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Chovelon B, Ranganathan V, Srinivasan S, McConnell EM, Faure P, Fiore E, Ravelet C, Peyrin E, DeRosa M. Noncompetitive Determination of Small Analytes by Sandwich-Type Lateral Flow Assay Based on an Aptamer Kissing Complex. Anal Chem 2024. [PMID: 38651263 DOI: 10.1021/acs.analchem.3c05472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Here, we present the proof-of-concept of a lateral flow assay (LFA) that is capable of detecting small-molecule targets in a noncompetitive manner by deploying a sandwich-type format based on the aptamer kissing complex (AKC) strategy. A fluorescently labeled hairpin aptamer served as the signaling agent, while a specific RNA hairpin grafted onto the strip served as the capture element. The hairpin aptamer switched from an unfolded to a folded form in the presence of the target, resulting in kissing interactions between the loops of the reporter and the capture agents. This design triggered a target-dependent fluorescent signal at the test line. The AKC-based LFA was developed for the detection of adenosine, achieving a detection limit in the micromolar range. The assay revealed the presence of the same analyte in urine. The method also proved effective with another small molecule (theophylline). We believe that the AKC-based LFA approach could overcome many of the shortcomings associated with conventional signal-off methods and competitive processes.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
- Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU-Biology and Pathology Institute, F-38041 Grenoble, France
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Velu Ranganathan
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Sathya Srinivasan
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Erin M McConnell
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
- Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU-Biology and Pathology Institute, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, CNRS, F-38041 Grenoble, France
| | - Maria DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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Billet B, Choisnard L, Faure P, Guicherd D, Cussigh E, Peyrin E, Ravelet C, Chovelon B. Stability of fecal calprotectin extracts using the Diasorin ® kit. Clin Chem Lab Med 2024; 62:e13-e15. [PMID: 37470268 DOI: 10.1515/cclm-2023-0472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/27/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Blandine Billet
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- DPM UMR 5063, University Grenoble Alpes, CNRS, Grenoble, France
| | - Luc Choisnard
- DPM UMR 5063, University Grenoble Alpes, CNRS, Grenoble, France
| | - Patrice Faure
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- DPM UMR 5063, University Grenoble Alpes, CNRS, Grenoble, France
| | - Denis Guicherd
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Elodie Cussigh
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Eric Peyrin
- DPM UMR 5063, University Grenoble Alpes, CNRS, Grenoble, France
| | - Corinne Ravelet
- DPM UMR 5063, University Grenoble Alpes, CNRS, Grenoble, France
| | - Benoit Chovelon
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- DPM UMR 5063, University Grenoble Alpes, CNRS, Grenoble, France
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Billet B, Chovelon B, McConnell EM, André D, Puillet-Anselme L, Fiore E, Faure P, Ravelet C, DeRosa MC, Peyrin E. Iodinated organic molecule as tag for inductively coupled Plasma-mass spectrometry aptamer assays. Talanta 2024; 267:125107. [PMID: 37672983 DOI: 10.1016/j.talanta.2023.125107] [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: 04/22/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) aptamer-based assays using metallic nanostructures or chelates as exogenous tags have gained growing attention in the last decade. We describe here a proof-of-concept study based on the exploitation of a simple organic molecule as a tag, i.e.l-thyroxine carrying four iodine atoms detectable by ICP-MS. A solid-phase assay involving the structure-switching format was deployed for the detection of the small molecule l-tyrosinamide as model target. The overall design involved (i) a reporter agent consisting of a DNA aptamer incorporating a single l-thyroxine label at its end and (ii) a capture agent, which is a partially complementary strand, immobilized on a microplate. Limit of detection in the nanomolar range was reported. The present labeling approach was further developed for the detection of a model protein (α-thrombin), using a sandwich mode, and proved effective in a biological matrix. We believe that the l-thyroxine tagging method could become a simple and robust alternative to commonly used labeling methods for ICP-MS aptamer-based assays.
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Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR, 5063, F-38041, Grenoble, France; CNRS, DPM UMR, 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU, Biology and Pathology Institute, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR, 5063, F-38041, Grenoble, France; CNRS, DPM UMR, 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU, Biology and Pathology Institute, F-38041, Grenoble, France; Department of Chemistry, Carleton University, Ottawa, Canada.
| | | | - Dominique André
- Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU, Biology and Pathology Institute, F-38041, Grenoble, France
| | - Laurence Puillet-Anselme
- Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU, Biology and Pathology Institute, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR, 5063, F-38041, Grenoble, France; CNRS, DPM UMR, 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR, 5063, F-38041, Grenoble, France; CNRS, DPM UMR, 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU, Biology and Pathology Institute, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR, 5063, F-38041, Grenoble, France; CNRS, DPM UMR, 5063, F-38041, Grenoble, France
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, Ottawa, Canada
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR, 5063, F-38041, Grenoble, France; CNRS, DPM UMR, 5063, F-38041, Grenoble, France.
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Chovelon B, Peyrin E, Ragot M, Salem N, Nguyen TG, Auvray B, Henry M, Petrillo MA, Fiore E, Bessy Q, Faure P, Ravelet C. Nile blue as reporter dye in salt aggregation based-colorimetric aptasensors for peptide, small molecule and metal ion detection. Anal Chim Acta 2023; 1243:340840. [PMID: 36697182 DOI: 10.1016/j.aca.2023.340840] [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: 10/13/2022] [Revised: 11/21/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Herein, we report a novel approach for the design of a colorimetric aptasensor, relying on a Dye Salt Aggregation-based Colorimetric Oligonucleotide assay (DYSACO assay). This method is based on the use of an intercalating agent, Nile Blue (NB), whose aggregation capacities (and thus modification of its absorption spectrum) are drastically amplified by adding salts to the working solution. The presence of an aptamer could protect NB from such aggregation process due to its intercalation into double-stranded DNA and/or interaction with nucleobases. In response to the addition of the specific ligand, the competition between NB and the target for binding to the aptamer occurs, resulting in an increase in the dye salt aggregation and then in the blue-to-blank color change of the solution. The proof-of-principle was demonstrated by employing the anti-l-tyrosinamide aptamer and the assay was successfully applied to the trace enantiomer detection, allowing the detection of an enantiomeric impurity down to approximately 2% in a non-racemic sample. Through a reversed mechanism based on the increased capture of NB by DNA upon analyte binding, the sensing platform was further demonstrated for the Hg(II) detection. Water samples of different origin were spiked with Hg(II) analyte at final range concentrations comprised between (0.5-15 μM). An excellent overall recovery of 122 ± 14%; 105 ± 14%; 99 ± 9%; was respectively obtained from river, tap and mineral water, suggesting that the sensor can be used under real sample conditions. The assay was also shown to work for sensing the ochratoxin A and d-arginine vasopressin compounds, revealing its simplicity and generalizability potentialities.
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Affiliation(s)
- Benoît Chovelon
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041, Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France.
| | - Mailys Ragot
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Nassim Salem
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Truong Giang Nguyen
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Benjamin Auvray
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Mickael Henry
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Mel-Alexandre Petrillo
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Quentin Bessy
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France
| | - Patrice Faure
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041, Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, UMR 5063, Grenoble Alpes University - CNRS, France.
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Charbonnier P, Chovelon B, Ravelet C, Ngo TD, Chevallet M, Deniaud A. ATP7B-Deficient Hepatocytes Reveal the Importance of Protein Misfolding Induced at Low Copper Concentration. Cells 2022; 11:cells11213400. [PMID: 36359796 PMCID: PMC9657033 DOI: 10.3390/cells11213400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Copper is a transition metal essential for human life. Its homeostasis is regulated in the liver, which delivers copper to the whole body and excretes its excess outside the organism in the feces through the bile. These functions are regulated within hepatocytes, and the ATP7B copper transporter is central to making the switch between copper use and excretion. In Wilson disease, the gene coding for ATP7B is mutated, leading to copper overload, firstly, in the liver and the brain. To better understand the role of ATP7B in hepatocytes and to provide a smart tool for the development of novel therapies against Wilson disease, we used the CrispR/Cas9 tool to generate hepatocyte cell lines with the abolished expression of ATP7B. These cell lines revealed that ATP7B plays a major role at low copper concentrations starting in the micromolar range. Moreover, metal stress markers are induced at lower copper concentrations compared to parental cells, while redox stress remains not activated. As shown recently, the main drawback induced by copper exposure is protein unfolding that is drastically exacerbated in ATP7B-deficient cells. Our data enabled us to propose that the zinc finger domain of DNAJ-A1 would serve as a sensor of Cu stress. Therefore, these Wilson-like hepatocytes are of high interest to explore in more detail the role of ATP7B.
