Evidence for the Universal Scaling Behaviour of a Freely Relaxing DNA Molecule

Relaxation measurements on a fluorescently labelled free DNA molecule after stretching by a Poiseuille flow in a capillary vessel reveal universal scaling features: at intermediate times the scaling exponent of the decay law for the molecule length as a function of time is found to be 0.51 +/- 0.05. This law is in agreement with the prediction of the Brochard-Wyart "stem and flower" model for the relaxation of a stretched polymer chain.Molecular and Cellular BiologyPhysic

Probing complex RNA structures by mechanical force

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure

Molecular transport and flow past hard and soft surfaces: Computer simulation of model systems

The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained polymer model. Hard, corrugated substrates are modelled by an FCC Lennard-Jones solid while polymer brushes are investigated as a prototypical example of a soft, deformable surface. From the molecular simulation we extract the coarse-grained parameters that characterise the equilibrium and flow properties of the liquid in contact with the substrate: the surface and interface tensions, and the parameters of the hydrodynamic boundary condition. The so-determined parameters enter a continuum description like the Stokes equation or the lubrication approximation.Comment: 41 pages, 13 figure

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p

The PUF family of RNA-binding proteins regulate gene expression post-transcriptionally. Saccharomyces cerevisiae Puf3p is characterised as binding nuclear-encoded mRNAs specifying mitochondrial proteins. Extensive studies of its regulation of COX17 demonstrate its role in mRNA decay. Using integrated genome-wide approaches we define an expanded set of Puf3p target mRNAs and quantitatively assessed the global impact of loss of PUF3 on gene expression using mRNA and polysome profiling and quantitative proteomics. In agreement with prior studies, our sequencing of affinity-purified Puf3-TAP associated mRNAs (RIP-seq) identified mRNAs encoding mitochondrially-targeted proteins. Additionally, we also found 720  new mRNA targets that predominantly encode proteins that enter the nucleus. Comparing transcript levels in wild-type and puf3∆ cells revealed that only a small fraction of mRNA levels alter, suggesting Puf3p determines mRNA stability for only a limited subset of its target mRNAs. Finally, proteomic and translatomic studies suggest that loss of Puf3p has widespread, but modest, impact on mRNA translation. Taken together our integrated multi-omics data point to multiple classes of Puf3p targets, which display coherent post-transcriptional regulatory properties and suggest Puf3p plays a broad, but nuanced, role in the fine-tuning of gene expression

Nonlinear diffusion and hyperuniformity from Poisson representation in systems with interaction mediated dynamics

We introduce a minimal model of interacting particles relying on conservation of the number of particles and interactions respecting conservation of the center of mass. The dynamics in our model is directly amenable to simple pairwise interactions between particles leading to particle displacements, ensues from this what we call interaction mediated dynamics. Inspired by binary reaction kinetics-like rules, we model systems of interacting agents activated upon pairwise contact. Using Poisson representations, our model is amenable to an exact nonlinear stochastic differential equation. We derive analytically its hydrodynamic limit, which turns out to be a nonlinear diffusion equation of porous medium type valid even far from steady state. We obtain exact self-similar solutions with subdiffusive scaling and compact support. The nonequilibrium steady state of our model in the dense phase displays hyperuniformity which we are able to predict from our analytical approach. We reinterpret hyperuniformity as stemming from correlations in particles displacements induced by the conservation of center of mass. Although quite simplistic, this model could in principle be realized experimentally at different scales by active particles systems

