Institut Des Sciences Analytiques

The different steps of the immobilization process of single-stranded DNA (ssDNA) on surfaces by means of chemical grafting have been investigated using systematic measurements of grafting and hybridization densities by means of radioactive labelling. The immobilization by chemical grafting to a dense monomolecular layer of N-hydroxysuccinimidyl ester reactive functions attached to silica plates was performed from a dilute solution of amino-terminated oligonucleotides (10 mol/l). The slow evaporation of the solvent allowed to increase the DNA grafting density by a factor of 10. A precise control of the rinsing process that followed the immobilization reaction allowed the discrimination between covalently bound and adsorbed oligonucleotides. Repeatable grafting densities, high signal-to-noise ratio and specific hybridization could be obtained if the adsorbed materials have been removed to completion at the rinsing steps. Repeatable hybridisation-denaturation cycles of complementary oligonucleotides could then be obtained at the surface. The most prominent advantages of the covalent binding associated with efficient rinsing are a better reproducibility and repeatability, and the reusability for the hybridization.

A biochip approach based on porous silicon as substrate is presented. The goal is to enhance the sensitivity of the biochip by increasing the specific surface area on the support. The elaboration of porous silicon layers has been optimized to guarantee good accessibility for large biomolecule targets. Oligonucleotide probes are synthesised directly on the surface using phosphoramidite chemistry. The high specific surface area of porous silicon allows the direct characterisation, by infrared spectroscopy, of the porous layer formation and the functionalisation steps. The monolayer grafting and derivatisation protocol is additionally characterized by wettability and fluorescence microscopy. The surface modification of porous layers (i.e. thermal oxidation and chemical derivatisation) ensures the stability of the structure against strong chemical reagents used during the direct oligonucleotide synthesis. Finally the protocol is successfully transferred to a flat Si/SiO 2 substrate, and validated by biological target specific recognition during hybridisation tests. In particular, radioactive measurements show a 10-fold enhancement of the oligonucleotide surface density on the porous silicon substrate compared to the flat thermal silica.

Parallel quantification of a large number of messenger RNA transcripts, using microarray technology, promises to provide unsuspected information about many cellular processes. Although experimental protocols on microarray applications are available, only limited methodological information on glass-slide manufacturing and signal interpretation has been published. The aim of this paper is to provide new insights into the practical aspects of the construction and hybridization of oligonucleotide-based microarrays. The intracellular symbiotic bacterium of aphids, Buchnera aphidicola, is used here as a model organism. The first part of the work is devoted to the optimization of procedures for printing slides, labeling of cDNA targets and hybridization. In the second part, based on a statistical analysis of the results, we discuss the influence of the probe attachment chemistry, of the labeling method, of the oligonucleotide position and of the concentration of a spotted oligonucleotide on signal intensity. The problem of signal specificity is also addressed, based on the calculation of the fluorescent ratio for each probe to its corresponding mismatch control probe. Lastly, the selection of internal spiked RNAs appropriate to our bacterial samples and useful for the data normalization step is presented. D

DNA microarrays are a powerful experimental tool for the detection of specific genomic sequences and are invaluable to a broad array of applications: clinical diagnosis, personalized medicine, drug research and development, gene therapy, food control technologies, and environmental sciences. Alloimmunization to human platelet antigens (HPAs) is commonly responsible for neonatal alloimmune thrombocytopenia, post-transfusional purpura and platelet transfusion refractoriness. Using DNA microarrays, we developed a diagnosis to type the biallelic HPA-1 platelet group. The region for the human genomic DNA sequence that contains the polymorphism responsible for HPA-1 alleles was amplified by polymerase chain reaction (PCR). The expected DNA fragments were hybridized on DNA microarrays, and the data were analyzed using specially developed software. Our initial results show that the two HPA-1 antigens polymorphisms containing a single base difference were detected using DNA microarrays.

Proteomic microarrays show a wide range of applications for the investigation of DNA-protein, enzyme-substrate as well as protein-protein interactions. Among many challenges to build a viable "protein microarray", the surface chemistry that will allow to immobilised various proteins to retain their biological activity is of paramount importance. Here we report a chemical functionalisation method allowing immobilisation of oligo-peptides onto silica surface (porous silica, glass, thermal silicon dioxide). Substrates were first derivatised with a monofunctional silane allowing the elaboration of dense and uniform monolayers in highly reproducible way. Prior to the oligo-peptides grafting, this organic layer was functionalised with an amino-polyethyleneglycol. The coupling step of oligo-peptides onto functionalised supports is achieved through activation of the C-terminal function of the oligo-peptides. Chemical surface modifications were followed by FTIR spectroscopy, AFM measurements and fluorescence scanning microscopy. A systematic study of the oligo-peptide grafting conditions (time, concentration, solvent) was carried out to optimise this step. The oligo-peptides grafting strategy implemented in this work ensure a covalent and oriented grafting of the oligo-peptides. This orientation is ensured through the use of fully protected peptide except the terminal primary amine. The immobilized peptides will be then deprotected before biological recognition. This strategy is crucial to retain the biological activity of thousands of oligo-probes assessed on a microarray.