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Affiliation(s)
- Peggy Charbonnier
- Université Grenoble Alpes, CNRS, CEA, IRIG Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Benoît Chovelon
- Service de Biochimie SB2TE, Institut de Biologie et Pathologie CHU Grenoble Alpes, F-38000 Grenoble, France
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, CNRS, UMR 5063, F-38041 Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, CNRS, UMR 5063, F-38041 Grenoble, France
| | - Tuan Dung Ngo
- Université Grenoble Alpes, CNRS, CEA, IRIG Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Mireille Chevallet
- Université Grenoble Alpes, CNRS, CEA, IRIG Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Aurélien Deniaud
- Université Grenoble Alpes, CNRS, CEA, IRIG Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
- Correspondence:
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Billet B, Chovelon B, Fiore E, Faure P, Ravelet C, Peyrin E. Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions. Biosens Bioelectron 2022; 205:114091. [PMID: 35217256 DOI: 10.1016/j.bios.2022.114091] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022]
Abstract
We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni2+ or Co2+ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.
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Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
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Leger M, Despinasse Q, Faure P, Arnaud J, Ravelet C, Chovelon B. Influence of delayed separation of plasma from whole blood and centrifugation protocol on Zn plasma concentration. Clin Chem Lab Med 2021; 58:e279-e281. [PMID: 32609637 DOI: 10.1515/cclm-2020-0380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/02/2020] [Indexed: 11/15/2022]
Affiliation(s)
- Mandy Leger
- Institute of Biology and Pathology, University Hospital of Grenoble and Alps, Grenoble, France
| | - Quentin Despinasse
- Institute of Biology and Pathology, University Hospital of Grenoble and Alps, Grenoble, France
| | - Patrice Faure
- Institute of Biology and Pathology, University Hospital of Grenoble and Alps, Grenoble, France
- University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, La Tronche, France
| | - Josiane Arnaud
- Institute of Biology and Pathology, University Hospital of Grenoble and Alps, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, Grenoble, France
- CNRS, DPM UMR 5063, Grenoble, France
| | - Benoit Chovelon
- Institute of Biology and Pathology, University Hospital of Grenoble and Alps, Grenoble, France
- University Grenoble Alpes, DPM UMR 5063, Grenoble, France
- CNRS, DPM UMR 5063, Grenoble, France
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Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo MA, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post-Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021; 60:12346-12350. [PMID: 33742515 DOI: 10.1002/anie.202102254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/13/2021] [Indexed: 12/11/2022]
Abstract
We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb2+ , Cd2+ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.
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Affiliation(s)
- Blandine Billet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Benoit Chovelon
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Emmanuelle Fiore
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Farid Oukacine
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | | | - Patrice Faure
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Corinne Ravelet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Eric Peyrin
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
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Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo M, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post‐Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Blandine Billet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Benoit Chovelon
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Emmanuelle Fiore
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Farid Oukacine
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | | | - Patrice Faure
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Corinne Ravelet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Eric Peyrin
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
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10
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Lu C, Saint-Pierre C, Gasparutto D, Roupioz Y, Ravelet C, Peyrin E, Buhot A. Melting Curve Analysis of Aptachains: Adenosine Detection with Internal Calibration. Biosensors (Basel) 2021; 11:112. [PMID: 33917864 PMCID: PMC8068264 DOI: 10.3390/bios11040112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/01/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022]
Abstract
Small molecules are ubiquitous in nature and their detection is relevant in various domains. However, due to their size, sensitive and selective probes are difficult to select and the detection methods are generally indirect. In this study, we introduced the use of melting curve analysis of aptachains based on split-aptamers for the detection of adenosine. Aptamers, short oligonucleotides, are known to be particularly efficient probes compared to antibodies thanks to their advantageous probe/target size ratio. Aptachains are formed from dimers with dangling ends followed by the split-aptamer binding triggered by the presence of the target. The high melting temperature of the dimers served as a calibration for the detection/quantification of the target based on the height and/or temperature shift of the aptachain melting peak.
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Affiliation(s)
- Chenze Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China;
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Christine Saint-Pierre
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Didier Gasparutto
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Yoann Roupioz
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Corinne Ravelet
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Eric Peyrin
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Arnaud Buhot
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
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11
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Zara L, Achilli S, Chovelon B, Fiore E, Toulmé JJ, Peyrin E, Ravelet C. Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants. Anal Chim Acta 2021; 1159:338382. [PMID: 33867041 DOI: 10.1016/j.aca.2021.338382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/28/2023]
Abstract
Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.
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Affiliation(s)
- Lorena Zara
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Novaptech, 2 Allée Du Doyen Georges Brus, 33600, Pessac, France
| | - Silvia Achilli
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | - Benoît Chovelon
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Service de Biochimie, Biologie Moléculaire, Toxicologie Environnementale, CHU de Grenoble-Alpes Site Nord- Institut de Biologie et de Pathologie, La Tronche, France
| | | | | | - Eric Peyrin
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France.
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12
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Despinasse Q, Choisnard L, Faure P, Guicherd D, Peyrin E, Ravelet C, Chovelon B. Stability of catecholamines in whole blood: influence of time between collection and centrifugation. Clin Chem Lab Med 2020; 59:e83-e85. [PMID: 33027041 DOI: 10.1515/cclm-2020-1291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/11/2020] [Indexed: 11/15/2022]
Affiliation(s)
- Quentin Despinasse
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Luc Choisnard
- University Grenoble Alpes, DPM UMR5063, Grenoble, France.,CNRS, DPM UMR5063, Grenoble, France
| | - Patrice Faure
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France.,University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, La Tronche, France
| | - Denis Guicherd
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR5063, Grenoble, France.,CNRS, DPM UMR5063, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR5063, Grenoble, France.,CNRS, DPM UMR5063, Grenoble, France
| | - Benoit Chovelon
- Unit of Biochemistry of Hormones and Nutrition, Institute of Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France.,University Grenoble Alpes, DPM UMR5063, Grenoble, France.,CNRS, DPM UMR5063, Grenoble, France
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13
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Broekgaarden M, Bulin AL, Porret E, Musnier B, Chovelon B, Ravelet C, Sancey L, Elleaume H, Hainaut P, Coll JL, Le Guével X. Surface functionalization of gold nanoclusters with arginine: a trade-off between microtumor uptake and radiotherapy enhancement. Nanoscale 2020; 12:6959-6963. [PMID: 32187249 DOI: 10.1039/d0nr01138j] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ultra-small gold nanoclusters (AuNCs) are increasingly investigated for cancer imaging and radiotherapy enhancement. While fine-tuning the AuNC surface chemistry can optimize their pharmacokinetics, its effects on radiotherapy enhancement remain largely unexplored. This study demonstrates that optimizing the surface chemistry of AuNCs for increased tumor uptake can significantly affect its potential to augment radiotherapy outcomes.
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Affiliation(s)
- Mans Broekgaarden
- Institute for Advanced Biosciences, Université Grenoble-Alpes, INSERM U1209, CNRS UMR 5309, Allée des Alpes, 38700 La Tronche, France.
