Institute of BiochemistryHeinrich-Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | | | | | - Samuel Lörcher
- Interdisciplinary Nanoscience Center, iNANOAarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
- Current address: Universitaet Basel 4056 Basel Switzerland
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center, iNANOAarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
- Department of ChemistryAarhus University 8000 Aarhus Denmark
| | - Vlada B. Urlacher
- Institute of BiochemistryHeinrich-Heine University Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center, iNANOAarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
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15
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Álvarez-Martos I, Møller A, Ferapontova EE. Dopamine Binding and Analysis in Undiluted Human Serum and Blood by the RNA-Aptamer Electrode. ACS Chem Neurosci 2019; 10:1706-1715. [PMID: 30605601 DOI: 10.1021/acschemneuro.8b00616] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Specific analysis of such neurotransmitters as dopamine by the aptamer electrodes in biological fluids is detrimentally affected by nonspecific adsorption of media, particularly pronounced at positive charges of the electrode surface at which dopamine oxidizes. Here, we show that dopamine analysis at the RNA-aptamer/cysteamine-modified electrodes is strongly inhibited in undiluted human serum and blood due to nonspecific interfacial adsorption of serum and blood components. We demonstrate that nonspecific adsorption of serum proteins (but not of blood components) could be minimized when analysis is performed in a flow and injections of serum samples are followed by washing steps in a phosphate buffer solution (PBS) carrier. Under those conditions, the dopamine-aptamer binding affinity in whole human serum of (1.9 ± 0.3) × 104 M-1 s-1 was comparable to the (3.7 ± 0.3) × 104 M-1 s-1 found in PBS, and the dopamine oxidation signal linearly depended on the dopamine concentration, providing a sensitivity of analysis of 73 ± 3 nA μM-1 cm-2 and a LOD of 114 ± 8 nM. The flow-injection apatmer-electrode system was used for direct analysis of basal levels of dopamine in undiluted human serum samples, without using any physical separators (membranes) or filtration procedures. The results suggest a simple strategy for combatting biosurface fouling, otherwise most pronounced at positive electrode potentials used for dopamine detection, and assist in designing more efficient antifouling strategies for biomedical applications.
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Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Arne Møller
- PET-Centre, Aarhus University Hospital, Aarhus, Denmark
- Center of Functionally Integrative Neuroscience, Aarhus University, Aarhus, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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16
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Kékedy‐Nagy L, Ferapontova EE. Directional Preference of DNA‐Mediated Electron Transfer in Gold‐Tethered DNA Duplexes: Is DNA a Molecular Rectifier? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- László Kékedy‐Nagy
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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Kékedy‐Nagy L, Ferapontova EE. Directional Preference of DNA‐Mediated Electron Transfer in Gold‐Tethered DNA Duplexes: Is DNA a Molecular Rectifier? Angew Chem Int Ed Engl 2019; 58:3048-3052. [DOI: 10.1002/anie.201809559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/26/2018] [Indexed: 12/20/2022]
Affiliation(s)
- László Kékedy‐Nagy
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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18
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Fapyane D, Nielsen JS, Ferapontova EE. Electrochemical Enzyme-Linked Sandwich Assay with a Cellulase Label for Ultrasensitive Analysis of Synthetic DNA and Cell-Isolated RNA. ACS Sens 2018; 3:2104-2111. [PMID: 30257555 DOI: 10.1021/acssensors.8b00662] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Electrochemical enzyme-linked sandwich assays on magnetic beads (MBs) refer to one of the most sensitive approaches for analysis of nonamplified nucleic acid samples, with redox enzymes being routinely used as labels. Here, we report a sensitive and inexpensive electrochemical nucleic acid sandwich assay on MBs that exploits a hydrolytic enzyme cellulase as a label, while MBs are used for preconcentration and bioseparation of analyzed samples. Binding of target DNA or RNA to capture DNA-modified MB triggers sandwich assembly and its labeling with cellulase. Application of the assembled sandwich to the electrodes covered with insulating nitrocellulose films induces film digestion by the cellulase label and pronounced changes in the electrical properties of the electrodes, the extent of the changes being proportional to the concentration of the analyzed nucleic acids. Down to 1 amol of Lactobacillus brevis specific synthetic DNA and rRNA isolated from L. brevis cells could be detected in 1 mL samples in the overall from 2 to 3 h assay. The assay is universal and can be adapted for point-of-care-testing and for in-field environmental and microbiomic analysis of unamplified samples of any DNA/RNA sequences.
