Université PSL

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Deposition kinetics of bi- and tridisperse colloidal suspensions in microchannels under the van der Waals regime
Laboratoire Microfluidique MEMS et nanostructures - Cesare M. Cejas, Lucrezia Maini, Fabrice Montia and Patrick Tabeling
Soft Matter - 15 7438-7447 - doi.org/10.1039/C9SM01098J - 2019
We investigate the kinetics of irreversible adsorption under the van der Waals regime, i.e. weakly Brownian polydisperse colloidal suspensions injected into shallow microchannels at high ionic strengths, where each suspension is represented by populations of particles with different particle sizes. We find that each population size of the particle in the suspension can be treated independently using an analytical solution based on the advection–diffusion equation and that the distribution of the adsorbed particles along the channel axis behaves according to a power law. The experimental measurements agree with Langevin simulations and are well accounted for by theory valid in the van der Waals regime. Operating in the van der Waals regime permits the present study to confirm the use of microfluidics as an effective in situ method to measure the Hamaker constant of particles under aqueous conditions.

Droplet generation at Hele-Shaw microfluidic T-junction
Laboratoire Microfluidique MEMS et nanostructures - I. Chakraborty, J. Ricouvier, P. Yazghur, P. Tabeling, A. Leshansky
Phys. Fluids - 31(2) 22010 - DOI: 10.1063/1.5086808 - 2019
Pairwise frictional profile between particles determines discontinuous shear thickening transition in non‐colloidal suspensions
Laboratoire Micromégas - J. Comtet, G. Chatté, A. Niguès, L. Bocquet, A. Siria, and A. Colin
Nat Commun - 8 15633 - DOI: 10.1038/ncomms15633 - 2019
The process by which sheared suspensions go through a dramatic change in viscosity is known as discontinuous shear thickening. Although well-characterized on the macroscale, the microscopic mechanisms at play in this transition are still poorly understood. Here, by developing new experimental procedures based on quartz-tuning fork atomic force microscopy, we measure the pairwise frictional profile between approaching pairs of polyvinyl chloride and cornstarch particles in solvent. We report a clear transition from a low-friction regime, where pairs of particles support a finite normal load, while interacting purely hydrodynamically, to a high-friction regime characterized by hard repulsive contact between the particles and sliding friction. Critically, we show that the normal stress needed to enter the frictional regime at nanoscale matches the critical stress at which shear thickening occurs for macroscopic suspensions. Our experiments bridge nano and macroscales and provide long needed demonstration of the role of frictional forces in discontinuous shear thickening.
Entrance Effects in Concentration-Gradient-Driven Flow Through an Ultrathin Porous Membrane
Laboratoire Micromégas - Daniel J. Rankin, Lydéric Bocquet, David M. Huang
J. Chem. Phys - 151 44705 - DOI:10.1063/1.5108700 - 2019
Transport of liquid mixtures through porous membranes is central to processes such as desalination, chemical separations and energy harvesting, with ultrathin membranes made from novel 2D nanomaterials showing exceptional promise. Here we derive, for the first time, general equations for the solution and solute fluxes through a circular pore in an ultrathin planar membrane induced by a solute concentration gradient. We show that the equations accurately capture the fluid fluxes measured in finite-element numerical simulations for weak solute-membrane interactions. We also derive scaling laws for these fluxes as a function of the pore size and the strength and range of solute-membrane interactions. These scaling relationships differ markedly from those for concentration-gradient-driven flow through a long cylindrical pore or for flow induced by a pressure gradient or electric field through a pore in an ultrathin membrane. These results have broad implications for transport of liquid mixtures through membranes with a thickness on the order of the characteristic pore size.
Osmosis, from molecular insights to large-scale applications
Laboratoire Micromégas - Sophie Marbach, Lyderic Bocquet
Phys. Chem. - 48 3102-3144 - DOI:10.1039/C8CS00420J - 2019
Osmosis is a universal phenomenon occurring in a broad variety of processes and fields. It is the archetype of entropic forces, both trivial in its fundamental expression - the van 't Hoff perfect gas law - and highly subtle in its physical roots. While osmosis is intimately linked with transport across membranes, it also manifests itself as an interfacial transport phenomenon: the so-called diffusio-osmosis and -phoresis, whose consequences are presently actively explored for example for the manipulation of colloidal suspensions or the development of active colloidal swimmers. Here we give a global and unifying view of the phenomenon of osmosis and its consequences with a multi-disciplinary perspective. Pushing the fundamental understanding of osmosis allows to propose new perspectives for different fields and we highlight a number of examples along these lines, for example introducing the concepts of osmotic diodes, active separation and far from equilibrium osmosis, raising in turn fundamental questions in the thermodynamics of separation. The applications of osmosis are also obviously considerable and span very diverse fields. Here we discuss a selection of phenomena and applications where osmosis shows great promises: osmotic phenomena in membrane science (with recent developments in separation, desalination, reverse osmosis for water purification thanks in particular to the emergence of new nanomaterials); applications in biology and health (in particular discussing the kidney filtration process); osmosis and energy harvesting (in particular, osmotic power and blue energy as well as capacitive mixing); applications in detergency and cleaning, as well as for oil recovery in porous media.