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14
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15
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. Kissing interactions for the design of a multicolour fluorescence anisotropy chiral aptasensor. Talanta 2019; 205:120098. [DOI: 10.1016/j.talanta.2019.06.098] [Citation(s) in RCA: 4] [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: 04/26/2019] [Revised: 06/23/2019] [Accepted: 06/27/2019] [Indexed: 01/03/2023]
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16
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Coussot G, Le Postollec A, Incerti S, Baqué M, Faye C, Vandenabeele-Trambouze O, Cottin H, Ravelet C, Peyrin E, Fiore E, Vigier F, Caron J, Chaput D, Przybyla B, Berger T, Dobrijevic M. Photochemistry on the Space Station-Aptamer Resistance to Space Conditions: Particles Exposure from Irradiation Facilities and Real Exposure Outside the International Space Station. Astrobiology 2019; 19:1063-1074. [PMID: 30817199 DOI: 10.1089/ast.2018.1896] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Some microarray-based instruments that use bioaffinity receptors such as antibodies or aptamers are under development to detect signatures of past or present life on planetary bodies. Studying the resistance of such instruments against space constraints and cosmic rays in particular is a prerequisite. We used several ground-based facilities to study the resistance of aptamers to various types of particles (protons, electrons, neutrons, and carbon ions) at different energies and fluences. We also tested the resistance of aptamers during the EXPOSE-R2 mission outside the International Space Station (ISS). The accumulated dose measured after the 588 days of this mission (220 mGy) corresponds to the accumulated dose that can be expected during a mission to Mars. We found that the recognition ability of fluorescently labeled aptamers was not significantly affected during short-term exposure experiments taking into account only one type of radiation at a time. However, we demonstrated that the same fluorescent dye was significantly affected by temperature variations (-21°C to +58°C) and storage throughout the entirety of the ISS experiment (60% of signal loss). This induced a large variability of aptamer signal in our analysis. However, we found that >50% of aptamers were still functional after the whole EXPOSE-R2 mission. We conclude that aptamer-based instruments are well suited for in situ analysis on planetary bodies, but the detection step requires additional investigations.
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Affiliation(s)
- Gaëlle Coussot
- 1Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélie Le Postollec
- 2Laboratoire d'Astrophysique de Bordeaux (LAB), Université de Bordeaux, CNRS, B18N, Pessac, France
| | - Sébastien Incerti
- 3Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), UMR 5797, Université de Bordeaux, Gradignan, France
| | - Mickaël Baqué
- 4German Aerospace Center (DLR), Institute of Planetary Research, Management and Infrastructure, Research Group Astrobiological Laboratories, Berlin, Germany
| | | | - Odile Vandenabeele-Trambouze
- 6IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO), Plouzané, France
| | - Hervé Cottin
- 7Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR 7583, Université Paris Est Créteil et Université Paris Diderot, Institut Pierre Simon Laplace, Créteil, France
| | - Corinne Ravelet
- 8Département de Pharmacochimie Moléculaire, UMR 5063, Université Grenoble Alpes, CNRS, St. Martin d'Hères, France
| | - Eric Peyrin
- 8Département de Pharmacochimie Moléculaire, UMR 5063, Université Grenoble Alpes, CNRS, St. Martin d'Hères, France
| | - Emmanuelle Fiore
- 8Département de Pharmacochimie Moléculaire, UMR 5063, Université Grenoble Alpes, CNRS, St. Martin d'Hères, France
| | | | - Jérôme Caron
- 9Département de Radiothérapie, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France
| | - Didier Chaput
- 10DCT/ME/EM, Centre National d'Etudes Spatiales, Toulouse, France
| | - Bartos Przybyla
- 11German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Thomas Berger
- 11German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Michel Dobrijevic
- 2Laboratoire d'Astrophysique de Bordeaux (LAB), Université de Bordeaux, CNRS, B18N, Pessac, France
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17
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Taiwe GS, Montnach J, Nicolas S, De Waard S, Fiore E, Peyrin E, El-Aziz TMA, Amar M, Molgó J, Ronjat M, Servent D, Ravelet C, De Waard M. Aptamer Efficacies for In Vitro and In Vivo Modulation of αC-Conotoxin PrXA Pharmacology. Molecules 2019; 24:molecules24020229. [PMID: 30634526 PMCID: PMC6359527 DOI: 10.3390/molecules24020229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 01/03/2023] Open
Abstract
The medical staff is often powerless to treat patients affected by drug abuse or misuse and poisoning. In the case of envenomation, the treatment of choice remains horse sera administration that poses a wealth of other medical conditions and threats. Previously, we have demonstrated that DNA-based aptamers represent powerful neutralizing tools for lethal animal toxins of venomous origin. Herein, we further pursued our investigations in order to understand whether all toxin-interacting aptamers possessed equivalent potencies to neutralize αC-conotoxin PrXA in vitro and in vivo. We confirmed the high lethality in mice produced by αC-conotoxin PrXA regardless of the mode of injection and further characterized myoclonus produced by the toxin. We used high-throughput patch-clamp technology to assess the effect of αC-conotoxin PrXA on ACh-mediated responses in TE671 cells, responses that are carried by muscle-type nicotinic receptors. We show that 2 out of 4 aptamers reduce the affinity of the toxin for its receptor, most likely by interfering with the pharmacophore. In vivo, more complex responses on myoclonus and mice lethality are observed depending on the type of aptamer and mode of administration (concomitant or differed). Concomitant administration always works better than differed administration indicating the stability of the complex in vivo. The most remarkable conclusion is that an aptamer that has no or a limited efficacy in vitro may nevertheless be functional in vivo probably owing to an impact on the biodistribution or pharmacokinetics of the toxin in vivo. Overall, the results highlight that a blind selection of aptamers against toxins leads to efficient neutralizing compounds in vivo regardless of the mode of action. This opens the door to the use of aptamer mixtures as substitutes to horse sera for the neutralization of life-threatening animal venoms, an important WHO concern in tropical areas.
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Affiliation(s)
- Germain Sotoing Taiwe
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
- Department of Zoology and Animal Physiology, Faculty of Sciences, University of Buea, P.O. Box 63, Buea, Cameroon.
| | - Jérôme Montnach
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Sébastien Nicolas
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Stéphan De Waard
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Emmanuelle Fiore
- CNRS, DPM UMR 5063, University Grenoble Alpes, 38041 Grenoble, France.
| | - Eric Peyrin
- CNRS, DPM UMR 5063, University Grenoble Alpes, 38041 Grenoble, France.
| | | | - Muriel Amar
- Service d'Ingénierie Moléculaire des Protéines, Institut des Sciences du Vivant Frédéric Joliot, Commissariat à l'Energie Atomique, Université Paris-Saclay, F-91191 Gif sur Yvette, France.
| | - Jordi Molgó
- Service d'Ingénierie Moléculaire des Protéines, Institut des Sciences du Vivant Frédéric Joliot, Commissariat à l'Energie Atomique, Université Paris-Saclay, F-91191 Gif sur Yvette, France.
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS/Université Paris-Sud, 91198 Gif sur Yvette, France.
| | - Michel Ronjat
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Denis Servent
- Service d'Ingénierie Moléculaire des Protéines, Institut des Sciences du Vivant Frédéric Joliot, Commissariat à l'Energie Atomique, Université Paris-Saclay, F-91191 Gif sur Yvette, France.
| | - Corinne Ravelet
- CNRS, DPM UMR 5063, University Grenoble Alpes, 38041 Grenoble, France.
| | - Michel De Waard
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
- Smartox Biotechnology, 6 rue des Platanes, 38120 Saint Egrève, France.
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18
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Lisi S, Fiore E, Scarano S, Pascale E, Boehman Y, Ducongé F, Chierici S, Minunni M, Peyrin E, Ravelet C. Non-SELEX isolation of DNA aptamers for the homogeneous-phase fluorescence anisotropy sensing of tau Proteins. Anal Chim Acta 2018; 1038:173-181. [DOI: 10.1016/j.aca.2018.07.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 02/07/2023]
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19
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Perrier S, Guieu V, Chovelon B, Ravelet C, Peyrin E. Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms. Anal Chem 2018. [PMID: 29513518 DOI: 10.1021/acs.analchem.7b04593] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.
