Polynucleotides in cellular mimics: Coacervates and lipid vesicles

In this review, we examine the interaction of nucleic acids with cell-like structures based on liquid–liquid phase separation of charged molecules (complex coacervation) and amphiphilic self-assembly (lipid vesicles). We discuss the mechanisms of their assembly and describe how they can be used as models for origin of life studies and for understanding two recently-described phenomena in modern cells: membrane-free organelles and exosomes. Hybrid cells with increased structural complexity are highlighted and we then briefly explore how strategies based on electrostatic and hydrophobic assembly can be used for designing and synthesizing delivery agents for therapeutic nucleic acids. While the physical mechanisms of self-assembly vary, both strategies provide viable routes for generating minimal compartmentalized systems, modeling cellular pathways, and for rational design of new synthetic cells for technological applications.     

Pathways for the formation and evolution of peptides in prebiotic environments

α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.     

Pattern formation and self-organization in a simple precipitation system

Various types of pattern formation and self-organization phenomena can be observed in biological, chemical, and geochemical systems due to the interaction of reaction with diffusion. The appearance of static precipitation patterns was reported first by Liesegang in 1896. Traveling waves and dynamically changing patterns can also exist in reaction-diffusion systems: the Belousov-Zhabotinsky reaction provides a classical example for these phenomena. Until now, no experimental evidence had been found for the presence of such dynamical patterns in precipitation systems. Pattern formation phenomena, as a result of precipitation front coupling with traveling waves, are investigated in a new simple reaction-diffusion system that is based on the precipitation and complex formation of aluminum hydroxide. A unique kind of self-organization, the spontaneous appearance of traveling waves, and spiral formation inside a precipitation front is reported. The newly designed system is a simple one (we need just two inorganic reactants, and the experimental setup is simple), in which dynamically changing pattern formation can be observed. This work could show a new perspective in precipitation pattern formation and geochemical self-organization.     

液晶的超分子系统及生物膜模拟

本文评述了自组织产生功能的原理及溶致性液晶对生命科学的重要意义。这些是生命发展及细胞产生功能的先决条件。在高分子材料科学中, 通过自组织作用产生功能的原理导致了新的液晶材料。分子的自组织作用形成超分子体系从而产生相应的功能。从高分子材料科学的观点出发, 我们尝试将这两个领域结合在一起, 并希望能促进它们之间的相互作用和联合处理。同时评述了液晶的超分子体系、生物膜模型, 高分子脂质体及其在化学与生物医学方面的应用。如果双分子层的组装概念能更一般地延伸到有机介质, 那么一种全新的化学分支将会产生。     

Control of heterogeneous structure of porous polymer microspheres prepared from polymerization system and preformed polymer system

The studies on control of heterogeneous structure of porous polymer microspheres prepared for suspension polymerization system and preformed polymer system in author’s research group were reviewed. Firstly, the phase-separation behavior in O/W suspension polymerization system for preparation of porous poly(divinylbenzene) microspheres was quantitatively studied by combining transmittance and gelation point measurement, from which the morphology can be manipulated. The same method can be employed to study the pore size control in W/O hydrophilic polymerization system. Because the simple porous microsphere could not satisfy new applications, we developed new methods to prepare gigaporous microsphere, which possessed much larger pores than those obtained by general diluents, for chromatographic separation media, as well as hollow-porous microsphere for construction of cell-like microreactor. Furthermore, in order to overcome the difficulty of heterogeneous structure control for preformed polymer system, we developed special methods to obtain porous, hollow-porous, and hollow chitosan microspheres. Finally, some application results by utilizing special morphologies were introduced.     

Molecular Architecture and Function of Polymeric Oriented Systems: Models for the Study of Organization,Surface Recognition,and Dynamics of Biomembranes

The Part and the Whole. The principle of self-organization for the creation of functional units is not an invention of modern natural sciences. It was already a basic idea of the ancient philosophies in Asia and Europe: only the mutuality of the parts creates the whole and its ability to function. Translated into the language of chemistry this means: the self-organization of molecules leads to supramolecular systems and is responsible for their functions. Thermotropic and lyotropic liquid crystals are such functional units, formed by self-organization. As highly oriented systems, they exhibit new properties. The importance of lyotropic liquid crystals for the life sciences has been known for a long time. They are a prerequisite for the development of life and the ability of cells to function. In materials sciences this concept of function through organization led to the development of new liquid-crystalline materials. From the point of view of macromolecular chemistry, this review tries to combine these two different fields and especially hopes to stimulate their interaction and joint treatment. To exemplify this, the molecular architecture of polymeric organized systems will be discussed. Polymeric liquid crystals combine the ability to undergo spontaneous self-organization–typical of liquid-crystalline phases–with the polymer-specific property of stabilizing these ordered states. As new materials, polymeric liquid crystals have already been investigated intensively. As model systems for biomembranes as well as for the simulation of biomembrane processes, they so far have been little discussed. The intention of this review article is to show that polymer science is able to contribute to the simulation of cellular processes such as the stabilization of biomembranes, specific surface recognition, or even the “uncorking” of cells. Polymer science, having an old tradition as an inter-disciplinary field, can no longer restrict itself to common plastics. Attempts to reach new horizons have already begun. The borderland between liquid crystals and cells will certainly play an important role. Basic requirements to work in this frontier area between organic chemistry, membrane biology, life science, and materials science will be the delight in scientific adventures as well as the courage to go ahead. The most important prerequisite will be the willingness to cooperate with disciplines which so far have not really accepted each other. From this point of view, this review does not aim at giving defined answers. It wants instead to encourage the scientific venture: too often we cling to painfully acquired knowledge, fearing adventures.     

