Université PSL



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Theoretical study of sequence-dependent nanopore unzipping of DNA
Laboratoire Nanobiophysiques - U. Bockelmann and V. Viasnoff
Biophys. J. - 94(7) :2716–24 - DOI:10.1529/biophysj.107.111732 - 2008
We theoretically investigate the unzipping of DNA electrically driven through a nanometer-size pore. Taking the DNA base sequence explicitly into account, the unpairing and translocation process is described by a biased random walk in a one-dimensional energy landscape determined by the sequential basepair opening. Distributions of translocation times are numerically calculated as a function of applied voltage and temperature. We show that varying these two parameters changes the dynamics from a predominantly diffusive behavior to a dynamics governed by jumps over local energy barriers. The work suggests experimentally studying sequence effects, by comparing the average value and standard deviation of the statistical distribution of translocation times.
Interference and crosstalk in double optical tweezers using a single laser source
Laboratoire Nanobiophysiques - P. Mangeol and U. Bockelmann
Rev Sci Instrum - 79(8) :083103 - DOI:10.1063/1.2957652 - 2008
Experimental studies of single molecule mechanics require high force sensitivity and low drift, which can be achieved with optical tweezers. We built an optical tweezer setup for force measurements in a two bead assay. A cw infrared laser beam is split by polarization and focused by a high numerical aperture objective to create two traps. The same laser is used to form both traps and to measure the force by back focal plane interferometry. We show that although the two beams entering the microscope are designed to exhibit orthogonal polarization, interference and a significant parasitic force signal occur. Comparing the experimental results with a ray optics model, we show that the interference patterns are caused by the rotation of polarization on microscope lens surfaces and slides. The model qualitatively describes the pattern and the dependence of the parasitic force signal on the experimental parameters. We present two different approaches to experimentally reduce the crosstalk, namely, polarization rectification and frequency shifting.
A caged retinoic acid for one- and two-photon excitation in zebrafish embryos
Laboratoire Physique des biomolécules - P. Neveu, I. Aujard, C. Benbrahim, T. Le Saux, J.-F. Allemand, S. Vriz, D. Bensimon and L. Jullien
Angew Chem Int Ed Engl. - 47(20) :3744–46 - DOI:10.1002/anie.200800037 - 2008
Specific Wetting Probed With Biomimetic Droplets
Laboratoire Pôle Microfluidique - J. Fattaccioli, J. Baudry, F. Brochard-Wyart, N. Henry and J. Bibette
Soft Matter - 4(12) :2334-40 - DOI:10.1039/B806635C - 2008
We have produced emulsion droplets of controlled size and composition coated by ligands, and studied the adhesion of these drops on a solid substrate coated by receptors and polymers. Using transmission, RICM and fluorescence microscopy we assess the size, contact angle and ligand density for each drop. We first show that non-specific interactions significantly enhance the proteins density within the adhesive patch. Then we show that binding within the patch is partially inhibited in good agreement with the hypothesis of an absence of translational diffusion. We confirm that the density of specific bonds sets the adhesive energy and therefore the final contact angle, and finally show that specific binding in our system is always associated with the existence of a positive line tension, which linearly increases with the density of receptors. These experiments describe a new scenario for specific wetting which raises the importance of the coupling between non-specific interactions and specific binding.
In situ quantitative measurement of concentration profiles in a microreactor with submicron resolution using multiplex CARS microscopy
Laboratoire Procédés - Plasmas - Microsystèmes - Dawn Schafer, Jeff A. Squier, Jan van Maarseveen, Daniel Bon, Mischa Bonn, Michiel Mu¨ller
JACS - 130(35) :11592-3 - DOI:10.1021/ja804158n - 2008
In situ quantitative imaging of concentration profiles of reactants and products inside a microfluidic reactor is achieved, with submicron spatial resolution with mM sensitivity and on ms time scales, for a given position. The label-free approach relies on quantitative vibrational spectroscopy, using Coherent Anti-Stokes Raman scattering microscopy in a spectrally resolved fashion, and is demonstrated on an elementary acid-base reaction.
A simple and universal tool to remove on-line impurities in mono- or two-dimensional liquid chromatography–mass spectrometry analysis
Laboratoire Spectrométrie de masse biologique et protéomique - Hesse A-M, Marcelo P, Rossier J and Vinh J.
J. Chrom. A - 1189(1-2) :175-82 - DOI:10.1016/j.chroma.2007.12.060 - 2008
Several recurrent problems have always hindered mono-dimensional liquid chromatography-mass spectrometry proteomic analyses. Polymer contamination is a major problem because polymers could co-elute with compounds of interest (peptides). In this case spectral suppression degrades dynamic range and sensitivity. Polyethylene glycol derivatives count among the major contaminants. They are targeted in this work. They are eluted at 35-40% acetonitrile from C18 phase in every single reversed-phase run. Moreover, they are also observed in two-dimensional liquid chromatography in every salt fraction. A simple and robust method is presented here for rapid and efficient on-line removal of these impurities using self-regenerating purification microdevices.