Molecular streaming and its voltage control in ångström-scale channels
Laboratoire Micromégas - Timothée Mouterde, Anthony R. Poggioli, Ashok Keerthi, Shafat Hussain Dar
Nature - 567(7746) 87-90 - DOI: 10.1038/s41586-019-0961-5 - 2019
Over the past decade, the ability to reduce the dimensions of fluidic devices to the nanometre scale (by using nanotubes1–5 or nanopores6–11, for example) has led to the discovery of unexpected water- and ion-transport phenomena12–14. More recently, van der Waals assembly of two-dimensional materials¹⁵ has allowed the creation of artificial channels with ångström-scale precision¹⁶. Such channels push fluid confinement to the molecular scale, wherein the limits of continuum transport equations¹⁷ are challenged. Water films on this scale can rearrange into one or two layers with strongly suppressed dielectric permittivity18,19 or form a room-temperature ice phase²⁰. Ionic motion in such confined channels²¹ is affected by direct interactions between the channel walls and the hydration shells of the ions, and water transport becomes strongly dependent on the channel wall material²². We explore how water and ionic transport are coupled in such confinement. Here we report measurements of ionic fluid transport through molecular-sized slit-like channels. The transport, driven by pressure and by an applied electric field, reveals a transistor-like electrohydrodynamic effect. An applied bias of a fraction of a volt increases the measured pressure-driven ionic transport (characterized by streaming mobilities) by up to 20 times. This gating effect is observed in both graphite and hexagonal boron nitride channels but exhibits marked material-dependent differences. We use a modified continuum framework accounting for the material-dependent frictional interaction of water molecules, ions and the confining surfaces to explain the differences observed between channels made of graphene and hexagonal boron nitride. This highly nonlinear gating of fluid transport under molecular-scale confinement may offer new routes to control molecular and ion transport, and to explore electromechanical couplings that may have a role in recently discovered mechanosensitive ionic channels²³.
Beyond the Trade-Off: Dynamic Selectivity in Ionic Transport and Current Rectification
Laboratoire Micromégas - A. Poggioli, A. Siria, L. Bocquet
Phys. Chem. - 123.5 1171-1185 - doi.org/10.1021/acs.jpcb.8b11202 - 2019
Traditionally, ion selectivity in nanopores and nanoporous membranes is understood to be a consequence of Debye overlap, in which the Debye screening length is comparable to the nanopore radius somewhere along the length of the nanopore(s). This criterion sets a significant limitation on the size of ion-selective nanopores, as the Debye length is on the order of 1–10 nm for typical ionic concentrations. However, the analytical results we present here demonstrate that surface conductance generates a dynamical selectivity in ion transport, and this selectivity is controlled by so-called Dukhin, rather than Debye, overlap. The Dukhin length, defined as the ratio of surface to bulk conductance, reaches values of hundreds of nanometers for typical surface charge densities and ionic concentrations, suggesting the possibility of designing large-nanopore (10–100 nm), high-conductance membranes exhibiting significant ion selectivity. Such membranes would have potentially dramatic implications for the efficiency of osmotic energy conversion and separation techniques. Furthermore, we demonstrate that this mechanism of dynamic selectivity leads ultimately to the rectification of ionic current, rationalizing previous studies, showing that Debye overlap is not a necessary condition for the occurrence of rectifying behavior in nanopores.