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Affiliation(s)
- Deby Fapyane
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jesper S. Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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19
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Kékedy-Nagy L, Ferapontova EE. Sequence-Specific Electron Transfer Mediated by DNA Duplexes Attached to Gold through the Alkanethiol Linker. J Phys Chem B 2018; 122:10077-10085. [DOI: 10.1021/acs.jpcb.8b07505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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20
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Kékedy-Nagy L, Sørensen KD, Ferapontova EE. Picomolar sensitive and SNP-selective “Off-On” hairpin genosensor based on structure-tunable redox indicator signals. Biosens Bioelectron 2018; 117:444-449. [DOI: 10.1016/j.bios.2018.06.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/10/2023]
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21
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Campos R, Kékedy-Nagy L, She Z, Sodhi R, Kraatz HB, Ferapontova EE. Electron Transfer in Spacer-Free DNA Duplexes Tethered to Gold via dA 10 Tags. Langmuir 2018; 34:8472-8479. [PMID: 29936843 DOI: 10.1021/acs.langmuir.8b01412] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Electrical properties of DNA critically depend on the way DNA molecules are integrated within the electronics, particularly on DNA-electrode immobilization strategies. Here, we show that the rate of electron transport in DNA duplexes spacer-free tethered to gold via the adenosine terminal region (a dA10 tag) is enhanced compared to the hitherto reported DNA-metal electrode tethering chemistries. The rate of DNA-mediated electron transfer (ET) between the electrode and methylene blue intercalated into the dA10-tagged DNA duplex approached 361 s-1 at a ca. half-monolayer DNA surface coverage ΓDNA (with a linear regression limit of 670 s-1 at ΓDNA → 0), being 2.7-fold enhanced compared to phosphorothioated dA5* tethering (6-fold for the C6-alkanethiol linker representing an additional ET barrier). X-ray photoelectron spectroscopy evidenced dA10 binding to the Au surface via the purine N, whereas dA5* predominantly coordinated to the surface via sulfur atoms of phosphothioates. The latter apparently induces the DNA strand twist in the point of surface attachment affecting the local DNA conformation and, as a result, decreasing the ET rates through the duplex. Thus, a spacer-free DNA coupling to electrodes via dA10 tags thus allows a perspective design of DNA electronic circuits and sensors with advanced electronic properties and no implication from more expensive, synthetic linkers.
