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Gutiérrez-Gálvez L, García-Fernández D, Barrio MD, Luna M, Torres Í, Zamora F, Navío C, Milán-Rois P, Castellanos M, Abreu M, Cantón R, Galán JC, Somoza Á, Miranda R, García-Mendiola T, Lorenzo E. Free PCR virus detection via few-layer bismuthene and tetrahedral DNA nanostructured assemblies. Talanta 2024; 269:125405. [PMID: 37984235 DOI: 10.1016/j.talanta.2023.125405] [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: 09/07/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 11/22/2023]
Abstract
In this work we describe a highly sensitive method based on a biocatalyzed electrochemiluminescence approach. The system combines, for the first time, the use of few-layer bismuthene (FLB) as a platform for the oriented immobilization of tetrahedral DNA nanostructures (TDNs) specifically designed and synthetized to detect a specific SARS-CoV-2 gene sequence. In one of its vertices, these TDNs contain a DNA capture probe of the open reading frame 1 ab (ORF1ab) of the virus, available for the biorecognition of the target DNA/RNA. At the other three vertices, there are thiol groups that enable the stable anchoring/binding to the FLB surface. This novel geometry/approach enables not only the binding of the TDNs to surfaces, but also the orientation of the capture probe in a direction normal to the bismuthine surface so that it is readily accessible for binding/recognition of the specific SARS-CoV-2 sequence. The analytical signal is based on the anodic electrochemiluminescence (ECL) intensity of luminol which, in turn, arises as a result of the reaction with H2O2, generated by the enzymatic reaction of glucose oxidation, catalyzed by the biocatalytic label avidin-glucose oxidase conjugate (Av-GOx), which acts as co-reactant in the electrochemiluminescent reaction. The method exhibits a limit of detection (LOD) of 4.31 aM and a wide linear range from 14.4 aM to 1.00 μM, and its applicability was confirmed by detecting SARS-CoV-2 in nasopharyngeal samples from COVID-19 patients without the need of any amplification process.
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Affiliation(s)
- Laura Gutiérrez-Gálvez
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid (UAM), 28049, Madrid, Spain
| | - Daniel García-Fernández
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid (UAM), 28049, Madrid, Spain
| | - Melisa Del Barrio
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid (UAM), 28049, Madrid, Spain
| | - Mónica Luna
- Instituto de Micro y Nanotecnología IMN-CNM, CSIC (CEI UAM+CSIC), 28760, Tres Cantos, Madrid, Spain
| | - Íñigo Torres
- Departamento de Química Inorgánica and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Félix Zamora
- Departamento de Química Inorgánica and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Cristina Navío
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Paula Milán-Rois
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | | | - Melanie Abreu
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Rafael Cantón
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Álvaro Somoza
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Rodolfo Miranda
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Tania García-Mendiola
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid (UAM), 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Encarnación Lorenzo
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid (UAM), 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain; IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
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Fasano A, Guendon C, Jacq-Bailly A, Kpebe A, Wozniak J, Baffert C, Barrio MD, Fourmond V, Brugna M, Léger C. A Chimeric NiFe Hydrogenase Heterodimer to Assess the Role of the Electron Transfer Chain in Tuning the Enzyme's Catalytic Bias and Oxygen Tolerance. J Am Chem Soc 2023; 145:20021-20030. [PMID: 37657413 DOI: 10.1021/jacs.3c06895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
The observation that some homologous enzymes have the same active site but very different catalytic properties demonstrates the importance of long-range effects in enzyme catalysis, but these effects are often difficult to rationalize. The NiFe hydrogenases 1 and 2 (Hyd 1 and Hyd 2) from E. coli both consist of a large catalytic subunit that embeds the same dinuclear active site and a small electron-transfer subunit with a chain of three FeS clusters. Hyd 1 is mostly active in H2 oxidation and resistant to inhibitors, whereas Hyd 2 also catalyzes H2 production and is strongly inhibited by O2 and CO. Based on structural and site-directed mutagenesis data, it is currently believed that the catalytic bias and tolerance to O2 of Hyd 1 are defined by the distal and proximal FeS clusters, respectively. To test these hypotheses, we produced and characterized a hybrid enzyme made of the catalytic subunit of Hyd 1 and the electron transfer subunit of Hyd 2. We conclude that catalytic bias and sensitivity to CO are set by the catalytic subunit rather than by the electron transfer chain. We confirm the importance of the proximal cluster in making the enzyme Hyd 1 resist long-term exposure to O2, but we show that other structural determinants, in both subunits, contribute to O2 tolerance. A similar strategy based on the design of chimeric heterodimers could be used in the future to elucidate various structure-function relationships in hydrogenases and other multimeric metalloenzymes and to engineer useful hydrogenases that combine the desirable properties of distinct, homologous enzymes.