Atomic rheology of gold nanojunctions
Laboratoire Micromégas - Jean Comtet, Antoine Lainé, Antoine Niguès, Lydéric Bocquet & Alessandro Siria
Nature - 569(7756) 393–397 - DOI : 10.1038/s41586-019-1178-3 - 2019
Despite extensive investigations of dissipation and deformation processes in micro- and nano-sized metallic samples1,2,3,4,5,6,7, the mechanisms at play during the deformation of systems with ultimate (molecular) size remain unknown. Although metallic nanojunctions, which are obtained by stretching metallic wires down to the atomic level, are typically used to explore atomic-scale contacts5,8,9,10,11, it has not been possible until now to determine the full equilibrium and non-equilibrium rheological flow properties of matter at such scales. Here, by using an atomic-force microscope equipped with a quartz tuning fork, we combine electrical and rheological measurements on ångström-size gold junctions to study the non-linear rheology of this model atomic system. By subjecting the junction to increasing subnanometric deformations we observe a transition from a purely elastic regime to a plastic one, and eventually to a viscous-like fluidized regime, similar to the rheology of soft yielding materials12,13,14, although orders of magnitude different in length scale. The fluidized state furthermore exhibits capillary attraction, as expected for liquid capillary bridges. This shear fluidization cannot be captured by classical models of friction between atomic planes15,16 and points to an unexpected dissipative behaviour of defect-free metallic junctions at ultimate scales. Atomic rheology is therefore a powerful tool that can be used to probe the structural reorganization of atomic contacts.

Ionic Coulomb blockade as a fractional Wien effect
Laboratoire Micromégas - Nikita Kavokine, Sophie Marbach, Alessandro Siria & Lydéric Bocquet
Nat. Nanotechnol. - 14 573–578 - doi.org/10.1038/s41565-019-0425-y - 2019
Recent advances in nanofluidics have allowed the exploration of ion transport down to molecular-scale confinement, yet artificial porins are still far from reaching the advanced functionalities of biological ion machinery. Achieving single ion transport that is tunable by an external gate—the ionic analogue of electronic Coulomb blockade—would open new avenues in this quest. However, an understanding of ionic Coulomb blockade beyond the electronic analogy is still lacking. Here, we show that the many-body dynamics of ions in a charged nanochannel result in quantized and strongly nonlinear ionic transport, in full agreement with molecular simulations. We find that ionic Coulomb blockade occurs when, upon sufficient confinement, oppositely charged ions form ‘Bjerrum pairs’, and the conduction proceeds through a mechanism reminiscent of Onsager’s Wien effect. Our findings open the way to novel nanofluidic functionalities, such as an ion pump based on ionic Coulomb blockade, inspired by its electronic counterpart.
MicroMegascope based dynamic surface force apparatus
Laboratoire Micromégas - Lainé, Antoine; Jubin, Laetitia; Canale, Luca; Bocquet, Lydéric; Siria, Alessandro; Donaldson, Stephen H., Jr.; Niguès, Antoine
Nanotechnology - 30 195502 - DOI: 10.1088/1361-6528/ab02ba - 2019
Surface force apparatus (SFA) allows accurate resolving of the interfacial properties of fluids confined between extended surfaces. The accuracy of the SFA makes it an ubiquitous tool for the nanoscale mechanical characterization of soft matter systems. The SFA traditionally measures force-distance profiles through interferometry with subnanometric distance precision. However, these techniques often require a dedicated and technically demanding experimental setup, and there remains a need for versatile and simple force-distance measurement tools. Here we present a MicroMegascope based dynamic SFA capable of accurate measurement of the dynamic force profile of a liquid confined between a millimetric sphere and a planar substrate. Normal and shear mechanical impedance is measured within the classical frequency modulation framework. We measure rheological and frictional properties from micrometric to molecular confinement. We also highlight the resolution of small interfacial features such as ionic liquid layering. This apparatus shows promise as a versatile force-distance measurement device for exotic surfaces or extreme environments.
Nanorheology of Interfacial Water during Ice Gliding
Laboratoire Micromégas - L. Canale, J. Comtet, A. Niguès, C. Cohen, C. Clanet, A. Siria, and L. Bocquet
Phys. Rev. X - 9 041025 - doi.org/10.1103/PhysRevX.9.041025 - 2019
The slipperiness of ice is an everyday-life phenomenon, which, surprisingly, remains controversial despite a long scientific history. The very small friction measured on ice is classically attributed to the presence of a thin self-lubricating film of meltwater between the slider and the ice. But while the macroscale friction behavior of ice and snow has been widely investigated, very little is known about the interfacial water film and its mechanical properties. In this work, we develop a stroke-probe force measurement technique to uncover the microscopic mechanisms underlying ice lubrication. We simultaneously measure the shear friction of a bead on ice and quantify the in situ mechanical properties of the interfacial film, as well as its thickness, under various regimes of speed and temperature. In contrast with standard views, meltwater is found to exhibit a complex viscoelastic rheology, with a viscosity up to 2 orders of magnitude larger than pristine water. The unconventional rheology of meltwater provides a new, consistent, rationale for ice slipperiness. Hydrophobic coatings are furthermore shown to strongly reduce friction due to a surprising change in the local viscosity, providing an unexpected explanation for waxing effects in winter sports. Beyond ice friction, our results suggest new avenues towards self-healing lubricants to achieve ultralow friction.