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Affiliation(s)
- Rui Campos
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Zhe She
- Department of Physical and Environmental Sciences, 1095 Military Trail , University of Toronto Scarborough , Toronto , Ontario M1C 1A4 , Canada
| | - Rana Sodhi
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , Toronto , Ontario M5S 3E5 , Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, 1095 Military Trail , University of Toronto Scarborough , Toronto , Ontario M1C 1A4 , Canada
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , Toronto , Ontario M5S 3E5 , Canada
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
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22
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Abstract
Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark;
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23
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Álvarez-Martos I, Ferapontova EE. Electrocatalytic Discrimination between Dopamine and Norepinephrine at Graphite and Basal Plane HOPG Electrodes. ELECTROANAL 2018. [DOI: 10.1002/elan.201700837] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
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24
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Álvarez-Martos I, Ferapontova EE. “Negative electrocatalysis”-based specific analysis of dopamine at basal plane HOPG in the presence of structurally related catecholamines. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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25
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Fapyane D, Kékedy-Nagy L, Sakharov IY, Ferapontova EE. Electrochemistry and electrocatalysis of covalent hemin-G4 complexes on gold. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2017.11.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Álvarez-Martos I, Ferapontova EE. A DNA sequence obtained by replacement of the dopamine RNA aptamer bases is not an aptamer. Biochem Biophys Res Commun 2017; 489:381-385. [PMID: 28576492 DOI: 10.1016/j.bbrc.2017.05.134] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
A unique specificity of the aptamer-ligand biorecognition and binding facilitates bioanalysis and biosensor development, contributing to discrimination of structurally related molecules, such as dopamine and other catecholamine neurotransmitters. The aptamer sequence capable of specific binding of dopamine is a 57 nucleotides long RNA sequence reported in 1997 (Biochemistry, 1997, 36, 9726). Later, it was suggested that the DNA homologue of the RNA aptamer retains the specificity of dopamine binding (Biochem. Biophys. Res. Commun., 2009, 388, 732). Here, we show that the DNA sequence obtained by the replacement of the RNA aptamer bases for their DNA analogues is not able of specific biorecognition of dopamine, in contrast to the original RNA aptamer sequence. This DNA sequence binds dopamine and structurally related catecholamine neurotransmitters non-specifically, as any DNA sequence, and, thus, is not an aptamer and cannot be used neither for in vivo nor in situ analysis of dopamine in the presence of structurally related neurotransmitters.
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Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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29
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Salimian R, Kékedy-Nagy L, Ferapontova EE. Specific Picomolar Detection of a Breast Cancer Biomarker HER-2/neu
Protein in Serum: Electrocatalytically Amplified Electroanalysis by the Aptamer/PEG-Modified Electrode. ChemElectroChem 2017. [DOI: 10.1002/celc.201700025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Razieh Salimian
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Center for DNA Nanotechnology (CDNA) at iNANO
- Sharif University of Technology; Teheran Iran
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Center for DNA Nanotechnology (CDNA) at iNANO
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Science and Technology; Aarhus University; Gustav Wieds Vej 14 8000 Aarhus C Denmark
- Center for DNA Nanotechnology (CDNA) at iNANO
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30
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Abstract
Electrochemical methods allow fast and inexpensive analysis of enzymatic activities. Here, we report a simple and yet efficient electrochemical assay for the total activity of cellulase, a hydrolytic enzyme widely used in food and textiles industries, and for production of bioethanol. The assay exploits the difference in electrochemical signals from a soluble redox indicator, ferricyanide, on nitrocellulose films treated by cellulases. Ferricyanide electrochemistry is totally inhibited on graphite electrodes modified with an insulating nitrocellulose film and is evoked after the cellulase treatment. Ferricyanide voltammetric responses correlate with the increased permeability of the films and electrochemically active surface area of electrodes becoming accessible to the ferricyanide reaction after nitrocellulose digestion by cellulase. Trichoderma and Aspergillus niger cellulases activities were determined in a 5 min assay with a sensitivity of 10-8 U per assay, being 103-104-fold more sensitive than the standard commercially available optical assays. That makes the developed electrochemical approach the most prospective cost-effective alternative both for research and automated industrial applications.
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Affiliation(s)
- Deby Fapyane
- Interdisciplinary Nanoscience Center, Faculty of Science and Technology, Aarhus University , Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center, Faculty of Science and Technology, Aarhus University , Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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31
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Kékedy-Nagy L, Ferapontova EE, Brand I. Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials. J Phys Chem B 2017; 121:1552-1565. [PMID: 28177253 DOI: 10.1021/acs.jpcb.6b12363] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT)25 or cytosine-guanine (dGdC)20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C6 alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT)25 molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC)20 helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.
