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Ahmed N, Al-Madhagi S, Ortiz M, O'Sullivan CK, Katakis I. Direct electrochemical detection of enzyme labelled, isothermally amplified DNA. Anal Biochem 2020; 598:113705. [PMID: 32246925 DOI: 10.1016/j.ab.2020.113705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
Abstract
Genosensors for the detection of DNA via hybridisation normally require post-amplification processing such as the generation of single-stranded DNA and pre-detection labelling, complicating and lengthening the assay. A straightforward electrochemical genosensor, for the direct detection of isothermally generated nucleic acid amplicons via hybridisation is reported. The detection of Karlodinium armiger, responsible for harmful algae blooms was used as a model system to demonstrate the proof of concept. The approach exploits the use of specifically modified primers designed to generate amplicons with a central duplex flanked by a single-stranded tail at one end of the duplex and a horse-radish peroxidase on the other end. Individual gold electrodes of an array were functionalised with self-assembled monolayers of short thiolated DNA probes, designed to hybridise with the single-stranded tailed amplicon with the reporter enzyme label incorporated. The optimum amplification time was determined to be 60 min, at a fixed temperature of 37 °C. The hybridisation time to the enzyme labelled amplicon was optimised to be 10 min, but 2 min hybridisation time was also adequate. In this first example of using horse radish peroxidase-labelled primer in solution-phase recombinase polymerase amplification for subsequent detection via solid-phase hybridisation, the detection limit achieved was 0.4 fM, equivalent to 27622 cells/L, and the developed genosensor was applied to the detection of synthetic as well as genomic DNA, which had been extracted from a seawater sample.
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Affiliation(s)
- Nihad Ahmed
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain
| | - Sallam Al-Madhagi
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain
| | - Mayreli Ortiz
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain
| | - Ciara K O'Sullivan
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain; ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
| | - Ioanis Katakis
- Interfibio Consolidated Research Group, Department of Chemical Engineering, Universitat Rovira I Virgili, Avinguda Països Catalans 26, 43007, Tarragona, Spain
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Magriñá I, Toldrà A, Campàs M, Ortiz M, Simonova A, Katakis I, Hocek M, O'Sullivan CK. Electrochemical genosensor for the direct detection of tailed PCR amplicons incorporating ferrocene labelled dATP. Biosens Bioelectron 2019; 134:76-82. [PMID: 30954929 DOI: 10.1016/j.bios.2019.03.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 01/09/2023]
Abstract
An electrochemical genosensor for the detection and quantification of Karlodinium armiger is presented. The genosensor exploits tailed primers and ferrocene labelled dATP analogue to produce PCR products that can be directly hybridised on a gold electrode array and quantitatively measured using square wave voltammetry. Tailed primers consist of a sequence specific for the target, followed by a carbon spacer and a sequence specifically designed not to bind to genomic DNA, resulting in a duplex flanked by single stranded binding primers. The incorporation of the 7-(ferrocenylethynyl)-7-deaza-2'-deoxyadenosine triphosphate was optimised in terms of a compromise between maximum PCR efficiency and the limit of detection and sensitivity attainable using electrochemical detection via hybridisation of the tailed, ferrocene labelled PCR product. A limit of detection of 277aM with a linear range from 315aM to 10 fM starting DNA concentration and a sensitivity of 122 nA decade-1 was achieved. The system was successfully applied to the detection of genomic DNA in real seawater samples.
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Affiliation(s)
- Ivan Magriñá
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Anna Toldrà
- IRTA, Ctra. Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - Mònica Campàs
- IRTA, Ctra. Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - Mayreli Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610, Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| | - Ioanis Katakis
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610, Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic.
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010, Barcelona, Spain.
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Krock B, Busch JA, Tillmann U, García-Camacho F, Sánchez-Mirón A, Gallardo-Rodríguez JJ, López-Rosales L, Andree KB, Fernández-Tejedor M, Witt M, Cembella AD, Place AR. LC-MS/MS Detection of Karlotoxins Reveals New Variants in Strains of the Marine Dinoflagellate Karlodinium veneficum from the Ebro Delta (NW Mediterranean). Mar Drugs 2017; 15:md15120391. [PMID: 29258236 PMCID: PMC5742851 DOI: 10.3390/md15120391] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/10/2017] [Accepted: 12/07/2017] [Indexed: 11/16/2022] Open
Abstract
A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the detection and quantitation of karlotoxins in the selected reaction monitoring (SRM) mode. This novel method was based upon the analysis of purified karlotoxins (KcTx-1, KmTx-2, 44-oxo-KmTx-2, KmTx-5), one amphidinol (AM-18), and unpurified extracts of bulk cultures of the marine dinoflagellate Karlodinium veneficum strain CCMP2936 from Delaware (Eastern USA), which produces KmTx-1 and KmTx-3. The limit of detection of the SRM method for KmTx-2 was determined as 2.5 ng on-column. Collision induced dissociation (CID) spectra of all putative karlotoxins were recorded to present fragmentation patterns of each compound for their unambiguous identification. Bulk cultures of K. veneficum strain K10 isolated from an embayment of the Ebro Delta, NW Mediterranean, yielded five previously unreported putative karlotoxins with molecular masses 1280, 1298, 1332, 1356, and 1400 Da, and similar fragments to KmTx-5. Analysis of several isolates of K. veneficum from the Ebro Delta revealed small-scale diversity in the karlotoxin spectrum in that one isolate from Fangar Bay produced KmTx-5, whereas the five putative novel karlotoxins were found among several isolates from nearby, but hydrographically distinct Alfacs Bay. Application of this LC-MS/MS method represents an incremental advance in the determination of putative karlotoxins, particularly in the absence of a complete spectrum of purified analytical standards of known specific potency.
