Liquid Crystal Ordering and Isotropic Gelation in Solutions of Four-Base-Long DNA Oligomers

In silico study of DNA mononucleotide self-assembly

Recent experiments have demonstrated the self-assembly and long-range ordering of concentrated aqueous solutions of DNA and RNA mononucleotides. These are found to form Watson-Crick pairs that stack into columns that become spatially organized into a columnar liquid-crystalline phase. In this work, we numerically investigate this phase behavior by adopting an extremely coarse-grained model in which nucleotides are represented as semi-disk-like polyhedra decorated with attractive (patchy) sites that mimic the stacking and pairing interactions. We carry out Monte Carlo simulations of these patchy polyhedra by adapting algorithms borrowed from computer graphics. This model reproduces the features of the experimental phase behavior, which essentially depends on the combination of pairing and stacking interactions.

Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer

DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions

Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.

Stability of the chiral crystal phase and breakdown of the cholesteric phase in mixtures of active-passive chiral rods

In this study, we aim to explore the effect of chirality on the phase behavior of active helical particles driven by two-temperature scalar activity. We first calculate the equation of state of soft helical particles of various intrinsic chiralities using molecular dynamics (MD) simulation. In equilibrium, the emergence of various liquid crystal (LC) phases such as nematic (N), cholesteric , smectic (Sm) and crystal (K) crucially depends on the presence of walls that induce planar alignment. Next, we introduce activity through the two-temperature model: keep increasing the temperature of half of the helical particles (labeled as 'hot' particles) while maintaining the temperature of the other half at a lower value (labeled as 'cold' particles). Starting from a homogeneous isotropic (I) phase, we find the emergence of 2-TIPS: two temperature-induced phase separations between the hot and cold particles. We also observe that the cold particles undergo an ordering transition to various LC phases even in the absence of a wall. This observation reveals that the hot-cold interface in the active system plays the role of a wall in the equilibrium system by inducing an alignment direction for the cold particles. However, in the case of a cholesteric phase, we observe that activity destabilizes the phase by inducing smectic ordering in the cold zone while an isotropic structure in the hot zone. The smectic ordering in the cold zone eventually transforms to a chiral crystal phase with high enough activity.

Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation

The layered liquid crystalline phases formed by DNA molecules, which include rigid and flexible segments ("gapped DNA"), enable the study of both end-to-end stacking and side-to-side (helix-to-helix) lateral interactions, forming a model system to study such interactions at physiologically relevant DNA and ion concentrations. The observed layer structure exhibits long-range interlayer and in-layer positional correlations. In particular, the in-layer order has implications for DNA condensation, as it reflects whether these normally repulsive interactions become attractive under certain ionic conditions. Using synchrotron small-angle X-ray scattering measurements, we investigate the impact of divalent Mg2+ cations (in addition to a constant 150 mM Na+) on the stability of the inter- and in-layer DNA ordering as a function of temperature between 5 and 65 °C. DNA constructs with different terminal base pairings were created to mediate the strength of the attractive end-to-end stacking interactions between the blunt ends of the gapped DNA constructs. We demonstrate that the stabilities at a fixed DNA concentration of both interlayer and in-layer order are significantly enhanced even at a few mM Mg2+ concentration. The stabilities are even higher at 30 mM Mg2+; however, a marked decrease is observed at 100 mM Mg2+, suggesting a change in the nature of side-by-side interactions within this Mg2+ concentration range. We discuss the implications of these results in terms of counterion-mediated DNA-DNA attraction and DNA condensation.

Primitive membraneless compartments as a window into the earliest cells

What did the first cells on Earth look like? This is an unanswered mystery investigated by researchers in the origins of life field. While at some point cells must have developed membranes, genetic components, and catalytic cycles and catalysts, when the earliest cells developed these is not clear. One system which could shed light into the structure and function of the first cells on Earth is membraneless compartments generated from phase separation, perhaps before or as a precursor to the advent of membrane-bound compartmentalization. Here, we briefly comment on two prebiotically relevant membraneless compartment systems: coacervates and polyester microdroplets. This discussion seeks to highlight the current understanding of these systems and to pose unanswered questions as a challenge to the field at large.

Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling

Modern cells are complex chemical compartments tightly regulated by an underlying DNA-encoded program. Achieving a form of coupling between molecular content, chemical reactions, and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells but remains challenging. Here, we design coacervate droplets that promote non-enzymatic oligonucleotide polymerization and that restructure as a result of the reaction dynamics. More specifically, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases-soft solids, liquid crystalline or isotropic coacervates droplets-each of them having a different impact on the reaction efficiency. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photo-isomerization is used to demonstrate cycles of light-actuated oligonucleotide ligation. Remarkably, changes in the population of polynucleotides during polymerization induce phase transitions due to length-based DNA self-sorting to produce multiphase coacervates. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our reactive coacervates provide a general route to the non-enzymatic synthesis of polynucleotides and pave the way to the emergence of a primitive compartment-content coupling in membrane-free protocells.

Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions

Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.

Cellulose: A Review of Water Interactions, Applications in Composites, and Water Treatment

Cellulose is known to interact well with water, but is insoluble in it. Many polysaccharides such as cellulose are known to have significant hydrogen bond networks joining the molecular chains, and yet they are recalcitrant to aqueous solvents. This review charts the interaction of cellulose with water but with emphasis on the formation of both natural and synthetic fiber composites. Covering studies concerning the interaction of water with wood, the biosynthesis of cellulose in the cell wall, to its dispersion in aqueous suspensions and ultimately in water filtration and fiber-based composite materials this review explores water-cellulose interactions and how they can be exploited for synthetic and natural composites. The suggestion that cellulose is amphiphilic is critically reviewed, with relevance to its processing. Building on this, progress made in using various charged and modified forms of nanocellulose to stabilize oil-water emulsions is addressed. The role of water in the aqueous formation of chiral nematic liquid crystals, and subsequently when dried into composite films is covered. The review will also address the use of cellulose as an aid to water filtration as one area where interactions can be used effectively to prosper human life.

Liquid Crystalline Systems from Nature and Interaction of Living Organisms with Liquid Crystals

Biomaterials, which are substances interacting with biological systems, have been extensively explored to understand living organisms and obtain scientific inspiration (such as biomimetics). However, many aspects of biomaterials have yet to be fully understood. Because liquid crystalline phases are ubiquitously found in biomaterials (e.g., cholesterol, amphiphile, DNA, cellulose, bacteria), therefore, a wide range of research has made attempts to approach unresolved issues with the concept of liquid crystals (LCs). This review presents these studies that address the interactive correlation between biomaterials and LCs. Specifically, intrinsic LC behavior of various biomaterials such as DNA, cellulose nanocrystals, and bacteriaare first introduced. Second, the dynamics of bacteria in LC media are addressed, with focus on how bacteria interact with LCs, and how dynamics of bacteria can be controlled by exploiting the characteristics of LCs. Lastly, how the strong correlation between LCs and biomaterials has been leveraged to design a new class of biosensors with additional functionalities (e.g., self-regulated drug release) that are not available in previous systems is reviewed. Examples addressed in this review convey the message that the intersection between biomaterials and LCs offers deep insights into fundamental understanding of biomaterials, and provides resources for development of transformative technologies.