Determination of nanoparticle diffusion coefficients by Taylor dispersion analysis using a capillary electrophoresis instrument
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - d'Orlye F, Varenne A, Gareil P.
J. Chrom. A - 1204(2) :226-32 - DOI:10.1016/j.chroma.2008.08.008 - 2008
The collective diffusion coefficient D(C) of diluted suspensions of positively charged iron oxide maghemite particles was experimentally investigated using a capillary electrophoresis instrument on the grounds of Taylor dispersion theory. Conditions for this approach to be applicable to nanoparticles of mean solid diameter below 10nm were set in this work, enabling precisions on D(C) determination of less than 2% relative standard deviation (RSD). Significantly different D(C) values were thus measured for particle populations differing in solid number mean diameter by only 2 nm. The obtained values were compared to the z-average diffusion coefficient derived from dynamic light scattering (DLS) experiments and used for the calculation of the Stokes radius. The measured diffusion coefficients appeared to be dependent on particle volume fraction and electrolyte ionic strength. These observations were eventually discussed in terms of particle interactions.
Signal enhancement in electronic detection of DNA hybridization
Laboratoire Nanobiophysiques - C. Gentil, G. Philippin, and U. Bockelmann
Phys. Rev. E - 75(1) :011926 - DOI:10.1103/PhysRevE.75.011926 - 2007
Electronic detection of the specific recognition between complementary DNA sequences is investigated. DNA probes are immobilized at different lateral positions on a Poly(L-lysine)-coated surface of an integrated silicon transistor array. Hybridization and field effect detection are done with the solid surface immersed in electrolyte solutions. Differential measurements are performed, where DNA hybridization leads to surface potential shifts between the transistors of the array. We experimentally show that these differential signals of hybridization can be enhanced significantly by changing the salt concentration between hybridization and detection.
Collective migration of an epithelial monolayer in response to a model wound
Laboratoire Physico-biologie aux méso-échelles - Poujade M., Grasland-Mongrain E., Hertzog A., Jouanneau J., Chavrier P., Ladoux B., Buguin A., Silberzan P.
Proc. Nat. Acad. Sci. USA - 104(41) :15988-93 - DOI:10.1073/pnas.0705062104 - 2007
Using an original microfabrication-based technique, we experimentally study situations in which a virgin surface is presented to a confluent epithelium with no damage made to the cells. Although inspired by wound-healing experiments, the situation is markedly different from classical scratch wounding because it focuses on the influence of the free surface and uncouples it from the other possible contributions such as cell damage and/or permeabilization. Dealing with Madin–Darby canine kidney cells on various surfaces, we found that a sudden release of the available surface is sufficient to trigger collective motility. This migration is independent of the proliferation of the cells that mainly takes place on the fraction of the surface initially covered. We find that this motility is characterized by a duality between collective and individual behaviors. On the one hand, the velocity fields within the monolayer are very long range and involve many cells in a coordinated way. On the other hand, we have identified very active “leader cells” that precede a small cohort and destabilize the border by a fingering instability. The sides of the fingers reveal a pluricellular actin “belt” that may be at the origin of a mechanical signaling between the leader and the followers. Experiments performed with autocrine cells constitutively expressing hepatocyte growth factor (HGF) or in the presence of exogenous HGF show a higher average velocity of the border and no leader.
Rigidity-driven growth and migration of epithelial cells on microstructured anisotropic substrates
Laboratoire Physico-biologie aux méso-échelles - Saez A., Ghibaudo M., Buguin A., Silberzan P., Ladoux B.
Proc. Nat. Acad. Sci. USA - 104(20) :8281-6 - DOI:10.1073/pnas.0702259104 - 2007
The physical properties of the cellular environment are involved in regulating the formation and maintenance of tissues. In particular, substrate rigidity appears to be a key factor dictating cell response on culture surfaces. Here we study the behavior of epithelial cells cultured on microfabricated substrates engineered to exhibit an anisotropic stiffness. The substrate consists of a dense array of micropillars of oval cross-section, so that one direction is made stiffer than the other. We demonstrate how such an anisotropic rigidity can induce directional epithelial growth and guide cell migration along the direction of greatest rigidity. Regions of high tractional stress and large cellular deformations within the sheets of cells are concentrated at the edges, in particular at the two poles of the islands along their long axis, in correlation with the orientation of actin stress fibers and focal adhesions. By inducing scattering activity of epithelial cells, we show that isolated cells also migrate along the direction of greatest stiffness. Taken together, these findings show that the mechanical interactions of cells with their microenvironment can be tuned to engineer particular tissue properties.

414 publications.