Complexation between oppositely charged polyelectrolytes: beyond the Random Phase Approximation

We consider the phase behavior of polymeric systems by calculating the structure factors beyond the Random Phase Approximation. The effect of this correction to the mean-field RPA structure factor is shown to be important in the case of coulombic systems. Two examples are given: simple electrolytes and mixtures of incompatible oppositely charged polyelectrolytes. In this last case, all former studies predicted an enhancement of compatibility for increasing charge densities; we also describe the complexation transition between the polyelectrolytes. We determine a phase diagram of the polyelectrolyte mixture that includes both complexation and incompatibility.Comment: 18 pages, 4 figures. Submitted to EPJ-

Comparing open and closed molecular self-assembly

We study theoretically in the present work the self-assembly of molecules in an open system, which is fed by monomers and depleted in partial or complete clusters. Such a scenario is likely to occur for example in the context of viral self-assembly. We provide a general formula for the mean-field size distribution which is valid both at equilibrium in a closed system, and in the stationary state in an open system. This allows us to explore in a simple way out-of-equilibrium features for self-assembly and compare them to equilibrium properties. In particular, we identify a region of parameter space for which the out-of-equilibrium size distribution in the presence of external fluxes is equal to the equilibrium size distribution in the absence of external fluxes, up to a constant renormalization factor. The range of validity of this result and its consequences are discussed.Comment: PACS 81.16.Fg - Supramolecular and biochemical assembly PACS 82.39.-k - Chemical kinetics in biological systems PACS 05.65.+b - Self-organized system

Charge Distribution on Annealed Polyelectrolytes

We investigate the equilibrium charge distribution along a single annealed polyelectrolyte chain under different conditions. The coupling between the conformation of the chain and the local charge distribution is described for various solvent qualities and salt concentration. In salt free solution, we find a slight charge depletion in the central part of the chain: the charges accumulate at the ends. The effect is less important if salt is added to the solution since the charge inhomogeneity is localized close to the chain ends over a distance of order of the Debye length. In the case of poor solvent conditions we find a different charging of beads and strings in the framework of the necklace model. This inhomogeneity leads to a charge instability and a first order transition between spherical globules and elongated chains.Comment: 20 pages, 4 figure

Osmotic pressure: resisting or promoting DNA ejection from phage

Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of experimental techniques (osmotic suppression without DNaseI monitored by UV absorbance, pulse-field electrophoresis, and cryo-EM visualization) and simple scaling modeling that intact genome (i.e. undigested) ejection in a crowded environment is, on the contrary, enhanced or eventually complete with the help of a pulling force resulting from DNA condensation induced by the osmotic stress itself. This demonstrates that in vivo, the osmotically stressed cell cytoplasm will promote phage DNA ejection rather than resisting it. The further addition of DNA-binding proteins under crowding conditions is shown to enhance the extent of ejection. We also found some optimal crowding conditions for which DNA content remaining in the capsid upon ejection is maximum, which correlates well with the optimal conditions of maximum DNA packaging efficiency into viral capsids observed almost 20 years ago. Biological consequences of this finding are discussed

Entropic control of particle sizes during viral self-assembly

Morphologic diversity is observed across all families of viruses. Yet these supra-molecular assemblies are produced most of the time in a spontaneous way through complex molecular self-assembly scenarios. The modeling of these phenomena remains a challenging problem within the emerging field of Physical Virology. We present in this work a theoretical analysis aiming at highlighting the particular role of configuration entropy in the control of viral particle size distribution. Specializing this model to retroviruses like HIV-1, we predict a new mechanism of entropic control of both RNA uptake into the viral particle, and of the particle's size distribution. Evidence of this peculiar behavior has been recently reported experimentally

