Topological Metadefects: Tangles of Dislocations.

The concept of topological defects is universal. In condensed matter, it applies to disclinations, dislocations, or vortices that are fingerprints of symmetry breaking during phase transitions. Using as a generic example the tangles of dislocations, we introduce the concept of topological metadefects, i.e., defects made of defects. We show that in cholesterics, dextrogyre and levogyre primary tangles are generated through the D_{2}→C_{2} symmetry breaking from the coplanar dislocation pair called Lehmann cluster submitted to a high enough tensile strain. The primary tangles can be wound up individually into double helices. They can also annihilate in pairs or associate into tangles of higher orders following simple algebraic rules.

Interplay of Structure and Dynamics in Lithium/Ionic Liquid Electrolytes: Experiment and Molecular Simulation.

Despite their promising use in electrochemical and electrokinetic devices, ionic-liquid-based electrolytes often exhibit complex behavior arising from a subtle interplay of their structure and dynamics. Here, we report a joint experimental and molecular simulation study of such electrolytes obtained by mixing 1-butyl 3-methylimidazolium tetrafluoroborate with lithium tetrafluoroborate. More in detail, experiments consisting of X-ray scattering, pulsed field gradient NMR, and complex impedance spectroscopy are analyzed in the light of molecular dynamics simulations to probe the structural, dynamical, and electrochemical properties of this ionic-liquid-based electrolyte. Lithium addition promotes the nanostructuration of the liquid as evidenced from the appearance of a scattering prepeak that becomes more pronounced. Microscopically, using the partial structure factors determined from molecular dynamics, this prepeak is shown to correspond to the formation of well-ordered positive/negative charge series and also large aggregates (Lin(BF4)4-m)(4-m+n)-, which develop upon lithium addition. Such nanoscale ordering entails a drastic decrease in both the molecular mobility and ionic conductivity. In particular, the marked association of Li+ cations with four BF4- anions and long ion pairing times, which are promoted upon lithium addition, are found to severely hinder the Li+ transport properties.

Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte.

The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape.

Communication: Investigation of ion aggregation in ionic liquids and their solutions with lithium salt under high pressure.

X-ray scattering measurements were utilized to probe the effects of pressure on a series of ionic liquids, N-alkyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide (Pyr1A-TFSI) (A = 3, 6, and 9), along with mixtures of ionic liquid and 30 mol. % lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt. No evidence was found for crystallization of the pure ionic liquids or salt mixtures even at pressures up to 9.2 GPa. No phase separation or demixing was observed for the ionic liquid and salt mixtures. Shifts in the peak positions are indicative of compression of the ionic liquids and mixtures up to 2 GPa, after which samples reach a region of relative incompressibility, possibly indicative of a transition to a glassy state. With the application of pressure, the intensity of the prepeak was found to decrease significantly, indicating a reduction in cation alkyl chain aggregation. Additionally, incompressibility of the scattering peak associated with the distance between like-charges in the pure ionic liquids compared to that in mixtures with lithium salt suggests that the application of pressure could inhibit Li+ coordination with TFSI- to form Li[TFSI2]- complexes. This inhibition occurs through the suppression of TFSI- in the trans conformer, in favor of the smaller cis conformer, at high pressures.

Identification of a major intermediate along the self-assembly pathway of an icosahedral viral capsid by using an analytical model of a spherical patch.

Viruses are astonishing edifices in which hundreds of molecular building blocks fit into the final structure with pinpoint accuracy. We established a robust kinetic model accounting for the in vitro self-assembly of a capsid shell derived from an icosahedral plant virus by using time-resolved small-angle X-ray scattering (TR-SAXS) data at high spatiotemporal resolution. By implementing an analytical model of a spherical patch into a global fitting algorithm, we managed to identify a major intermediate species along the self-assembly pathway. With a series of data collected at different protein concentrations, we showed that free dimers self-assembled into a capsid through an intermediate resembling a half-capsid. The typical lifetime of the intermediate was a few seconds and yet the presence of so large an oligomer was not reported before. The progress in instrumental detection along with the development of powerful algorithms for data processing contribute to shedding light on nonequilibrium processes in highly complex systems such as viruses.

Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates.

Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.

Weighing polyelectrolytes packaged in viruslike particles.

This Letter reports on the remarkable selectivity of capsid proteins for packaging synthetic polyelectrolytes in viruslike particles. By applying the contrast variation method in small-angle neutron scattering, we accurately estimated the mean mass of packaged polyelectrolytes ⟨Mp⟩ and that of the surrounding capsid ⟨Mcap⟩. Remarkably, the mass ratio ⟨Mp⟩/⟨Mcap⟩ was invariant for polyelectrolyte molecular weights spanning more than 2 orders of magnitude. To do so, capsids either packaged several chains simultaneously or selectively retained the shortest chains that could fit the capsid interior. Our data are in qualitative agreement with theoretical predictions based on free energy minimization and emphasize the importance of protein self-energy. These findings may give new insights into the nonspecific origin of genome selectivity for a number of viral systems.

Influence of pDNA availability on transfection efficiency of polyplexes in non-proliferative cells.

We succeeded in visualizing plasmid DNA (pDNA) in the nucleus and cytosol of non-proliferative cells after transfection with linear polyethylenemine (lPEI) and histidinylated lPEI (His16-lPEI). This was possible with confocal microscope by using pDNA labelled with quantum dots. Indeed pDNA labelled with Cy3 leads to false positive nuclear localization because the saturation of the fluorescence signal overestimated the volume occupied by Cy3-pDNA. Moreover, Cy3 brightness was too weak to detect low amount of pDNA. About 20 to 40 pDNA copies were detected in the nucleus after the transfection of pDNA labelled with quantum dots. Transfection efficiency and cellular imaging data suggested that the cytosolic availability of pDNA, including endosome escape and/or polyplexes dissociation, is crucial for its nuclear delivery. In vitro transcription assay and transfection of cells allowing cytosolic gene expression concluded to better cytosolic availability of pDNA within His16-lPEI polyplexes. Cryo-TEM analyses revealed that His16-lPEI polyplexes exhibited a spherical shape and an amorphous internal structure which differed from the high degree of order of lPEI polyplexes. Altogether, this comparative study indicated that the high transfection efficiency of non-proliferative cells with His16-lPEI polyplexes was related to the amorphous structure and the facilitated dissociation of the assemblies.

Unusual self-assembly properties of Norovirus Newbury2 virus-like particles.

In the Caliciviridae family of nonenveloped, positive-stranded RNA viruses, Noroviruses are major causes of human and animal gastroenteritis worldwide. The Norovirus T=3 icosahedral capsid is made of 180 copies of the VP1 protein, as exemplified in the crystal structure of the virus-like particle (VLP) of the human Norwalk virus (NV). It was previously shown that the ca 40-nm recombinant NV VLP can be disassembled and reassembled in vitro. Here we report on the disassembly and self-assembly properties for the related (VP1 sequence identity of 50%) bovine Newbury2 Norovirus (NB2) VLP. Using a panel of biophysical techniques, we show that while the NB2 VLP displays disassembly properties similar to the NV VLP, NB2-VP1 shows remarkable self-assembly properties heretofore unreported for NV-VP1 or any other calicivirus capsid protein. These properties include the capabilities of self-assembling not only into regular T=3 capsids but also into larger VLP (up to 76 nm in diameter) and of tolerating substitution of the spike domain for that of a distantly related Calicivirus. In conditions favoring the natural, T=3 capsid, NB2-VP1 reproducibly assembles by an apparent two-phase process. Our results establish a robust new system with which to probe the dynamics of viral capsid self-assembly.

Norovirus capsid proteins self-assemble through biphasic kinetics via long-lived stave-like intermediates.

