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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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2
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Zhang J, Lucas RA, Gu Y, Yang Y, Sun K, Li H. Nanopore-Based Electrodes for Quinotrione Detection: Host-Guest-Induced Electrochemical Signal Switching. Anal Chem 2021; 93:5430-5436. [PMID: 33760588 DOI: 10.1021/acs.analchem.0c05033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanopore-based detection techniques, with a wide range of transport properties, exhibit impressive selectivity and sensitivity for analytes. To expand the application of nanoporous sensors, real-time and fast detection of targets, all within a portable device, is highly desired for nanopore-based sensors. In addition, to improve the accuracy of the output signal, more appropriate readout methods also need to be explored. In this manuscript, we describe a nanopore-based electrode, regarded as NAC-P6-PC@AuE, prepared by coupling a pillararene-based nanoporous membrane with an electrochemical impedance measurement method. The fabricated device is demonstrated by exposing pillararene-based receptors to trace amounts of pesticide molecules. NAC-P6-PC@AuE devices exhibit distinguished selectivity to quinotrione, as well as the ability to quantify quinotrione with a limit of quantitation (LOQ) of 10 nM. The mechanism that allows sensing was verified using finite-element simulations and may be explained as host-guest-induced surface charge shielding, which influences the electrochemical response of probe molecules. The applications of this nanopore-based electrode may be extended toward other target molecules by decorating the nanopore surfaces with specifically chosen receptors.
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Affiliation(s)
- Jin Zhang
- National Engineering Research Center for Fine Petrochemical Intermediates, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou730000, P. R. China.,Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Rachel A Lucas
- Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Yulin Gu
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Yuxia Yang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Kunpeng Sun
- National Engineering Research Center for Fine Petrochemical Intermediates, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou730000, P. R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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Bonnet H, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Negative SPR Signals during Low Molecular Weight Analyte Recognition. Anal Chem 2021; 93:4134-4140. [PMID: 33577288 DOI: 10.1021/acs.analchem.1c00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface plasmon resonance (SPR) is a powerful technique for studying biomolecular interactions mainly due to its sensitivity and real-time and label free advantages. While SPR signals are usually positive, only a few studies have reported sensorgrams with negative signals. The aim of the present work is to investigate and to explain the observation of negative SPR signals with the hypothesis that it reflects major changes in ligand conformation resulting from target binding. We demonstrated that these negative unconventional signals were due to the negative complex (ligand/analyte) refractive index increment (RII) deviation from the sum of the RII of the individual entities which counterbalanced the theoretical increase of the signal triggered by the target recognition and the ligand folding. We also found that the conformation change of biomolecules can induce a negative or a positive complex RII deviation depending on its sequence and immobilization mode.
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Affiliation(s)
- H Bonnet
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - L Coche-Guérente
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - E Defrancq
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - N Spinelli
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - A Van der Heyden
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - J Dejeu
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
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Hao C, Xu L, Kuang H, Xu C. Artificial Chiral Probes and Bioapplications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1802075. [PMID: 30656745 DOI: 10.1002/adma.201802075] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/29/2018] [Indexed: 06/09/2023]
Abstract
The development of artificial chiral architectures, especially chiral inorganic nanostructures, has greatly promoted research into chirality in nanoscience. The nanoscale chirality of artificial chiral nanostructures offers many new application opportunities, including chiral catalysis, asymmetric synthesis, chiral biosensing, and others that may not be allowed by natural chiral molecules. Herein, the progress achieved during the past decade in chirality-associated biological applications (biosensing, biolabeling, and bioimaging) combined with individual chiral nanostructures (such as chiral semiconductor nanoparticles and chiral metal nanoparticles) or chiral assemblies is discussed.
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Affiliation(s)
- Changlong Hao
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Liguang Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
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Vignon A, Flaget A, Michelas M, Djeghdir M, Defrancq E, Coche-Guerente L, Spinelli N, Van der Heyden A, Dejeu J. Direct Detection of Low-Molecular-Weight Compounds in 2D and 3D Aptasensors by Biolayer Interferometry. ACS Sens 2020; 5:2326-2330. [PMID: 32786219 DOI: 10.1021/acssensors.0c00925] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The direct biolayer interferometry (BLI) measurement of low-molecular-weight (LMW) analytes (<200 Da) still represents a challenge, in particular, when low receptor densities are used. BLI is a powerful optical technique for the label-free, real-time characterization and quantification of biomolecular interactions at interfaces. We demonstrate herein that the quantification of biomolecular recognition is possible by BLI using either 2D-like or 3D platforms for aptamer ligand immobilization. The influence of the aptamer density on the interaction was evaluated and compared for the two sensor architectures. Despite the LMW of the analyte, BLI monitoring led to signals that are exploitable for affinity and kinetic studies, even at low aptamer density. We demonstrate that the immobilization format as well as the aptamer density has a crucial influence on the determination of the recognition parameters.
