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

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

Colloidal fibers as structurant for worm-like micellar solutions

We investigate the rheological properties of a simplified version of a liquid detergent composed of an aqueous solution of the linear alkylbenzene sulphonate (LAS) surfactant, in which a small amount of fibers made of hydrogenated castor oil (HCO) is dispersed. At the concentration typically used in detergents, LAS is in a worm-like micellar phase exhibiting a Maxwellian behavior. The presence of HCO fibers provides elastic properties, such that the system behaves as a simple Zener body, mechanically characterized by a parallel connection of a spring and a Maxwell element. Despite this apparent independence of the contributions of the fibers and the surfactant medium to the mechanical characteristics of the system, we find that the low frequency modulus increases with increasing LAS concentration. This indicates that LAS induces attractive interactions among the HCO fibers, resulting in the formation of a stress-bearing structure that withstands shear at HCO concentrations, where the HCO fibers in the absence of attractive interactions would not sufficiently overlap to provide stress-bearing properties to the system

Emerging applications of label-free optical biosensors

Innovative technical solutions to realize optical biosensors with improved performance are continuously proposed. Progress in material fabrication enables developing novel substrates with enhanced optical responses. At the same time, the increased spectrum of available biomolecular tools, ranging from highly specific receptors to engineered bioconjugated polymers, facilitates the preparation of sensing surfaces with controlled functionality. What remains often unclear is to which extent this continuous innovation provides effective breakthroughs for specific applications. In this review, we address this challenging question for the class of label-free optical biosensors, which can provide a direct signal upon molecular binding without using secondary probes. Label-free biosensors have become a consolidated approach for the characterization and screening of molecular interactions in research laboratories. However, in the last decade, several examples of other applications with high potential impact have been proposed. We review the recent advances in label-free optical biosensing technology by focusing on the potential competitive advantage provided in selected emerging applications, grouped on the basis of the target type. In particular, direct and real-time detection allows the development of simpler, compact, and rapid analytical methods for different kinds of targets, from proteins to DNA and viruses. The lack of secondary interactions facilitates the binding of small-molecule targets and minimizes the perturbation in single-molecule detection. Moreover, the intrinsic versatility of label-free sensing makes it an ideal platform to be integrated with biomolecular machinery with innovative functionality, as in case of the molecular tools provided by DNA nanotechnology

Viscoelasticity of nematic liquid crystals at a glance

Polarised microscopy is shown to be a powerful alternative to light scattering for the determination of the viscoelasticity of aligned nematic liquid crystals. We perform experiments in a wide range of temperatures by using an adapted version of the recently introduced differential dynamic microscopy technique, which enables us to extract scattering information directly from the microscope images. A dynamic analysis of the images acquired in different geometries provides the splay, twist and bend viscoelastic ratios. A static analysis allows a successful determination of the bend elastic constant. All our results are in excellent agreement with those obtained with the far more time-consuming depolarised light scattering techniques. Remarkably, a noteworthy extension of the investigated temperature-range is observed, owing to the lower sensitivity of microscopy to multiple scattered light. Moreover, we show that the unique space-resolving capacities of our method enable us to investigate nematics in the presence of spatial disorder, where traditional light scattering fails. Our findings demonstrate that the proposed scattering-with-images approach provides a space-resolved probe of the local sample properties, applicable also to other optically anisotropic soft materials

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

Hierarchical Propagation of Chirality through Reversible Polymerization: The Cholesteric Phase of DNA Oligomers

Unveiling the subtle rules that control the buildup of macroscopic chirality starting from chiral molecular elements is a challenge for theory and computations. In this context, a remarkable phenomenon is the formation of helically twisted nematic (cholesteric) phases, with pitch in the micrometer range, driven by self-assembly of relatively small chiral species into supramolecular semiflexible polymers. We have developed a theoretical framework to connect the cholesteric organization to the shape and chirality of the constituents, described with molecular detail, in this kind of system. The theory has been tested against new accurate measurements for solutions of short DNA duplexes. We show that the cholesteric organization is determined by steric repulsion between duplexes, and we identify distinctive features of linear self-assembly in the temperature and concentration dependence of the pitch