Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation.

The layered liquid crystalline phases formed by DNA molecules, which include rigid and flexible segments ("gapped DNA"), enable the study of both end-to-end stacking and side-to-side (helix-to-helix) lateral interactions, forming a model system to study such interactions at physiologically relevant DNA and ion concentrations. The observed layer structure exhibits long-range interlayer and in-layer positional correlations. In particular, the in-layer order has implications for DNA condensation, as it reflects whether these normally repulsive interactions become attractive under certain ionic conditions. Using synchrotron small-angle X-ray scattering measurements, we investigate the impact of divalent Mg2+ cations (in addition to a constant 150 mM Na+) on the stability of the inter- and in-layer DNA ordering as a function of temperature between 5 and 65 °C. DNA constructs with different terminal base pairings were created to mediate the strength of the attractive end-to-end stacking interactions between the blunt ends of the gapped DNA constructs. We demonstrate that the stabilities at a fixed DNA concentration of both interlayer and in-layer order are significantly enhanced even at a few mM Mg2+ concentration. The stabilities are even higher at 30 mM Mg2+; however, a marked decrease is observed at 100 mM Mg2+, suggesting a change in the nature of side-by-side interactions within this Mg2+ concentration range. We discuss the implications of these results in terms of counterion-mediated DNA-DNA attraction and DNA condensation.

Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions.

Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.

Mono- and bilayer smectic liquid crystal ordering in dense solutions of "gapped" DNA duplexes.

Although its mesomorphic properties have been studied for many years, only recently has the molecule of life begun to reveal the true range of its rich liquid crystalline behavior. End-to-end interactions between concentrated, ultrashort DNA duplexes-driving the self-assembly of aggregates that organize into liquid crystal phases-and the incorporation of flexible single-stranded "gaps" in otherwise fully paired duplexes-producing clear evidence of an elementary lamellar (smectic-A) phase in DNA solutions-are two exciting developments that have opened avenues for discovery. Here, we report on a wider investigation of the nature and temperature dependence of smectic ordering in concentrated solutions of various "gapped" DNA (GDNA) constructs. We examine symmetric GDNA constructs consisting of two 48-base pair duplex segments bridged by a single-stranded sequence of 2 to 20 thymine bases. Two distinct smectic layer structures are observed for DNA concentration in the range [Formula: see text] mg/mL. One exhibits an interlayer periodicity comparable with two-duplex lengths ("bilayer" structure), and the other has a period similar to a single-duplex length ("monolayer" structure). The bilayer structure is observed for gap length ≳10 bases and melts into the cholesteric phase at a temperature between 30 °C and 35 °C. The monolayer structure predominates for gap length ≲10 bases and persists to [Formula: see text]C. We discuss models for the two layer structures and mechanisms for their stability. We also report results for asymmetric gapped constructs and for constructs with terminal overhangs, which further support the model layer structures.

Pretransitional behavior of viscoelastic parameters at the nematic to twist-bend nematic phase transition in flexible n-mers.

We report dynamic light scattering measurements of the orientational (Frank) elastic constants and associated viscosities among a homologous series of a liquid crystalline dimer, trimer, and tetramer exhibiting a uniaxial nematic (N) to twist-bend nematic (NTB) phase transition. The elastic constants for director splay (K11), twist (K22) and bend (K33) exhibit the relations K11 > K22 > K33 and K11/K22 > 2 over the bulk of the N phase. Their behavior near the N-NTB transition shows dependency on the parity of the number (n) of the rigid mesomorphic units in the flexible n-mers. Namely, the bend constant K33 in the dimer and tetramer turns upward and starts increasing close to the transition, following a monotonic decrease through most of the N phases. In contrast, K33 for the trimer flattens off just above the transition and shows no pretransitional enhancement. The twist constant K22 increases pretransitionally in both even and odd n-mers, but more weakly so in the trimer, while K11 increases steadily on cooling without evidence of pretransitional behavior in any n-mer. The viscosities associated with pure splay, twist-dominated twist-bend, and pure bend fluctuations in the N phase are comparable in magnitude to those of rod-like monomers. All three viscosities increase with decreasing temperature, but the bend viscosity in particular grows sharply near the N-NTB transition. The N-NTB pretransitional behavior is shown to be in qualitative agreement with the predictions of a coarse-grained theory, which models the NTB phase as a "pseudo-layered" structure with the symmetry (but not the mass density wave) of a smectic-A* phase.

Distinct differences in the nanoscale behaviors of the twist-bend liquid crystal phase of a flexible linear trimer and homologous dimer.