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Affiliation(s)
- Sandrine Perrier
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Valérie Guieu
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Benoit Chovelon
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France.,Département de Biochimie, Toxicologie et Pharmacologie , CHU de Grenoble Site Nord-Institut de Biologie et de Pathologie , F-38041 Grenoble , France
| | - Corinne Ravelet
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Eric Peyrin
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
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20
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. Mirror-image aptamer kissing complex for arginine-vasopressin sensing. Anal Chim Acta 2017; 1001:143-150. [PMID: 29291797 DOI: 10.1016/j.aca.2017.11.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/03/2017] [Accepted: 11/13/2017] [Indexed: 12/31/2022]
Abstract
The recently reported aptamer kissing complex (AKC) strategy has allowed for the development of a new kind of sandwich-like sensing tools. Currently AKC assays have been only applied to low molecular weight molecules and their functionality in complex matrices remains challenging. The objective of the present study broken down into two sub-aims; exploring the propensity to broaden the scope of detectable analytes and designing a more robust system for potential applications to realistic samples. An all L-configuration aptaswitch module derived from a hairpin spiegelmer specific to a larger target, i.e. the arginine-vasopressin (AVP) hormone, was elaborated. The target-induced AKC formation in presence of a specific mirror-image RNA hairpin (L-aptakiss) probe were analyzed by using fluorescence anisotropy. The mirror-image kissing complex was successfully formed when the L-AVP target bound to the engineered L-aptaswitch element. It was also established that the use of methanol as cosolvent significantly improved the assay sensitivity through the stabilization of the ternary complex. Finally, the capability of the mirror-image method to operate in 10-fold diluted, untreated human serum was illustrated. The current work revealed that the AKC concept can be expanded to a wider range of targets and converted to a L-configuration sensing platform especially suitable for bioanalysis purposes.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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21
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Lisi S, Scarano S, Fedeli S, Pascale E, Cicchi S, Ravelet C, Peyrin E, Minunni M. Toward sensitive immuno-based detection of tau protein by surface plasmon resonance coupled to carbon nanostructures as signal amplifiers. Biosens Bioelectron 2017; 93:289-292. [DOI: 10.1016/j.bios.2016.08.078] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 11/28/2022]
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22
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Tohala L, Oukacine F, Ravelet C, Peyrin E. Sequence requirements of oligonucleotide chiral selectors for the capillary electrophoresis resolution of low-affinity DNA binders. Electrophoresis 2017; 38:1383-1390. [PMID: 28256731 DOI: 10.1002/elps.201600516] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/21/2017] [Accepted: 02/28/2017] [Indexed: 12/23/2022]
Abstract
We recently reported that a great variety of DNA oligonucleotides (ONs) used as chiral selectors in partial-filling capillary electrophoresis (CE) exhibited interesting enantioresolution properties toward low-affinity DNA binders. Herein, the sequence prerequisites of ONs for the CE enantioseparation process were studied. First, the chiral resolution properties of a series of homopolymeric sequences (Poly-dT) of different lengths (from 5 to 60-mer) were investigated. It was shown that the size increase-dependent random coil-like conformation of Poly-dT favorably acted on the apparent selectivity and resolution. The base-unpairing state constituted also an important factor in the chiral resolution ability of ONs as the switch from the single-stranded to double-stranded structure was responsible for a significant decrease in the analyte selectivity range. Finally, the chemical diversity enhanced the enantioresolution ability of single-stranded ONs. The present work could lay the foundation for the design of performant ON chiral selectors for the CE separation of weak DNA binder enantiomers.
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Affiliation(s)
- Luma Tohala
- DPM, UMR 5063, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Farid Oukacine
- DPM, UMR 5063, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Corinne Ravelet
- DPM, UMR 5063, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Eric Peyrin
- DPM, UMR 5063, Université Grenoble Alpes, CNRS, Grenoble, France
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23
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Goux E, Dausse E, Guieu V, Azéma L, Durand G, Henry M, Choisnard L, Toulmé JJ, Ravelet C, Peyrin E. A colorimetric nanosensor based on a selective target-responsive aptamer kissing complex. Nanoscale 2017; 9:4048-4052. [PMID: 28276559 DOI: 10.1039/c7nr00612h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein, we report a novel approach for the design of a colorimetric aptasensor based on functionalized gold nanoparticle probes. This approach relies on the conjugation of nanoparticles by two functional DNA and RNA hairpins that engage specific kissing (loop-loop) interactions in response to the addition of a small analyte ligand, leading to particle aggregation and then red-to-purple colour change of the colloidal solution.
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Affiliation(s)
- E Goux
- University Grenoble Alpes, DPM CNRS UMR 5063, F-38041 Grenoble, France.
| | - E Dausse
- Laboratoire ARNA, University of Bordeaux, Inserm U1212, CNRS UMR5320, F-33076 Bordeaux, France
| | - V Guieu
- University Grenoble Alpes, DPM CNRS UMR 5063, F-38041 Grenoble, France.
| | - L Azéma
- Laboratoire ARNA, University of Bordeaux, Inserm U1212, CNRS UMR5320, F-33076 Bordeaux, France
| | - G Durand
- Laboratoire ARNA, University of Bordeaux, Inserm U1212, CNRS UMR5320, F-33076 Bordeaux, France
| | - M Henry
- University Grenoble Alpes, DPM CNRS UMR 5063, F-38041 Grenoble, France.
| | - L Choisnard
- University Grenoble Alpes, DPM CNRS UMR 5063, F-38041 Grenoble, France.
| | - J-J Toulmé
- Laboratoire ARNA, University of Bordeaux, Inserm U1212, CNRS UMR5320, F-33076 Bordeaux, France
| | - C Ravelet
- University Grenoble Alpes, DPM CNRS UMR 5063, F-38041 Grenoble, France.
| | - E Peyrin
- University Grenoble Alpes, DPM CNRS UMR 5063, F-38041 Grenoble, France.
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24
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. A lifetime-sensitive fluorescence anisotropy probe for DNA-based bioassays: The case of SYBR Green. Biosens Bioelectron 2016; 90:140-145. [PMID: 27886600 DOI: 10.1016/j.bios.2016.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/01/2016] [Accepted: 11/20/2016] [Indexed: 12/12/2022]
Abstract
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer. On the basis of ligand-induced changes in the molar fractions of bound and free forms of SG, the approach provides an unprecedented means for the FA monitoring of the ligand binding to short DNA molecules, allowing the elaboration of a variety of intercalator displacement assays and label-free biosensors that involve diverse DNA structures (duplex, hairpin, G-quadruplex and single-stranded), ligand types (ion, small organic molecule and protein) and binding modes (intercalation, minor groove, allosteric switch). These findings open up promising avenues in the design of a new generation of FA assays.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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Challier L, Miranda-Castro R, Barbe B, Fave C, Limoges B, Peyrin E, Ravelet C, Fiore E, Labbé P, Coche-Guérente L, Ennifar E, Bec G, Dumas P, Mavré F, Noël V. Multianalytical Study of the Binding between a Small Chiral Molecule and a DNA Aptamer: Evidence for Asymmetric Steric Effect upon 3'- versus 5'-End Sequence Modification. Anal Chem 2016; 88:11963-11971. [PMID: 27934108 DOI: 10.1021/acs.analchem.6b04046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acid aptamers are involved in a broad field of applications ranging from therapeutics to analytics. Deciphering the binding mechanisms between aptamers and small ligands is therefore crucial to improve and optimize existing applications and to develop new ones. Particularly interesting is the enantiospecific binding mechanism involving small molecules with nonprestructured aptamers. One archetypal example is the chiral binding between l-tyrosinamide and its 49-mer aptamer for which neither structural nor mechanistic information is available. In the present work, we have taken advantage of a multiple analytical characterization strategy (i.e., using electroanalytical techniques such as kinetic rotating droplet electrochemistry, fluorescence polarization, isothermal titration calorimetry, and quartz crystal microbalance) for interpreting the nature of binding process. Screening of the binding thermodynamics and kinetics with a wide range of aptamer sequences revealed the lack of symmetry between the two ends of the 23-mer minimal binding sequence, showing an unprecedented influence of the 5' aptamer modification on the bimolecular binding rate constant kon and no significant effect on the dissociation rate constant koff. The results we have obtained lead us to conclude that the enantiospecific binding reaction occurs through an induced-fit mechanism, wherein the ligand promotes a primary nucleation binding step near the 5'-end of the aptamer followed by a directional folding of the aptamer around its target from 5'-end to 3'-end. Functionalization of the 5'-end position by a chemical label, a polydA tail, a protein, or a surface influences the kinetic/thermodynamic constants up to 2 orders of magnitude in the extreme case of a surface immobilized aptamer, while significantly weaker effect is observed for a 3'-end modification. The reason is that steric hindrance must be overcome to nucleate the binding complex in the presence of a modification near the nucleation site.
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Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Bertrand Barbe
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes , 470 rue de la chimie, 38400 Saint-Martin d'Hères, France
| | - Pierre Labbé
- Département de Chimie Moléculaire, CNRS, UMR 5250, Université Grenoble Alpes , FR 2607, 570 rue de la chimie, B.P. 53, 38400 Grenoble, France
| | - Liliane Coche-Guérente
- Département de Chimie Moléculaire, CNRS, UMR 5250, Université Grenoble Alpes , FR 2607, 570 rue de la chimie, B.P. 53, 38400 Grenoble, France
| | - Eric Ennifar
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - Guillaume Bec
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - Philippe Dumas
- "Architecture et Réactivité de l'ARN", Biophysique et Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg , 15 rue René Descartes, 67084 Strasbourg, France
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité , 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
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Durand G, Dausse E, Goux E, Fiore E, Peyrin E, Ravelet C, Toulmé JJ. A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers. Nucleic Acids Res 2016; 44:4450-9. [PMID: 27067541 PMCID: PMC4872101 DOI: 10.1093/nar/gkw206] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 01/22/2023] Open
Abstract
Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 106 RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with KDs in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy.
