Liquid crystal formation in supercoiled DNA solutions

Colloidal Particle-Induced Microstructural Transition in Cellulose/Ionic Liquid/Water Mixtures

The role of colloidal particles in enhancing the mechanical and thermal properties of liquid crystalline (LC) gels formed in microcrystalline cellulose/1-allyl-3-methylimidazolium chloride/water mixtures is experimentally investigated by means of rheology and polarized optical microscopy (POM). The overshoot in loss modulus and increase in the melting temperature of LC domains as observed in differential scanning calorimetry signal a stronger interaction of cellulose with both hydrophobic polystyrene and hydrophilic silica nanoparticles which in turn point to considerable amphiphilic nature of cellulose. The aggregation of nanoparticles observed by POM and the rheological behavior point to the development of a sample-spanning network of cellulose-nanoparticle clusters during the sol-gel transition with an increase in concentration of water. Furthermore, the LC gels obey Chambon-Winter (CW) criterion, indicating a self-similar gel network, except at very high particle loadings. Moreover, the LC domains show a temporal evolution into a space-spanning network of cellulose spherulites. The evolution process largely depends on the particle concentration, with highly loaded samples showing quicker evolution, which leads to a violation of the CW criterion. Furthermore, the temperature-induced microstructural transition (with and without shear) is also examined.

Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes

Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.

Rheology and microstructure of concentrated microcrystalline cellulose (MCC)/1-allyl-3-methylimidazolium chloride (AmimCl)/water mixtures

Water added to a solution of microcrystalline cellulose (MCC) in 1-allyl-3-methylimidazolium chloride (AmimCl) reduces the solvent quality and causes significant changes in the flow properties and microstructure due to restructuring and aggregation of cellulose molecules. We report an experimental investigation by means of polarization optical microscopy (POM) and rheology of the distinct phases formed in 5-20 wt% MCC/AmimCl solutions due to the addition of water. With increase in the cellulose concentration, the MCC/AmimCl/water mixtures showed different morphologies such as the non-aligned cholesteric liquid crystalline (LC) domain, the coexistence of spherulite-like structures within the LC domain and a space-spanning network of spherulite-like structures at high concentrations of water. In situ microscopy during shear and POM observations pre and post shear revealed a significant increase in the size of the birefringent domains as the shear rate is increased, which continued to exist even after the cessation of shear. With an increase in the concentration of water, the zero shear viscosity of the MCC/AmimCl/water mixtures was found to go through a minimum, beyond which the aggregation of cellulose commenced. The corresponding oscillatory shear response showed a sol-gel transition with an increase in water concentration. Moreover, at high cellulose concentrations (12-20 wt%), the MCC/AmimCl/water gels exhibited self-similarity and followed the Chambon-Winter (CW) criterion. The similar phase behavior and rheological response observed for MCC dissolved in 1-butyl-3 methylimidazolium chloride (BmimCl) indicated the generality of the presented results.

A histone-like protein induces plasmid DNA to form liquid crystals in vitro and gene compaction in vivo

The liquid crystalline state is a universal phenomenon involving the formation of an ordered structure via a self-assembly process that has attracted attention from numerous scientists. In this study, the dinoflagellate histone-like protein HCcp3 is shown to induce super-coiled pUC18 plasmid DNA to enter a liquid crystalline state in vitro, and the role of HCcp3 in gene condensation in vivo is also presented. The plasmid DNA (pDNA)-HCcp3 complex formed birefringent spherical particles with a semi-crystalline selected area electronic diffraction (SAED) pattern. Circular dichroism (CD) titrations of pDNA and HCcp3 were performed. Without HCcp3, pUC18 showed the characteristic B conformation. As the HCcp3 concentration increased, the 273 nm band sharply shifted to 282 nm. When the HCcp3 concentration became high, the base pair (bp)/dimer ratio fell below 42/1, and the CD spectra of the pDNA-HCcp3 complexes became similar to that of dehydrated A-form DNA. Microscopy results showed that HCcp3 compacted the super-coiled gene into a condensed state and that inclusion bodies were formed. Our results indicated that HCcp3 has significant roles in gene condensation both in vitro and in histone-less eukaryotes in vivo. The present study indicates that HCcp3 has great potential for applications in non-viral gene delivery systems, where HCcp3 may compact genetic material to form liquid crystals.

