Tommaso P. Fraccia

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.

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.

Evidence of Liquid Crystal–Assisted Abiotic Ligation of Nucleic Acids

The emergence of early life must have been marked by the appearance in the prebiotic era of complex molecular structures and systems, motivating the investigation of conditions that could not only facilitate appropriate chemical synthesis, but also provide the mechanisms of molecular selection and structural templating necessary to pilot the complexification toward specific molecular patterns. We recently proposed and demonstrated that these functions could be afforded by the spontaneous ordering of ultrashort nucleic acids oligomers into Liquid Crystal (LC) phases. In such supramolecular assemblies, duplex-forming oligomers are held in average end-to-end contact to form chemically discontinuous but physically continuous double helices. Using blunt ended duplexes, we found that LC formation could both provide molecular selection mechanisms and boost inter-oligomer ligation. This paper provides an essential extension to this notion by investigating the catalytic effects of LC ordering in duplexes with mutually interacting overhangs. Specifically, we studied the influence of LC ordering of 5’-hydroxy-3’-phosphate partially self-complementary DNA 14mers with 3’-CG sticky-ends, on the efficiency of non-enzymatic ligation reaction induced by water-soluble carbodiimide EDC as condensing agent. We investigated the ligation products in mixtures of DNA with poly-ethylene glycol (PEG) at three PEG concentrations at which the system phase separates creating DNA-rich droplets that organize into isotropic, nematic LC and columnar LC phases. We observe remarkable LC-enhanced chain lengthening, and we demonstrate that such lengthening effectively promotes and stabilizes LC domains, providing the kernel of a positive feedback cycle by which LC ordering promotes elongation, in turn stabilizing the LC ordering.

Non-linear optical measurement of the twist elastic constant in thermotropic and DNA lyotropic chiral nematics

Throughout the whole history of liquid crystals science, the balancing of intrinsic elasticity with coupling to external forces has been the key strategy for most application and investigation. While the coupling of the optical field to the nematic director is at the base of a wealth of thoroughly described optical effects, a significant variety of geometries and materials have not been considered yet. Here we show that by adopting a simple cell geometry and measuring the optically induced birefringence, we can readily extract the twist elastic coefficient K22 of thermotropic and lyotropic chiral nematics (N*). The value of K22 we obtain for chiral doped 5CB thermotropic N* well matches those reported in the literature. With this same strategy, we could determine for the first time K22 of the N* phase of concentrated aqueous solutions of DNA oligomers, bypassing the limitations that so far prevented measuring the elastic constants of this class of liquid crystalline materials. The present study also enlightens the significant nonlinear optical response of DNA liquid crystals.

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.

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.

Giant optical nonlinearity in DNA lyotropic liquid crystals

We report the experimental evidence of nonlinear optical response in DNA lyotropic nematic liquid crystals. Pump-probe experiments indicate that the non-linearity is remarkably large. Quantitative assessment of the non-linear optical coefficient by transient optical grating demonstrates that the response is of the same order of the well-known Giant Optical Nonlinearity (GON) of thermotropic nematics. These results represent a further incentive to the current investigation of potential applications of DNA in biophotonics.

Phase separations, liquid crystal ordering and molecular partitioning in mixtures of PEG and DNA oligomers

ABSTRACT Liquid crystals (LCs) ordering of DNA and RNA oligomers relies on the presence of inter-duplex end-to-end attraction, driving the formation of linear aggregates. Such interactions are gauged, at a macroscopic level, by the osmotic pressure at the isotropic-nematic and nematic-columnar phase transitions. We studied aqueous solutions of PEG and DNA duplex-forming oligomers, finding that there is a wide range of concentrations in which these mixtures phase separate into coexisting PEG-rich and DNA-rich phases, the latter being either in the isotropic state or ordered as a nematic or columnar LC. We determined the phase diagram in mixtures of PEG and DNA duplexes with different terminal motifs – blunt ends, sticky overhangs, aggregation-preventing overhangs – and measured the partitioning of the species in the coexisting phases. On this basis, we determined the osmotic pressure as a function of the DNA concentration across the phase diagram. We compared the equation of state obtained in this way with both the Carnahan–Starling equation of state for hard spheres and with the pressure predicted by computer simulations of a system of aggregating cylinders. We obtain a good agreement between experiments and simulations, and end-to-end attraction energies of the order of 6 kcal/mol, a bit larger than expected, but still in agreement with the current models for DNA-DNA interactions. Graphical Abstract

Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly

Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.