This paper presents a comprehensive theory and experimental characterisation of the modulation of the fluorescence intensity by the construction of optical interferences on oxidised silicon substrates used for DNA microarrays. The model predicts a 90-fold variation of the fluorescence signal depending on the oxide thickness. For a Cy3 dye, the signal is maximal for a 90 nm oxide thickness corresponding to a 7.5-fold enhancement with respect to a standard glass substrate. For experimental validation of the model, we have prepared Si/SiO 2 substrates with different parallel steps of decreasing oxide thicknesses on the same sample using a buffered oxide etch (BOE) etching process after thermal oxidation. The SiO 2 surface has been functionalised by a silane monolayer before in situ synthesis of L185 oligonucleotide probes. After hybridisation with complementary targets, the variations of the fluorescence intensity versus oxide thickness are in very good accordance with the theoretical model. The experimental comparison against a glass substrate shows a 10-fold enhancement of the detection sensitivity. Our results demonstrate that a Si/SiO 2 substrate is an attractive alternative to standard glass slides for the realisation of fluorescence DNA microarrays whenever detection sensitivity is an important issue.

Using two different 25-mer oligonucleotide probes covalently grafted on a silicon substrate, we demonstrate how efficient atomic force microscopy (AFM) can be for monitoring each step of DNA chip preparation: from probe immobilization to hybridization on the molecular scale. We observed the probe-molecule organization on the chip after immobilization, and the target molecules, which hybridized with probes could be individually identified. This article presents a method of straightforwardly identifying not only single and double DNA strands, but also, and more significantly, the hybridized part on them.

An acrylate monolith has been synthesized into a cyclic olefin copolymer microdevice for reversed-phase electrochromatography purposes. Microchannels, designed by hot embossing, were filled up with an acrylate monolith to serve as a hydrophobic stationary phase. A lauryl acrylate monolith was formulated to suit the hydrophobic material, by implementing 100% organic porogenic solvent. This new composition was tested in capillary prior to its transfer into the microfluidic device. Surface functionalization of the cyclic olefin copolymer surface was applied using UV-grafting technique to improve the covalent attachment of this monolith to the plastic walls of the microfluidic chip. The on-chip performances of this monolith were evaluated in detail for the reversed-phase electrochromatographic separation of polycyclic aromatic hydrocarbons, with plate heights reaching down to 10 μm when working at optimal velocity.

A micro-immunoaffinity monolithic column (IAC) was developed and in-line coupled with capillary zone electrophoresis in a fully automated way with Ochratoxin A as test solute. The in-line microimmunoaffinity columns based on monolithic methacrylate polymers (EDMA-GMA) were prepared in situ at the inlet end of a PTFE coated fused silica capillary by UV initiated polymerization and subsequently grafted with antibodies. These IACs were thoroughly characterized. The synthesis of the polymeric support was first demonstrated to be reproducible in terms of permeability, surface properties and efficiency. The antibodies immobilization was then studied by a new original hydrodynamic method (ADECA) allowing the in situ quantitative determination (at a miniaturized scale) of the total amount of immobilized antibodies. The combination of this measurement with the binding capacity of the IAC allowed, for the first time, the in situ determination of immobilized antibody activity. A total of 260 ± 15 ng (1.6 ± 0.1 pmol) of IgG antibodies/cm in 75 m i.d. monolithic column (i.e. 18 g mg −1 ) was obtained with (anti-Ochratoxin A/Ochratoxin A) as antibody/antigen model. 40% of the immobilized antibodies remain active corresponding to a binding capacity of 1.2 ± 0.2 pmol antigen/cm (i.e. 600 pg/cm of our test solute OTA), a very high capacity when dealing with trace analysis and with regard to the detection limits (30 pg and 0.5 pg with UV and LIF detection, respectively). The recovery yields were quantitative with negligible non-specific adsorption and allow analysis of diluted samples (1 ng mL −1 ) for a percolated volume of 10 L. It was also demonstrated that despite the progressive denaturation of antibodies consecutive to the elution step, the binding capacity of the IAC remained high enough to implement at least 15 consecutive analyses with the same column and in a fully automated way.