Turning fluorescent dyes into Cu(II) nanosensors

There is great interest in the self-organization of the proper subunits as a new strategy for the realization of fluorescent chemosensors. In this article, it is shown that commercially available fluorescent dyes, functionalized with triethoxysilane moieties, can be converted into fluorescent chemosensors by simple inclusion into silica nanostructures. Dye-doped silica nanoparticles and thin films detect Cu(II) ions in the micromolar range by the quenching of fluorescence emission. The different response toward Zn(II), Ni(II), and Co(II) metal ions was also investigated and is reported. The self-organization of the silica structures leads, at the same time, to the formation of metal ion binding sites as well as to the linking of a fluorescent reporter in their proximity. Structural features of the materials, particularly particle size and network porosity, strongly affect their ability to act as fluorescent sensors.     

Advanced Polymeric Materials for High-tech Innovations

High technology is advancing our society and modernizing our life and advanced materials play an important role in the technological innovations. My research group has been working on the development of advanced polymeric materials and in this talk I will report our recent work on the creation of new conjugated polymers with novel molecular structures and unique materials properties.1-18 Our work include the design of molecular structures of monomeric building blocks, development of stable, effective and environmentally benign "green” polymerization catalysts, discovery of new polymerization reactions, synthesis of functional macromolecules, fabrication of nanodimensional composites, assembly and control of hierarchical structures, and construction of electrooptical devices. We have revealed the liquid crystallinity, light emission, photoconductivity, optical limiting, nano-hybridization, solvatochromism, optical activity, self-organization, and biological activity of the linear polyacetylenes and hyperbranched polyarylenes. The utilization of the advanced polymers and their interesting materials properties for high-tech innovations will be discussed.     

Synthesis of trisubstituted imidazoles via a convergent reaction network from methyl ketones and benzoins

A novel method for constructing trisubstituted imidazoles has been created using simple and readily available aromatic ketones, benzoins, and ammonium acetate as starting materials. The new synthetic strategy utilized a convergent integration of two self-labor domino sequences, providing a typical example for logical self-organization synthesis.     

The need for the historical understanding of nature in physics and chemistry

During the last decades the physico-chemical conception of self-organization of chemical systems has been created. The chemical systems in natural-historical processes do not have any creator: they rise up from irreversible processes by self-organization. The issue of self-organization in physics has led to a new interpretation of the laws of nature. As Ilya Prigogine has shown, they do not express certainties but possibilities and describe a world that must be understood in a historical way. In the new philosophical understanding of nature priority is not ascribed to any single type or level of entity, but to historical processes, to processes of endless generation and change.     

半导体荧光量子点标记技术

生命体系中化学、生物信息的活体、原位、实时、动态和高灵敏获取，是当前生命科学研究中迫切需要解决的关键问题之一，发展相关的新技术与新方法至关重要。半导体荧光量子点因其优异的荧光特性可望在解决此类难题中发挥重要作用而日益受到关注。本文将根据我们课题组多年来的研究工作经验，就半导体荧光量子点标记技术的相关基础问题、在生物医学领域中的应用以及发展前景等做简要评述。     

Structural identification of new glycolipids based on cyclodextrin using high-resolution positive and negative electrospray ionization mass spectrometry

In the continuing challenge to increase the performance of cyclodextrins (CDs) for various applications, new phospholipidyl-cyclodextrin derivatives showing improved self-organization properties in water have been synthesized, as new carriers for drug vectorization, starting from natural beta-cyclodextrin. Due to the important chemical modifications of the original cyclic oligosaccharide molecules, simple nuclear magnetic resonance (NMR) experiments do not easily lead to both an unambiguous assignment of the structures and to a rapid evaluation of the purity of the final products. However, positive and negative ion electrospray ionization (ESI-MS) in combination with accurate mass measurements and tandem mass spectrometry (MS/MS) led to the positive structural identification of the first series of these new amphiphilic compounds.     

利用微信公众平台加强基础化学实验室管理的探索和实践

新媒体微信公众号具有简单、便捷、精准、可持续、学生乐于接受等特点,已渗透到高校学习、生活的每一个角落,也直接影响着高校实验室的信息化建设与管理。为了提高教学实验室的科学化管理水平,本文提出了利用微信公众号构建基础化学实验室管理系统,介绍了相关的应用与实践,这将使实验室管理和实验教学突破时空的限制,提高实验室利用效率,为实验教学和人才培养提供更高水平的服务。     

Engineering Polymersome Protocells

The field of biomimicry is embracing the construction of complex assemblies that imitate both biological structure and function. Advancements in the design of these mimetics have generated a growing vision for creating an artificial or proto- cell. Polymersomes are vesicles that can be made from synthetic, biological or hybrid polymers and can be used as a model template to build cell-like structures. In this perspective, we discuss various areas where polymersomes have been used to mimic cell functions as well as areas in which the synthetic flexibility of polymersomes would make them ideal candidates for a biomembrane mimetic. Designing a polymersome that comprehensively displays the behaviors discussed herein has the potential to lead to the development of an autonomous, responsive particle that resembles the intelligence of a biological cell.     

