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Kavand A, Robin P, Mayoraz L, Mensi M, Gerber-Lemaire S. Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry. RSC Adv 2023; 13:34003-34011. [PMID: 38020007 PMCID: PMC10660212 DOI: 10.1039/d3ra04928k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be precisely controlled to achieve the required accuracy and sensitivity. In particular, achieving high hybridization density at the sensing surface is a prerequisite to reach a low limit of detection. We herein describe a strategy based on peptides as anchoring units to immobilize DNA probes at the surface of borosilicate slides. While the coating pathway involves copper-catalyzed click chemistry, a copper-free variation is also reported. The resulting biochips display a high hybridization density (2.9 pmol per cm2) with their targeted gene sequences.
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Affiliation(s)
- Alireza Kavand
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Perrine Robin
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Lucas Mayoraz
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
| | - Mounir Mensi
- ISIC-XRDSAP, EPFL Valais-Wallis Rue de l'Industrie 17 CH-1951 Sion Switzerland
| | - Sandrine Gerber-Lemaire
- Group for Functionalized Biomaterials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne CH-1015 Lausanne Switzerland
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Zhang G, Shan D, Dong H, Cosnier S, Al-Ghanim KA, Ahmad Z, Mahboob S, Zhang X. DNA-Mediated Nanoscale Metal–Organic Frameworks for Ultrasensitive Photoelectrochemical Enzyme-Free Immunoassay. Anal Chem 2018; 90:12284-12291. [DOI: 10.1021/acs.analchem.8b03762] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Dan Shan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | | | - Serge Cosnier
- University of Grenoble Alpes-CNRS, DCM UMR 5250, F-38000 Grenoble, France
| | - Khalid Abdullah Al-Ghanim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Zubair Ahmad
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department of Zoology, Government College University, Faisalabad, Pakistan
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Forato F, Liu H, Benoit R, Fayon F, Charlier C, Fateh A, Defontaine A, Tellier C, Talham DR, Queffélec C, Bujoli B. Comparison of Zirconium Phosphonate-Modified Surfaces for Immobilizing Phosphopeptides and Phosphate-Tagged Proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5480-5490. [PMID: 27166821 DOI: 10.1021/acs.langmuir.6b01020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Different routes for preparing zirconium phosphonate-modified surfaces for immobilizing biomolecular probes are compared. Two chemical-modification approaches were explored to form self-assembled monolayers on commercially available primary amine-functionalized slides, and the resulting surfaces were compared to well-characterized zirconium phosphonate monolayer-modified supports prepared using Langmuir-Blodgett methods. When using POCl3 as the amine phosphorylating agent followed by treatment with zirconyl chloride, the result was not a zirconium-phosphonate monolayer, as commonly assumed in the literature, but rather the process gives adsorbed zirconium oxide/hydroxide species and to a lower extent adsorbed zirconium phosphate and/or phosphonate. Reactions giving rise to these products were modeled in homogeneous-phase studies. Nevertheless, each of the three modified surfaces effectively immobilized phosphopeptides and phosphopeptide tags fused to an affinity protein. Unexpectedly, the zirconium oxide/hydroxide modified surface, formed by treating the amine-coated slides with POCl3/Zr(4+), afforded better immobilization of the peptides and proteins and efficient capture of their targets.