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Affiliation(s)
- Andrea Fasano
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Chloé Guendon
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Aurore Jacq-Bailly
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Arlette Kpebe
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Jérémy Wozniak
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Carole Baffert
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Melisa Del Barrio
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, 28040 Madrid, Spain
| | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Myriam Brugna
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, CNRS, Aix Marseille Université, UMR 7281, Marseille, France
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3
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Luna-López G, Del Barrio M, Fize J, Artero V, Margarida Coito A, A C Pereira I, Carlos Conesa J, Iglesias-Juez A, De Lacey AL, Pita M. Photobio-electrocatalytic production of H 2 using fluorine-doped tin oxide (FTO) electrodes covered with a NiO-In 2S 3 p-n junction and NiFeSe hydrogenase. Bioelectrochemistry 2023; 150:108361. [PMID: 36621050 DOI: 10.1016/j.bioelechem.2022.108361] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Clean energy vectors are needed towards a fossil fuel-free society, diminishing both greenhouse effect and pollution. Electrochemical water splitting is a clean route to obtain green hydrogen, the cleanest fuel; although efficient electrocatalysts are required to avoid high overpotentials in this process. The combination of inorganic semiconductors with biocatalysts for photoelectrochemical H2 production is an alternative approach to overcome this challenge. N-type semiconductors can be coupled to a co-catalyst for H2 production in the presence of a sacrificial electron donor in solution, but the replacement of the latter with an electrode is a challenge. In this work we attach a NiFeSe-hydrogenase with high activity for H2 production with the n-type semiconductor indium sulfide, which upon visible irradiation is able to transfer its excited electrons to the enzyme. In order to enhance the transfer of the generated holes towards the electrode for their replenishment, we have explored the inclusion of a p-type material, NiO, to induce a p-n junction for H2 production in a photoelectrochemical biocatalytic system in absence of sacrificial reagents.
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Affiliation(s)
- Gabriel Luna-López
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Melisa Del Barrio
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain; Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid 28049, Spain
| | - Jennifer Fize
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 38000 Grenoble, France
| | - Vincent Artero
- Univ Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 38000 Grenoble, France
| | - Ana Margarida Coito
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - José Carlos Conesa
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Ana Iglesias-Juez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Antonio L De Lacey
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Marcos Pita
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
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Caserta G, Papini C, Adamska-Venkatesh A, Pecqueur L, Sommer C, Reijerse E, Lubitz W, Gauquelin C, Meynial-Salles I, Pramanik D, Artero V, Atta M, Del Barrio M, Faivre B, Fourmond V, Léger C, Fontecave M. Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O 2 Resistance and Catalytic Bias? J Am Chem Soc 2018; 140:5516-5526. [PMID: 29595965 DOI: 10.1021/jacs.8b01689] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[FeFe]-hydrogenases, HydAs, are unique biocatalysts for proton reduction to H2. However, they suffer from a number of drawbacks for biotechnological applications: size, number and diversity of metal cofactors, oxygen sensitivity. Here we show that HydA from Megasphaera elsdenii (MeHydA) displays significant resistance to O2. Furthermore, we produced a shorter version of this enzyme (MeH-HydA), lacking the N-terminal domain harboring the accessory FeS clusters. As shown by detailed spectroscopic and biochemical characterization, MeH-HydA displays the following interesting properties. First, a functional active site can be assembled in MeH-HydA in vitro, providing the enzyme with excellent hydrogenase activity. Second, the resistance of MeHydA to O2 is conserved in MeH-HydA. Third, MeH-HydA is more biased toward proton reduction than MeHydA, as the result of the truncation changing the rate limiting steps in catalysis. This work shows that it is possible to engineer HydA to generate an active hydrogenase that combines the resistance of the most resistant HydAs and the simplicity of algal HydAs, containing only the H-cluster.