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Affiliation(s)
- Guillaume Durand
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Emma Goux
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Eric Peyrin
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Corinne Ravelet
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
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Chovelon B, Durand G, Dausse E, Toulmé JJ, Faure P, Peyrin E, Ravelet C. ELAKCA: Enzyme-Linked Aptamer Kissing Complex Assay as a Small Molecule Sensing Platform. Anal Chem 2016; 88:2570-5. [PMID: 26832823 DOI: 10.1021/acs.analchem.5b04575] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report herein a novel sandwich-type enzyme-linked assay for the "signal-on" colorimetric detection of small molecules. The approach (referred to as enzyme-linked aptamer kissing complex assay (ELAKCA)) relied on the kissing complex-based recognition of the target-bound hairpin aptamer conformational state by a specific RNA hairpin probe. The aptamer was covalently immobilized on a microplate well surface to act as target capture element. Upon small analyte addition, the folded aptamer was able to bind to the biotinylated RNA hairpin module through loop-loop interaction. The formed ternary complex was then revealed by the introduction of the streptavidin-horseradish peroxidase conjugate that catalytically converted the 3,3',5,5'-tetramethylbenzidine substrate into a colorimetric product. ELAKCA was successfully designed for two different systems allowing detecting the adenosine and theophylline molecules. The potential practical applicability in terms of biological sample analysis (human plasma), temporal stability, and reusability was also reported. Owing to the variety of both hairpin functional nucleic acids, kissing motifs, and enzyme-based signaling systems, ELAKCA opens up new prospects for developing small molecule sensing platforms of wide applications.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France.,Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie , F-38041 Grenoble, France
| | - Guillaume Durand
- Laboratoire ARNA, Université Bordeaux, Inserm U869, F-33076 Bordeaux, France
| | - Eric Dausse
- Laboratoire ARNA, Université Bordeaux, Inserm U869, F-33076 Bordeaux, France
| | - Jean-Jacques Toulmé
- Laboratoire ARNA, Université Bordeaux, Inserm U869, F-33076 Bordeaux, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble Site Nord - Institut de Biologie et de Pathologie , F-38041 Grenoble, France.,University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France
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Goux E, Lespinasse Q, Guieu V, Perrier S, Ravelet C, Fiore E, Peyrin E. Fluorescence anisotropy-based structure-switching aptamer assay using a peptide nucleic acid (PNA) probe. Methods 2015; 97:69-74. [PMID: 26455538 DOI: 10.1016/j.ymeth.2015.09.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/04/2015] [Accepted: 09/18/2015] [Indexed: 01/04/2023] Open
Abstract
This study describes for the first time the feasibility of using peptide nucleic acids (PNAs) as an alternative to the DNA probes in structure-switching aptamer fluorescence polarisation assays. The effects of experimental parameters such as the length of the PNA strand, the nature of dye and the buffer conditions on the assay performances are first explored using two different methodologies based on the competition between the PNA/aptamer hydribridisation and the target/aptamer complexation. D-ATP can be detected from 1 to 25 μM in a linear range and a detection limit (LOD) of 3 μM can be reached. For this target, this lowers by a factor >5 the LOD reported with conventional DNA-based fluorescent structure switching aptamer-based assays and by a factor 3 the LOD observed with non-competitive fluorescent sensing platform indicating the usefulness of the PNA-based approach.
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Affiliation(s)
- Emma Goux
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Quentin Lespinasse
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Valérie Guieu
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France.
| | - Sandrine Perrier
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France.
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Fiore E, Dausse E, Dubouchaud H, Peyrin E, Ravelet C. Ultrafast capillary electrophoresis isolation of DNA aptamer for the PCR amplification-based small analyte sensing. Front Chem 2015; 3:49. [PMID: 26322305 PMCID: PMC4533002 DOI: 10.3389/fchem.2015.00049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/27/2015] [Indexed: 01/14/2023] Open
Abstract
Here, we report a new homogeneous DNA amplification-based aptamer assay for small analyte sensing. The aptamer of adenosine chosen as the model analyte was split into two fragments able to assemble in the presence of target. Primers were introduced at extremities of one fragment in order to generate the amplifiable DNA component. The amount of amplifiable fragment was quantifiable by Real-Time Polymerase Chain Reaction (RT-PCR) amplification and directly reliable on adenosine concentration. This approach combines the very high separation efficiency and the homogeneous format (without immobilization) of capillary electrophoresis (CE) and the sensitivity of real time PCR amplification. An ultrafast isolation of target-bound split aptamer (60 s) was developed by designing a CE input/ouput scheme. Such method was successfully applied to the determination of adenosine with a LOD of 1 μM.
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Affiliation(s)
- Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Eric Dausse
- Laboratoire ARNA, Institut National de la Santé et de la Recherche Médicale U869, Université Bordeaux Bordeaux, France
| | - Hervé Dubouchaud
- Laboratoire de Bioénergétique Fondamentale et Appliquée, Institut National de la Santé et de la Recherche Médicale U1055, University Grenoble Alpes Grenoble, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire UMR 5063, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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Abstract
Herein, we studied the chiral resolution properties of a repertoire of arbitrarily chosen DNA oligonucleotides (ON). Ten oligonucleotidic sequences characterized by diverse base compositions, sizes, and structural features, ranging from secondary structure-free homo-oligonucleotides to duplex, hairpin, and three-way junction architectures, were investigated as potential chiral selectors. Their enantioselective features were assessed by using ONs as running buffer additives in partial-filling capillary electrophoresis. It was shown that all the screened sequences displayed enantiodiscrimination capabilities toward small aromatic compounds. Under (sub)millimolar DNA concentration conditions, the combination of only three oligonucleotidic sequences provided the chiral resolution of around 20 racemates, including drugs, illegal drugs, amino-acids, and nucleosides. This work represents the first demonstration of such analyte selectivity spectrum for nucleic acid-based chiral separation tools.
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Affiliation(s)
- Luma Tohala
- Université Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Farid Oukacine
- Université Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Corinne Ravelet
- Université Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Eric Peyrin
- Université Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, CNRS, DPM UMR 5063, F-38041 Grenoble, France
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Durand G, Lisi S, Ravelet C, Dausse E, Peyrin E, Toulmé JJ. Riboswitches Based on Kissing Complexes for the Detection of Small Ligands. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400402] [Citation(s) in RCA: 13] [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: 12/26/2022]
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Durand G, Lisi S, Ravelet C, Dausse E, Peyrin E, Toulmé JJ. Riboswitches based on kissing complexes for the detection of small ligands. Angew Chem Int Ed Engl 2014; 53:6942-5. [PMID: 24916019 DOI: 10.1002/anie.201400402] [Citation(s) in RCA: 34] [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: 01/14/2014] [Indexed: 01/08/2023]
Abstract
Biosensors derived from aptamers were designed for which folding into a hairpin shape is triggered by binding of the cognate ligand. These aptamers (termed aptaswitches) thus switch between folded and unfolded states in the presence and absence of the ligand, respectively. The apical loop of the folded aptaswitch is recognized by a second hairpin called the aptakiss through loop-loop or kissing interactions, whereas the aptakiss does not bind the unfolded aptaswitch. Therefore, the formation of a kissing complex signals the presence of the ligand. Aptaswitches were designed that enable the detection of GTP and adenosine in a specific and quantitative manner by surface plasmon resonance when using a grafted aptakiss or in solution by anisotropy measurement with a fluorescently labeled aptakiss. This approach is generic and can potentially be extended to the detection of any molecule for which hairpin aptamers have been identified, as long as the apical loop is not involved in ligand binding.
