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Electronic hybridization detection in microarray format and DNA genotyping
Antoine Blin, Ismaïl Cissé and Ulrich Bockelmann
Scientific Reports - 4(n°4194) - DOI: 10.1038/srep04194 - 2013
We describe an approach to substituting a fluorescence microarray with a surface made of an arrangement of electrolyte-gated field effect transistors. This was achieved using a dedicated blocking of non-specific interactions and comparing threshold voltage shifts of transistors exhibiting probe molecules of different base sequence. We apply the approach to detection of the 35delG mutation, which is related to non-syndromic deafness and is one of the most frequent mutations in humans. The process involves barcode sequences that are generated by Tas-PCR, a newly developed replication reaction using polymerase blocking. The barcodes are recognized by hybridization to surface attached probes and are directly detected by the semiconductor device.
Revealing the competition between peeled DNA, melting bubbles, and S-DNA during DNA overstretching using fluorescence microscopy
Graeme A. Kinga, Peter Grossa, Ulrich Bockelmannb, Mauro Modestic, Gijs J. L. Wuitea, and Erwin J. G. Petermana
Proc. Nat. Acad. Sci. USA - vol.110 (n°10) 3859–64 - DOI: 10.1073/pnas.1213676110 - 2013
Mechanical stress plays a key role in many genomic processes, such as DNA replication and transcription. The ability to predict the response of double-stranded (ds) DNA to tension is a cornerstone of understanding DNA mechanics. It is widely appreciated that torsionally relaxed dsDNA exhibits a structural transition at forces of ∼65 pN, known as overstretching, whereby the contour length of the molecule increases by ∼70%. Despite extensive investigation, the structural changes occurring in DNA during overstretching are still generating considerable debate. Three mechanisms have been proposed to account for the increase in DNA contour length during overstretching: strand unpeeling, localized base-pair breaking (yielding melting bubbles), and formation of S-DNA (strand unwinding, while base pairing is maintained). Here we show, using a combination of fluorescence microscopy and optical tweezers, that all three structures can exist, uniting the often contradictory dogmas of DNA overstretching. We visualize and distinguish strand unpeeling and melting-bubble formation using an appropriate combination of fluorescently labeled proteins, whereas remaining B-form DNA is accounted for by using specific fluorescent molecular markers. Regions of S-DNA are associated with domains where fluorescent probes do not bind. We demonstrate that the balance between the three structures of overstretched DNA is governed by both DNA topology and local DNA stability. These findings enhance our knowledge of DNA mechanics and stability, which are of fundamental importance to understanding how proteins modify the physical state of DNA.
Surface functionalization of COC microfluidic materials by plasma and click chemistry processes
Y. Ladner, F. D’orlye, C. Perrard, B. Da Silva, C. Guyon, M. Tatoulian, S. Griveau, F. Bedioui & A. Varenne
Plasma Process - 10(11) :959-69 - DOI:10.1002/ppap.201300066 - 2013
A robust method for COC surfaces functionalization was developed for the first time by plasma polymerization. 1-bromopropane in the vapor phase allowed the formation of a brominated deposit on COC surfaces, which stability, homogeneity and chemical nature were evaluated for different experimental conditions. The analysis of vapor phase was achieved by mass spectrometry to control brominated precursor fragmentation. Following nucleophilic exchange in the presence of NaN3 to convert the brominated surface to azide-bearing surface, these modified COC were further functionalized with a fluorescent alkyne, via the copper-catalyzed azide–alkyne cycloaddition reaction, i.e. “click” reaction. Surface modifications were characterized by water contact angle measurement, ellipsometry, electrochemical microscopy, XPS, IR and fluorescence microscopy. This new process was proved to be efficient and stable in time up to 7 days.