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Affiliation(s)
- Giorgio Caserta
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Cecilia Papini
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Agnieszka Adamska-Venkatesh
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Constanze Sommer
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Edward Reijerse
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
| | - Charles Gauquelin
- LISBP , Université de Toulouse, CNRS, INRA, INSA , Toulouse , France
| | | | - Debajyoti Pramanik
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Vincent Artero
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes, CEA/BIG, CNRS , 17 rue des martyrs , 38000 Grenoble , France
| | - Melisa Del Barrio
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
| | - Vincent Fourmond
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Christophe Léger
- Aix Marseille Université , CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 , 13400 Marseille , France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques , Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University , 11 place Marcelin Berthelot , 75005 Paris , France
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5
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Del Barrio M, Sensi M, Fradale L, Bruschi M, Greco C, de Gioia L, Bertini L, Fourmond V, Léger C. Interaction of the H-Cluster of FeFe Hydrogenase with Halides. J Am Chem Soc 2018; 140:5485-5492. [PMID: 29590528 DOI: 10.1021/jacs.8b01414] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
FeFe hydrogenases catalyze H2 oxidation and production using an "H-cluster", where two Fe ions are bound by an aza-dithiolate (adt) ligand. Various hypotheses have been proposed (by us and others) to explain that the enzyme reversibly inactivates under oxidizing, anaerobic conditions: intramolecular binding of the N atom of adt, formation of the so-called "Hox/inact" state or nonproductive binding of H2 to isomers of the H-cluster. Here, we show that none of the above explains the new finding that the anaerobic, oxidative, H2-dependent reversible inactivation is strictly dependent on the presence of Cl- or Br-. We provide experimental evidence that chloride uncompetitively inhibits the enzyme: it reversibly binds to catalytic intermediates of H2 oxidation (but not to the resting "Hox" state), after which oxidation locks the active site into a stable, saturated, inactive form, the structure of which is proposed here based on DFT calculations. The halides interact with the amine group of the H-cluster but do not directly bind to iron. It should be possible to stabilize the inhibited state in amounts compatible with spectroscopic investigations to explore further this unexpected reactivity of the H-cluster of hydrogenase.
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Affiliation(s)
- Melisa Del Barrio
- Aix Marseille Université , CNRS, Bioénergétique et Ingénierie des Protéines , Marseille , France
| | - Matteo Sensi
- Aix Marseille Université , CNRS, Bioénergétique et Ingénierie des Protéines , Marseille , France
| | - Laura Fradale
- Aix Marseille Université , CNRS, Bioénergétique et Ingénierie des Protéines , Marseille , France
| | - Maurizio Bruschi
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , 20126 Milan , Italy
| | - Claudio Greco
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , 20126 Milan , Italy
| | - Luca de Gioia
- Department of Biotechnologies and Biosciences , University of Milano-Bicocca , 20126 Milan , Italy
| | - Luca Bertini
- Department of Biotechnologies and Biosciences , University of Milano-Bicocca , 20126 Milan , Italy
| | - Vincent Fourmond
- Aix Marseille Université , CNRS, Bioénergétique et Ingénierie des Protéines , Marseille , France
| | - Christophe Léger
- Aix Marseille Université , CNRS, Bioénergétique et Ingénierie des Protéines , Marseille , France
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