Michi Nakata

End-to-End Stacking and Liquid Crystal Condensation of 6– to 20–Base Pair DNA Duplexes

Short complementary B-form DNA oligomers, 6 to 20 base pairs in length, are found to exhibit nematic and columnar liquid crystal phases, even though such duplexes lack the shape anisotropy required for liquid crystal ordering. Structural study shows that these phases are produced by the end-to-end adhesion and consequent stacking of the duplex oligomers into polydisperse anisotropic rod-shaped aggregates, which can order into liquid crystals. Upon cooling mixed solutions of short DNA oligomers, in which only a small fraction of the DNA present is complementary, the duplex-forming oligomers phase-separate into liquid crystal droplets, leaving the unpaired single strands in isotropic solution. In a chemical environment where oligomer ligation is possible, such ordering and condensation would provide an autocatalytic link whereby complementarity promotes the extended polymerization of complementary oligomers.

Helical Nanofilament Phases

Packing Bananas and Boomerangs Assembling achiral molecules typically generates achiral domains. However, odd things can happen when the molecules are banana-or boomerang-shaped—their cores can twist out of plain to form left- or right-handed helices, which can then pack into chiral domains that will polarize light (see the Perspective by Amabilino). Hough et al. (p. 452) show that if you make the situation even more complex by frustrating the packing of adjacent layers, you can create a material that appears to be macroscopically isotropic with only very local positional and orientational ordering of the molecules but still shows an overall chirality. In a second paper, Hough et al. (p. 456) also show that if you change the chemistry of the molecules to allow for better overall packing, you can create a situation where helical filaments form that also tend to pack in layered structures. However, the frustration between the two types of packing leads to macroscopically chiral and mesoporous structures. Molecules lacking handedness can form layered, mesoporous helical structures. In the formation of chiral crystals, the tendency for twist in the orientation of neighboring molecules is incompatible with ordering into a lattice: Twist is expelled from planar layers at the expense of local strain. We report the ordered state of a neat material in which a local chiral structure is expressed as twisted layers, a state made possible by spatial limitation of layering to a periodic array of nanoscale filaments. Although made of achiral molecules, the layers in these filaments are twisted and rigorously homochiral—a broken symmetry. The precise structural definition achieved in filament self-assembly enables collective organization into arrays in which an additional broken symmetry—the appearance of macroscopic coherence of the filament twist—produces a liquid crystal phase of helically precessing layers.

Chiral Isotropic Liquids from Achiral Molecules

Packing Bananas and Boomerangs Assembling achiral molecules typically generates achiral domains. However, odd things can happen when the molecules are banana-or boomerang-shaped—their cores can twist out of plain to form left- or right-handed helices, which can then pack into chiral domains that will polarize light (see the Perspective by Amabilino). Hough et al. (p. 452) show that if you make the situation even more complex by frustrating the packing of adjacent layers, you can create a material that appears to be macroscopically isotropic with only very local positional and orientational ordering of the molecules but still shows an overall chirality. In a second paper, Hough et al. (p. 456) also show that if you change the chemistry of the molecules to allow for better overall packing, you can create a situation where helical filaments form that also tend to pack in layered structures. However, the frustration between the two types of packing leads to macroscopically chiral and mesoporous structures. Banana-shaped molecules lacking handedness form a macroscopically isotropic fluid that still has overall chirality. A variety of simple bent-core molecules exhibit smectic liquid crystal phases of planar fluid layers that are spontaneously both polar and chiral in the absence of crystalline order. We found that because of intralayer structural mismatch, such layers are also only marginally stable against spontaneous saddle splay deformation, which is incompatible with long-range order. This results in macroscopically isotropic fluids that possess only short-range orientational and positional order, in which the only macroscopically broken symmetry is chirality—even though the phases are formed from achiral molecules. Their conglomerate domains exhibit optical rotatory powers comparable to the highest ever found for isotropic fluids of chiral molecules.

Twist-bend heliconical chiral nematic liquid crystal phase of an achiral rigid bent-core mesogen.

The chiral, heliconical (twist-bend) nematic ground state is reported in an achiral, rigid, bent-core mesogen (UD68). Similar to the nematic twist-bend (N(TB)) phase observed in bent molecular dimers, the N(TB) phase of UD68 forms macroscopic, smecticlike focal-conic textures and exhibits nanoscale, periodic modulation with no associated modulation of the electron density, i.e., without a detectable lamellar x-ray reflection peak. The N(TB) helical pitch is p(TB) ∼ 14 nm. When an electric field is applied normal to the helix axis, a weak electroclinic effect is observed, revealing 50-μm-scale left- and right-handed domains in a chiral conglomerate.