Catkin liked nano-Co3O4 catalyst built-in organic microreactor by PEMOCVD method for trace CO oxidation at room temperature
G. L. Chen,C. Guyon,Z. X. Zhang,B. Da Silva,P. Da Costa,S. Ognier,D. Bonn,M. Tatoulian
Microfluidics and Nanofluidics - 16(1-2) :141-148 - DOI:10.10.1007/s10404-013-1220-y - 2013
In this paper, tricobalt tetraoxide (Co3O4) catalyst was coated on the polydimethylsiloxane microchannel by the plasma-enhanced metal-organic chemical vapor deposition technology. The obtained Co3O4 film was characterized by SEM, XRD, XPS, and TEM, and the results show that the as-deposited Co3O4 film was initially composed of many cauliflowers-shaped microclusters. Also, the microcauliflower was transformed from an amorphous phase to a crystal phase when the Co3O4 film was treated by Ar and O2 plasma for more than 20 min, and the crystal lattice line occurred on the surface of nano-sized-Co3O4 particles. Meanwhile, the interface of Co3O4 particles with diameter between 3 and 12 nm became obvious and some nano-catkin structures were also formed on the Co3O4 film. The ratio of Co3+/Co2+ in the spinel-type Co3O4 was nearly 2, and the nano-particles predominantly expose their {311}, {111}, and {220} planes. These morphologies and structure characteristics were found to be ideal for increasing the catalytic activity efficiency of Co3O4 for CO oxidation, and the catalytic stability of Co3O4 coated on the organic microreactor lasted nearly 85 h for trace CO oxidation at room temperature.
The different structure characteristics of nanosized Co3O 4 film crystallized by the annealing and plasma techniques
G.L. Chen, C. Guyon, Z.X., Zhang, S. Ognier, J. Beem, M.Tatoulian
Microfluidics and Nanofluidics - 107 :1111 – 114 - DOI:10.1016/j.matlet.2013.05.071 - 2013
In this study, we deposited nano-Co3O4 film on silicon substrate using plasma-enhanced metal—organic chemical vapor deposition (PEMOCVD), and the structure difference of Co3O4 crystallized by the annealing and the Ar/O2 plasma techniques were explored by SEM, TEM, XRD, and XPS. Compared to the net morphology of Co3O4 film treated with high calcinations temperature, the cauliflowers-shaped micro-clusters were changed to nano-catkin when the sample was treated with Ar and O2 plasma for 40 min. Additionally, both samples (annealed and plasma-treated) showed the formation of both the {311} and {220} planes. The surface richness of active Co3+ sites on the exposed {220} plane indicated that the as-deposited nano-Co3O4 films have potential catalytic properties for CO and hydrocarbon oxidation.
Cyclic Olefin Copolymer Plasma millireactors
Schelcher G, Guyon C, Ognier S, Cavadias S, Martinez E, Taniga V, Malaquin L, Tabeling P and Tatoulian M
Lab. Chip - 14(16) 3037-42 - DOI: 10.1039/c4lc00423j - 2013
The novelty of this paper lies in the development of a multistep process for the manufacturing of plasma millireactors operating at atmospheric pressure. The fabrication process relies on the integration of metallic electrodes over a cyclic olefin copolymer chip by a combination of photopatterning and sputtering. The developed plasma millireactors were successfully tested by creating air discharges in the gas volume of the millichannel. A sputtered silica layer was deposited on the channel walls to provide a barrier between the plasma and the polymer in order to prevent the alteration of polymer surfaces during the plasma treatment. Interest in this process of employing plasma millireactor as a high reactive environment is demonstrated here by the degradation of a volatile organic compound (acetaldehyde) in ambient air. In this miniaturized device, we obtained a high acetaldehyde conversion (98%) for a specific input energy lower than 200 J L(-1).
Aptamer-conjugated nanoparticles: Preservation of targeting functionality demonstrated by microchip electrophoresis in frontal mode
M. Girardot, F. d'Orlye, S. Descroix, A. Varenne.
Analytical Biochemistry - 435 150-152 - PMID:23333271 - 2013
Aptamer-conjugated nanoparticles (Apt-NPs) are increasingly being developed for biomedical purposes and especially for diagnosis and therapy. However, there is no quantitative study of the targeting functionality of such grafted aptamers compared with free aptamers. Thus, we report the first determination of binding parameters for Apt-NP/target complexes, thanks to a continuous frontal analysis in a microchip electrophoresis format (named FACMCE), based on a methodology previously developed by our group. As a model system, the targeting ability of a lysozyme-binding aptamer conjugated to fluorescent maghemite nanoparticles was evaluated and showed evidence that the conjugation does not alter the affinity of this aptamer.