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Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus-C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus-C, Denmark
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg , 26111 Oldenburg, Germany
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32
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Ostatná V, Kasalová-Vargová V, Kékedy-Nagy L, Černocká H, Ferapontova EE. Chronopotentiometric sensing of specific interactions between lysozyme and the DNA aptamer. Bioelectrochemistry 2016; 114:42-47. [PMID: 28063413 DOI: 10.1016/j.bioelechem.2016.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 01/08/2023]
Abstract
Specific DNA-protein interactions are vital for cellular life maintenance processes, such as transcriptional regulation, chromosome maintenance, replication and DNA repair, and their monitoring gives valuable information on molecular-level organization of those processes. Here, we propose a new method of label-free electrochemical sensing of sequence specific binding between the lysozyme protein and a single stranded DNA aptamer specific for lysozyme (DNAapta) that exploits the constant current chronopotentiometric stripping (CPS) analysis at modified mercury electrodes. Specific lysozyme-DNAapta binding was distinguished from nonspecific lysozyme-DNA interactions at thioglycolic acid-modified mercury electrodes, but not at the dithiothreitol-modified or bare mercury electrodes. Stability of the surface-attached lysozyme-DNAapta layer depended on the stripping current (Istr) intensity, suggesting that the integrity of the layer critically depends on the time of its exposure to negative potentials. Stabilities of different lysozyme-DNA complexes at the negatively polarized electrode surface were tested, and it was shown that structural transitions of the specific lysozyme-DNAapta complexes occur in the Istr ranges different from those observed for assemblies of lysozyme with DNA sequences capable of only nonspecific lysozyme-DNA interactions. Thus, the CPS allows distinct discrimination between specific and non-specific protein-DNA binding and provides valuable information on stability of the nucleic acid-protein interactions at the polarized interfaces.
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Affiliation(s)
- Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic.
| | - Veronika Kasalová-Vargová
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University, Gustav Wieds Vej 14, DK 8000 Aarhus-C, Denmark
| | - Hana Černocká
- Institute of Biophysics, The Czech Academy of Science, v.v.i., Královopolská 135, 61265 Brno, Czech Republic
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University, Gustav Wieds Vej 14, DK 8000 Aarhus-C, Denmark
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33
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Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
| | - Andrey Kartashov
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO); Aarhus University; Gustav Wieds Vej 14 DK-8000 Aarhus C Denmark
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34
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Affiliation(s)
- Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO); Center for DNA Nanotechnology (CDNA); Aarhus University; Gustav Wieds Vej 1590-14 DK-8000 Aarhus C Denmark
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35
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Fapyane D, Ferapontova EE. Enhanced electron transfer between gold nanoparticles and horseradish peroxidase reconstituted onto alkanethiol-modified hemin. Electrochem commun 2016. [DOI: 10.1016/j.elecom.2016.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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36
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Shipovskov S, Bonamore A, Boffi A, Ferapontova EE. Electrocatalytic interconversion of NADH and NAD(+) by Escherichia coli flavohemoglobin. Chem Commun (Camb) 2016; 51:16096-8. [PMID: 26389555 DOI: 10.1039/c5cc06317e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
E. coli flavohemoglobin, oriented at electrodes via amphiphilic polymyxin B, electrocatalytically interconverts NADH and NAD(+) at its heme potentials operating as an electron transfer relay between the electrode and the protein FAD, where NADH/NAD(+) is transformed. The results are crucial for the development of NAD(+)-dependent bioelectrodes for biosynthesis, biosensors and biofuel cells.