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Affiliation(s)
- Anthony Vignon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Arthur Flaget
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Maxime Michelas
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Mehdi Djeghdir
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Nicolas Spinelli
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
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Lu H, Wang Z, Fan X, Wang H, Zhang Q, Fu M, Ning G, Zhang Y, Wang H. Electrochemical chiral amino acid biosensor based on dopamine-localized gold nanoparticles @ left-handed spiral chiral carbon nanotubes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3901-3908. [PMID: 32716415 DOI: 10.1039/d0ay00921k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The high electrocatalytic performance plays a decisive role in the efficient electrochemical sensing of electrocatalysts. A spiral chiral carbon tube (HLCNT) loaded with gold nanoparticles (AuNPs) was prepared by electrochemical methods. Dopamine was first electropolymerized on the surface of the HLCNT, and then it acted as a localizer to uniformly load the AuNPs onto the surface of the HLCNT. The dopamine-localized gold nanoparticles @ left-handed spiral chiral carbon nanotubes (HLCNT-AuNPs-2) material combined the chiral structure of chiral carbon nanotubes and the high conductivity of AuNPs. The HLCNT-AuNPs-2 realized the qualitative and quantitative detection of tyrosine (Tyr) and tryptophan (Trp) isomers by their different oxidation potentials and current signals. Through quantitative detection, the analytical results showed that the detection limit of l-Trp was calculated to be 5.31 μM, and the detection limit of l-Tyr was 9.04 μM. More importantly, the material realized the real sample detection of amino acids, which is of great significance for the practical detection of amino acid isomers in medicine and biology.
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Affiliation(s)
- Haijun Lu
- Key Laboratory of Analytical Science and Technology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province, P. R. China.
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Lu Q, Liu X, Hou J, Yuan Q, Li Y, Chen S. Selection of Aptamers Specific for DEHP Based on ssDNA Library Immobilized SELEX and Development of Electrochemical Impedance Spectroscopy Aptasensor. Molecules 2020; 25:molecules25030747. [PMID: 32050451 PMCID: PMC7038136 DOI: 10.3390/molecules25030747] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 12/20/2022] Open
Abstract
A selection of aptamers specific for di(2-ethylhexyl) phthalate (DEHP) and development of electrochemical impedance spectroscopy (EIS) aptasensor are described in this paper. The aptamers were selected from an immobilized ssDNA library using the systematic evolution of ligands by exponential enrichment (SELEX). The enrichment was monitored using real-time quantitative PCR (Q-PCR), and the aptamers were identified by high-throughput sequencing (HTS), gold nanoparticles (AuNPs) colorimetric assay, and localized surface plasmon resonance (LSPR). The EIS aptasensor was developed to detect DEHP in water samples. After eight rounds of enrichment, HTS, AuNPs colorimetric assay, and LSPR analysis indicated that four aptamers had higher binding activity, and aptamer 31 had the highest affinity (Kd = 2.26 ± 0.06 nM). The EIS aptasensor had a limit of detection (LOD) of 0.103 pg/mL with no cross-reactivity to DEHP analogs and a mean recovery of 76.07% to 141.32% for detection of DEHP in water samples. This aptamer is novel with the highest affinity and sensitivity.
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Affiliation(s)
- Qi Lu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi 435002, China; (Q.L.); (Q.Y.); (Y.L.); (S.C.)
| | - Xixia Liu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi 435002, China; (Q.L.); (Q.Y.); (Y.L.); (S.C.)
- Hubei Engineering Research Center of typical wild vegetable Breeding and Comprehensive Utilization Technology; Hubei Normal University, Huangshi 435002, China
- National Demonstration Center for Experimental Biology Education, Hubei Normal University, Huangshi 435002, China
- Correspondence: (X.L.); (J.H.)
| | - Jianjun Hou
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi 435002, China; (Q.L.); (Q.Y.); (Y.L.); (S.C.)