We synthesized the liquid crystal dimer and trimer members of a series of flexible linear oligomers and characterized their microscopic and nanoscopic properties using resonant soft X-ray scattering and a number of other experimental techniques. On the microscopic scale, the twist-bend phases of the dimer and trimer appear essentially identical. However, while the liquid crystal dimer exhibits a temperature-dependent variation of its twist-bend helical pitch varying from 100 to 170 Å on heating, the trimer exhibits an essentially temperature-independent pitch of 66 Å, significantly shorter than those reported for other twist-bend forming materials in the literature. We attribute this to a specific combination of intrinsic conformational bend of the trimer molecules and a sterically favorable intercalation of the trimers over a commensurate fraction (two-thirds) of the molecular length. We develop a geometric model of the twist-bend phase for these materials with the molecules arranging into helical chain structures, and we fully determine their respective geometric parameters.

Indication of a twist-grain-boundary-twist-bend phase of flexible core bent-shape chiral dimers.

The effect of the molecular chirality of chiral additives on the nanostructure of the twist-bend nematic (NTB) liquid crystal phase with ambidextrous chirality and nanoscale pitch due to spontaneous symmetry breaking is studied. It is found that the ambidextrous nanoscale pitch of the NTB phase increases by 50% due to 3% chiral additive, and the chiral transfer among the biphenyl groups disappears in the NTB* phase. Most significantly, a twist-grain boundary (TGB) type phase is found at c > 1.5 wt% chiral additive concentrations below the usual N* phase and above the non-CD active NTB* phase. In such a TGB type phase, the adjacent blocks of pseudo-layers of the nanoscale pitch rotate across the grain boundaries.

Elastic and viscous properties of the nematic dimer CB7CB.

We present a comprehensive set of measurements of optical, dielectric, diamagnetic, elastic, and viscous properties in the nematic (N) phase formed by a liquid crystalline dimer. The studied dimer, 1,7-bis-4-(4'-cyanobiphenyl) heptane (CB7CB), is composed of two rigid rodlike cyanobiphenyl segments connected by a flexible aliphatic link with seven methyl groups. CB7CB and other nematic dimers are of interest due to their tendency to adopt bent configurations and to form two states possessing a modulated nematic director structure, namely, the twist-bend nematic, N_{TB}, and the oblique helicoidal cholesteric, Ch_{OH}, which occurs when the achiral dimer is doped with a chiral additive and exposed to an external electric or magnetic field. We characterize the material parameters as functions of temperature in the entire temperature range of the N phase, including the pretransitional regions near the N-N_{TB} and N-to-isotropic (I) transitions. The splay constant K_{11} is determined by two direct and independent techniques, namely, detection of the Frederiks transition and measurement of director fluctuation amplitudes by dynamic light scattering (DLS). The bend K_{33} and twist K_{22} constants are measured by DLS. K_{33}, being the smallest of the three constants, shows a strong nonmonotonous temperature dependence with a negative slope in both N-I and N-N_{TB} pretransitional regions. The measured ratio K_{11}/K_{22} is larger than 2 in the entire nematic temperature range. The orientational viscosities associated with splay, twist, and bend fluctuations in the N phase are comparable to those of nematics formed by rodlike molecules. All three show strong temperature dependence, increasing sharply near the N-N_{TB} transition.

Smectic phase in suspensions of gapped DNA duplexes.

Smectic ordering in aqueous solutions of monodisperse stiff double-stranded DNA fragments is known not to occur, despite the fact that these systems exhibit both chiral nematic and columnar mesophases. Here, we show, unambiguously, that a smectic-A type of phase is formed by increasing the DNA's flexibility through the introduction of an unpaired single-stranded DNA spacer in the middle of each duplex. This is unusual for a lyotropic system, where flexibility typically destabilizes the smectic phase. We also report on simulations suggesting that the gapped duplexes (resembling chain-sticks) attain a folded conformation in the smectic layers, and argue that this layer structure, which we designate as smectic-fA phase, is thermodynamically stabilized by both entropic and energetic contributions to the system's free energy. Our results demonstrate that DNA as a building block offers an exquisitely tunable means to engineer a potentially rich assortment of lyotropic liquid crystals.

Elasticity, viscosity, and orientational fluctuations of a lyotropic chromonic nematic liquid crystal disodium cromoglycate.

Using dynamic light scattering, we study orientational fluctuation modes in the nematic phase of a self-assembled lyotropic chromonic liquid crystal (LCLC) disodium cromoglycate and measure the Frank elastic moduli and viscosity coefficients. The elastic moduli of splay (K1) and bend (K3) are in the order of 10 pN while the twist modulus (K2) is an order of magnitude smaller. The splay constant K1 and the ratio K1/K3 both increase substantially as the temperature T decreases, which we attribute to the elongation of the chromonic aggregates at lower temperatures. The bend viscosity is comparable to that of thermotropic liquid crystals, while the splay and twist viscosities are several orders of magnitude larger. The temperature dependence of bend viscosity is weak. The splay and twist viscosities change exponentially with the temperature. In addition to the director modes, the fluctuation spectrum reveals an additional mode that is attributed to diffusion of structural defects in the column-like aggregates.

Nanostructures of nematic materials of laterally branched molecules.