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Affiliation(s)
- Guillaume Durand
- Univ. Bordeaux, IECB, Laboratoire ARNA, 2 rue Robert Escarpit, 33607 Pessac (France); Inserm U869, Laboratoire ARNA, 146 rue Léo Saignat, 33076 Bordeaux (France)
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Perrier S, Zhu Z, Fiore E, Ravelet C, Guieu V, Peyrin E. Capillary gel electrophoresis-coupled aptamer enzymatic cleavage protection strategy for the simultaneous detection of multiple small analytes. Anal Chem 2014; 86:4233-40. [PMID: 24716781 DOI: 10.1021/ac5010234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This novel, multi small-analyte sensing strategy is the result of combining the target-induced aptamer enzymatic protection approach with the CGE-LIF (capillary gel electrophoresis with laser-induced fluorescence) technique. The implemented assay principle is based on an analysis of the phosphodiesterase I (PDE I)-mediated size variation of a fluorescein-labeled aptamer (FApt), the enzyme catalyzing the removal of nucleotides from DNA in the 3' to 5' direction. In the absence of the target, the unfolded aptamer was enzymatically cleaved into short DNA fragments. Upon target binding, the DNA substrate was partially protected against enzymatic hydrolysis. The amount of bound aptamer remaining after the exonuclease reaction was proportional to the concentration of the target. The CGE technique, which was used to determine the separation of FApt species from DNA digested products, permitted the quantification of adenosine (A), ochratoxin A (O), and tyrosinamide (T) under the same optimized enzymatic conditions. This assay strategy was subsequently applied to the simultaneous detection of A, O, and T in a single capillary under buffered conditions using corresponding FApt probes of different lengths (23, 36, and 49 nucleotides, respectively). Additionally, the detection of these three small molecules was successfully achieved in a complex medium (diluted, heat-treated human serum) showing a good recovery. It is worth noting that the multiplexed analysis was accomplished for targets with different charge states by using aptamers possessing various structural features. This sensing platform constitutes a rationalized and reliable approach with an expanded potential for a high-throughput determination of small analytes in a single capillary.
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Affiliation(s)
- Sandrine Perrier
- Université Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble, France
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Zhu Z, Ravelet C, Perrier S, Guieu V, Fiore E, Peyrin E. Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules. Anal Chem 2012; 84:7203-11. [PMID: 22793528 DOI: 10.1021/ac301552e] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.
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Affiliation(s)
- Zhenyu Zhu
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble cedex 9, France
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Zhu Z, Schmidt T, Mahrous M, Guieu V, Perrier S, Ravelet C, Peyrin E. Optimization of the structure-switching aptamer-based fluorescence polarization assay for the sensitive tyrosinamide sensing. Anal Chim Acta 2011; 707:191-6. [PMID: 22027138 DOI: 10.1016/j.aca.2011.09.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 08/31/2011] [Accepted: 09/14/2011] [Indexed: 11/19/2022]
Abstract
In this paper, a structure-switching aptamer assay based on a fluorescence polarization (FP) signal transduction approach and dedicated to the L-tyrosinamide sensing was described and optimized. A fluorescently labelled complementary strand (CS) of the aptamer central region was used as a probe. The effects of critical parameters such as buffer composition and pH, temperature, aptamer:CS stoichiometry, nature of the dye (Fluorescein (F) or Texas Red (TR)) and length of the CS (15-, 12-, 9- and 6-mer) on the assay analytical performances were evaluated. Under optimized experimental conditions (10 mM Tris-HCl, 5 mM MgCl(2) and 25 mM NaCl, pH 7.5 temperature of 22°C and stoichiometry 1:1), the results showed that, for a 12-mer CS, the F dye moderately increased the method sensitivity in comparison to the TR label. The F labelled 9-mer CS, however, did not allow the hybrid formation with the functional nucleic acid, thus emphasizing the importance of the nature of the fluorophore. In contrast, the same 9-mer CS labelled with the TR dye was able to effectively associate with the aptamer and was easily displaced upon target binding as demonstrated by a significant improvement of the sensitivity and a detection limit of 250 nM, comparable to those reported with direct aptasensing methods. The present study demonstrates that not only the CS length but also the nature of the dye played a preponderant role in the performance of the structure-switching aptamer assay, highlighting the importance of interdependently controlling these two factors for an optimal FP-based sensing platform.
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Affiliation(s)
- Zhenyu Zhu
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, ICMG FR 2607, Université Grenoble I, Saint-Martin d'Hères, France
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36
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Guieu V, Ravelet C, Perrier S, Zhu Z, Cayez S, Peyrin E. Aptamer enzymatic cleavage protection assay for the gold nanoparticle-based colorimetric sensing of small molecules. Anal Chim Acta 2011; 706:349-53. [PMID: 22023872 DOI: 10.1016/j.aca.2011.08.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/27/2011] [Accepted: 08/31/2011] [Indexed: 11/30/2022]
Abstract
A label-free, homogeneous aptamer-based sensor strategy was designed for the facile colorimetric detection of small target molecules. The format relied on the target-induced protection of DNA aptamer from the enzymatic digestion and its transduction into a detectable signal through the length-dependent adsorption of single-stranded DNA onto unmodified gold nanoparticles (AuNPs). The proof-of-principle of the approach was established by employing the anti-tyrosinamide aptamer as a model functional nucleic acid. In the absence of target, the aptamer was cleaved by the phosphodiesterase I enzymatic probe, leading to the release of mononucleotides and short DNA fragments. These governed effective electrostatic stabilization of AuNPs so that the nanoparticles remained dispersed and red-colored upon salt addition. Upon tyrosinamide binding, the enzymatic cleavage was impeded, resulting in the protection of the aptamer structure. As this long DNA molecule was unable to electrostatically stabilize AuNPs, the resulting colloidal solution turned blue after salt addition due to the formation of nanoparticle aggregates. The quantitative determination of the target can be achieved by monitoring the ratio of absorbance at 650 and 520 nm of the gold colloidal solution. A limit of detection of ~5 μM and a linear range up to 100 μM were obtained. The sensing platform was further applied, through the same experimental protocol, to the adenosine detection by using its DNA aptamer as recognition tool. This strategy could extend the potentialities, in terms of both simplicity and general applicability, of the aptamer-based sensing approaches.
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Affiliation(s)
- Valérie Guieu
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, ICMG FR 2607, Université Grenoble 1, Campus Universitaire, Saint-Martin d'Hères, France
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37
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Baqué M, Le Postollec A, Ravelet C, Peyrin E, Coussot G, Desvignes I, Incerti S, Moretto P, Dobrijevic M, Vandenabeele-Trambouze O. Investigation of low-energy proton effects on aptamer performance for astrobiological applications. Astrobiology 2011; 11:207-211. [PMID: 21434764 DOI: 10.1089/ast.2010.0520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biochips are promising instruments for the search for organic molecules in planetary environments. Nucleic acid aptamers are powerful affinity receptors known for their high affinity and specificity, and therefore are of great interest for space biochip development. A wide variety of aptamers have already been selected toward targets of astrobiological interest (from amino acids to microorganisms). We present a first study to test the resistance of these receptors to the constraints of the space environment. The emphasis is on the effect of cosmic rays on the molecular recognition properties of DNA aptamers. Experiments on beam-line facilities have been conducted with 2 MeV protons and fluences much higher than expected for a typical mission to Mars. Our results show that this irradiation process did not affect the performances of DNA aptamers as molecular recognition tools.
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Affiliation(s)
- M Baqué
- Institut des Biomolécules Max Mousseron-IBMM, Centre National de la Recherche Scientifique, Université de Montpellier, Unité Mixte de Recherche, France
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38
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Zhu Z, Ravelet C, Perrier S, Guieu V, Roy B, Perigaud C, Peyrin E. Multiplexed detection of small analytes by structure-switching aptamer-based capillary electrophoresis. Anal Chem 2010; 82:4613-20. [PMID: 20446673 DOI: 10.1021/ac100755q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Affinity probe capillary electrophoresis (APCE) assays, combining the separation power of CE with the specificity of interactions occurring between a target and a molecular recognition element (MRE), have become important analytical tools in many application fields. In this report, a rationalized strategy, derived from the structure-switching aptamer concept, is described for the design of a novel APCE mode dedicated to small molecule detection. Two assay configurations were reported. The first one, developed for the single-analyte determination, was based on the use of a cholesteryl-tagged aptamer (Chol-Apt) as the MRE and its fluorescein-labeled complementary strand (CS*) as the tracer (laser-induced fluorescence detection). Under micellar electrokinetic chromatography (MEKC) conditions, free CS* and the hybrid formed with Chol-Apt (duplex*) were efficiently separated (and then quantified) through the specific shift of the electrophoretic mobility of the cholesteryl-tagged species in the presence of a neutral micellar phase. When the target was introduced into the preincubated sample, the hybridized form was destabilized, resulting in a decrease in the duplex* peak area and a concomitant increase in the free CS* peak area. The second format, especially designed for multianalyte sensing, employed dually cholesteryl- and fluorescein-labeled complementary strands (Chol-CS*) of different lengths and unmodified aptamers (Apt). The size-dependent electrophoretic separation of different Chol-CS* forms from each other and from their corresponding duplexes* was also accomplished under MEKC conditions. The simultaneous detection of multiple analytes in a single capillary was performed by monitoring accurately each target-induced duplex-to-complex change. This method could expand significantly the potential of small solute APCE analysis in terms of simplicity, adaptability, generalizability, and high-throughput analysis capability.