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Affiliation(s)
- Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Chemische Ökologie, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Julia A Busch
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Chemische Ökologie, Am Handelshafen 12, 27570 Bremerhaven, Germany.
- Common Wadden Sea Secretariat, Virchowstr. 1, 26382 Wilhelmshaven, Germany.
| | - Urban Tillmann
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Chemische Ökologie, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | | | | | - Juan J Gallardo-Rodríguez
- Department of Chemical Engineering, Faculty of Engineering, University of Concepción, Concepción 4030000, Chile.
| | | | - Karl B Andree
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Ctra Poble Nou km 5.5, 43540 Sant Carles de la Rapita, Tarragona, Spain.
| | - Margarita Fernández-Tejedor
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Ctra Poble Nou km 5.5, 43540 Sant Carles de la Rapita, Tarragona, Spain.
| | - Matthias Witt
- Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany.
| | - Allan D Cembella
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Chemische Ökologie, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Allen R Place
- Institute of Marine and Environmental Technology, UMCES, Baltimore, MD 21613, USA.
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Busch JA, Andree KB, Diogène J, Fernández-Tejedor M, Toebe K, John U, Krock B, Tillmann U, Cembella AD. Toxigenic algae and associated phycotoxins in two coastal embayments in the Ebro Delta (NW Mediterranean). HARMFUL ALGAE 2016; 55:191-201. [PMID: 28073532 DOI: 10.1016/j.hal.2016.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 06/06/2023]
Abstract
Harmful Algal Bloom (HAB) surveillance is complicated by high diversity of species and associated phycotoxins. Such species-level information on taxonomic affiliations and on cell abundance and toxin content is, however, crucial for effective monitoring, especially of aquaculture and fisheries areas. The aim addressed in this study was to determine putative HAB taxa and related phycotoxins in plankton from aquaculture sites in the Ebro Delta, NW Mediterranean. The comparative geographical distribution of potentially harmful plankton taxa was established by weekly field sampling throughout the water column during late spring-early summer over two years at key stations in Alfacs and Fangar embayments within the Ebro Delta. Core results included not only confirmed identification of HAB taxa that are common for the time period and geographical area, but also provided evidence of potentially new taxa. At least 25 HAB taxa were identified to species level, and an additional six genera were confirmed, by morphological criteria under light microscopy and/or by molecular genetics approaches involving qPCR and next generation DNA pyrosequencing. In particular, new insights were gained by the inclusion of molecular techniques, which focused attention on the HAB genera Alexandrium, Karlodinium, and Pseudo-nitzschia. Noteworthy is the discovery of Azadinium sp., a potentially new HAB species for this area, and Gymnodinium catenatum or Gymnodinium impudicum by means of light microscopy. In addition, significant amounts of the neurotoxin domoic acid (DA) were found for the first time in phytoplankton samples in the Ebro Delta. While the presence of the known DA-producing diatom genus Pseudo-nitzschia was confirmed in corresponding samples, the maximal toxin concentration did not coincide with highest cell abundances of the genus and the responsible species could not be identified. Combined findings of microscopic and molecular detection approaches underline the need for a synoptic strategy for HAB monitoring, which integrates the respective advantages and compensates for limitations of individual methods.
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Affiliation(s)
- Julia A Busch
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, 26111 Oldenburg, Germany; Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany.
| | - Karl B Andree
- IRTA, Ctra Poble Nou km 5,5, 43540 Sant Carles de la Rapita, Tarragona, Spain.
| | - Jorge Diogène
- IRTA, Ctra Poble Nou km 5,5, 43540 Sant Carles de la Rapita, Tarragona, Spain.
| | | | - Kerstin Toebe
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany.
| | - Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany.
| | - Bernd Krock
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany.
| | - Urban Tillmann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany.
| | - Allan D Cembella
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany.
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