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Affiliation(s)
- Florian Forato
- Chimie et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230 , 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Hao Liu
- Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Roland Benoit
- CRMD-CNRS, 1B rue de la férollerie, 45071 Orléans Cedex 2, France
| | - Franck Fayon
- CNRS, CEMHTI UPR3079, Université de Orléans , F-45071 Orléans, France
| | - Cathy Charlier
- Fonctionnalité et Ingénierie des Protéines (UFIP), Université de Nantes, CNRS, UMR 6286 , 2 rue de la Houssinière BP 92208, 44322 Nantes Cedex 3, France
| | - Amina Fateh
- Fonctionnalité et Ingénierie des Protéines (UFIP), Université de Nantes, CNRS, UMR 6286 , 2 rue de la Houssinière BP 92208, 44322 Nantes Cedex 3, France
| | - Alain Defontaine
- Fonctionnalité et Ingénierie des Protéines (UFIP), Université de Nantes, CNRS, UMR 6286 , 2 rue de la Houssinière BP 92208, 44322 Nantes Cedex 3, France
| | - Charles Tellier
- Fonctionnalité et Ingénierie des Protéines (UFIP), Université de Nantes, CNRS, UMR 6286 , 2 rue de la Houssinière BP 92208, 44322 Nantes Cedex 3, France
| | - Daniel R Talham
- Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Clémence Queffélec
- Chimie et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230 , 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Bruno Bujoli
- Chimie et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230 , 2 rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
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Zhang GY, Deng SY, Cai WR, Cosnier S, Zhang XJ, Shan D. Magnetic zirconium hexacyanoferrate(II) nanoparticle as tracing tag for electrochemical DNA assay. Anal Chem 2015; 87:9093-100. [PMID: 26259126 DOI: 10.1021/acs.analchem.5b02395] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Novel multifunctional magnetic zirconium hexacyanoferrate nanoparticles (ZrHCF MNPs) were prepared, which consisted of magnetic beads (MBs) inner core and zirconium hexacyanoferrate(II) (ZrHCF) outer shell. As an artificial peroxidase, the ZrHCF MNPs exhibited remarkable electrocatalytic properties in the reduction of H2O2 at 0.2 V vs saturated calomel electrode (SCE). On the basis of the bonding interaction between Zr (IV) of the shell ZrHCF framework and phosphonate groups, the 5'-phosphorylated ssDNA probes with a consecutive stretch of guanines as a spacer could be incorporated in ZrHCF MNPs easily. Thus, DNA-grafted ZrHCF MNPs could be simply obtained by magnetic separation. The prepared nanoelectrocatalyst was further used as signal nanoprobe for the ultrasensitive electrochemical DNA assay. Under optimal conditions, the proposed biosensor presents high sensitivity for detecting target DNA with a linear range from 1.0 fM to 1.0 nM and a low detection limit of 0.43 fM. Moreover, it exhibits good performance with excellent selectivity, high stability, and acceptable fabrication reproducibility.
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Affiliation(s)
- Guang-Yao Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Sheng-Yuan Deng
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Wen-Rong Cai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Serge Cosnier
- University of Grenoble Alpes-CNRS , DCM UMR 5250, F-38000 Grenoble, France
| | - Xue-Ji Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
| | - Dan Shan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing, Jiangsu 210094, China
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Liu H, Queffélec C, Charlier C, Defontaine A, Fateh A, Tellier C, Talham DR, Bujoli B. Design and optimization of a phosphopeptide anchor for specific immobilization of a capture protein on zirconium phosphonate modified supports. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13949-13955. [PMID: 25365756 DOI: 10.1021/la5036085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The attachment of affinity proteins onto zirconium phosphonate coated glass slides was investigated by fusing a short phosphorylated peptide sequence at one extremity to enable selective bonding to the active surface via the formation of zirconium phosphate coordinate covalent bonds. In a model study, the binding of short peptides containing zero to four phosphorylated serine units and a biotin end-group was assessed by surface plasmon resonance-enhanced ellipsometry (SPREE) as well as in a microarray format using fluorescence detection of AlexaFluor 647-labeled streptavidin. Significant binding to the zirconated surface was only observed in the case of the phosphopeptides, with the best performance, as judged by streptavidin capture, observed for peptides with three or four phosphorylation sites and when spotted at pH 3. When fusing similar phosphopeptide tags to the affinity protein, the presence of four phosphate groups in the tag allows efficient immobilization of the proteins and efficient capture of their target.
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Affiliation(s)
- Hao Liu
- Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
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Wang R, Wan J, Ma X, Xu X, Liu L. Anchored [RuCl2(p-cymene)]2 in hybrid zirconium phosphate–phosphonate coated and pillared with double-stranded hydrophobic linear polystyrene as heterogeneous catalyst suitable for aqueous asymmetric transfer hydrogenation. Dalton Trans 2013; 42:6513-22. [DOI: 10.1039/c3dt33015j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Queffélec C, Petit M, Janvier P, Knight DA, Bujoli B. Surface modification using phosphonic acids and esters. Chem Rev 2012; 112:3777-807. [PMID: 22530923 DOI: 10.1021/cr2004212] [Citation(s) in RCA: 550] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Clémence Queffélec
- LUNAM Université, CNRS, UMR, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation, UFR Sciences et Techniques, Nantes, France
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Engineering of a phosphorylatable tag for specific protein binding on zirconium phosphonate based microarrays. J Biol Inorg Chem 2011; 17:399-407. [DOI: 10.1007/s00775-011-0863-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 11/15/2011] [Indexed: 10/14/2022]
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9
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Hu R, Wu ZS, Zhang S, Shen GL, Yu R. Robust electrochemical system for screening single nucleotide polymorphisms. Chem Commun (Camb) 2011; 47:1294-6. [DOI: 10.1039/c0cc03884a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sethi D, Kumar A, Gandhi RP, Kumar P, Gupta KC. New protocol for oligonucleotide microarray fabrication using SU-8-coated glass microslides. Bioconjug Chem 2010; 21:1703-8. [PMID: 20712300 DOI: 10.1021/bc100262n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microarray technology has become an important tool for detection and analysis of nucleic acid targets. Immobilization of modified and unmodified oligonucleotides on epoxy-functionalized glass surfaces is often used in microarray fabrication. Here, we demonstrate a protocol that employs coating of SU-8 (glycidyl ether of bisphenol A) onto glass microslides to obtain high density of epoxy functions for efficient immobilization of aminoalkyl-, thiophosphoryl-, and phosphorylated oligonucleotides with uniform spot morphology. The resulting microarrays exhibited high immobilization (∼65%) and hybridization efficiency (30-36%) and were sufficiently stable over a range of temperature and pH conditions. The prominent feature of the protocol is that spots can be visualized distinctly at 0.05 μM probe (a 20-mer oligonucleotide) concentration. The constructed microarrays were subsequently used for detection of base mismatches and bacterial diseases (meningitis and typhoid).