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Affiliation(s)
- S Shipovskov
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - A Bonamore
- Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University "La Sapienza", 00185 Rome, Italy
| | - A Boffi
- Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University "La Sapienza", 00185 Rome, Italy
| | - E E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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37
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Kékedy-Nagy L, Shipovskov S, Ferapontova EE. Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes. Anal Chem 2016; 88:7984-90. [DOI: 10.1021/acs.analchem.6b01020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary
Nanoscience Center, and ‡Center for DNA Nanotechnology at
iNANO, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
| | - Stepan Shipovskov
- Interdisciplinary
Nanoscience Center, and ‡Center for DNA Nanotechnology at
iNANO, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary
Nanoscience Center, and ‡Center for DNA Nanotechnology at
iNANO, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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38
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Castaing V, Álvarez-Martos I, Ferapontova EE. Wiring of Glucose Oxidizing Flavin Adenine Dinucleotide-Dependent Enzymes by Methylene Blue-Modified Third Generation Poly(amidoamine) Dendrimers Attached to Spectroscopic Graphite Electrodes. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.01.217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Álvarez-Martos I, Ferapontova EE. Electrochemical Label-Free Aptasensor for Specific Analysis of Dopamine in Serum in the Presence of Structurally Related Neurotransmitters. Anal Chem 2016; 88:3608-16. [PMID: 26916821 DOI: 10.1021/acs.analchem.5b04207] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cellular and brain metabolism of dopamine can be correlated with a number of neurodegenerative disorders, and as such, in vivo analysis of dopamine in the presence of structurally related neurotransmitters (NT) represents a holy grail of neuroscience. Interference from those NTs generally does not allow selective electroanalysis of dopamine, which redox transformation overlaps with those of other catecholamines. In our previous work, we reported an electrochemical RNA-aptamer-based biosensor for specific analysis of dopamine (Analytical Chemistry, 2013; Vol. 85, p 121). However, the overall design of the biosensor restricted its stability and impeded its operation in serum. Here, we show that specific biorecognition and electroanalysis of dopamine in serum can be performed by the RNA aptamer tethered to cysteamine-modified gold electrodes via the alkanethiol linker. The stabilized dopamine aptasensor allowed continuous 20 h amperometric analysis of dopamine in 10% serum within the physiologically important 0.1-1 μM range and in the presence of catechol and such dopamine precursors and metabolites as norepinephrine and l-DOPA. In a flow-injection mode, the aptasensor response to dopamine was ∼1 s, the sensitivity of analysis, optimized by adjusting the aptamer surface coverage, was 67 ± 1 nA μM(-1) cm(-2), and the dopamine LOD was 62 nM. The proposed design of the aptasensor, exploiting both the aptamer alkanethiol tethering to the electrode and screening of the catecholamine-aptamer electrostatic interactions, allows direct monitoring of dopamine levels in biological fluids in the presence of competitive NT and thus may be further applicable in biomedical research.
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Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO) and ‡Danish National Research Foundation: Center for DNA Nanotechnology (CDNA), Aarhus University , Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and ‡Danish National Research Foundation: Center for DNA Nanotechnology (CDNA), Aarhus University , Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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Jarczewska M, Kékedy-Nagy L, Nielsen JS, Campos R, Kjems J, Malinowska E, Ferapontova EE. Electroanalysis of pM-levels of urokinase plasminogen activator in serum by phosphorothioated RNA aptamer. Analyst 2016; 140:3794-802. [PMID: 25620243 DOI: 10.1039/c4an02354d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein biomarkers of cancer allow a dramatic improvement in cancer diagnostics as compared to the traditional histological characterisation of tumours by enabling a non-invasive analysis of cancer development and treatment. Here, an electrochemical label-free assay for urokinase plasminogen activator (uPA), a universal biomarker of several cancers, has been developed based on the recently selected uPA-specific fluorinated RNA aptamer, tethered to a gold electrode via a phosphorothioated dA tag, and soluble redox indicators. The binding properties of the uPA-aptamer couple and interference from the non-specific adsorption of bovine serum albumin (BSA) were modulated by the electrode surface charge. A nM uPA electroanalysis at positively charged surfaces, complicated by the competitive adsorption of BSA, was tuned to the pM uPA analysis at negative surface charges of the electrode, being improved in the presence of negatively charged BSA. The aptamer affinity for uPA displayed via the binding/dissociation constant relationship correspondingly increased, ca. three orders of magnitude, from 0.441 to 367. Under optimal conditions, the aptasensor allowed 10(-12)-10(-9) M uPA analysis, also in serum, being practically useful for clinical applications. The proposed strategy for optimization of the electrochemical protein sensing is of particular importance for the assessment and optimization of in vivo protein ligand binding by surface-tethered aptamers.