A liquid crystal world for the origins of life

Nucleic acids (NAs) in modern biology accomplish a variety of tasks, and the emergence of primitive nucleic acids is broadly recognized as a crucial step for the emergence of life. While modern NAs have been optimized by evolution to accomplish various biological functions, such as catalysis or transmission of genetic information, primitive NAs could have emerged and been selected based on more rudimental chemical-physical properties, such as their propensity to self-assemble into supramolecular structures. One such supramolecular structure available to primitive NAs are liquid crystal (LC) phases, which are the outcome of the collective behavior of short DNA or RNA oligomers or monomers that self-assemble into linear aggregates by combinations of pairing and stacking. Formation of NA LCs could have provided many essential advantages for a primitive evolving system, including the selection of potential genetic polymers based on structure, protection by compartmentalization, elongation, and recombination by enhanced abiotic ligation. Here, we review recent studies on NA LC assembly, structure, and functions with potential prebiotic relevance. Finally, we discuss environmental or geological conditions on early Earth that could have promoted (or inhibited) primitive NA LC formation and highlight future investigation axes essential to further understanding of how LCs could have contributed to the emergence of life.

Liquid crystal phase formation and non-Newtonian behavior of oligonucleotide formulations

Viscosity behavior of liquid oligonucleotide therapeutics and its dependence on formulation properties has been poorly studied to date. We observed a high increase in viscosity and solidification of therapeutic oligonucleotide formulations with increasing oligonucleotide concentration creating challenges during drug product manufacturing. In this study, we characterized the viscosity behavior of three different single strand DNA oligonucleotides based on oligonucleotide concentration and formulation composition. We subsequently studied the underlying mechanism for increased viscosity at higher oligonucleotide concentrations by dynamic light scattering (DLS), 1H nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), and polarized light microscopy. Viscosity was highly dependent on formulation composition, oligonucleotide sequence, and concentration, and especially dependent on the presence and combination of different individual ions, such as the presence of sodium chloride in the formulation. In samples with elevated viscosity, the viscosity behavior was characterized by non-Newtonian, shear-thinning flow behavior. We further studied these samples by DLS and 1H NMR, which revealed the presence of supra-molecular assemblies, and further characterization by polarized light and DSC characterized these assemblies as liquid crystals in the formulation. The present study links the macroscopic viscosity behavior of oligonucleotide formulations to the formation of supra-molecular assemblies and to the presence of liquid crystals, and highlights the importance of formulation composition selection for these therapeutics.

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments

Understanding of the pairing statistics in solutions populated by a large number of distinct solute species with mutual interactions is a challenging topic, relevant in modeling the complexity of real biological systems. Here we describe, both experimentally and theoretically, the formation of duplexes in a solution of random-sequence DNA (rsDNA) oligomers of length L = 8, 12, 20 nucleotides. rsDNA solutions are formed by 4^L distinct molecular species, leading to a variety of pairing motifs that depend on sequence complementarity and range from strongly bound, fully paired defectless helices to weakly interacting mismatched duplexes. Experiments and theory coherently combine revealing a hybridization statistics characterized by a prevalence of partially defected duplexes, with a distribution of type and number of pairing errors that depends on temperature. We find that despite the enormous multitude of inter-strand interactions, defectless duplexes are formed, involving a fraction up to 15% of the rsDNA chains at the lowest temperatures. Experiments and theory are limited here to equilibrium conditions.

Several biological processes require that specific partner molecules succeed in binding after negotiating their way through a huge number of interactions with other molecules. How such molecular recognition emerges among millions distinct molecular species is an open problem. We have studied, both experimentally and theoretically, such process of “molecular recognition” in pools of highly diverse random DNA oligomers, which binds preferentially, but not exclusively, to its perfect complementary sequence. We find a complex behavior, in which some perfect pairing takes place with a non-trivial temperature dependence that we understand thorough statistical mechanics modelling. The pairing pattern of short random DNA is relevant in the context of the origin of life since the so-called “RNA World” was most probably based on the mutual recognition of random chains.

