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

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

A self-assembled periodic nanoporous framework in aqueous solutions of the DNA tetramer GCCG

The collective behavior of the shortest DNA oligomers in high concentration aqueous solutions is an unexplored frontier of DNA science and technology. Here we broaden the realm of DNA nanoscience by demonstrating that single-component aqueous solutions of the DNA 4-base oligomer GCCG can spontaneously organize into three-dimensional (3D) periodic mesoscale frameworks. This oligomer can form B-type double helices by Watson-Crick (WC) pairing, into tiled brickwork-like duplex strands, which arrange into mutually parallel arrays and form the nematic and columnar liquid crystal phases, as is typical for long WC chains. However, at DNA concentrations above 400mg/mL, these solutions nucleate and grow an additional mesoscale framework phase, comprising a periodic network on a three dimensional body-centered cubic (BCC) lattice. This lattice is an array of nodes (valence-8, each formed by a pair of quadruplexes of GCCG terminal Gs), connected with a separation of 6.6 nm by struts (6-GCCG-long WC duplexes). This 3D-ordered DNA framework is of low density (DNA volume fraction ~0.2), but, due to its 3D crystal structure, is osmotically incompressible over its phase range. Atomistic simulations confirm the stability of such structures, which promise to form the basis of novel families of simply and inexpensively made nanoscale frameworks for templating and selection applications.Comment: 33 pages, 8 figure

Elasticity and Viscosity of DNA Liquid Crystals

Concentrated solutions of blunt-ended DNA oligomer duplexes self-assemble in living polymers and order into lyotropic nematic liquid crystal phase. Using the optical torque provided by three distinct illumination geometries, we induce independent splay, twist, and bend deformations of the DNA nematic and measure the corresponding elastic coefficient

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

Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution

Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth

Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides

Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating sub-cellular compartment structure and function. While complex coacervation of flexible single stranded nucleic acids is broadly investigated, coacervation of double stranded DNA (dsDNA) is less studied because of its propensity to generate solid precipitates. Here, we reverse this perspective by showing that short dsDNA and poly-L-lysine coacervates can escape precipitation while displaying a surprisingly complex phase diagram, including the full set of liquid crystal (LC) mesophases observed to date in bulk dsDNA. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA and peptide concentrations, which allow continuous transitions between all accessible phases. A deeper understanding of LC-coacervates can gain insights to decipher structures and phase transition mechanisms within biomolecular condensates, to design stimuli-responsive multi-phase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides.</p

Liquid Crystal Ordering of Four-Base-Long DNA Oligomers with Both G–C and A–T Pairing

We report the liquid crystal (LC) ordering in an aqueous solution of four-base-long DNA oligomers 5′-GCTA-3′. In such systems, the formation of the chiral nematic (N*) LC phase is the result of a continuous self-assembly process in which double helix stability is achieved only through linear chaining of multiple DNA strands. The thermal stability of the aggregates and their LC phase diagram have been experimentally investigated, quantitatively interpreted with theoretical models and compared with recent results on four-base sequences with only G–C or only A–T pairing motifs. N* phase is found at GCTA concentration, cDNA, between 240 and 480 mg/mL and at temperature T &lt; 30 °C. The twist of the nematic director is found to be left-handed with pitch (p) in the optical range, increasing with cDNA and decreasing with T