Adsorption Kinetics in Open Nanopores as a Source of Low-Frequency Noise
Laboratoire Micromégas - Simon Gravelle, Roland R. Netz, and Lydéric Bocquet
Nano Lett. - 19(10) 7265-7272 - doi.org/10.1021/acs.nanolett.9b02858 - 2019
Ionic current measurements through solid-state nanopores consistently show a power spectral density that scales as 1/f α at low frequency f, with an exponent α ∼ 0.5–1.5, but strikingly, the physical origin of this behavior remains elusive. Here, we perform simulations of particles reversibly adsorbing at the surface of a nanopore and show that the fluctuations in the number of adsorbed particles exhibit low-frequency pink noise. We furthermore propose theoretical modeling for the time-dependent adsorption of particles on the nanopore surface for various geometries, which predicts a frequency spectrum in very good agreement with the simulation results. Altogether, our results highlight that the low-frequency noise takes its origin in the reversible adsorption of ions at the pore surface combined with the long-lasting excursions of the ions in the reservoirs. The scaling regime of the power spectrum extends down to a cutoff frequency which is far smaller than simple diffusion estimates. Using realistic values for the pore dimensions and the adsorption–desorption kinetics, this predicts the observation of pink noise for frequencies down to the hertz for a typical solid-state nanopore, in good agreement with experiments.
Beyond the Tradeoff: Dynamic Selectivity in Ionic Transport and Current Selectivity
Laboratoire Micromégas - Anthony R. Poggioli, Alessandro Siria, Lyderic Bocquet
J. Phys. Chem. B. - 123(5) 1171--1185 - DOI:10.1021/acs.jpcb.8b11202 - 2019
Traditionally, ion-selectivity in nanopores and nanoporous membranes is understood to be a consequence of Debye overlap, in which the Debye screening length is comparable to the nanopore radius somewhere along the length of the nanopore(s). This criterion sets a significant limitation on the size of ion-selective nanopores, as the Debye length is on the order of 1 - 10 nm for typical ionic concentrations. However, the analytical results we present here demonstrate that surface conductance generates a dynamical selectivity in ion transport, and this selectivity is controlled by so-called Dukhin, rather than Debye, overlap. The Dukhin length, defined as the ratio of surface to bulk conductance, reaches values of hundreds of nanometers for typical surface charge densities and ionic concentrations, suggesting the possibility of designing large-nanopore (10 - 100 nm), high-conductance membranes exhibiting significant ion-selectivity. Such membranes would have potentially dramatic implications for the efficiency of osmotic energy conversion and separation techniques. Furthermore, we demonstrate that this mechanism of dynamic selectivity leads ultimately to the rectification of ionic current, rationalizing previous studies showing that Debye overlap is not a necessary condition for the occurrence of rectifying behavior in nanopores.
Nano-on-Micro Fibrous Extracellular Matrices for Scalable Expansion of Human Es/Ips Cells
Laboratoire Nanobioscience et Microsystèmes group - L. Liu, K.-i. Kamei, M. Yoshioka, M. Nakajima, J. Li, N. Fujimoto, S. Terada, Y. Tokunaga, Y. Koyama, H. Sato, K. Hasegawa, N. Nakatsuji and Y. Chen
Biomaterials - 124 47-54 - DOI: 10.1016/j.biomaterials.2017.01.039 - 2019
Human pluripotent stem cells (hPSCs) hold great potential for industrial and clinical applications. Clinical-grade scaffolds and high-quality hPSCs are required for cell expansion as well as easy handling and manipulation of the products. Current hPSC culture methods do not fulfill these requirements because of a lack of proper extracellular matrices (ECMs) and cell culture wares. We developed a layered nano-on-micro fibrous cellular matrix mimicking ECM, named "fiber-on-fiber (FF)" matrix, which enables easy handling and manipulation of cultured cells. While non-woven sheets of cellulose and polyglycolic acid were used as a microfiber layer facilitating mechanical stability, electrospun gelatin nanofibers were crosslinked on the microfiber layer, generating a mesh structure with connected nanofibers facilitating cell adhesion and growth. Our results showed that the FF matrix supports effective hPSC culture with maintenance of their pluripotency and normal chromosomes over two months, as well as effective scaled-up expansion, with fold increases of 54.1 ± 15.6 and 40.4 ± 8.4 in cell number per week for H1 human embryonic stem cells and 253G1 human induced pluripotent stem cells, respectively. This simple approach to mimick the ECM may have important implications after further optimization to generate lineage-specific products.