The synthesis and small-angle X-ray scattering (SAXS) characterization is reported for 20 laterally branched mesogenic molecules, which are derived from the common rod-shaped 2,5-bis([4-(octyloxy)phenyl]carbonyloxy) benzoic acid unit. These compounds have a varying degree of flexibility, in that their lateral branch is formed upon conversion of the acid to either an ester or an amide, and most laterally branched molecules exhibit relatively wide nematic liquid-crystal phases with a direct nematic-to-crystal transition at lower temperatures. SAXS studies reveal the presence of smectic-like nanostructures (clusters) with short-range order in the nematic phase, with characteristic correlation lengths from 3 to over 10 nm. The smectic layers that are contained in these clusters are tilted with respect to the nematic director by angles ranging from 0° (i.e. untilted) to 55°. In some compounds, the intensity of the SAXS peak corresponding to the smectic layer spacing depends strongly on temperature. The main features of the nanostructures can be understood based on the molecular structure; therefore, guiding future synthetic work towards more precisely controlled and technologically useful nanostructures in nematics.

Dielectric properties of mixtures of a bent-core and a calamitic liquid crystal.

Dielectric spectroscopy measurements have been performed on a bent-core nematic liquid crystal and on its binary mixtures with a calamitic nematic. We have detected more dispersions in the bent-core compound than in the calamitic one, including one at an unusually low frequency of a few kilohertz. The dispersions detected in the mixtures have been identified and the spectra have been split into contributions of the constituents. In order to connect the dielectric increment with the molecular dipole moment we have applied a sophisticated conformational calculation not performed before for a large, flexible mesogen molecule with numerous polar groups.

Thermal conductivity and particle agglomeration in alumina nanofluids: experiment and theory.

In recent years many experimentalists have reported an anomalously enhanced thermal conductivity in liquid suspensions of nanoparticles. Despite the importance of this effect for heat transfer applications, no agreement has emerged about the mechanism of this phenomenon, or even about the experimentally observed magnitude of the enhancement. To address these issues, this paper presents a combined experimental and theoretical study of heat conduction and particle agglomeration in nanofluids. On the experimental side, nanofluids of alumina particles in water and ethylene glycol are characterized using thermal conductivity measurements, viscosity measurements, dynamic light scattering, and other techniques. The results show that the particles are agglomerated, with an agglomeration state that evolves in time. The data also show that the thermal conductivity enhancement is within the range predicted by effective medium theory. On the theoretical side, a model is developed for heat conduction through a fluid containing nanoparticles and agglomerates of various geometries. The calculations show that elongated and dendritic structures are more efficient in enhancing the thermal conductivity than compact spherical structures of the same volume fraction, and that surface (Kapitza) resistance is the major factor resulting in the lower than effective medium conductivities measured in our experiments. Together, these results imply that the geometry, agglomeration state, and surface resistance of nanoparticles are the main variables controlling thermal conductivity enhancement in nanofluids.

Director dynamics in liquid-crystal physical gels.

Nematic liquid-crystal (LC) elastomers and gels have a rubbery polymer network coupled to the nematic director. While LC elastomers show a single, non-hydrodynamic relaxation mode, dynamic light-scattering studies of self-assembled liquid-crystal gels reveal orientational fluctuations that relax over a broad time scale. At short times, the relaxation dynamics exhibit hydrodynamic behavior. In contrast, the relaxation dynamics at long times are non-hydrodynamic, highly anisotropic, and increase in amplitude at small scattering angles. We argue that the slower dynamics arise from coupling between the director and the physically associated network, which prevents director orientational fluctuations from decaying completely at short times. At long enough times the network restructures, allowing the orientational fluctuations to fully decay. Director dynamics in the self-assembled gels are thus quite distinct from those observed in LC elastomers in two respects: they display soft orientational fluctuations at short times, and they exhibit at least two qualitatively distinct relaxation processes.

Dynamics of distorted cholesterics in a mesogenic versus isotropic polymer network.

The dynamics of the distorted cholesteric director is studied in a complex matrix, such as mesogenic and istotropic polymer networks, by means of dynamic light scattering. We employ polymer-stabilized cholesteric diffraction gratings as our system to measure thermal fluctuations of the cholesteric director in photostabilized low-molecular-weight polymer networks. The relaxation rates of fast and slow dynamical modes of the distorted cholesteric directors are measured in two scattering geometries, where the scattering vector is either parallel or perpendicular to the helical axis. The dispersion relations for fluctuation wave vectors along the helical axis are found to be fundamentally different for the two types of polymer networks. Experimental dispersion curves are in agreement with the theoretical predictions developed in the present paper. A possible understanding of dispersion in distorted cholesterics is developed and the experimental results for polymer stabilized cholesteric diffraction gratings are presented in this report. We also discuss the coupling of a slow relaxation mode of distorted cholesterics in a mesogenic versus isotropic polymer network.