Cholesteric and nematic liquid crystalline phase behavior of double-stranded DNA stabilized single-walled carbon nanotube dispersions

The first lyotropic cholesteric single-walled carbon nanotube (SWNT) liquid crystal phase was obtained by dispersing SWNTs in an aqueous solution of double-stranded DNA (dsDNA). Depending on the dispersion methodology, the polydomain nematic phase previously reported for other lyotropic carbon nanotube dispersions could also be obtained. The phase behavior and dispersion microstructure were affected by the relative concentrations of dsDNA and SWNT and whether small bundles were removed prior to concentrating the dispersions. This readily controlled phase behavior opens new routes for producing SWNT films with controlled morphology.

Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations

With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.

Polarization-sensitive two-photon microscopy study of the organization of liquid-crystalline DNA

Highly concentrated DNA solutions exhibit self-ordering properties such as the generation of liquid-crystalline phases. Such organized domains may play an important role in the global chromatin topology but can also be used as a simple model for the study of more complex 3D DNA structures. In this work, using polarized two-photon fluorescence microscopy, we report on the orientation of DNA molecules in liquid-crystalline phases. For this purpose, we analyze the signal emitted by fluorophores that are noncovalently bound to DNA strands. In nonlinear processes, excitation occurs exclusively in the focal volume, which offers advantages such as the reduction of photobleaching of out-of-focus molecules and intrinsic 3D sectioning capability. Propidium iodide and Hoechst, two fluorophores with different DNA binding modes, have been considered. Polarimetric measurements show that the dyes follow the alignment with respect to the DNA strands and allow the determination of the angles between the emission dipoles and the longitudinal axis of the DNA double strand. These results provide a useful starting point toward the application of two-photon polarimetry techniques to determine the local orientation of condensed DNA in physiological conditions.

Conformational response of supercoiled DNA to confinement in a nanochannel

Monte Carlo simulations were done to study the conformation of supercoiled DNA confined in a nanochannel. The molecule has a superhelical density of around -0.05 and is bathed in a monovalent salt solution with an ionic strength of 2, 10, or 150 mM. The cross-sectional diameter of the circular shaped nanochannel was varied in the range of 10 to 80 nm. The conformational properties were characterized by the writhing number and the distribution in the distance between the two opposing strands of the superhelix. With increasing confinement, as set by a smaller tube diameter and/or decreased screening of the Coulomb interaction, the supercoil becomes more tightly interwound and long-range structural features such as branching and the formation of hairpins are progressively suppressed. Analysis of the energetics shows a concurrent increase in electrostatic energy and energy of interaction of the supercoil with the wall, but the elastic twisting energy decreases. Confinement in a nanochannel or otherwise hence results in a decrease in the absolute value of the twist exerted on the duplex. The bending energy remains approximately constant, which means that there are no significant deflections from the wall. The simulation results are interpreted with theory based on the wormlike chain model, including the effects of the wall, charge, elasticity, and configurational entropy. It was found that the theory is reasonably successful in predicting the structural response to the confinement at the local level of the diameter and pitch of the supercoil.

Amylose Crystallization from Concentrated Aqueous Solution

Maize amylose, separated from granular starch by means of an aqueous leaching process, was used to investigate spherulite formation from concentrated mixtures of starch in water. Amylose (10-20%, w/w) was found to form a spherulitic semicrystalline morphology over a wide range of cooling rates (1-250 degrees C/min), provided it was first heated to >170 degrees C. This is explained through the effect of temperature on chain conformation. A maximum quench temperature of approximately 70 degrees C was required to produce spherulitic morphology. Quench temperatures between 70 and 110 degrees C produced a gel-like morphology. This is explained on the basis of the relative kinetics of liquid-liquid phase separation vis-à-vis crystallization. The possibility of the presence of a liquid crystalline phase affecting the process of spherulite formation is discussed.

Pharmaceutical liquid crystals: the relevance of partially ordered systems

Pharmaceutical solids have generally been characterized as either three-dimensional crystals or amorphous solids based on X-ray powder diffraction and modulated temperature differential scanning calorimetry. In contrast, fewer examples of thermotropic and lyotropic liquid crystals, or mesophases, appear in the pharmaceutical literature, and that literature teaches that the aforementioned analytical techniques should be complemented with polarized light microscopy and small-angle X-ray scattering in order to effectively identify potential liquid crystalline states. Lyotropic liquid crystals are induced by the presence of solvent, and have been extensively described elsewhere in the context of emulsion technology; however, other pharmaceutical examples are emerging. Thermotropic liquid crystals are induced by a change in temperature and are essentially free of solvent, where more pharmaceutical applications appear in the literature. In the present review the general structural characteristics that favor the formation of liquid crystalline mesophases are categorized by therapeutic target and molecular size, and the analytical means of their identification are presented.

Information content and complexity in the high-order organization of DNA

Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.