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Affiliation(s)
- D Sethi
- Indian Institute of Toxicology Research (CSIR), Mahatma Gandhi Marg, Lucknow, India
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Sethi D, Gandhi RP, Kuma P, Gupta KC. Chemical strategies for immobilization of oligonucleotides. Biotechnol J 2010; 4:1513-29. [PMID: 19844919 DOI: 10.1002/biot.200900162] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The development of oligonucleotide-based microarrays (biochips) is a major thrust area in the rapidly growing biotechnology industry, which encompasses a diverse range of research areas including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Microarray experiments have proved to be unique in offering cost-effective and efficient analysis at the genomic level. In the last few years, biochips have gained increasing acceptance in the study of genetic and cellular processes. As the increase in experimental throughput has posed many challenges to the research community, considerable progress has been made in the advancement of microarray technology. In this review, chemical strategies for immobilization of oligonucleotides have been highlighted with special emphasis on post-synthetic immobilization of oligonucleotides on glass surface. The major objective of this article is to make the researchers acquainted with some most recent advances in this area.
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Affiliation(s)
- Dalip Sethi
- Institute of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
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Cinier M, Petit M, Williams MN, Fabre RM, Pecorari F, Talham DR, Bujoli B, Tellier C. Bisphosphonate Adaptors for Specific Protein Binding on Zirconium Phosphonate-based Microarrays. Bioconjug Chem 2009; 20:2270-7. [DOI: 10.1021/bc9002597] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mathieu Cinier
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Marc Petit
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Monique N. Williams
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Roxane M. Fabre
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Frédéric Pecorari
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Daniel R. Talham
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Bruno Bujoli
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
| | - Charles Tellier
- Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, UFR Sciences et Techniques, Université de Nantes, CNRS, UMR 6204, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, France, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France, and Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
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Fabre RM, Talham DR. Stable supported lipid bilayers on zirconium phosphonate surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:12644-12652. [PMID: 19711922 DOI: 10.1021/la901920y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Supported lipid bilayers that can fully represent biological cell membranes are attractive biomimetic models for biophysical and biomedical applications. In this study, we develop a new approach to engineering stable supported lipid membranes and demonstrate their utility for the study of protein-membrane interactions. This system uses a zirconium phosphonate monolayer to modify a substrate and generate a reactive surface that tethers the lipid membrane via a highly covalent bond between surface zirconium ions and divalent phosphate groups in the lipid assembly, for example, from phosphatidic acid. An advantage of the approach is that the zirconium phosphonate modifier can be applied to nearly any surface, allowing the same methods to be used on glass, gold, silicon, or plastic supports. The lipid bilayers are formed by vesicle fusion, either directly on the zirconated surface to form symmetric bilayers or following deposition of a Langmuir-Blodgett lipid layer to generate asymmetric bilayers. The membrane formation was studied by surface plasmon resonance enhanced ellipsometry (SPREE) as the phosphatidic acid composition was varied. We found that 10% of phosphatidic acid generates supported lipid bilayers stable to dehydration. The two-dimensional fluidity of these systems was characterized by fluorescence recovery after photobleaching (FRAP) measurements. Uniform, mobile supported lipid bilayers with lipid diffusion coefficients of approximately 4 mum(2)/s were obtained. SPREE was also used to measure kinetic parameters of the binding of melittin, a bee venom peptide, to asymmetric lipid bilayers with different electrostatic properties. The results are comparable to those obtained by other research groups, confirming that the model membranes behave as expected. Overall, the results of this study prove that supported lipid bilayers on zirconium phosphonate inorganic surfaces make up an attractive biomimetic system that is highly stable, can be used with multiple substrates, and does not require any biomolecule synthetic modifications.
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Affiliation(s)
- Roxane M Fabre
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA
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