- Hubei Engineering Research Center of typical wild vegetable Breeding and Comprehensive Utilization Technology; Hubei Normal University, Huangshi 435002, China
- National Demonstration Center for Experimental Biology Education, Hubei Normal University, Huangshi 435002, China
- Correspondence: (X.L.); (J.H.)
| | - Qiuxue Yuan
- National Demonstration Center for Experimental Biology Education, Hubei Normal University, Huangshi 435002, China
| | - Yani Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi 435002, China; (Q.L.); (Q.Y.); (Y.L.); (S.C.)
| | - Sirui Chen
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi 435002, China; (Q.L.); (Q.Y.); (Y.L.); (S.C.)
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8
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Oukacine F, Ravelet C, Peyrin E. Enantiomeric sensing and separation by nucleic acids. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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9
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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] [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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Zhang J, Wang Z, Lv S, Zeng X, Sun Y, Li H, Zhang R. The chiral interfaces fabricated by d/l-alanine-pillar[5]arenes for selectively adsorbing ctDNA. Chem Commun (Camb) 2019; 55:778-781. [PMID: 30569920 DOI: 10.1039/c8cc09696a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this paper, the d/l-AP5-interfaces are firstly fabricated by attaching d-alanine-pillar[5]arene and l-alanine-pillar[5]arene (d/l-AP5) onto the gold surface, and they exhibit a significantly different chiral influence on the morphology and the adsorption quantity of the adsorbed ctDNA molecules. The research provides an ideal chiral platform for investigating chiral phenomena in biological systems.
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Affiliation(s)
- Jin Zhang
- The First Hospital of Shanxi Medical University, The Affiliated Cancer Hospital of Shanxi Medical University, Taiyuan 030001, China.
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11
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Guyon H, Mavré F, Catala M, Turcaud S, Brachet F, Limoges B, Tisné C, Micouin L. Use of a redox probe for an electrochemical RNA-ligand binding assay in microliter droplets. Chem Commun (Camb) 2018; 53:1140-1143. [PMID: 28054050 DOI: 10.1039/c6cc07785d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we report an affordable, sensitive, fast and user-friendly electroanalytical method for monitoring the binding between unlabeled RNA and small compounds in microliter-size droplets using a redox-probe and disposable miniaturized screen-printed electrochemical cells.
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Affiliation(s)
- Hélène Guyon
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France. and Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - Marjorie Catala
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Serge Turcaud
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France.
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris, France.
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 4 av. de l'Observatoire, 75006 Paris, France.
| | - Laurent Micouin
- Laboratoire de Chimie et Biochimie pharmacologiques et toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints Pères, 75006 Paris, France.
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Maistrenko VN, Sidel’nikov AV, Zil’berg RA. Enantioselective Voltammetric Sensors: New Solutions. JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1134/s1061934818010057] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Enantioselective analysis of Moxifloxacin hydrochloride enantiomers with graphene-β-Cyclodextrin-nanocomposite modified carbon paste electrode using adsorptive stripping differential pulse Voltammetry. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.07.141] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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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] [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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Du X, Jiang D, Hao N, Qian J, Dai L, Zhou L, Hu J, Wang K. Building a Three-Dimensional Nano-Bio Interface for Aptasensing: An Analytical Methodology Based on Steric Hindrance Initiated Signal Amplification Effect. Anal Chem 2016; 88:9622-9629. [PMID: 27600624 DOI: 10.1021/acs.analchem.6b02368] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The development of novel detection methodologies in electrochemiluminescence (ECL) aptasensor fields with simplicity and ultrasensitivity is essential for constructing biosensing architectures. Herein, a facile, specific, and sensitive methodology was developed unprecedentedly for quantitative detection of microcystin-LR (MC-LR) based on three-dimensional boron and nitrogen codoped graphene hydrogels (BN-GHs) assisted steric hindrance amplifying effect between the aptamer and target analytes. The recognition reaction was monitored by quartz crystal microbalance (QCM) to validate the possible steric hindrance effect. First, the BN-GHs were synthesized via self-assembled hydrothermal method and then applied as the Ru(bpy)32+ immobilization platform for further loading the biomolecule aptamers due to their nanoporous structure and large specific surface area. Interestingly, we discovered for the first time that, without the aid of conventional double-stranded DNA configuration, such three-dimensional nanomaterials can directly amplify the steric hindrance effect between the aptamer and target analytes to a detectable level, and this facile methodology could be for an exquisite assay. With the MC-LR as a model, this novel ECL biosensor showed a high sensitivity and a wide linear range. This strategy supplies a simple and versatile platform for specific and sensitive determination of a wide range of aptamer-related targets, implying that three-dimensional nanomaterials would play a crucial role in engineering and developing novel detection methodologies for ECL aptasensing fields.
