Folding transition of a single semiflexible polyelectrolyte chain through toroidal bundling of loop structures

Conformational behavior of a semiflexible dipolar chain with a variable relative size of charged groups via molecular dynamics simulations

The conformational behavior of an isolated semiflexible dipolar chain has been studied by molecular dynamics simulations. The dipolar chain was modeled as a backbone chain of charged beads, each containing an oppositely charged unit connected to it by a rigid spring. The main focus was on the effect of the backbone chain rigidity and the size of the charged groups on the morphology of the collapsed states of the chain formed in low-polar media where the electrostatic interactions are essential. It has been found that the stable globular conformations of the long chain of N = 256 backbone beads are a toroid and an elliptical globule. The macroscopic parameters (such as the radius of gyration and shape factors) as well as the local characteristics of these conformations (radial density distributions of ions, orientational correlations of chain segments, dipoles etc.) are studied depending on the chain stiffness. The regions of stability of a torus and an elliptical globule are found for the dipolar chains with variable dipole length and stiffness, which depend on the strength of electrostatic interactions. It has been shown that a size asymmetry of oppositely charged beads destabilizes globular states favoring elongated chain conformations. A coexistence of various metastable states was demonstrated for shorter chains of N = 128, 64, and 32.

Self-assembly of bis-salphen compounds: from semiflexible chains to webs of nanorings

The recently-observed self-assembly of certain salphen-based compounds into neuron-like networks of microrings interconnected with nano-thin strings may suggest a new highly-potent tool for nanoscale patterning. However, the mechanism behind such phenomena needs to be clarified before they can be applied in materials design. Here we show that, in contrast with what was initially presumed, the emergence of a "rings-and-rods" pattern is unlikely to be explained by merging, collapse and piercing of vesicles as in previously reported cases of nanorings self-assembly via non-bonding interactions. We propose an alternative explanation: the compounds under study form a 1D coordination polymer, the fibres of which are elastic enough to fold into toroidal globules upon solvent evaporation, while being able to link separate chains into extended networks. This becomes possible because the structure of the compound's scaffold is found to adopt a very different conformation from that inferred in the original work. Based on ab initio and molecular dynamics calculations we propose a step-by-step description of self-assembly process of a supramolecular structure which explains all the observed phenomena in a simple and clear way. The individual roles of the compound' s scaffold structure, coordination centres, functional groups and solvent effects are also explained, opening a route to control the morphology of self-assembled networks and to synthesize new compounds exhibiting similar behaviour.

Coexistence of coil and globule domains within a single confined DNA chain

The highly charged DNA chain may be either in an extended conformation, the coil, or condensed into a highly dense and ordered structure, the toroid. The transition, also called collapse of the chain, can be triggered in different ways, for example by changing the ionic conditions of the solution. We observe individual DNA molecules one by one, kept separated and confined inside a protein shell (the envelope of a bacterial virus, 80 nm in diameter). For subcritical concentrations of spermine (4+), part of the DNA is condensed and organized in a toroid and the other part of the chain remains uncondensed around. Two states coexist along the same DNA chain. These ‘hairy’ globules are imaged by cryo-electron microscopy. We describe the global conformation of the chain and the local ordering of DNA segments inside the toroid.

Modeling DNA condensation on freestanding cationic lipid membranes

Motivated by recent experimental observations of a rapid spontaneous DNA coil-globule transition on freestanding cationic lipid bilayers, we propose simple theoretical models for DNA condensation on cationic lipid membranes. First, for a single DNA rod, we examine the conditions of full wrapping of a cylindrical DNA-like semi-flexible polyelectrolyte by an oppositely charged membrane. Then, for two parallel DNA rods, we self-consistently analyze the shape and the extent of the membrane enveloping them, focusing on membrane elastic deformations and the membrane-DNA embracing angle, which enables us to compute the membrane-mediated DNA-DNA interactions. We examine the effects of the membrane composition and its charge density, which are the experimentally tunable parameters. We show that membrane-driven rod-rod attraction is more pronounced for higher charge densities and for smaller surface tensions of the membrane. Thus, we demonstrate that for a long DNA chain adhered to a cationic lipid membrane, such membrane-induced DNA-DNA attraction can trigger compaction of DNA.

Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness

We investigated the folding transition between an elongated coil state and a compact state on a single polymer chain confined in a small space with different stiffness with the aid of Monte Carlo simulation. In a flexible polymer, the folding transition is retarded in a confined space. In contrast, the transition is promoted for a semiflexible chain, in which the discontinuity of the volume change occupied by a single chain is diminished by confinement. This unique confinement effect is interpreted in terms of conformational entropy and self-avoiding repulsive interaction.

In vitro HIV-1 selective integration into the target sequence and decoy-effect of the modified sequence

Although there have been a few reports that the HIV-1 genome can be selectively integrated into the genomic DNA of cultured host cell, the biochemistry of integration selectivity has not been fully understood. We modified the in vitro integration reaction protocol and developed a reaction system with higher efficiency. We used a substrate repeat, 5′-(GTCCCTTCCCAGT)_n(ACTGGGAAGGGAC)_n-3′, and a modified sequence DNA ligated into a circular plasmid. CAGT and ACTG (shown in italics in the above sequence) in the repeat units originated from the HIV-1 proviral genome ends. Following the incubation of the HIV-1 genome end cDNA and recombinant integrase for the formation of the pre-integration (PI) complex, substrate DNA was reacted with this complex. It was confirmed that the integration selectively occurred in the middle segment of the repeat sequence. In addition, integration frequency and selectivity were positively correlated with repeat number n. On the other hand, both frequency and selectivity decreased markedly when using sequences with deletion of CAGT in the middle position of the original target sequence. Moreover, on incubation with the deleted DNAs and original sequence, the integration efficiency and selectivity for the original target sequence were significantly reduced, which indicated interference effects by the deleted sequence DNAs. Efficiency and selectivity were also found to vary discontinuously with changes in manganese dichloride concentration in the reaction buffer, probably due to its influence on the secondary structure of substrate DNA. Finally, integrase was found to form oligomers on the binding site and substrate DNA formed a loop-like structure. In conclusion, there is a considerable selectivity in HIV-integration into the specified sequence; however, similar DNA sequences can interfere with the integration process, and it is therefore difficult for in vivo integration to occur selectively in the actual host genome DNA.

Finite-width bundle is most stable in a solution with salt

We applied the mean-field approach to a columnar bundle assembled by the parallel arrangement of stiff polyelectrolyte rods in a salt bath. The electrostatic potential can be divided into two regions: inside the bundle for condensed counterions and outside the bundle for free small ions. To determine the distribution of condensed counterions inside the bundle, we use a local self-consistent condition that depends on the charge density, the electrostatic potential, and the net polarization. The results showed that, upon bundle formation, the electric charge of polyelectrolytes, even those inside the bundle, tends to survive in an inhomogeneous manner, and thus their width remains finite under thermal equilibrium because of the long-range effect of charge instability.