Electrokinetic characterization of superparamagnetic nanoparticle–aptamer conjugates: design of new highly specific probes for miniaturized molecular diagnostics
M. Girardot, F. d'Orlye, A. Varenne
Anal. Bioanal. Chem - 406(4) :1089-98 - DOI:10.1007/s00216-013-7265-7 - 2013
With the view of designing new nanoparticle (NP)-aptamer conjugates and proving their suitability as biorecognition tools for miniaturized molecular diagnostics, new maghemite-silica core-shell NP-aptamer conjugates were characterized for the first time in terms of grafting rate and colloidal stability under electrophoretic conditions using capillary electrophoresis. After the grafting rate (on the order of six to 50) of the lysozyme-binding aptamer had been estimated, the electrophoretic stability and peak dispersion of the resulting oligonucleotide-NP conjugates were estimated so as to determine the optimal separation conditions in terms of buffer pH, ionic strength and nature, as well as temperature and electric field strength. The effective surface charge density of the NPs was close to zero for pH lower than 5, which led to some aggregation. The NPs were stable in the pH range from 5 to 9, and an increase in electrophoretic mobility was evidenced with increasing pH. Colloidal stability was preserved at physiological pH for both non-grafted NPs and grafted NPs in the 10-100 mM ionic strength range and in the 15-60 °C temperature range. A strong influence of the nature of the buffer counterion on NP electrophoretic mobility and peak dispersion was evidenced, thus indicating some interactions between buffer components and NP-aptamer conjugates. Whereas an electric field effect (50-900 V cm(-1)) on NP electrophoretic mobility was evidenced, probably linked to counterion dissociation, temperature seems to have an appreciable effect on the zeta potential and aptamer configuration as well. This information is crucial for estimating the potentialities of such biorecognition tools in electrophoretic systems.
Red blood celles decorated with functionalized core-shell magnetic nanoparticles : elucidation of the adsorption mechanism
T. D. Mai, F. D’Orlyé, C. Menager, A. Varenne, M. Siaugue
Chem. Comm. - 49(47) :5393-5 - DOI:10.1039/c3cc41513a. - 2013
The decoration of red blood cells (RBCs) with aminated and carboxylated core-shell magnetic nanoparticles (CSMNs) was studied and elucidated. It was demonstrated that only aminated CSMNs could decorate the RBCs and their adsorption interaction is mainly ruled by electrostatic attraction between the positively charged amino groups on CSMNs and the abundant sialic acid groups on the outer surface of RBCs.
Surface functionalization of COC microfluidic materials by plasma and click chemistry processes
Y. Ladner, F. D’orlye, C. Perrard, B. Da Silva, C. Guyon, M. Tatoulian, S. Griveau, F. Bedioui & A. Varenne
Plasma Process - 10(11) :959-69 - DOI:10.1002/ppap.201300066 - 2013
A robust method for COC surfaces functionalization was developed for the first time by plasma polymerization. 1-bromopropane in the vapor phase allowed the formation of a brominated deposit on COC surfaces, which stability, homogeneity and chemical nature were evaluated for different experimental conditions. The analysis of vapor phase was achieved by mass spectrometry to control brominated precursor fragmentation. Following nucleophilic exchange in the presence of NaN3 to convert the brominated surface to azide-bearing surface, these modified COC were further functionalized with a fluorescent alkyne, via the copper-catalyzed azide–alkyne cycloaddition reaction, i.e. “click” reaction. Surface modifications were characterized by water contact angle measurement, ellipsometry, electrochemical microscopy, XPS, IR and fluorescence microscopy. This new process was proved to be efficient and stable in time up to 7 days.

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579 publications.