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Affiliation(s)
- Xiaojiao Du
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Ding Jiang
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Nan Hao
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Jing Qian
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Liming Dai
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Jianping Hu
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Kun Wang
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, and ‡School of Food and Biological Engineering, Jiangsu University , Zhenjiang, Jiangsu 212013, People's Republic of China
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16
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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17
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18
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Straightforward grafting approach for cyclam-functionalized screen-printed electrodes for selective Cu(II) determination. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.03.141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Perrier S, Bouilloud P, De Oliveira Coelho G, Henry M, Peyrin E. Small molecule aptamer assays based on fluorescence anisotropy signal-enhancer oligonucleotides. Biosens Bioelectron 2016; 82:155-61. [PMID: 27085946 DOI: 10.1016/j.bios.2016.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/23/2016] [Accepted: 04/04/2016] [Indexed: 12/24/2022]
Abstract
Herein, we design novel fluorescence anisotropy (FA) aptamer sensing platforms dedicated to small molecule detection. The assay strategy relied on enhanced fluctuations of segmental motion dynamics of the aptamer tracer mediated by an unlabelled, partially complementary oligonucleotide. The signal-enhancer oligonucleotide (SEO) essentially served as a free probe fraction revealer. By targeting specific regions of the signalling functional nucleic acid, the SEO binding to the unbound aptamer triggered perturbations of both the internal DNA flexibility and the localized dye environment upon the free probe to duplex structure transition. This potentiating effect determined increased FA variations between the duplex and target bound states of the aptameric probe. FA assay responses were obtained with both pre-structured (adenosine) and unstructured (tyrosinamide) aptamers and with dyes of different photochemical properties (fluorescein and texas red). The multiplexed analysis ability was further demonstrated through the simultaneous multicolour detection of the two small targets. The FA method appears to be especially simple, sensitive and widely applicable.
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Affiliation(s)
- Sandrine Perrier
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Prisca Bouilloud
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Gisella De Oliveira Coelho
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Mickael Henry
- 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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20
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He Z, Zang S, Liu Y, He Y, Lei H. A multi-walled carbon nanotubes-poly(l-lysine) modified enantioselective immunosensor for ofloxacin by using multi-enzyme-labeled gold nanoflower as signal enhancer. Biosens Bioelectron 2015; 73:85-92. [DOI: 10.1016/j.bios.2015.05.054] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/02/2015] [Accepted: 05/24/2015] [Indexed: 12/28/2022]
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21
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Souard F, Perrier S, Noël V, Fave C, Fiore E, Peyrin E, Garcia J, Vanhaverbeke C. Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling. Chemistry 2015; 21:15740-8. [PMID: 26356596 DOI: 10.1002/chem.201501527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
Abstract
Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
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Affiliation(s)
- Florence Souard
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
| | - Sandrine Perrier
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Emmanuelle Fiore
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Eric Peyrin
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Julian Garcia
- DCM, Université Grenoble Alpes, Grenoble, 38000 (France).,DCM, CNRS, Grenoble, 38000 (France)
| | - Cécile Vanhaverbeke
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
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22
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Osypova A, Thakar D, Dejeu J, Bonnet H, Van der Heyden A, Dubacheva GV, Richter RP, Defrancq E, Spinelli N, Coche-Guérente L, Labbé P. Sensor Based on Aptamer Folding to Detect Low-Molecular Weight Analytes. Anal Chem 2015; 87:7566-74. [PMID: 26122480 DOI: 10.1021/acs.analchem.5b01736] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aptamers have emerged as promising biorecognition elements in the development of biosensors. The present work focuses on the application of quartz crystal microbalance with dissipation monitoring (QCM-D) for the enantioselective detection of a low molecular weight target molecule (less than 200 Da) by aptamer-based sensors. While QCM-D is a powerful technique for label-free, real-time characterization and quantification of molecular interactions at interfaces, the detection of small molecules interacting with immobilized receptors still remains a challenge. In the present study, we take advantage of the aptamer conformational changes upon the target binding that induces displacement of water acoustically coupled to the sensing layer. As a consequence, this phenomenon leads to a significant enhancement of the detection signal. The methodology is exemplified with the enantioselective recognition of a low molecular weight model compound, L-tyrosinamide (L-Tym). QCM-D monitoring of L-Tym interaction with the aptamer monolayer leads to an appreciable signal that can be further exploited for analytical purposes or thermodynamics studies. Furthermore, in situ combination of QCM-D with spectroscopic ellipsometry unambiguously demonstrates that the conformational change induces a nanometric decrease of the aptamer monolayer thickness. Since QCM-D is sensitive to the whole mass of the sensing layer including water that is acoustically coupled, a decrease in thickness of the highly hydrated aptamer layer induces a sizable release of water that can be easily detected by QCM-D.