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Affiliation(s)
- Marta Jarczewska
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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41
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Farjami E, Campos R, Ferapontova EE. Correction to "Effect of the DNA End of Tethering to Electrodes on Electron Transfer in Methylene Blue-Labeled DNA Duplexes". Langmuir 2016; 32:928. [PMID: 26756700 DOI: 10.1021/acs.langmuir.5b03487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Álvarez-Martos I, Campos R, Ferapontova EE. Surface state of the dopamine RNA aptamer affects specific recognition and binding of dopamine by the aptamer-modified electrodes. Analyst 2015; 140:4089-96. [PMID: 25882962 DOI: 10.1039/c5an00480b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Specific monitoring of dopamine, in the presence of structurally related neurotransmitters, is critical for diagnosis, treatment and mechanistic understanding of a variety of human neuropathologies, but nevertheless the proper tools are scarce. Recently, an electrochemical aptasensor for specific analysis of dopamine, exploiting dopamine biorecognition by the RNA aptamer electrostatically adsorbed onto a cysteamine-modified electrode, has been reported (Analytical Chemistry 85 (2013) 121). However it was not clear which way dopamine biorecognition and binding by such aptamer layers proceed and if they can be improved. Here, we show that the aptamer surface state, in particular the aptamer surface density, in a bell-shaped manner affects the dopamine binding, being maximal for the 3.5 ± 0.3 pmol cm(-2) monolayer coverage of the aptamer molecules lying flat on the surface. Therewith, the aptamer affinity for dopamine increases one order of magnitude due to electrostatically regulated immobilization, with the aptamer-dopamine dissociation constant of 0.12 ± 0.01 μM versus 1.6 ± 0.17 μM shown in solution. Under optimal conditions, 0.1-2 μM dopamine was specifically and 85.4 nA μM(-1) cm(-2) sensitively detected, with no interference from structurally related catecholamines. The results allow improvement of the robustness of dopamine monitoring by aptamer-modified electrodes in biological systems, within the 0.01-1 μM dopamine fluctuation range.
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Affiliation(s)
- Isabel Álvarez-Martos
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark.
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Fapyane D, Kartashov A, von Wachenfeldt C, Ferapontova EE. Gated electron transfer reactions of truncated hemoglobin from Bacillus subtilis differently orientated on SAM-modified electrodes. Phys Chem Chem Phys 2015; 17:15365-74. [DOI: 10.1039/c5cp00960j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Electron transfer in truncated hemoglobin depends on the SAMs it is attached to demonstrating a new type of electronic responsivity.
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Affiliation(s)
- Deby Fapyane
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Andrey Kartashov
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | | | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- DK-8000 Aarhus C
- Denmark
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44
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Lopes P, Ferapontova EE. Electrochemical analysis Aβ42 peptide adsorption and aggregation on spectroscopic graphite. Monatsh Chem 2014. [DOI: 10.1007/s00706-014-1362-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Campos R, Kotlyar A, Ferapontova EE. DNA-mediated electron transfer in DNA duplexes tethered to gold electrodes via phosphorothioated dA tags. Langmuir 2014; 30:11853-11857. [PMID: 25267302 DOI: 10.1021/la502766g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The efficiency of DNA-based bioelectronic devices strongly depends on the way DNA molecules are linked to the electronic component. Commonly, DNA is tethered to metal electrodes via an alkanethiol linker representing an additional barrier for electron transport. Here we demonstrate that the replacement of the alkanethiol linker for a phosphorothioated adenosine tag increases the rate of DNA-mediated electron transfer (ET) up to 259 s(-1), representing the highest hitherto reported rate of electrochemically-modulated ET, and improves the stability of DNA-electrode surface binding. Both results offer pronounced technological and scientific benefits for DNA-based electronics.
