Gregory P. Smith

Liquid crystal self-assembly of random-sequence DNA oligomers.

In biological systems and nanoscale assemblies, the self-association of DNA is typically studied and applied in the context of the evolved or directed design of base sequences that give complementary pairing, duplex formation, and specific structural motifs. Here we consider the collective behavior of DNA solutions in the distinctly different regime where DNA base sequences are chosen at random or with varying degrees of randomness. We show that in solutions of completely random sequences, corresponding to a remarkably large number of different molecules, e.g., approximately 1012 for random 20-mers, complementary still emerges and, for a narrow range of oligomer lengths, produces a subtle hierarchical sequence of structured self-assembly and organization into liquid crystal (LC) phases. This ordering follows from the kinetic arrest of oligomer association into long-lived partially paired double helices, followed by reversible association of these pairs into linear aggregates that in turn condense into LC domains.

Spontaneous liquid crystal and ferromagnetic ordering of colloidal magnetic nanoplates.

Ferrofluids are familiar as colloidal suspensions of ferromagnetic nanoparticles in aqueous or organic solvents. The dispersed particles are randomly oriented but their moments become aligned if a magnetic field is applied, producing a variety of exotic and useful magnetomechanical effects. A longstanding interest and challenge has been to make such suspensions macroscopically ferromagnetic, that is having uniform magnetic alignment in the absence of a field. Here we report a fluid suspension of magnetic nanoplates that spontaneously aligns into an equilibrium nematic liquid crystal phase that is also macroscopically ferromagnetic. Its zero-field magnetization produces distinctive magnetic self-interaction effects, including liquid crystal textures of fluid block domains arranged in closed flux loops, and makes this phase highly sensitive, with it dramatically changing shape even in the Earths magnetic field.

Metal oxide formation by serine and cysteine proteases

Silicatein-α, a member of the cathepsin-L family of protease enzymes, has previously been identified as a mediator for the formation of metal oxides such as silica (K. Shimizu, J. Cha, G. D. Stucky and D. E. Morse, Proc. Natl. Acad. Sci. U. S. A., 1998, 95, 6234). The active site of silicatein-α, a serine-histidine-asparagine triad, prompted us to investigate metal oxide formation in protease enzymes with similar active sites. Three enzymes were explored: the cysteine proteases papain and TEV (tobacco etch virus protease), and the serine protease trypsin. It was observed that papain and trypsin were able to mediate the formation of titania at room temperature and neutral pH. Only papain was able to mediate the formation of silica, and TEV was unable to mediate the formation of either titania or silica. The metal oxide formation activities of papain and trypsin were inhibited by heat denaturation, suggesting a role of protein tertiary structure on condensation activity. These activities are discussed in terms of sequence homology to silicatein-α and active site accessibility.

Abiotic ligation of DNA oligomers templated by their liquid crystal ordering

It has been observed that concentrated solutions of short DNA oligomers develop liquid crystal ordering as the result of a hierarchically structured supramolecular self-assembly. In mixtures of oligomers with various degree of complementarity, liquid crystal microdomains are formed via the selective aggregation of those oligomers that have a sufficient degree of duplexing and propensity for physical polymerization. Here we show that such domains act as fluid and permeable microreactors in which the order-stabilized molecular contacts between duplex terminals serve as physical templates for their chemical ligation. In the presence of abiotic condensing agents, liquid crystal ordering markedly enhances ligation efficacy, thereby enhancing its own phase stability. The coupling between order-templated ligation and selectivity provided by supramolecular ordering enables an autocatalytic cycle favouring the growth of DNA chains, up to biologically relevant lengths, from few-base long oligomers. This finding suggests a novel scenario for the abiotic origin of nucleic acids.

Alignment of the columnar liquid crystal phase of nano-DNA by confinement in channels

We demonstrate that topographic confinement in micro-channels can produce aligned domains of the columnar liquid crystal phase of complementary duplex short deoxyribonucleic acid (DNA) oligomers. Optical microscopy probing birefringence and fluorescence polarisation showed that the columnar liquid crystal phase of a 1:1 mixture of the complementary dodecamers 5′–CCTCAAAACTCC–3′ and 5′–GGAGTTTTGAGG–3′ in aqueous solution was aligned with the duplex DNA chains oriented normal to the channel axis.

Phases and structures of sunset yellow and disodium cromoglycate mixtures in water

We study phases and structures of mixtures of two representative chromonic liquid crystal materials, sunset yellow FCF (SSY) and disodium cromoglycate (DSCG), in water. A variety of combinations of isotropic, nematic (N), and columnar (also called M) phases are observed depending on their concentrations, and a phase diagram is made. We find a tendency for DSCG-rich regions to show higher-order phases while SSY-rich regions show lower-order ones. We observe uniform mesophases only when one of the materials is sparse in the N phases. Their miscibility in M phases is so low that essentially complete phase separation occurs. X-ray scattering and spectroscopy studies confirm that SSY and DSCG molecules do not mix when they form chromonic aggregates and neither do their aggregates when they form M phases.

Corrigendum: Abiotic ligation of DNA oligomers templated by their liquid crystal ordering.

Nature Communications 6: Article number: 6424 (2015); Published 10 March 2015; Updated 17 June 2015 The original version of this Article contained an error in the spelling of the author Youngwoo Yi, which was incorrectly given as Yougwooo Yi. This has now been corrected in both the PDF and HTML versions of the Article.

Nuclear pore complex frequency in CA1 pyramidal cells of the aging rat

The frequency and the diameter of nuclear pore complexes, and the nuclear perimeter, were studied in CA1 pyramidal cells of the hippocampi from 3-, 9-, 24-, and 30-month-old rats (Fischer 344). No changes with age in any of these parameters were observed. This finding is discussed in terms of varied responses of different brain areas to the effects of aging.

Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson–Crick selectivity

Significance The columnar liquid crystal phases reported here are physical associations of the smallest molecular species to self-assemble into the duplex base-paired stacked columnar double-helical structures of nucleic acids. These assemblies of monomers can provide starting states capable of partitioning appropriate molecules from solution with a high degree of selectivity, acting as pathways for the prebiotic appearance of molecular selection, self-assembly, and, ultimately, of the sequence-directed assembly of polymers. We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson–Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.