The self-assembly kinetics for a norovirus capsid protein were probed by time-resolved small-angle X-ray scattering and then analyzed by singular value decomposition and global fitting. Only three species contribute to the total scattering intensities: dimers, intermediates comprising some 11 dimers, and icosahedral T = 3 capsids made up of 90 dimers. Three-dimensional reconstructions of the intermediate robustly show a stave-like shape consistent with an arrangement of two pentameric units connected by an interstitial dimer. Upon triggering of self-assembly, the biphasic kinetics consist of a fast step in which dimers are assembled into intermediates, followed by a slow step in which intermediates interlock into capsids. This simple kinetic model reproduces experimental data with an excellent agreement over 6 decades in time and with nanometer resolution. The extracted form factors are robust against changes in experimental conditions. These findings challenge and complement currently accepted models for the assembly of norovirus capsids.

Phase behavior and structure of stable complexes between a long polyanion and a branched polycation.

The association between oppositely charged branched polyethylenimine (BPEI) and polymethacrylic acid (PMA) in the dilute regime is investigated using turbidimetric titration and electrophoretic mobility measurements. The complexation is controlled by tuning continuously the pH-sensitive charge of the polyacid in acidic solution. The formation of soluble and stable positively charged complexes is a cooperative process characterized by the existence of two regimes of weak and strong complexation. In the regime of weak complexation, a long PMA chain overcharged by several BPEI molecules forms a binary complex. As the charge of the polyacid increases, these binary complexes condense at a well defined charge ratio of the mixture to form large positively charged aggregates. The overcharging and the existence of two regimes of complexation are analyzed in the light of recent theories. The structure of the polyelectrolytes is investigated at higher polymer concentration by small angle neutron scattering. Binary complexes of finite size present an open structure where the polyacid chains connecting a small number of BPEI molecules have shrunk slightly. In the condensed complexes, BPEI molecules, wrapped by polyacid chains, form networks of stretched necklaces.

PEO-PPO block copolymer vectors do not interact directly with DNA but with lipid membranes.

Small angle neutron (SANS) and light scattering was used to study the interaction between fragments of double stranded deoxyribonucleic acid (DNA) and a synthetic triblock [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] amphiphilic polymer, known as L64, a potential vector for gene therapy. The mechanism of action of this vector is yet unknown. The contrast variation method was used to separate the partial structure factors of the different components in mixtures of triblock and DNA. It has been found that the copolymer and DNA molecules exhibit repulsive interactions. Further, the interaction between the copolymer and a model lipid membrane was investigated in order to explain the action of the vector. Electrical measurements on black lipid membranes indicated that the main effect of L64 as a vector is to permeabilize the cell's membrane.

Negatively charged self-assembling DNA/poloxamine nanospheres for in vivo gene transfer.

Over the past decade, numerous nonviral cationic vectors have been synthesized. They share a high density of positive charges and efficiency for gene transfer in vitro. However, their positively charged surface causes instability in body fluids and cytotoxicity, thereby limiting their efficacy in vivo. Therefore, there is a need for developing alternative molecular structures. We have examined tetrabranched amphiphilic block copolymers consisting of four polyethyleneoxide/polypropyleneoxide blocks centered on an ethylenediamine moiety. Cryo-electron microscopy, ethidium bromide fluorescence and light and X-ray scattering experiments performed on vector-DNA complexes showed that the dense core of the nanosphere consisted of condensed DNA interacting with poloxamine molecules through electrostatic, hydrogen bonding and hydrophobic interactions, with DNA molecules also being exposed at the surface. The supramolecular organization of block copolymer/DNA nanospheres induced the formation of negatively charged particles. These particles were stable in a solution that had a physiological ionic composition and were resistant to decomplexation by heparin. The new nanostructured material, the structure of which clearly contrasted with that of lipoplexes and polyplexes, efficiently transferred reporter and therapeutic genes in skeletal and heart muscle in vivo. Negatively charged supramolecular assemblies hold promise as therapeutic gene carriers for skeletal and heart muscle-related diseases and expression of therapeutic proteins for local or systemic uses.