Polarization Induced Electro-Functionalization of Pore Walls: A Contactless Technology.

This review summarizes recent advances in micro- and nanopore technologies with a focus on the functionalization of pores using a promising method named contactless electro-functionalization (CLEF). CLEF enables the localized grafting of electroactive entities onto the inner wall of a micro- or nano-sized pore in a solid-state silicon/silicon oxide membrane. A voltage or electrical current applied across the pore induces the surface functionalization by electroactive entities exclusively on the inside pore wall, which is a significant improvement over existing methods.

Carbohydrates as new probes for the identification of closely related Escherichia coli strains using surface plasmon resonance imaging.

Prevention of foodborne diseases depends highly on our ability to control rapidly and accurately a possible contamination of food. So far, standard procedures for bacterial detection require time-consuming bacterial cultures on plates before the pathogens can be detected and identified. We present here an innovative biochip, based on direct differential carbohydrate recognitions of five closely related Escherichia coli strains, including the enterohemorragic E.

Electrochemical transduction of DNA hybridization at modified electrodes by using an electroactive pyridoacridone intercalator.

A synthetic redox probe structurally related to natural pyridoacridones was designed and electrochemically characterised. These heterocycles behave as DNA intercalators due to their extended planar structure that promotes stacking in between nucleic acid base pairs. Electrochemical characterization by cyclic voltammetry revealed a quasi-reversible electrochemical behaviour occurring at a mild negative potential in aqueous solution.

Binding of chondroitin 4-sulfate to cathepsin S regulates its enzymatic activity.

Human cysteine cathepsin S (catS) participates in distinct physiological and pathophysiological cellular processes and is considered as a valuable therapeutic target in autoimmune diseases, cancer, atherosclerosis, and asthma. We evaluated the capacity of negatively charged glycosaminoglycans (heparin, heparan sulfate, chondroitin 4/6-sulfates, dermatan sulfate, and hyaluronic acid) to modulate the activity of catS. Chondroitin 4-sulfate (C4-S) impaired the collagenolytic activity (type IV collagen) and inhibited the peptidase activity (Z-Phe-Arg-AMC) of catS at pH 5.

Microwave heating for the rapid generation of glycosylhydrazides.

Conditions for simple derivatization of reducing carbohydrates via adipic acid dihydrazide microwave-assisted condensation are described. We demonstrate with a diverse set of oligo- and polysaccharides how to improve a restrictive and labor intensive conventional conjugation protocol by using microwave-assisted chemistry. We show that 5 min of microwave heating in basic or acidic conditions are adequate to generate, in increased yields, intact and functional glycosylhydrazides, whereas hours to days and acidic conditions are generally required under conventional methods.

Polarization-induced local pore-wall functionalization for biosensing: from micropore to nanopore.

The use of biological-probe-modified solid-state pores in biosensing is currently hindered by difficulties in pore-wall functionalization. The surface to be functionalized is small and difficult to target and is usually chemically similar to the bulk membrane. Herein, we demonstrate the contactless electrofunctionalization (CLEF) approach and its mechanism.

Polypyrrole-oligosaccharide microarray for the measurement of biomolecular interactions by surface plasmon resonance imaging.

The polypyrrole approach initially developed for the construction of DNA chips, has been extended to other biochemical compounds such as proteins and more recently oligosaccharides. The copolymerization of a pyrrole monomer with a biomolecule bearing a pyrrole group by an electrochemical process allows a very fast coupling of the biomolecule (probe) to a gold layer used as a working electrode. Fluorescence-based detection is the reference method to detect interactions on biochips; however an alternative label free method, could be more convenient for rapid screening of biointeractions.

Blood cell capture on antibody microarrays and monitoring of the cell capture using surface plasmon resonance imaging.

Blood is a tremendous source of data for diagnostic purposes. Thanks to the qualitative and quantitative analysis of the different cell types carried into the blood stream. To that end, cell capture of several cell types at different locations on a microarray is an interesting alternative to classical techniques run 'in solution' as it allows simultaneous characterization of several cells on a single device.

Polypyrrole-peptide microarray for biomolecular interaction analysis by SPR imaging.

Nowadays, high-throughput analysis of biological events is a great challenge which could take benefit of the recent development of microarray devices. The great potential of such technology is related to the availability of a chip bearing a large set of probes, stable and easy to obtain, and suitable for ligand-binding detection. Here, we describe a new method based on polypyrrole chemistry, allowing the covalent immobilization of peptides in a microarray format and on a gold surface compatible with the use of surface plasmon resonance.

Electropolymerisable pyrrole-oligonucleotide: synthesis and analysis of ODN hybridisation by fluorescence and QCM.

Conducting polymer films, such as polypyrrole, appear particularly attractive for the immobilisation of biological molecules by entrapment or covalent grafting. We describe here a new pyrrole phosphorarnidite building block allowing the synthesis of oligonucleotide (ODN) bearing a pyrrole moiety. The electropolymerisable pyrrole moiety was then introduced on the 5' end of the oligonucleotide.

Surface plasmon resonance imaging on polypyrrole protein chips: application to streptavidin immobilization and immunodetection.

Initially developed for the construction of DNA chips, the polypyrrole approach has been extended to other biochemical compounds (mainly proteins and oligosaccharides). This method allows one to copolymerize a pyrrole monomer with a biomolecule bearing a pyrrole group; this reaction is based on an electrochemical process allowing a very fast coupling of the biomolecule (probe) to a gold layer used as a working electrode. Fluorescence-based detection processes are classically used for evidence biorecognition on biochips; in order to avoid the labeling of the targets, we propose an alternative method--surface plasmon resonance imaging (SPRi).

Polypyrrole oligosaccharide array and surface plasmon resonance imaging for the measurement of glycosaminoglycan binding interactions.