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Affiliation(s)
- Rui Campos
- Interdisciplinary Nanoscience Center (iNANO) and ‡Center for DNA Nanotechnology (CDNA) at iNANO, Science and Technology, Aarhus University , Gustav Wieds Vej 14, 8000 Aarhus, Denmark
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Sosna M, Fapyane D, Ferapontova EE. Reconstitution of peroxidase onto hemin-terminated alkanethiol self-assembled monolayers on gold. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2014.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Lopes P, Xu M, Zhang M, Zhou T, Yang Y, Wang C, Ferapontova EE. Direct electrochemical and AFM detection of amyloid-β peptide aggregation on basal plane HOPG. Nanoscale 2014; 6:7853-7857. [PMID: 24934601 DOI: 10.1039/c4nr02413c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Amyloidogenesis is associated with more than 30 human diseases, including Alzheimer's which is related to aggregation of β-amyloid peptide (Aβ). Here, consecutive stages of Aβ42 aggregation and amyloid fibril formation were followed electrochemically via oxidation of tyrosines in Aβ42 adsorbed on the basal plane graphite electrode and directly correlated with Aβ42 morphological changes observed by atomic force microscopy of the same substrate. The results offer new tools for analysis of mechanisms of Aβ aggregation.
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Affiliation(s)
- Paula Lopes
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000, Aarhus C, Denmark.
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Mirbagheri N, Chevallier J, Kibsgaard J, Besenbacher F, Ferapontova EE. Electrocatalysis of Water Oxidation by H2O-Capped Iridium-Oxide Nanoparticles Electrodeposited on Spectroscopic Graphite. Chemphyschem 2014; 15:2844-50. [DOI: 10.1002/cphc.201402079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Indexed: 11/10/2022]
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49
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Abi A, Lin M, Pei H, Fan C, Ferapontova EE, Zuo X. Electrochemical switching with 3D DNA tetrahedral nanostructures self-assembled at gold electrodes. ACS Appl Mater Interfaces 2014; 6:8928-8931. [PMID: 24802004 DOI: 10.1021/am501823q] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanomechanical switching of functional three-dimensional (3D) DNA nanostructures is crucial for nanobiotechnological applications such as nanorobotics or self-regulating sensor and actuator devices. Here, DNA tetrahedral nanostructures self-assembled onto gold electrodes were shown to undergo the electronically addressable nanoswitching due to their mechanical reconfiguration upon external chemical stimuli. That enables construction of robust surface-tethered electronic nanodevices based on 3D DNA tetrahedra. One edge of the tetrahedron contained a partially self-complementary region with a stem-loop hairpin structure, reconfigurable upon hybridization to a complementary DNA (stimulus DNA) sequence. A non-intercalative ferrocene (Fc) redox label was attached to the reconfigurable tetrahedron edge in such a way that reconfiguration of this edge changed the distance between the electrode and Fc.
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Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, ‡Center for DNA Nanotechnology (CDNA) at iNANO, and §Sino-Danish Centre for Education and Research (SDC) at iNANO, Aarhus University , Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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50
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Mirbagheri N, Wang D, Peng C, Wang J, Huang Q, Fan C, Ferapontova EE. Visible Light Driven Photoelectrochemical Water Oxidation by Zn- and Ti-Doped Hematite Nanostructures. ACS Catal 2014. [DOI: 10.1021/cs500372v] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Degao Wang
- Division
of Physical Biology, Bioimaging Center, Shanghai Synchrotron Radiation
Facility, CAS Key Laboratory of Interfacial Physics and Technology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Cheng Peng
- Division
of Physical Biology, Bioimaging Center, Shanghai Synchrotron Radiation
Facility, CAS Key Laboratory of Interfacial Physics and Technology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jianqiang Wang
- Division
of Physical Biology, Bioimaging Center, Shanghai Synchrotron Radiation
Facility, CAS Key Laboratory of Interfacial Physics and Technology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division
of Physical Biology, Bioimaging Center, Shanghai Synchrotron Radiation
Facility, CAS Key Laboratory of Interfacial Physics and Technology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division
of Physical Biology, Bioimaging Center, Shanghai Synchrotron Radiation
Facility, CAS Key Laboratory of Interfacial Physics and Technology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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