Self-propelled water drops on bare glass substrates in air: fast, controllable and easy transport powered by surfactants
Laboratoire Nanobioscience et Microsystèmes group - P. E. Galy, S. Rudiuk, M. Morel, D. Baigl
Langmuir - 36, 25 6916–6923 - doi : 10.1021/acs.langmuir.9b03727 - 2019
Self-propelled drops are capable of motion without external intervention. As such, they constitute attractive entities for fundamental investigations in active soft matter, hydrodynamics, and surface sciences, as well as promising systems for autonomous microfluidic operations. In contrast with most of the examples relying on organic drops or specifically treated substrates, here we describe the first system of nonreactive water drops in air that can propel themselves on a commercially available ordinary glass substrate that was used as received. This is achieved by exploiting the dynamic adsorption behavior of common n-alkyltrimethylammonium bromide (CnTAB) surfactants added to the drop. We precisely analyze the drop motion for a broad series of surfactants carrying n = 6 to 18 carbon atoms in their tail and establish how the motion characteristics (speed, probability of motion) are tuned by both the hydrophobicity and the concentration of the surfactant. We show that motion occurs regardless of the n value but only in a specific concentration range with a maximum speed at around one tenth of the critical micelle concentration (CMC/10) for most of the tested surfactants. Surfactants of intermediate hydrophobicity are shown to be the best candidates to power drops that can move at a high speed (1−10 cm s−1), the optimal performance being reached with [C12TAB] = 800 μM. We propose a mechanism where the motion originates from the anisotropic wettability of the substrate created by the electrostatic adsorption of surfactants beneath the moving drop. Simply drawing lines with a marker pen allows us to create guiding paths for drop motion and to achieve operations such as complex trajectory control, programmed drop fusion, drop refilling, as well as drop moving vertically against gravity. This work revisits the role of surfactants in dynamic wetting and self-propelled motion as well as brings an original strategy to build the future of microfluidics with lower-cost, simpler, and more autonomous portable devices that could be made available to everyone and everywhere.
Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure
Laboratoire Physique des biomolécules - Allemand JF, Tardin C, Salomé L.
Nat. Methods - 1;169 46-56 - doi: 10.1016/j.ymeth.2019.07.020. - 2019
Tethering beads to DNA offers a panel of single molecule techniques for the refined analysis of the conformational dynamics of DNA and the elucidation of the mechanisms of enzyme activity. Recent developments include the massive parallelization of these techniques achieved by the fabrication of dedicated nanoarrays by soft nanolithography. We focus here on two of these techniques: the Tethered Particle motion and Magnetic Tweezers allowing analysis of the behavior of individual DNA molecules in the absence of force and under the application of a force and/or a torque, respectively. We introduce the experimental protocols for the parallelization and discuss the benefits already gained, and to come, for these single molecule investigations.
Anisotropic cellular forces support mechanical integrity of the Stratum Corneum barrier
Laboratoire Physique des biomolécules - Guo S, Domanov Y, Donovan M, Ducos B, Pomeau Y, Gourier C, Perez E, Luengo GS.
Chem. Mater - 92 45231 - doi: 10.1016/j.jmbbm.2018.12.027 - 2019
The protective function of biological surfaces that are exposed to the exterior of living organisms is the result of a complex arrangement and interaction of cellular components. This is the case for the most external cornified layer of skin, the stratum corneum (SC). This layer is made of corneocytes, the elementary 'flat bricks' that are held together through adhesive junctions. Despite the well-known protective role of the SC under high mechanical stresses and rapid cell turnover, the subtleties regarding the adhesion and mechanical interaction among the individual corneocytes are still poorly known. Here, we explore the adhesion of single corneocytes at different depths of the SC, by pulling them using glass microcantilevers, and measuring their detachment forces. We measured their interplanar adhesion between SC layers, and their peripheral adhesion among cells within a SC layer. Both adhesions increased considerably with depth. At the SC surface, with respect to adhesion, the corneocyte population exhibited a strong heterogeneity, where detachment forces differed by more than one order of magnitude for corneocytes located side by side. The measured detachment forces indicated that in the upper-middle layers of SC, the peripheral adhesion was stronger than the interplanar one. We conclude that the stronger peripheral adhesion of corneocytes in the SC favors an efficient barrier which would be able to resist strong stresses.
Anisotropic cellular forces support mechanical integrity of the Stratum Corneum barrier
Laboratoire Physique des biomolécules - Guo S, Domanov Y, Donovan M, Ducos B, Pomeau Y, Gourier C, Perez E, Luengo GS.
Chem. Mater - 92 45231 - doi: 10.1016/j.jmbbm.2018.12.027 - 2019
The protective function of biological surfaces that are exposed to the exterior of living organisms is the result of a complex arrangement and interaction of cellular components. This is the case for the most external cornified layer of skin, the stratum corneum (SC). This layer is made of corneocytes, the elementary 'flat bricks' that are held together through adhesive junctions. Despite the well-known protective role of the SC under high mechanical stresses and rapid cell turnover, the subtleties regarding the adhesion and mechanical interaction among the individual corneocytes are still poorly known. Here, we explore the adhesion of single corneocytes at different depths of the SC, by pulling them using glass microcantilevers, and measuring their detachment forces. We measured their interplanar adhesion between SC layers, and their peripheral adhesion among cells within a SC layer. Both adhesions increased considerably with depth. At the SC surface, with respect to adhesion, the corneocyte population exhibited a strong heterogeneity, where detachment forces differed by more than one order of magnitude for corneocytes located side by side. The measured detachment forces indicated that in the upper-middle layers of SC, the peripheral adhesion was stronger than the interplanar one. We conclude that the stronger peripheral adhesion of corneocytes in the SC favors an efficient barrier which would be able to resist strong stresses.
PICH and TOP3A cooperate to induce positive DNA supercoiling
Laboratoire Physique des biomolécules - Anna Hélène Bizard, Jean-Francois Allemand, Tue Hassenkam, Manikandan Paramasivam
Nature - 26(4) 1 - DOI: 10.1038/s41594-019-0201-6 - 2019
All known eukaryotic topoisomerases are only able to relieve torsional stress in DNA. Nevertheless, it has been proposed that the introduction of positive DNA supercoiling is required for efficient sister-chromatid disjunction by Topoisomerase 2a during mitosis. Here we identify a eukaryotic enzymatic activity that introduces torsional stress into DNA. We show that the human Plk1-interacting checkpoint helicase (PICH) and Topoisomerase 3a proteins combine to create an extraordinarily high density of positive DNA supercoiling. This activity, which is analogous to that of a reverse-gyrase, is apparently driven by the ability of PICH to progressively extrude hypernegatively supercoiled DNA loops that are relaxed by Topoisomerase 3a. We propose that this positive supercoiling provides an optimal substrate for the rapid disjunction of sister centromeres by Topoisomerase 2a at the onset of anaphase in eukaryotic cells.
Mechanistic characterization of the DEAD-box RNA helicase Ded1 from yeast as revealed by a novel technique using single-molecule magnetic tweezers
Laboratoire Physique des biomolécules - Saurabh Raj, Debjani Bagchi, Jessica Valle Orero, Josette Banroques, N Kyle Tanner, Vincent Croquette
Nucleic Acids Res. - 47(7) 3699–3710 - doi.org/10.1093/nar/gkz057 - 2019
DEAD-box helicases are involved in all steps of RNA metabolism. They are ATP-dependent RNA binding proteins and RNA-dependent ATPases. They can displace short duplexes, but they lack processivity. Their mechanism and functioning are not clearly understood; classical or bulk biochemical assays are not sufficient to answer these questions. Single-molecule techniques provide useful tools, but they are limited in cases where the proteins are nonprocessive and give weak signals. We present here a new, magnetic-tweezers-based, single-molecule assay that is simple and that can sensitively measure the displacement time of a small, hybridized, RNA oligonucleotide. Tens of molecules can be analyzed at the same time. Comparing the displacement times with and without a helicase gives insights into the enzymatic activity of the protein. We used this assay to study yeast Ded1, which is orthologous to human DDX3. Although Ded1 acts on a variety of substrates, we find that Ded1 requires an RNA substrate for its ATP-dependent unwinding activity and that ATP hydrolysis is needed to see this activity. Further, we find that only intramolecular single-stranded RNA extensions enhance this activity. We propose a model where ATP-bound Ded1 stabilizes partially unwound duplexes and where multiple binding events may be needed to see displacement.

638 publications.