A racemic layer structure in a chiral bent-core ferroelectric liquid crystal

A fluid smectic phase of a chiral bent-core liquid crystal was found to have a ground state structure that is anticlinic in tilt and ferroelectric in polar order, SmCAPF*. The layer chirality of this structure alternates from layer to layer despite their being composed of chiral mesogens. Observations of the optical second harmonic generation signal from well-aligned domains confirm that the ground state of this phase is bistable ferroelectric. In addition to the ground state two types of metastable domains are also observed.

Right-handed double-helix ultrashort DNA yields chiral nematic phases with both right- and left-handed director twist

Concentrated solutions of duplex-forming DNA oligomers organize into various mesophases among which is the nematic (N∗), which exhibits a macroscopic chiral helical precession of molecular orientation because of the chirality of the DNA molecule. Using a quantitative analysis of the transmission spectra in polarized optical microscopy, we have determined the handedness and pitch of this chiral nematic helix for a large number of sequences ranging from 8 to 20 bases. The B-DNA molecule exhibits a right-handed molecular double-helix structure that, for long molecules, always yields N∗ phases with left-handed pitch in the μm range. We report here that ultrashort oligomeric duplexes show an extremely diverse behavior, with both left- and right-handed N∗ helices and pitches ranging from macroscopic down to 0.3 μm. The behavior depends on the length and the sequence of the oligomers, and on the nature of the end-to-end interactions between helices. In particular, the N∗ handedness strongly correlates with the oligomer length and concentration. Right-handed phases are found only for oligomers shorter than 14 base pairs, and for the sequences having the transition to the N∗ phase at concentration larger than 620 mg/mL. Our findings indicate that in short DNA, the intermolecular double-helical interactions switch the preferred liquid crystal handedness when the columns of stacked duplexes are forced at high concentrations to separations comparable to the DNA double-helix pitch, a regime still to be theoretically described.

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Using optical microscopy, we have studied the phase behavior of mixtures of 12- to 22-bp-long nanoDNA oligomers. The mixtures are chosen such that only a fraction of the sample is composed of mutually complementary sequences, and hence the solutions are effectively mixtures of single-stranded and double-stranded (duplex) oligomers. When the concentrations are large enough, such mixtures phase-separate via the nucleation of duplex-rich liquid crystalline domains from an isotropic background rich in single strands. We find that the phase separation is approximately complete, thus corresponding to a spontaneous purification of duplexes from the single-strand oligos. We interpret this behavior as the combined result of the energy gain from the end-to-end stacking of duplexes and of depletion-type attractive interactions favoring the segregation of the more rigid duplexes from the flexible single strands. This form of spontaneous partitioning of complementary nDNA offers a route to purification of short duplex oligomers and, if in the presence of ligation, could provide a mode of positive feedback for the preferential synthesis of longer complementary oligomers, a mechanism of possible relevance in prebiotic environments.

Physical polymerization and liquid crystallization of RNA oligomers.

Ultrashort complementary RNA oligomers, as short as six base pairs in length, are found to exhibit chiral nematic and columnar liquid crystal phases in aqueous solution, through end-to-end adhesion into physically bound, but chemically segmented, polymers. Geometrical constraints indicate that the phosphate helix is continuous along the aggregated chain. The end-to-end adhesion is due to a base-staking type interaction, whose energy and temperature dependence are determined.

Alignment of liquid crystals by topographically patterned polymer films prepared by nanoimprint lithography

Nanoimprint lithographically (NIL) prepared polymer film replicas of micrometer scale topographic master patterns are used as liquid crystal alignment surfaces. Depolarized transmission light microscopy study of nematic liquid crystal cells made using the replicas as one window shows that the NIL generated linear line patterns and two-dimensional square grid patterns align the liquid crystal in planar mono- and bistable states.

Collective Molecular Motion during V-Shaped Switching in a Smectic Liquid Crystal.

The molecular motion during V-shaped switching in a homogeneously aligned smectic C*-like liquid crystal (LC) cell has been investigated by measuring the effective optical anisotropy Δneff, apparent tilt angle θapp, switching current, and second-harmonic generation and comparing them with the simulated results based on two extreme models, i.e., random model and collective model, where molecules switch randomly and collectively, respectively. The comparison revealed that the collective switching motion of LC molecules is more reasonable than the random motion. Moreover, it was also confirmed that the observed infrared absorption anisotropy of the phenyl stretching mode due to LC molecular distributions strongly supports the collective model. From these results, it was demonstrated that LC molecules do not switch randomly but all the LC molecules rotate collectively on a cone under the driving field.