In order to construct tools able to screen oligosaccharide-protein interactions, we have developed a polypyrrole-based oligosaccharide chip constructed via a copolymerization process of pyrrole and pyrrole-modified oligosaccharide. For our study, GAG (glycosaminoglycans) or GAG fragments, which are involved in many fundamental biological processes, were modified by the pyrrole moiety on their reducing end and then immobilized on the chip. The parallel binding events on the upperside of the surface can be simultaneously monitored and quantified in real time and without labeling by surface plasmon resonance imaging (SPRi).

Clinically related protein-peptide interactions monitored in real time on novel peptide chips by surface plasmon resonance imaging.

Background: Developing rapid, high-throughput assays for detecting and characterizing protein-protein interactions is a great challenge in the postgenomic era. We have developed a new method that allows parallel analysis of multiple analytes in biological fluids and is suitable for biological and medical studies.

Methods: This technology for studying peptide-antibody interactions is based on polypyrrole-peptide chips and surface plasmon resonance imaging (SPRi).

A polypyrrole protein microarray for antibody-antigen interaction studies using a label-free detection process.

Protein microarray is a promising technology that should combine rapidity and easy use with high throughput and versatility. This article describes a method in which an electrocopolymerization process is employed to graft biological molecules on to a chip so that surface plasmon resonance imaging may be used to detect molecular interactions. Copolymerization of pyrrole-modified protein and pyrrole is an efficient grafting process which immobilizes molecules at defined positions on a gold surface.

Versatile analysis of multiple macromolecular interactions by SPR imaging: application to p53 and DNA interaction.

The greatest challenge in the postgenomic era is the description of proteome interactions, such as protein-protein or protein-DNA interactions. Surface plasmon resonance (SPR) is an optical technique in which binding of an analyte to the surface changes the refractive index at the surface/solution interface. Molecular interactions are analysed in real time without a labeling step.

New acridone derivatives for the electrochemical DNA-hybridisation labelling.

In the field of DNA sensing, DNA hybridisation detection is generally performed by fluorescence microscopy. However, fluorescence instrumentation is difficult to miniaturise in order to produce fully integrated DNA chips. In this context, electrochemical detection of DNA hybridisation may avoid this limitation.

Polypyrrole based DNA hybridization assays: study of label free detection processes versus fluorescence on microchips.

In this paper, we present different ways to detect DNA hybridization on a solid support. The grafting chemistry is based on the electro-controlled copolymerization of a pyrrole-modified oligonucleotide and pyrrole. This process allows an easy functionalization of conducting materials.

Electropolymerization as a versatile route for immobilizing biological species onto surfaces. Application to DNA biochips.

Biosensors based on electronic conducting polymers appear particularly well suited to the requirements of modern biological analysis--multi-parametric assays, high information density, and miniaturization. We describe a new methodology for the preparation of addressed DNA matrices. The process includes an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing on their 5' end a pyrrole moiety.

Characterization and optimization of a real-time, parallel, label-free, polypyrrole-based DNA sensor by surface plasmon resonance imaging.

We describe in this paper a methodology to quantify multispot parallel DNA hybridizations and denaturations on gold surfaces by using, on one hand, a polypyrrole-based surface functionalization based on an electrospotting process and, on the other hand, surface plasmon resonance imaging allowing real-time measurements on several DNA spots at a time. Two characterization steps were performed in order to optimize the immobilization of oligonucleotide probes and, thus, to increase the signal-to-noise ratio of monitored hybridization signals: the first step consisted of characterizing the signal dependence upon the density of immobilized 15-mer probes, and, the second step, in analyzing the hybridization response versus spot thickness. We further demonstrated that a surface density of polypyrrole/DNA probes of approximately 130 fmol/ mm2 (590 pg/mm2) optimizes the hybridization signal that can be detected directly.

Electroconducting polymers for the construction of DNA or peptide arrays on silicon chips.

We wish to show in this paper new developments and new applications of the pyrrole copolymerization process allowing the addressing of pyrrole-modified biomolecules on microelectrode arrays. Two main developments are described: the first one concerns the development of multiplexed silicon chips bearing 128 microelectrodes instead of 48 for the passive chips. The second one deals with new applications of this grafting process concerning not only DNA chips but peptide chips too.

Polypyrrole DNA chip on a silicon device: example of hepatitis C virus genotyping.

We describe in this article an oligonucleotide array constructed on a silicon device bearing a matrix of addressable 50-microns microelectrodes. Each electrode was covered by a conducting polymer (polypyrrole) grafted by an oligonucleotide (ODN). The DNA chip was prepared by successive electrochemically addressed copolymerizations of 5' pyrrole-labeled ODN and pyrrole.

Preparation of a DNA matrix via an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group.

A new methodology for the preparation of addressed DNA matrices is described. The process includes an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing on their 5' end a pyrrole moiety introduced by phosphoramidite chemistry. The electro-controlled synthesis of the copolymer (poly-pyrrole) gives, in one step, a solid conducting film deposited on the surface of an electrode.

Chemical synthesis of a biologically active natural tRNA with its minor bases.

The complete chemical synthesis of an E. coli tRNA(Ala) with its specific minor nucleosides, dihydrouridine, ribothymidine and pseudouridine, is reported. The method makes use of protected 2'-O-tertiobutyldimethylsilyl-ribonucleoside-3'-O-(2-cyanoethyl-N- ethyl-N- methyl)phosphoramidites.

[Total chemical synthesis of natural transfer RNA].

New improvements in the chemical synthesis of oligoribonucleotides are reported and they are applied to the first total chemical synthesis of a natural RNA. This E. coli K12 alanine tRNA contains in its sequence dihydrouridine, ribothymidine and pseudo-uridine.