X-ray Fiber Diffraction and Computational Analyses of Stacked Hexads in Supramolecular Polymers: Insight into Self-Assembly in Water by Prospective Prebiotic Nucleobases

Altering the structures of 3D supramolecular assemblies from melamine and cyanuric acid derivatives in water

Herein, we obtained two supramolecular assemblies with layered structures from melamine, N-methylmelamine, and hexynyl-cyanuric acid in water. By combination of X-ray diffraction, electron microscopy, and molecular dynamics studies, we found that introducing one methyl group in melamine alters the arrangement of the layers in these structures.

X-ray diffraction and its emerging applications in the food industry

X-ray diffraction (XRD) is an analytical technique that has found several applications focusing on the identification of crystal structure, space groups, plane, and orientation, in addition to qualitative and quantitative phase identification, and polymorphism behavior. An XRD diffractogram pattern/Bragg's peak can also provide valuable information that can be used for various food applications. While this review details the fundamental principles of XRD, the types of XRD systems, instrumentation, and the components thereof, the focus is to serve as a structured resource on explored applications of XRD in food, majorly revolving around food quality and safety. While recent studies relevant to the field are highlighted, leads for futuristic prospects are presented. With its unique approach, the XRD analysis can prove to be a rapid, robust, and sensitive nondestructive approach to food quality evaluation. Recent reports indicate its scope for nonconventional applications such as the assessment of 3D printability of foods, ice crystal formation, and screening food adulterants. Studies also highlight its scope to complement or replace conventional food quality testing approaches that involve the usage of chemicals, extensive sample preparation procedures, derivatization steps and demand long testing times.

One-Pot Formation of Pairing Proto-RNA Nucleotides and Their Supramolecular Assemblies

Most contemporary theories for the chemical origins of life include the prebiotic synthesis of informational polymers, including strong interpretations of the RNA World hypothesis. Existing challenges to the prebiotic emergence of RNA have encouraged exploration of the possibility that RNA was preceded by an ancestral informational polymer, or proto-RNA, that formed more easily on the early Earth. We have proposed that the proto-nucleobases of proto-RNA would have readily formed glycosides with ribose and that these proto-nucleosides would have formed base pairs as monomers in aqueous solution, two properties not exhibited by the extant nucleosides or nucleotides. Here we demonstrate that putative proto-nucleotides of the model proto-nucleobases barbituric acid and melamine can be formed in the same one-pot reaction with ribose-5-phosphate. Additionally, the proto-nucleotides formed in these reactions spontaneously form assemblies that are consistent with the presence of Watson-Crick-like base pairs. Together, these results provide further support for the possibility that heterocycles closely related to the extant bases of RNA facilitated the prebiotic emergence of RNA-like molecules, which were eventually replaced by RNA over the course of chemical and biological evolution.

Motorized Photomodulator: Making A Non-photoresponsive Supramolecular Gel Switchable by Light

Introducing photo-responsive molecules offers an attractive approach for remote and selective control and dynamic manipulation of material properties. However, it remains highly challenging how to use a minimal amount of photo-responsive units to optically modulate materials that are inherently inert to light irradiation. Here we show the application of a light-driven rotary molecular motor as a "motorized photo-modulator" to endow a typical H-bond-based gel system with the ability to respond to light irradiation and create a reversible sol-gel transition. The key molecular design feature is the introduction of a minimal amount (2 mol %) of molecular motors into the supramolecular network as photo-switchable non-covalent crosslinkers. Advantage is taken of the subtle interplay of the large geometry change during photo-isomerization of the molecular motor guest and the dynamic nature of a supramolecular gel host system. As a result, a tiny amount of molecular motors is enough to switch the mechanical modulus of the entire supramolecular systems. This study proves the concept of designing photo-responsive materials with minimum use of non-covalent light-absorbing units.

Twisted Structures in Natural and Bioinspired Molecules: Self-Assembly and Propagation of Chirality Across Multiple Length Scales

Several biomolecules can form dynamic aggregates in water, whose nanometric structures often reflect the chirality of the monomers in unexpected ways. Their twisted organization can be further propagated to the mesoscale, in chiral liquid crystalline phases, and even to the macroscale, where chiral, layered architectures contribute to the chromatic and mechanical properties of various plant, insect, and animal tissues. At all scales, the resulting organization is determined by a subtle balance among chiral and nonchiral interactions, whose understanding and fine-tuning is fundamental also for applications. We present recent advances in the chiral self-assembly and mesoscale ordering of biological and bioinspired molecules in water, focusing on systems based on nucleic acids or related aromatic molecules, oligopeptides, and their hybrid stuctures. We highlight the common features and key mechanisms governing this wide range of phenomena, together with novel characterization approaches.

Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions

Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.

Dietary supplementation for female infertility: Recent advances in the nutritional therapy for premature ovarian insufficiency

Premature ovarian insufficiency (POI) ranks top in the reproductive disorders that may impair multiple functioning systems, reduce the quality of life and ultimately deprive patients of their fertility among women. Symptoms can be partially alleviated by present hormone replacement therapy that cannot improve conception or decrease occurrence rates of systemic complication. Nutritional dietary supplements are attracting more and more attention because of their safety, bioavailability, and efficacy for well-being. Nutrients in the daily food are composed of carbohydrates, fat and lipoprotein, protein and polypeptide, vitamins, and vegetable or fruits containing phytoestrogens. These are functional nutrients due to the proliferative, anti-inflammatory, anti-oxidant, and mitochondria-protective potential during the course of menopause. Apart from dietary nutrients, microbe-related nutritional substances, including probiotics, prebiotics and the combination-synbiotics, display high potential as well in supporting estrous cycle, ovarian viability and modulating other vital reproductive functions. The present review will discuss dietary and microbial nutrients and their roles and applications in the living body based upon animal or human research, evaluate possible effect mechanisms from molecular, cellular and tissue levels, and provide insights into nutritional therapy for prolonging reproductive lifespan in female patients.

Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions

The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.

Structural Analysis of the Poly(thymidine)-Melamine Assembly

Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.

Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate

The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA

The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.