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.

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.

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.

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.

Conductive and dielectric defects, and anisotropic and isotropic turbulence in liquid crystals: Electric power fluctuation measurements.

Fluctuations of the injected electric power during electroconvection (EHC) of liquid crystals are reported in both the conductive and the dielectric regime of convection. The amplitude and the frequency of the fluctuations, as well as the probability density functions have been compared in these two regimes and substantial differences have been found both in defect turbulence of EHC and at the DSM1-->DSM2 transition.

Persistent global power fluctuations near a dynamic transition in electroconvection.

This is a study of the global fluctuations in power injection and light transmission through a liquid crystal just above the onset of electroconvection. The source of the fluctuations is identified as the creation and annihilation of defects. They are spatially uncorrelated and yet temporally correlated. The temporal correlation is seen to persist for extremely long times. There seems to be an especially close relation between defect creation or annihilation in electroconvection and thermal plumes in Rayleigh-Bénard convection.