PREBIOTIC FORMATION OF HIGHER MOLECULAR WEIGHT COMPOUNDS FROM THE PHOTOLYSIS OF AQUEOUS ACETIC ACID

In the study of chemical evolution, experiments simulating primitive earth conditions have shown that many compounds of biological significance can be produced from simple precursors. In an attempt to search for the origin of polycarboxylic acids, the UV irradiation of aqueous acetic acid was performed. Among the products detected were succinic, citric and malonic acids which are key compounds in metabolic pathways, suggesting that these compounds might have been formed on the primitive Earth prior to life itself.     

Dancing waves in reaction-diffusion systems

The mechanism of pattern formation in reaction-diffusion systems is treated as an interesting subject, generally for understanding self-organization observed in living systems and natural phenomena. Several spatial patterns appear in the reaction-diffusion systems where an activator and an inhibitor coexist as an intermediate, as represented by a traveling wave, a stationary wave called a Turing structure, etc. Here, we show new kinds of waves in reaction-diffusion systems, which exhibit reciprocating motion without colliding into each other or blinking periodically. These patterns have never been observed in the conventional numerical models, although experimentally oscillating spots have been often observed. Our model demonstrates that other than the ratio of diffusion coefficients for both intermediates, the thickness of reaction media acts to generate inhibitory effect. The spatial factor of the medium contributes to new pattern formation in reaction-diffusion systems. For the design of new functional materials, the concept might be useful as a simple controlling method for pattern dynamics.     

A New Route for the Prebiotic Synthesis of Nucleobases and Hydantoins in Water/Ice Solutions Involving the Photochemistry of Acetylene

The origin of nucleobases and other heterocycles is a classic question in the chemistry of the origins of life. The construction of laboratory models for the abiotic synthesis of nitrogen heterocycles in plausible natural conditions also aids the understanding and prediction of chemical species in the Solar System. Here, we report a new explanation for the origin of hydantoins, purines, and pyrimidines in eutectic water/ice/urea solutions driven by ultraviolet irradiation (in the 185–254 nm range, UVC) of acetylene under anoxic conditions. An analysis of the products indicates the synthesis of hydantoin and 5‐hydroxyhydantoin, the purines uric acid, xanthine, and guanine, and the pyrimidines uracil and cytosine. The synthesis occurred together with the photo‐oxidation of bases in a complex process for which possible pathways are proposed. In conclusion, an acetylene‐containing atmosphere could contribute to the origin of nucleobases in the presence of a urea/water system by an HCN‐independent mechanism. The presence of ice has a dual role as a favorable medium for the synthesis of nucleobases and protection against degradation and as a source of free radicals for the synthesis of highly oxidized heterocycles. A mechanism for the origin of hydantoins and uracil from urea in plausible conditions for prebiotic chemistry is also proposed.     

Flexible self-organization of two size-scales oxide nanotubes on Ti45Nb alloy

We report on the growth of anodic oxide nanotubes grown on a simple Ti45Nb alloy that show self-organization on two size-scales. The well-ordered nanotube layers consist of large and small diameter tubes that are arranged in an alternating two-dimensional (2D) structure. This bimodal morphology and the thickness of the nanotube layer are affected by the electrochemical conditions used. The bimodal feature can be obtained over a wide potential range (between 15 and 55 V), resulting in a linear diameter variation from 80 to 330 nm for the larger and 50–180 nm for the smaller tubes. The organization into two size-scales takes place during the first hour of the anodization process. This result of flexible two size-scale self-organization using a simple two element alloy is of significant importance not only for fundamental research but also for specific applications that can benefit from bimodal properties.     

Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks

The origin of life on Earth was a chemical affair. So how did primitive biochemical systems originate from geochemical and cosmochemical processes on the young planet? Contemporary research into the origins of life subscribes to the Darwinian principle of material causes operating in an evolutionary context, as advocated by A. I. Oparin and J. B. S. Haldane in the 1920s. In its simplest form (e.g., a bacterial cell) extant biological complexity relies on the functional integration of metabolic networks and replicative genomes inside a lipid boundary. Different research programmes have explored the prebiotic plausibility of each of these autocatalytic subsystems and combinations thereof: self-maintained networks of small molecules, template chemistry, and self-reproductive vesicles. This tutorial review focuses on the debates surrounding the origin of metabolism and offers a brief overview of current studies on the evolution of metabolic networks. I suggest that a leitmotif in the origin and evolution of metabolism is the role played by catalysers' substrate ambiguity and multifunctionality.