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Affiliation(s)
- Alina Osypova
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Dhruv Thakar
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Jérôme Dejeu
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Hugues Bonnet
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Angéline Van der Heyden
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | | | - Ralf P Richter
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France.,§CIC biomaGUNE, 20009 Donostia-San Sebastian, Spain.,∥Max-Planck-Institute for Intelligent Systems, 70569 Stuttgart, Germany
| | - Eric Defrancq
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Nicolas Spinelli
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Liliane Coche-Guérente
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Pierre Labbé
- †Université Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France.,‡CNRS, DCM UMR 5250, F-38000 Grenoble, France
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23
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Jiang H, Ling K, Tao X, Zhang Q. Theophylline detection in serum using a self-assembling RNA aptamer-based gold nanoparticle sensor. Biosens Bioelectron 2015; 70:299-303. [PMID: 25840014 DOI: 10.1016/j.bios.2015.03.054] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/17/2015] [Accepted: 03/23/2015] [Indexed: 01/02/2023]
Abstract
Recently, DNA aptamer-gold nanoparticle (AuNP) conjugates have emerged as novel biosensing tools. Although RNA aptamers are more advantageous than DNA aptamers, their vulnerable nature during the construction of these conjugates restricts the development of RNA aptasensors. In this study, we developed an RNA aptamer-based AuNP sensor for the detection of theophylline in serum, combining the high binding affinity and selectivity of a theophylline RNA aptamer and the fluorescence quenching ability of AuNPs. In order to prevent nuclease degradation during the experimental process, the single strand of the theophylline RNA aptamer (33-mer) was split at the end loop region into two shorter halves, which were able to reassemble to form the theophylline-binding pocket. One fragment was linked to a DNA sequence that included a 15 thymine (T15) spacer and a polyadenine (polyA, A12) tail. The chimeric RNA/DNA oligonucleotide was attached to AuNPs within a few minutes via adsorption of the polyA tail. The other fragment was labeled with a fluorophore (Cy3). The two individual fragments self-assembled in the presence of theophylline. Upon ligand binding, the fragments came into close proximity, resulting in fluorescence quenching. This sensor exhibited a low detection limit of 0.05 µM, with a linear dynamic range from 0.1 to 10 µM in serum. Moreover, the sensor did not recognize theophylline-related compounds (e.g., caffeine and theobromine), demonstrating its high selectivity. This strategy offers new possibilities for the application of RNA aptasensors in clinical settings.
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Affiliation(s)
- Hongyan Jiang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Biomedical Material of Tianjin, Tianjin 300192, PR China
| | - Kai Ling
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Biomedical Material of Tianjin, Tianjin 300192, PR China
| | - Xiaojun Tao
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Biomedical Material of Tianjin, Tianjin 300192, PR China
| | - Qiqing Zhang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Biomedical Material of Tianjin, Tianjin 300192, PR China.
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24
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Mondal PC, Fontanesi C, Waldeck DH, Naaman R. Field and chirality effects on electrochemical charge transfer rates: spin dependent electrochemistry. ACS NANO 2015; 9:3377-84. [PMID: 25752750 DOI: 10.1021/acsnano.5b00832] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This work examines whether electrochemical redox reactions are sensitive to the electron spin orientation by examining the effects of magnetic field and molecular chirality on the charge transfer process. The working electrode is either a ferromagnetic nickel film or a nickel film that is coated with an ultrathin (5-30 nm) gold overlayer. The electrode is coated with a self-assembled monolayer that immobilizes a redox couple containing chiral molecular units, either the redox active dye toluidine blue O with a chiral cysteine linking unit or cytochrome c. By varying the direction of magnetization of the nickel, toward or away from the adsorbed layer, we demonstrate that the electrochemical current depends on the orientation of the electrons' spin. In the case of cytochrome c, the spin selectivity of the reduction is extremely high, namely, the reduction occurs mainly with electrons having their spin-aligned antiparallel to their velocity.