Dynamical DNA accessibility induced by chromatin remodeling and protein binding

International audienceChromatin remodeling factors are enzymes being able to alter locally chromatin structure at the nucleosomal level and they actively participate in the regulation of gene expression. Using simple rules for individual nucleosome motion induced by a remodeling factor, we designed simulations of the remodeling of oligomeric chromatin, in order to address quantitatively collective effects in DNA accessibility upon nucleosome mobilization. Our results suggest that accessibility profiles are inhomogeneous thanks to borders effects like protein binding. Remarkably, we show that the accessibility lifetime of DNA sequence is roughly doubled in the vicinity of borders as compared to its value in bulk regions far from the borders. These results are quantitatively interpreted as resulting from the confined diffusion of a large nucleosome depleted region

DNA heats up : Energetics of genome ejection from phage revealed by isothermal titration calorimetry

Most bacteriophages are known to inject their double-stranded DNA into bacteria upon receptor binding in an essentially spontaneous way. This downhill thermodynamic process from the intact virion toward the empty viral capsid plus released DNA is made possible by the energy stored during active packaging of the genome into the capsid. Only indirect measurements of this energy have been available until now using either single-molecule or osmotic suppression techniques. In this paper, we describe for the first time the use of isothermal titration calorimetry to directly measure the heat released (or equivalently the enthalpy) during DNA ejection from phage lambda, triggered in solution by a solubilized receptor. Quantitative analyses of the results lead to the identification of thermodynamic determinants associated with DNA ejection. The values obtained were found to be consistent with those previously predicted by analytical models and numerical simulations. Moreover, the results confirm the role of DNA hydration in the energetics of genome confinement in viral capsids.Comment: 24 pages including figures and tabl

Challenging packaging limits and infectivity of phage λ

The terminase motors of bacteriophages have been shown to be among the strongest active machines in the biomolecular world, being able to package several tens of kilobase pairs of viral genome into a capsid within minutes. Yet these motors are hindered at the end of the packaging process by the progressive build-up of a force resisting packaging associated with already packaged DNA. In this experimental work, we raise the issue of what sets the upper limit on the length of the genome that can be packaged by the terminase motor of phage λ and still yield infectious virions, and the conditions under which this can be efficiently performed. Using a packaging strategy developed in our laboratory of building phage λ from scratch, together with plaque assay monitoring, we have been able to show that the terminase motor of phage λ is able to produce infectious particles with up to 110% of the wild-type (WT) λ-DNA length. However, the phage production rate, and thus the infectivity, decreased exponentially with increasing DNA length, and was a factor of 103 lower for the 110% λ-DNA phage. Interestingly, our in vitro strategy was still efficient in fully packaging phages with DNA lengths as high as 114% of the WT length, but these viruses were unable to infect bacterial cells efficiently. Further, we demonstrated that the phage production rate is modulated by the presence of multivalent ionic species. The biological consequences of these finding are discussed

RNA Control of HIV-1 Particle Size Polydispersity

HIV-1, an enveloped RNA virus, produces viral particles that are known to be much more heterogeneous in size than is typical of non-enveloped viruses. We present here a novel strategy to study HIV-1 Viral Like Particles (VLP) assembly by measuring the size distribution of these purified VLPs and subsequent viral cores thanks to Atomic Force Microscopy imaging and statistical analysis. This strategy allowed us to identify whether the presence of viral RNA acts as a modulator for VLPs and cores size heterogeneity in a large population of particles. These results are analyzed in the light of a recently proposed statistical physics model for the self-assembly process. In particular, our results reveal that the modulation of size distribution by the presence of viral RNA is qualitatively reproduced, suggesting therefore an entropic origin for the modulation of RNA uptake by the nascent VLP

Electrophoresis of positioned nucleosomes

We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as wrapped length of DNA on the electrophoretic mobility of the complex. The predictions of the model are in qualitative agreement with experimental results on mononucleosomes assembled on short DNA fragments (<400bp). Influence of additional experimental parameters like gel concentration, ionic strength, effective charges is also discussed in the framework of the model, and is found to be qualitatively consistent with experiments when available. Based on the present model, we propose a simple semi-empirical formula describing positioning of nucleosomes as seen through electrophoresis.Comment: to appear in Biophys. J. 29 page