Growth of two dimensional domains in copolymer thin films

Quenching experiments on very thin films (≃ 1 000 Å) of symmetric diblock copolymer deposited on solid substrates result in the formation of circular relief domains at the free surface of the sample. It is due to the quantization of the possible thicknesses of the sample which accompanies the lamellar ordering of the two species parallel to the substrate. Depending on the average thickness of the film, the domains can be depressions or elevations. Based on the conjecture of a simple dislocation structure of the domain edge, equations governing the time evolution of the domain size distribution are proposed. The flows involved in the domain growth are shown to be confined into a bilayer which is disrupted at the dislocation lines. The hypothesis is made that interlayer frictions dominate. The growth kinetics of a single hole in a finite film is finally solved explicitely. Its radius is found to decay as a 1/3 power law of its life time.Lorsqu'on trempe des films très minces (1 000 Å d'épaisseur) de copolymères déposés sur un substrat solide, des domaines circulaires apparaissent en relief à la surface de l'échantillon. Ce phénomène est dû à la formation d'un ordre lamellaire dans le film qui s'accompagne d'une quantification de son épaisseur locale. Les domaines peuvent correspondre à des dépressions ou des élévations, selon l'épaisseur du film initial. Après avoir postulé que la structure des bords des domaines est une simple dislocation, on établit les équations qui gouvernent leur croissance. On montre en particulier que les écoulements de polymère qui permettent cette évolution doivent prendre place dans une bicouche incomplète enfermée entre deux monocouches complètes, et on fait l'hypothèse que la dissipation provient essentiellement du frottement entre couches. Le cas d'un trou unique dans un film de surface finie est finalement examiné en détail. Son rayon évolue comme la puissance 1/3 de sa durée de vie

Atomic force microscopy of three-dimensional membrane protein crystals. Ca-ATPase of sarcoplasmic reticulum.

We have observed three-dimensional crystals of the calcium pump from sarcoplasmic reticulum by atomic force microscopy (AFM). From AFM images of dried crystals, both on graphite and mica, we measured steps in the crystal thickness, corresponding to the unit cell spacing normal to the substrate. It is known from transmission electron microscopy that crystal periodicity in the plane of the substrate is destroyed by drying, and it was therefore not surprising that we were unable to observe this periodicity by AFM. Thus, we were motivated to use the AFM on hydrated crystals. In this case, crystal adsorption appeared to be a limiting factor, and our studies indicate that adsorption is controlled by the composition of the medium and by the physical-chemical properties of the substrate. We used scanning electron microscopy to determine the conditions yielding the highest adsorption of crystals, and, under these conditions, we have obtained AFM images of hydrated crystals with a resolution similar to that observed with dried samples (i.e., relatively poor). In the same preparations, we have observed lipid bilayers with a significantly better resolution, indicating that the poor quality of crystal images was not due to instrumental limitations. Rather, we attribute poor images to the intrinsic flexibility of these multilamellar crystals, which apparently allow movement of one layer relative to another in response to shear forces from the AFM tip. We therefore suggest some general guidelines for future studies of membrane proteins with AFM

Light scattering study of a lower critical consolute point in a micellar system

We have studied aqueous micellar solutions of sodium dodecyl sulfate, butanol and sodium chloride. Due to the screening of electrostatic repulsive forces by the ionic atmosphere and to the existence of attractive forces (possibly related to hydration) between the micelles, lower critical consolute points can be found in these mixtures. Our data from surface and bulk light scattering are in perfect agreement with the renormalization group theories for critical phenomena. Moreover, the critical region happens to be wider than that predicted by the decorated Ising models used to describe lower critical consolute points.Nous avons étudié les solutions micellaires aqueuses de sulfate de dodécyle et de sodium, butanol et chlorure de sodium. En raison de l'écrantage des forces électrostatiques répulsives par les nuages ioniques et de l'existence de forces attractives entre les micelles (éventuellement reliées à l'hydratation), des points critiques inférieurs de démixtion peuvent être trouvés dans ces mélanges. Nos mesures par diffusion de lumière, de volume et de surface, sont en parfait accord avec les théories du groupe de renormalisation pour les phénomènes critiques. De plus, la région critique apparaît plus large que prévue par les modèles d'Ising décorés utilisés pour décrire les points critiques inférieurs

Light scattering study of microemulsions and its relation to percolation phenomena

The characteristics of the light scattered by microemulsions in the vicinity of a percolation threshold indicate the existence of strong and long range attractive forces between micelles. Hydrodynamic interactions are also present but show no evidence of long range character.Les caractéristiques de la lumière diffusée par des microémulsions au voisinage d'un seuil de percolation indiquent l'existence de forces attractives à longue portée entre micelles. Les interactions hydrodynamiques sont également présentes, mais n'ont pas de comportement à longue portée