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Affiliation(s)
| | - Claudio Fontanesi
- †Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
- ‡Department of Chemical and Geological Science, University of Modena and Reggio Emilia, Via G. Campi 183, 41125 Modena, Italy
| | - David H Waldeck
- §Department of Chemistry, Pittsburgh University, Pittsburgh Pennsylvania 15260, United States
| | - Ron Naaman
- †Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Feagin TA, Olsen DPV, Headman ZC, Heemstra JM. High-throughput enantiopurity analysis using enantiomeric DNA-based sensors. J Am Chem Soc 2015; 137:4198-206. [PMID: 25747268 DOI: 10.1021/jacs.5b00923] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Distinguishing between the two enantiomers of a molecule is a challenging task due to their nearly identical physical properties. Time-consuming chromatography methods are typically required for this task, which greatly limits the throughput of analysis. Here we describe a fluorescence-based method for the rapid and high-throughput analysis of both small-molecule enantiopurity and concentration. Our approach relies on selective molecular recognition of one enantiomer of the target molecule using a DNA aptamer, and the ability of aptamer-based biosensors to transduce the presence of a target molecule into a dose-dependent fluorescence signal. The key novel aspect of our approach is the implementation of enantiomeric DNA biosensors, which are synthesized from D- and L-DNA, but labeled with orthogonal fluorophores. According to the principle of reciprocal chiral substrate specificity, these biosensors will bind to opposite enantiomers of the target with equal affinity and selectivity, enabling simultaneous quantification of both enantiomers of the target. Using the previously reported DNA biosensor for L-tyrosinamide (L-Tym), we demonstrate the ability to rapidly and accurately measure both enantiopurity and concentration for mixtures of L- and D-Tym. We also apply our enantiomeric biosensors to the optimization of reaction conditions for the synthesis of D-Tym and provide mathematical modeling to suggest that DNA biosensors having only modest binding selectivity can also be used for fluorescence-based enantiopurity measurement. This research provides a generalizable method for high-throughput analysis of reaction mixtures, which is anticipated to significantly accelerate reaction optimization for the synthesis of high-value chiral small molecules.
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Affiliation(s)
- Trevor A Feagin
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - David P V Olsen
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zachary C Headman
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jennifer M Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
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26
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Zor E, Bingol H, Ramanaviciene A, Ramanavicius A, Ersoz M. An electrochemical and computational study for discrimination ofd- andl-cystine by reduced graphene oxide/β-cyclodextrin. Analyst 2015; 140:313-21. [DOI: 10.1039/c4an01751j] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This study indicates the applicability of two different techniques (electrochemical and computational study) for the discrimination of cystine enantiomers (d- andl-cystine) by reduced graphene oxide/β-cyclodextrin (rGO/β-CD) hybrid material.
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Affiliation(s)
- Erhan Zor
- Selcuk University
- Institute of Science
- Department of Chemistry
- Konya
- Turkey
| | - Haluk Bingol
- Necmettin Erbakan University
- A.K. Education Faculty
- Chemistry Department
- Konya
- Turkey
| | - Almira Ramanaviciene
- Vilnius University
- Faculty of Chemistry
- Centre of Nanotechnology and Materials Science
- Vilnius
- Lithuania
| | - Arunas Ramanavicius
- Vilnius University
- Faculty of Chemistry
- Centre of Nanotechnology and Materials Science
- Vilnius
- Lithuania
| | - Mustafa Ersoz
- Selcuk University
- Advanced Technology Research and Application Center
- Konya
- Turkey
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27
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Souada M, Piro B, Reisberg S, Anquetin G, Noël V, Pham MC. Label-free electrochemical detection of prostate-specific antigen based on nucleic acid aptamer. Biosens Bioelectron 2014; 68:49-54. [PMID: 25569871 DOI: 10.1016/j.bios.2014.12.033] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/01/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022]
Abstract
We report a label-free aptasensor to make direct detection of prostate specific antigen (PSA, a biomarker of prostate cancer) using a quinone-containing conducting copolymer acting as redox transducer and grafting matrix for immobilization of the short aptamer strands. It is shown that capture of PSA generates a current decrease (signal-off) measured by Square Wave Voltammetry. This current decrease is specific for PSA above a limit of quantification in the ng mL(-1) range. The change in current is used to determine the PSA-aptamer dissociation constant K(D), of ca. 2.6 nM. To consolidate the proof of concept, a heterogeneous competitive exchange with a complementary DNA strand which breaks PSA-aptamer interactions is studied. This double-check followed by a current increase provides full assurance of a perfectly specific recognition.