Mono- and bilayer smectic liquid crystal ordering in dense solutions of "gapped" DNA duplexes

Although its mesomorphic properties have been studied for many years, only recently has the molecule of life begun to reveal the true range of its rich liquid crystalline behavior. End-to-end interactions between concentrated, ultrashort DNA duplexes-driving the self-assembly of aggregates that organize into liquid crystal phases-and the incorporation of flexible single-stranded "gaps" in otherwise fully paired duplexes-producing clear evidence of an elementary lamellar (smectic-A) phase in DNA solutions-are two exciting developments that have opened avenues for discovery. Here, we report on a wider investigation of the nature and temperature dependence of smectic ordering in concentrated solutions of various "gapped" DNA (GDNA) constructs. We examine symmetric GDNA constructs consisting of two 48-base pair duplex segments bridged by a single-stranded sequence of 2 to 20 thymine bases. Two distinct smectic layer structures are observed for DNA concentration in the range [Formula: see text] mg/mL. One exhibits an interlayer periodicity comparable with two-duplex lengths ("bilayer" structure), and the other has a period similar to a single-duplex length ("monolayer" structure). The bilayer structure is observed for gap length ≳10 bases and melts into the cholesteric phase at a temperature between 30 °C and 35 °C. The monolayer structure predominates for gap length ≲10 bases and persists to [Formula: see text]C. We discuss models for the two layer structures and mechanisms for their stability. We also report results for asymmetric gapped constructs and for constructs with terminal overhangs, which further support the model layer structures.

Dendrimer-mediated columnar mesophase of surfactants

The columnar mesophase, in which the molecular or supramolecular building blocks with rod-like geometry pack into two-dimensional (2D) lattices, is an important class of mesomorphic structure having been found in various liquid crystalline materials for practical applications. The cylindrical micelles assembled by amphiphilic surfactants may also form columnar mesophases with the micelle packing symmetry being tunable by the molecular characteristics of the surfactants. In this study, we demonstrate that a positively charged tree-like polymer, poly(amidoamine) (PAMAM) G4 dendrimer, acted as an effective structure-directing agent for the columnar mesophase of a common anionic surfactant, sodium dodecyl sulfate (SDS), via their electrostatic interaction. By adjusting the dendrimer charge density and the nominal binding ratio (Xn) of SDS to dendrimer, the electrostatic complexes self-assembled to form a body-centered cubic (BCC) sphere phase, wherein the dendrimers were staggered between the interspaces of the SDS spherical micelles packed in the BCC lattice. Four types of 2D columnar mesophase composed of SDS cylindrical micelles and dendrimers were accommodated within the interstitial tunnels, including the hexagonal columnar phase (Colhex), simple rectangular columnar phase (Colsr), oblique columnar phase (Colob) and centered rectangular columnar phase (Colcr). A detailed analysis of the geometry of the dendrimer in the columnar mesophases revealed that the structural transition was governed by the interplay among the lateral and axial deformations of the dendrimer, and the deformation of the SDS micelle cross section for achieving effective charge matching and accommodation of the dendrimer. The present study demonstrated the power of the dendrimer in directing the long-range ordered packing of oppositely charged cylinders to yield a rich structural polymorphism of the columnar mesophase that may be exploited for the development of functional materials.

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

Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating subcellular 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. Short dsDNA supramolecular aggregation and packing in the dense coacervate phase are the main parameters regulating the global LC-coacervate phase behavior. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA, and peptide concentrations, which allow continuous reversible 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 multiphase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides.

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.

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 coefficients K₁, K₂, and K₃, and viscosities η_splay, η_twist, and η_bend. We find the viscoelasticity of the system to be remarkably soft, as the viscoelastic coefficients are smaller than in other lyotropic liquid crystals. We find K₁ > K₃ > K₂, in agreement with the elasticity of the nematic phase of flexible polymers, and η_bend > η_splay > η_twist a behavior that is nonconventional in the context of chromonic, polymeric, and thermotropic liquid crystals, indicating a possible role of the weakness and reversibility of the DNA aggregates.