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Affiliation(s)
- Zhenyu Zhu
- Departement de Pharmacochimie Moléculaire, UMR 5063 CNRS, ICMG FR 2607, Université Grenoble I, Campus universitaire, Saint-Martin d'Hères, France
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Zaher M, Ravelet C, Vanhaverbeke C, Baussanne I, Perrier S, Fize J, Décout JL, Peyrin E. Enantioseparation by MEKC using a ligand exchange-based chiral pseudostationary phase. Electrophoresis 2010; 30:2869-73. [PMID: 19637217 DOI: 10.1002/elps.200800832] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this paper, a new ligand-exchange -MEKC mode, based on the design of a unique lipohilic species (4'-octadecylneamine derivative), which served both as micelle-forming surfactant (by its hydrophobic part) and central ion-complexing ligand (by its hydrophilic part) is described. The CMC of the used lipophilic neamine derivative was first determined by surface tension measurements. Subsequent NMR experiments were performed in order to investigate the Cu(II) binding properties of the neamine micellar phase. The enantioseparation properties of both the octadecylneamine derivative-Cu(II) MEKC and the native neamine-Cu(II) CE systems were evaluated and compared using the tryptophan racemate as a probe analyte. The effects of several different electrophoretic conditions on the enantiomer migration behavior in the ligand-exchange-MEKC mode were examined. The developed methodology was also applied to the enantioseparation of other analytes such as 1-methyl-tryptophan, 3,5-diiodo-tyrosine and 1-naphtyl-alanine.
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Affiliation(s)
- Mustapha Zaher
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, Institut de Chimie Moléculaire de Grenoble FR 2607, Université Grenoble I (Joseph Fourier), UFR de Pharmacie, Grenoblex, France
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Perrier S, Ravelet C, Guieu V, Fize J, Roy B, Perigaud C, Peyrin E. Rationally designed aptamer-based fluorescence polarization sensor dedicated to the small target analysis. Biosens Bioelectron 2009; 25:1652-7. [PMID: 20034782 DOI: 10.1016/j.bios.2009.12.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 11/27/2009] [Accepted: 12/02/2009] [Indexed: 11/19/2022]
Abstract
A direct fluorescence polarization (FP) assay strategy, dedicated to the small molecule sensing and based on the unique induced-fit binding mechanism of end-labelled nucleic acid aptamers, has been recently developed by our group. Small target binding has been successfully converted into a significant increase of the fluorescence anisotropy signal presumably produced by the reduction of the local motional freedom of the dye. In order to generalize the approach, a rational FP sensor methodology was established herein, by engineering instability in the secondary structure of an aptameric recognition element. The anti-adenosine DNA aptamer, labelled by a single fluorescein dye at its 3' extremity, was employed as a model functional nucleic acid probe. The terminal stem of the stem-loop structure was shortened to induce a destabilized/denatured conformation which promoted the local segmental mobility of the dye and then a significant depolarization process. Upon target binding, the structural change of the aptamer induced the formation of a stable stem-loop structure, leading to the reduction of the dye mobility and the increase in the fluorescence anisotropy signal. This reasoned approach was applied to the sensing of adenosine and adenosine monophosphate and their chiral analysis.
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Affiliation(s)
- Sandrine Perrier
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, ICMG FR 2607, Université Grenoble I, Campus universitaire, 70, rue de la Chimie, 38240 Saint-Martin d'Hères, France
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41
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Ruta J, Perrier S, Ravelet C, Fize J, Peyrin E. Noncompetitive fluorescence polarization aptamer-based assay for small molecule detection. Anal Chem 2009; 81:7468-73. [PMID: 19630421 DOI: 10.1021/ac9014512] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this paper, a new fluorescence polarization (FP) assay strategy is described reporting the first demonstration of a noncompetitive FP technique dedicated to the small molecule sensing. This approach was based on the unique induced-fit binding mechanism of nucleic acid aptamers which was exploited to convert the small target binding event into a detectable fluorescence anisotropy signal. An anti-L-tyrosinamide DNA aptamer, labeled by a single fluorescent dye at its extremity, was employed as a model functional nucleic acid probe. The DNA conformational change generated by the L-tyrosinamide binding was able to induce a significant increase in the fluorescence anisotropy signal. The method allowed enantioselective sensing of tyrosinamide and analysis in practical samples. The methodology was also applied to the L-argininamide detection, suggesting the potential generalizability of the direct FP-based strategy. Such aptamer-based assay appeared to be a sensitive analytical system of remarkable simplicity and ease of use.
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Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble cedex 9, France
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Ruta J, Perrier S, Ravelet C, Roy B, Perigaud C, Peyrin E. Aptamer-modified micellar electrokinetic chromatography for the enantioseparation of nucleotides. Anal Chem 2009; 81:1169-76. [PMID: 19128144 DOI: 10.1021/ac802443j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this paper, a new aptamer-based capillary electrophoresis (CE) method, which was able to separate the enantiomers of an anionic target (adenosine monophosphate, AMP) displaying the same electrophoretic mobility as that of the oligonucleotidic chiral selector, is reported. The design of the aptamer-modified micellar electrokinetic chromatography (MEKC) mode consisted of nonionic micelles which acted as a pseudostationary phase and a hydrophobic cholesteryl group-tagged aptamer (Chol-Apt) which partitioned into the uncharged micellar phase. Under partial-filling format and suppressed electroosmotic flow conditions, the strong mobility alteration of Chol-Apt permitted AMP enantiomers to pass through the micelle-anchored aptamer zone and promoted the target enantioseparation. The influence of several electrophoretic parameters (such as concentration and nature of the nonionic surfactant, preincubation of the Chol-Apt and surfactant, capillary temperature, and applied voltage) on the AMP enantiomer migration was investigated in order to define the utilization conditions of the aptamer-modified MEKC mode. The chiral resolution, in a single run, of three adenine nucleotides, i.e., AMP, ADP (adenosine diphosphate), and ATP (adenosine triphosphate), was further accomplished using such methodology. This approach demonstrates the possibility to extend the CE applicability of aptamer chiral selectors to potentially any target, without restriction on its charge-to-mass ratio.
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Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble Cedex 9, France
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43
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Ruta J, Ravelet C, Baussane I, Fize J, Décout JL, Peyrin E. Competitive affinity capillary electrophoresis assay based on a "hybrid" pre-incubation/on-capillary mixing format using an enantioselective aptamer as affinity ligand. J Sep Sci 2008; 31:2239-43. [PMID: 18546393 DOI: 10.1002/jssc.200700633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this paper, we describe an aptamer-based competitive affinity CE (ACE) assay involving (i) the pre-incubation of the target (D-arginine) and the specific ligand (anti-D-arginine-L-RNA aptamer) before (ii) the competition with the labeled target (dansylated D-arginine) through an on-capillary mixing strategy. The effects of some critical operating parameters such as the applied voltage and the sample-aptamer mixture plug length on the assay sensitivity were investigated. The ACE assay appeared particularly dependent on the plug length of the pre-incubated sample-aptamer solution. It was shown that this "hybrid" strategy significantly improved the assay sensitivity relative to that obtained with a "full" on-capillary mixing approach.
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Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire, Institut de Chimie Moléculaire de Grenoble, Université Grenoble I (Joseph Fourier), UFR de Pharmacie, Grenoble, France
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Abstract
Two kinds of chiral stationary phases (CSPs) can be distinguished: (i) the "conventional" CSPs for which the selectivity is not pre-determined and (ii) the CSPs which are characterized by a predictable elution order, depending on the target enantiomer used for the selection of the chiral selector. At the present time, three general methodologies have been described to create chiral selectors specifically designed against the racemate to resolve: the molecular imprinting technology, the production of antibodies and the combinatorial approach. The latter methodology involves two categories of procedures to develop CSPs: an approach from a small library of low-molecular weight selectors and an approach from a very large library of single-stranded oligonucleotides (DNA and RNA aptamers). In this review, the recent advances in the HPLC applications of the chiral selectors identified through these two combinatorial procedures are addressed.
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Affiliation(s)
- Corinne Ravelet
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, Institut de Chimie Moléculaire de Grenoble, France
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45
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Ruta J, Ravelet C, Désiré J, Décout JL, Peyrin E. Covalently bonded DNA aptamer chiral stationary phase for the chromatographic resolution of adenosine. Anal Bioanal Chem 2007; 390:1051-7. [PMID: 17899039 DOI: 10.1007/s00216-007-1552-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 08/07/2007] [Accepted: 08/09/2007] [Indexed: 10/22/2022]
Abstract
In this work, a target-specific aptamer chiral stationary phase (CSP) based on the oligonucleotidic selector binding to silica particles through a covalent linkage was developed. An anti-D-adenosine aptamer was coupled, using an in-situ method, by way of an amide bond to macroporous carboxylic acid based silica. Frontal chromatography analysis was performed to evaluate the column properties, i.e., determination of the stationary phase binding capacity and the dissociation constant of the target-immobilized aptamer complex. It was found that such covalent immobilization was able to maintain the aptamer binding properties at a convenient level for an efficient enantioseparation. Subsequently, the separation of adenosine enantiomers was investigated under different operating conditions, including changes in the eluent's ionic strength and the proportion of organic modifiers as well as column temperatures. It was demonstrated that, under various conditions of use and storage, the present CSP was stable over time.
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Affiliation(s)
- Joséphine Ruta
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, Université Joseph Fourier-CNRS, 3804, Grenoble, France
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Ruta J, Ravelet C, Baussanne I, Décout JL, Peyrin E. Aptamer-based enantioselective competitive binding assay for the trace enantiomer detection. Anal Chem 2007; 79:4716-9. [PMID: 17511423 DOI: 10.1021/ac070469d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [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: 11/28/2022]
Abstract
The development of highly enantioselective assays and sensors has received much attention for the determination of enantiomeric impurities at a low level. For chiral compounds, the efficient monitoring of the in selection procedure has allowed the isolation of nucleic acid aptamers which are able to strongly discriminate the target enantiomers. In this paper, we demonstrated for the first time that an aptamer can be successfully used to design a highly enantioselective tool for the trace enantiomer detection. The aptamer-based stereoselective assay was developed using an affinity capillary electrophoresis-based competitive, homogeneous format and an on-capillary mixing approach. Detection of as low as 0.01% of the minor enantiomer in a nonracemic mixture can be achieved, in a short analysis time (<5 min).
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Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, ICMG FR 2607, Université Joseph Fourier, UFR de Pharmacie de Grenoble, 5, Avenue de Verdun, 38240 Meylan, France
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Ruta J, Ravelet C, Grosset C, Fize J, Ravel A, Villet A, Peyrin E. Enantiomeric separation using an l-RNA aptamer as chiral additive in partial-filling capillary electrophoresis. Anal Chem 2007; 78:3032-9. [PMID: 16642990 DOI: 10.1021/ac060033i] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [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: 11/28/2022]
Abstract
In this paper, we report the chiral resolution of arginine using an anti-arginine l-RNA aptamer chiral selector in partial-filling CE. The effects of the capillary temperature, sample load, and aptamer plug length on the enantiomeric separation were assessed. Very high chiral resolving capability was observed at low or moderate capillary temperatures (the target peak being not detected in the separation window), whereas the practical chiral resolution was achieved only at high enough temperatures (50-60 degrees C). Over this high-temperature range, the electrophoretic behavior of the target enantiomer appeared to result from a combination of binding site heterogeneity, slow desorption kinetics, and concentration overload of aptamer binding sites. From additional thermal UV melting experiments, three RNA conformations were identified for the 50-60 degrees C temperatures. It was suggested that the presence of these different RNA conformations was a plausible source of the binding site heterogeneity.
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Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, ICMG FR 2607, Université Joseph Fourier, UFR de Pharmacie de Grenoble, Avenue de Verdun, 38240 Meylan, France
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48
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Abstract
An immobilized anti-L-arginine d-RNA aptamer, used as a target-specific chiral stationary phase (CSP), was found to be very quickly degraded by RNases under usual chromatographic utilization and storage. To overcome this severe limitation for a practical use, a CSP based on the L-RNA aptamer, that is, the mirror image of the D-RNA aptamer, was created. It was shown that this mirror-image approach was a very simple and powerful strategy to develop a highly stable stationary phase due to the intrinsic insensitivity of l-RNA to the RNase degradation. In addition, such an approach allowed one to reverse the enantiomer elution order relative to that obtained with the corresponding d-RNA CSP.
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Affiliation(s)
- Agnès Brumbt
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, Institut de Chimie Moléculaire de Grenoble FR 2607, Université Joseph Fourier, UFR de Pharmacie de Grenoble, Avenue de Verdun, 38240 Meylan, France
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49
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Ravelet C, Ravel A, Grosset C, Villet A, Geze A, Wouessidjewe D, Peyrin E. STOICHIOMETRY AND FORMATION CONSTANTS OF SIX PAHs WITH γ-CYCLODEXTRIN, DETERMINED BY HPLC USING A CYANO STATIONARY PHASE. J LIQ CHROMATOGR R T 2006. [DOI: 10.1081/jlc-120008757] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Corinne Ravelet
- a Laboratoire de Chimie Analytique , UFR de Pharmacie , Domaine de la Merci, 38700, La Tronche, France
| | - Anne Ravel
- a Laboratoire de Chimie Analytique , UFR de Pharmacie , Domaine de la Merci, 38700, La Tronche, France
| | - Catherine Grosset
- a Laboratoire de Chimie Analytique , UFR de Pharmacie , Domaine de la Merci, 38700, La Tronche, France
| | - Annick Villet
- a Laboratoire de Chimie Analytique , UFR de Pharmacie , Domaine de la Merci, 38700, La Tronche, France
| | - Annabelle Geze
- b Laboratoire de Pharmacotechnie , UFR de Pharmacie , 5 Avenue de Verdun, 38243, Meylan Cedex, France
| | - Denis Wouessidjewe
- b Laboratoire de Pharmacotechnie , UFR de Pharmacie , 5 Avenue de Verdun, 38243, Meylan Cedex, France
| | - Eric Peyrin
- a Laboratoire de Chimie Analytique , UFR de Pharmacie , Domaine de la Merci, 38700, La Tronche, France
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Ruta J, Grosset C, Ravelet C, Fize J, Villet A, Ravel A, Peyrin E. Chiral resolution of histidine using an anti-D-histidine L-RNA aptamer microbore column. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 845:186-90. [PMID: 16870513 DOI: 10.1016/j.jchromb.2006.06.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/15/2006] [Accepted: 06/17/2006] [Indexed: 11/30/2022]
Abstract
In this paper, we report a new anti-amino acid aptamer chiral stationary phase (CSP). The enantiomers of histidine were separated using an immobilized histidine-specific L-RNA aptamer (40-mer) and an aqueous buffer as mobile phase. The effects of the variation of different operating parameters, including the mobile phase pH and the MgCl2 concentration as well as the column temperature, on the solute retention were assessed. The results suggested that (i) the protonated form of histidine was involved in the stereospecific RNA binding and (ii) Mg2+ was essential for the target enantiomer binding to the specific aptamer sites. From a practical point of view, it appeared that the baseline resolution in a minimum analysis time can be achieved at a column temperature of 35 degrees C for an eluent containing 10 mM of MgCl2, pH 5.5.
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Affiliation(s)
- Josephine Ruta
- Département de Pharmacochimie Moléculaire UMR 5063 CNRS, Institut de Chimie Moléculaire de Grenoble FR 2607, Université Joseph Fourier, UFR de Pharmacie de Grenoble, Avenue de Verdun, 38240 Meylan, France
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