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Affiliation(s)
- M Souada
- Univ. Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - B Piro
- Univ. Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France.
| | - S Reisberg
- Univ. Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - G Anquetin
- Univ. Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - V Noël
- Univ. Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - M C Pham
- Univ. Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
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28
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Zhuang J, He Y, Chen G, Tang D. Binding-induced internal-displacement of inverted aptamer beacon: Toward a novel electrochemical detection platform. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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29
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Hun X, Xu Y, Bai L. A chemiluminescence assay for L-histidine based on controlled DNAzyme catalytic reactions on magnetic microparticles. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1359-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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30
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Qiang W, Liu H, Li W, Chen X, Xu D. Label-free detection of adenosine based on fluorescence resonance energy transfer between fluorescent silica nanoparticles and unmodified gold nanoparticles. Anal Chim Acta 2014; 828:92-8. [DOI: 10.1016/j.aca.2014.04.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/10/2014] [Accepted: 04/19/2014] [Indexed: 12/20/2022]
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31
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Song W, Li H, Liang H, Qiang W, Xu D. Disposable electrochemical aptasensor array by using in situ DNA hybridization inducing silver nanoparticles aggregate for signal amplification. Anal Chem 2014; 86:2775-83. [PMID: 24490908 DOI: 10.1021/ac500011k] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Nanomaterials as tracing tags have been widely used in biosensors with high sensitivity and selectivity. In this work, a signal amplification electrochemical aptamer sensing strategy for the detection of protein was designed by combining the hybridization-inducing aggregate of DNA-functionalized silver nanoparticles (AgNPs) and differential pulse stripping voltammetry (DPSV) detection. The multiprobes containing hybridization DNA and aptamers were anchored onto the silver nanoparticles. The protein assay was prepared through the immobilization of capture aptamer that specifically recognizes platelet-derived growth factor (PDGF-BB) on gold nanoparticles modified screen-printed electrode (SPE) array. After a sandwich-type reaction, two kinds of DNA-modified AgNPs were simultaneously added on the electrode surface for specifically recognizing PDGF-BB and forming the AgNPs aggregate caused by in situ hybridization of DNA. Compared to the signal-labeled tag, the tracing aggregate tags showed a strong electroactivity for signal amplification through stripping detection of silver after preoxidation. By using the hybridization-inducing aggregate as electrochemical readouts, the sensor showed wide linear range and low detection limit. The hybridization-inducing AgNPs aggregate were further used as tracing tags in multiplied proteins assays for PDGF-BB and thrombin by using the SPE array chip as sensing platform. The cross-talk between different aptamer-modified electrodes on the same array was avoided because of the advantage of labeled AgNPs. The array detection was also applied in the logic gate operation. The proposed method described here is ideal for multianalytes determination in clinical diagnostics with good analytical performance.
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Affiliation(s)
- Wei Song
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, People's Republic of China
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Moreau J, Challier L, Lalaoui N, Mavré F, Noël V, Limoges B, Schöllhorn B, Fave C. Rational design of a redox-labeled chiral target for an enantioselective aptamer-based electrochemical binding assay. Chemistry 2014; 20:2953-9. [PMID: 24519626 DOI: 10.1002/chem.201302979] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Indexed: 12/18/2022]
Abstract
A series of redox-labeled L-tyrosinamide (L-Tym) derivatives was prepared and the nature of the functional group and the chain length of the spacer were systematically varied in a step-by-step affinity optimization process of the tracer for the L-Tym aptamer. The choice of the labeling position on L-Tym proved to be crucial for the molecular recognition event, which could be monitored by cyclic voltammetry and is based on the different diffusion rates of free and bound targets in solution. From this screening approach an efficient electroactive tracer emerged. Comparable dissociation constants Kd were obtained for the unlabeled and labeled targets in direct or competitive binding assays. The enantiomeric tracer was prepared and its enantioselective recognition by the corresponding anti-D-Tym aptamer was demonstrated. The access to both enantiomeric tracer molecules opens the door for the development of one-pot determination of the enantiomeric excess when using different labels with well-separated redox potentials for each enantiomer.
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Affiliation(s)
- Julie Moreau
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris Cedex 13 (France)
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Cao Y, Chen D, Chen W, Yu J, Chen Z, Li G. Aptamer-based homogeneous protein detection using cucurbit[7]uril functionalized electrode. Anal Chim Acta 2014; 812:45-9. [PMID: 24491763 DOI: 10.1016/j.aca.2014.01.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/27/2013] [Accepted: 01/05/2014] [Indexed: 12/12/2022]
Abstract
A new strategy for homogeneous protein detection is developed based on a cucurbit[7]uril (CB[7]) functionalized electrode. The analytical procedure consists of the binding of target protein to its aptamer in the test solution, followed by an exonuclease-catalyzed digestion of methylene blue (MB) tag labeled DNA oligonucleotides. Since CB[7] molecules immobilized on the electrode may efficiently capture the released MB-labeled nucleotides, the MB tags are concentrated to the electrode surface and subsequently yield highly sensitive electrochemical signal, which is related to the concentration of the target protein. The method combines the host-guest properties of CB[7] with the immobilization-free homogeneous assay, providing a powerful tool for protein detection. Taking the detection of osteopontin as an example, the proposed method can have a linear response to the target protein in a range from 50 to 500 ng mL(-1) with a detection limit of 10.7 ng mL(-1). It can also show high specificity and good reproducibility, and can be used directly for the assay of osteopontin in serum samples.
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Affiliation(s)
- Ya Cao
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Dehu Chen
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China; Department of Hepatobiliary Surgery, The Affiliated Hospital, Nantong University, Nantong 226001, China
| | - Weiwei Chen
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jiacui Yu
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Zhong Chen
- Department of Hepatobiliary Surgery, The Affiliated Hospital, Nantong University, Nantong 226001, China.
| | - Genxi Li
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China; Department of Biochemistry and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China.
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Challier L, Miranda-Castro R, Marchal D, Noël V, Mavré F, Limoges B. Kinetic Rotating Droplet Electrochemistry: A Simple and Versatile Method for Reaction Progress Kinetic Analysis in Microliter Volumes. J Am Chem Soc 2013; 135:14215-28. [DOI: 10.1021/ja405415q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Lylian Challier
- ITODYS, UMR 7086 CNRS, and ‡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
| | - Rebeca Miranda-Castro
- ITODYS, UMR 7086 CNRS, and ‡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
| | - Damien Marchal
- ITODYS, UMR 7086 CNRS, and ‡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, and ‡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
| | - François Mavré
- ITODYS, UMR 7086 CNRS, and ‡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
- ITODYS, UMR 7086 CNRS, and ‡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
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Catalytic DNA-based fluorescence polarization chiral sensing platform for L-histidine detection at trace level. Anal Bioanal Chem 2013; 406:1173-9. [PMID: 23877180 DOI: 10.1007/s00216-013-7208-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/17/2013] [Accepted: 07/02/2013] [Indexed: 12/11/2022]
Abstract
This paper reports a novel fluorescence polarization (FP) chiral sensor approach based on a catalytic DNA. This platform involves an enzyme module (E), which was able to trigger the L-histidine-dependent cleavage of an RNA phosphoester bond of a substrate domain (S), whereas it did not accept the D-enantiomer as cofactor. Two assay formats were proposed, based on bi- and unimolecular strategies. The bimolecular design was related to the use of separate E and fluorescently labelled S* sequences. The two oligonucleotide strands were pre-assembled via complementary regions at their extremities. As the result of the large molecular volume of the formed assembly, the S* probe displayed a high fluorescence anisotropy signal. Upon addition of the L-histidine, the DNAzyme cleaved the phosphoester bond of the S* component, leading to the loss of stem stability and the release of single-stranded products of lower size. This was accompanied by a significant decrease in the fluorescence anisotropy response. As a simpler alternative, the unimolecular design, where E and S sequences are linked together through a loop to form a single fluorescent probe E-S*, was also investigated. It was found that the unimolecular approach provided an improved FP response relative to the bimolecular one. Under optimized operating conditions, such a chiral sensing platform allowed the detection of as low as 0.05% of the L-histidine enantiomer in a non-racemic mixture.
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Manoli K, Magliulo M, Torsi L. Chiral Sensor Devices for Differentiation of Enantiomers. Top Curr Chem (Cham) 2013; 341:133-76. [DOI: 10.1007/128_2013_444] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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37
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Feng L, Xu B, Ren J, Zhao C, Qu X. A human telomeric DNA-based chiral biosensor. Chem Commun (Camb) 2012; 48:9068-70. [DOI: 10.1039/c2cc34776h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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