Liquid crystal ordering of nucleic acids

Several analytical calculations and computer simulations propose that cylindrical monodispersive rods having an aspect ratio (ratio of length to diameter) greater than 4 can exhibit liquid crystal (LC) ordering. But, recent experiments demonstrated the signature of LC ordering in systems of 4- to 20-base pair (bp) long nucleic acids (NAs) that do not satisfy the shape anisotropy criterion. Mechanisms of end-to-end adhesion and stacking have been proposed to explain this phenomenon. In this study, using all-atom molecular dynamics (MD) simulation, we explicitly verify the end-to-end stacking of double-stranded RNA (dsRNA) and demonstrate the LC ordering at the microscopic level. Using umbrella sampling (US) calculation, we quantify the potential of mean force (PMF) between two dsRNAs for various reaction coordinates (RCs) and compare our results with previously reported PMFs for double-stranded DNA (dsDNA). The PMF profiles demonstrate the anisotropic nature of inter-NA interaction. We find that, like dsDNA, dsRNA also prefers to stack on top of each other while repelling sideways, leading to the formation of supra-molecular-columns that undergo LC ordering at high NA volume fraction (φ). We also demonstrate and quantify the nematic ordering of the RNAs using several hundred nanosecond-long MD simulations that remain almost invariant for different initial configurations and under different external physiological conditions.

Manipulation of cholesteric liquid crystal phase behavior and molecular assembly by molecular chirality

Molecular simulation is used to study the effect of molecular chirality on liquid crystalline phase transition and molecular assembly behavior. Based on a flexible chain (FCh) model with helical arrangement of side beads, the phase behavior of FCh models with various molecular chiralities are studied as functions of pressure (or density). By modifying the molecular chirality of FCh, we can manipulate the relative stability of the nematic and cholesteric phases continuously; and we found that increasing molecular chirality may destabilize cholesteric order due to the effective reduction of chiral interactions. A semismectic phase is identified in the high-density region, in which the two-dimensional fluid layers overlap due to shift alignment formed by FCh particles. The global phase diagram of the FCh model is constructed and the potential energy surface is calculated to elucidate the formation of cholesteric phase in terms of two-body interactions.

Amplification of Chirality by Adenosine Monophosphate-Capped Luminescent Gold Nanoclusters in Nematic Lyotropic Chromonic Liquid Crystal Tactoids

Amplification of chirality across length scales is a key concept pertinent to many models aiming to unravel the origin of homochirality. Tactoids of lyotropic chromonic liquid crystals formed by DNA, dyes, and other flat ionic molecules in water in the biphasic nematic + isotropic regime turn out to be a particularly relevant system to investigate chirality transfer and amplification. Herein, we present experiments to determine the amplification of chirality by luminescent gold nanoclusters decorated with adenosine monophosphate inducing chiral nematic tactoids formed by disodium cromoglycate in water. Polarized optical microscopy investigations of the induced homochiral tactoids reveal that adenosine monophosphate shows a higher optical activity when bound to the surface of such gold nanoclusters in comparison to free adenosine monophosphate, despite a three-time lower overall concentration. Free adenosine monophosphate also induces the opposite chiral twist both in the bulk nematic phase as shown by induced thin film circular dichroism spectropolarimetry and in the tactoids in comparison to adenosine monophosphate bound to the gold nanocluster. Overall, these experiments demonstrate that lyotropic chromonic liquid crystal tactoids are powerful systems to image and quantify chirality amplification by key biological chiral molecules that would have played a role in the origin of homochirality.

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.

Prebiotic Evolution and Self-Assembly of Nucleic Acids

Prebiotic evolution is the stage that is assumed to have taken place prior to the emergence of the first living entities, during which time the abiotic synthesis of monomers, oligomers, and supramolecular systems that led to the hypothesized RNA world occurred. In this Perspective, the success of one-pot Miller-Urey type synthesis of organic compounds is compared with the multipot syntheses developed within the framework of systems chemistry, which attempts to demonstrate that RNA could have been formed directly in the primitive environment. The prebiotic significance of liquid-crystal ordering of nucleic acid oligomers and self-organizing assemblages of RNA and DNA that are formed in the absence of membranes or mineral matrices is also addressed.

Chirality amplification by desymmetrization of chiral ligand-capped nanoparticles to nanorods quantified in soft condensed matter

Induction, transmission, and manipulation of chirality in molecular systems are well known, widely applied concepts. However, our understanding of how chirality of nanoscale entities can be controlled, measured, and transmitted to the environment is considerably lacking behind. Future discoveries of dynamic assemblies engineered from chiral nanomaterials, with a specific focus on shape and size effects, require exact methods to assess transmission and amplification of nanoscale chirality through space. Here we present a remarkably powerful chirality amplification approach by desymmetrization of plasmonic nanoparticles to nanorods. When bound to gold nanorods, a one order of magnitude lower number of chiral molecules induces a tighter helical distortion in the surrounding liquid crystal-a remarkable amplification of chirality through space. The change in helical distortion is consistent with a quantification of the change in overall chirality of the chiral ligand decorated nanomaterials differing in shape and size as calculated from a suitable pseudoscalar chirality indicator.

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

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.

Chiral lyotropic chromonic liquid crystals composed of disodium cromoglycate doped with water-soluble chiral additives

We investigated the pitches of cholesteric liquid crystals prepared by mixing disodium cromoglycate (DSCG) in water with 5 different water-soluble chiral additives. The measurements are based on the Grandjean-Cano wedge cell method. Overall, the twisting effect is weak, and the shortest pitch of 2.9 ± 0.2 μm is obtained using trans-4-hydroxy-l-proline, by which the cholesteric sample is iridescent at certain viewing angles. Freeze-fracture transmission electron microscopy (FFTEM) was also performed for the first time on both the nematic and cholesteric phases, revealing that stacked chromonic aggregates are very long, up to a few hundred nm, which explains why cholesteric chromonic liquid crystals hardly have pitches in the visible wavelength region.

Cholesteric ordering predicted using a coarse-grained polymeric model with helical interactions

The understanding of cholesteric liquid crystals at a molecular level is challenging. Limited insights are available to bridge between molecular structures and macroscopic chiral organization. In the present study, we introduce a novel coarse-grained (CG) molecular model, which is represented by flexible chain particles with helical interactions (FCh), to study the liquid crystalline phase behavior of cholesteric molecules such as double strand DNA and α-helix polypeptides using molecular dynamics (MD) simulations. The isotropic-cholesteric phase transitions of FCh molecules were simulated for varying chain flexibilities. A wall confinement was used to break the periodicity along the cholesteric helix director in order to predict the equilibrium cholesteric pitch. The left-handed cholesteric phase was shown for FCh molecules with right-handed chiral interactions, and a spatially inhomogeneous distribution of the nematic order parameter profile was observed in cholesteric phases. It was found that the chain flexibility plays an important role in determining the macroscopic cholesteric pitch and the structure of the cholesteric liquid crystal phase. The simulations provide insight into the relationship between microscopic molecular characteristics and the macroscopic phase behavior.

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.

Lyotropic Liquid Crystal Phases from Anisotropic Nanomaterials

Liquid crystals are an integral part of a mature display technology, also establishing themselves in other applications, such as spatial light modulators, telecommunication technology, photonics, or sensors, just to name a few of the non-display applications. In recent years, there has been an increasing trend to add various nanomaterials to liquid crystals, which is motivated by several aspects of materials development. (i) addition of nanomaterials can change and thus tune the properties of the liquid crystal; (ii) novel functionalities can be added to the liquid crystal; and (iii) the self-organization of the liquid crystalline state can be exploited to template ordered structures or to transfer order onto dispersed nanomaterials. Much of the research effort has been concentrated on thermotropic systems, which change order as a function of temperature. Here we review the other side of the medal, the formation and properties of ordered, anisotropic fluid phases, liquid crystals, by addition of shape-anisotropic nanomaterials to isotropic liquids. Several classes of materials will be discussed, inorganic and mineral liquid crystals, viruses, nanotubes and nanorods, as well as graphene oxide.

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.

Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA

Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration.