Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets

Higher-order structures that originate from the specific and reversible DNA-directed self-assembly of microscopic building blocks hold great promise for future technologies. Here, we functionalized biotinylated soft colloid oil-in-water emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker. We show the components of this modular linking system to be stable and to induce sequence-specific aggregation of binary mixtures of emulsion droplets. Three length scales were thereby involved: nanoscale DNA base pairing linking microscopic building blocks resulted in macroscopic aggregates visible to the naked eye. The aggregation process was reversible by changing the temperature and electrolyte concentration and by the addition of competing oligonucleotides. The system was reset and reused by subsequent refunctionalization of the emulsion droplets. DNA-directed self-assembly of oil-in-water emulsion droplets, therefore, offers a solid basis for programmable and recyclable soft materials that undergo structural rearrangements on demand and that range in application from information technology to medicine.     

Integrative self-sorting is a programming language for high level self-assembly

Starting from the basis of a simple 4-component self-sorting system of crown ethers and ammonium ions, we design 6 building blocks in which 2 identical or different binding sites are incorporated. These building blocks can be mixed in many different ways to yield quite distinctly different pseudorotaxane assemblies. The self-sorting process integrates all building blocks in specific places so that this approach permits us to exert positional control and can widely influence the resulting assemblies with respect to the details of their structures. At maximum, we report quadruply interlocked species with up to 5 subunits that form specific assemblies. Although NMR methods are limited to the analysis of simpler complexes, ESI-MS and, in particular, tandem mass spectrometry is highly useful to analyze the assemblies'' connectivities.     

Self-assembly of soft-matter quasicrystals and their approximants

The surprising recent discoveries of quasicrystals and their approximants in soft-matter systems poses the intriguing possibility that these structures can be realized in a broad range of nanoscale and microscale assemblies. It has been theorized that soft-matter quasicrystals and approximants are largely entropically stabilized, but the thermodynamic mechanism underlying their formation remains elusive. Here, we use computer simulation and free-energy calculations to demonstrate a simple design heuristic for assembling quasicrystals and approximants in soft-matter systems. Our study builds on previous simulation studies of the self-assembly of dodecagonal quasicrystals and approximants in minimal systems of spherical particles with complex, highly specific interaction potentials. We demonstrate an alternative entropy-based approach for assembling dodecagonal quasicrystals and approximants based solely on particle functionalization and shape, thereby recasting the interaction-potential-based assembly strategy in terms of simpler-to-achieve bonded and excluded-volume interactions. Here, spherical building blocks are functionalized with mobile surface entities to encourage the formation of structures with low surface contact area, including non-close-packed and polytetrahedral structures. The building blocks also possess shape polydispersity, where a subset of the building blocks deviate from the ideal spherical shape, discouraging the formation of close-packed crystals. We show that three different model systems with both of these features-mobile surface entities and shape polydispersity-consistently assemble quasicrystals and/or approximants. We argue that this design strategy can be widely exploited to assemble quasicrystals and approximants on the nanoscale and microscale. In addition, our results further elucidate the formation of soft-matter quasicrystals in experiment.     

Correlating the magic numbers of inorganic nanomolecular assemblies with a {Pd84} molecular-ring Rosetta Stone

Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate {Pd₈₄}-ring cluster 3.3 nm in diameter; [Pd₈₄O₄₂(OAc)₂₈(PO₄)₄₂]^70- ({Pd₈₄} ≡ {Pd₁₂}₇) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the {Pd₈₄}-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the {Pd₈₄} we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a “Rosetta Stone” to rationalize the “magic numbers” defining a number of other systems. This is because the discovery of {Pd₈₄} allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families.     

Helices

Helices are among the simplest shapes that are observed in the filamentary and molecular structures of nature. The local mechanical properties of such structures are often modeled by a uniform elastic potential energy dependent on bending and twist, which is what we term a rod model. Our first result is to complete the semi-inverse classification, initiated by Kirchhoff, of all infinite, helical equilibria of inextensible, unshearable uniform rods with elastic energies that are a general quadratic function of the flexures and twist. Specifically, we demonstrate that all uniform helical equilibria can be found by means of an explicit planar construction in terms of the intersections of certain circles and hyperbolas. Second, we demonstrate that the same helical centerlines persist as equilibria in the presence of realistic distributed forces modeling nonlocal interactions as those that arise, for example, for charged linear molecules and for filaments of finite thickness exhibiting self-contact. Third, in the absence of any external loading, we demonstrate how to construct explicitly two helical equilibria, precisely one of each handedness, that are the only local energy minimizers subject to a nonconvex constraint of self-avoidance.     

Unfolding free energy of a two-domain transmembrane sugar transport protein

Understanding how an amino acid sequence folds into a functional, three-dimensional structure has proved to be a formidable challenge in biological research, especially for transmembrane proteins with multiple alpha helical domains. Mechanistic folding studies on helical membrane proteins have been limited to unusually stable, single domain proteins such as bacteriorhodopsin. Here, we extend such work to flexible, multidomain proteins and one of the most widespread membrane transporter families, the major facilitator superfamily, thus showing that more complex membrane proteins can be successfully refolded to recover native substrate binding. We determine the unfolding free energy of the two-domain, Escherichia coli galactose transporter, GalP; a bacterial homologue of human glucose transporters. GalP is reversibly unfolded by urea. Urea causes loss of substrate binding and a significant reduction in alpha helical content. Full recovery of helical structure and substrate binding occurs in dodecylmaltoside micelles, and the unfolding free energy can be determined. A linear dependence of this free energy on urea concentration allows the free energy of unfolding in the absence of urea to be determined as +2.5 kcal·mol(-1). Urea has often been found to be a poor denaturant for transmembrane helical structures. We attribute the denaturation of GalP helices by urea to the dynamic nature of the transporter structure allowing denaturant access via the substrate binding pocket, as well as to helical structure that extends beyond the membrane. This study gives insight into the final, critical folding step involving recovery of ligand binding for a multidomain membrane transporter.     

Thermal and Mechanical Studies of Perlite Concrete Casing for Chimneys in Residential Buildings

Chimneys are structures designed to convey exhaust gases from heating devices to the outside of buildings. The materials from which they are made have a great impact on their fire safety, as well as on the safety of the whole building. As current trends in the construction industry are moving towards improving the environmental impact and fire safety, changes to building materials are constantly being introduced. This also applies to the development of chimney technology, as there is still a recognised need for new solutions when it comes to materials used in the production of chimney systems. This article presents the findings of tests carried out on a chimney made from innovative perlite concrete blocks. Four different perlite concrete blocks that differed in bulk densities were analysed. The obtained results were then compared with widely used leca (lightweight expanded clay aggregate) concrete blocks. The test results confirmed high insulation properties of the perlite concrete block, from which the innovative chimney casing was made. The fire safety level was maintained even in high temperatures that occur during soot fire (1000 °C). These properties were retained despite there being no additional insulation of the flue duct. Even though the thermal load decreased the compressive strength of the chimney blocks, they still displayed sufficient average strength of 4.03 MPa. Additionally, the test results confirmed the possibility of recovering heat from the chimney with the efficiency of 23–30%, which constitutes a considerable increase compared to chimneys made from leca concrete blocks.     

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularity-free self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.     

DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires

DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of approximately 25 nm and have been observed with lengths up to 20 microm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods.     

How Properties of Kenaf Fibers from Burkina Faso Contribute to the Reinforcement of Earth Blocks

Physicochemical characteristics of Hibiscus cannabinus (kenaf) fibers from Burkina Faso were studied using X-ray diffraction (XRD), infrared spectroscopy, thermal gravimetric analysis (TGA), chemical analysis and video microscopy. Kenaf fibers (3 cm long) were used to reinforce earth blocks, and the mechanical properties of reinforced blocks, with fiber contents ranging from 0.2 to 0.8 wt%, were investigated. The fibers were mainly composed of cellulose type I (70.4 wt%), hemicelluloses (18.9 wt%) and lignin (3 wt%) and were characterized by high tensile strength (1 ± 0.25 GPa) and Young’s modulus (136 ± 25 GPa), linked to their high cellulose content. The incorporation of short fibers of kenaf reduced the propagation of cracks in the blocks, through the good adherence of fibers to the clay matrix, and therefore improved their mechanical properties. Fiber incorporation was particularly beneficial for the bending strength of earth blocks because it reinforces these blocks after the failure of soil matrix observed for unreinforced blocks. Blocks reinforced with such fibers had a ductile tensile behavior that made them better building materials for masonry structures than unreinforced blocks.     

Bioelectrocatalytic hydrogels from electron-conducting metallopolypeptides coassembled with bifunctional enzymatic building blocks

Here, we present two bifunctional protein building blocks that coassemble to form a bioelectrocatalytic hydrogel that catalyzes the reduction of dioxygen to water. One building block, a metallopolypeptide based on a previously designed triblock polypeptide, is electron-conducting. A second building block is a chimera of artificial alpha-helical leucine zipper and random coil domains fused to a polyphenol oxidase, small laccase (SLAC). The metallopolypeptide has a helix-random-helix secondary structure and forms a hydrogel via tetrameric coiled coils. The helical and random domains are identical to those fused to the polyphenol oxidase. Electron-conducting functionality is derived from the divalent attachment of an osmium bis-bipyrdine complex to histidine residues within the peptide. Attachment of the osmium moiety is demonstrated by mass spectroscopy (MS-MALDI-TOF) and cyclic voltammetry. The structure and function of the alpha-helical domains are confirmed by circular dichroism spectroscopy and by rheological measurements. The metallopolypeptide shows the ability to make electrical contact to a solid-state electrode and to the redox centers of modified SLAC. Neat samples of the modified SLAC form hydrogels, indicating that the fused alpha-helical domain functions as a physical cross-linker. The fusion does not disrupt dimer formation, a necessity for catalytic activity. Mixtures of the two building blocks coassemble to form a continuous supramolecular hydrogel that, when polarized, generates a catalytic current in the presence of oxygen. The specific application of the system is a biofuel cell cathode, but this protein-engineering approach to advanced functional hydrogel design is general and broadly applicable to biocatalytic, biosensing, and tissue-engineering applications.     

Asymmetric catalysis in complex target synthesis

This article describes three distinct strategies by which stereochemically complex molecules are synthesized and the ways asymmetric catalysis can impact on all three. The development of general methods to prepare synthetically useful building blocks leads to an expanded "chiral pool" of potential starting materials for asymmetric synthesis. The possibility of discovering new reactions to access new types of building blocks is particularly attractive and serves to help define the frontiers of the field. Asymmetric catalysis can also be applied to diastereoselective synthesis such that the stereochemistry of the catalyst, and not that of the substrate, determines the relative configuration of the product. Finally, in reactions where multiple stereocenters are generated simultaneously or in tandem, catalyst and substrate control can operate in a complementary manner to achieve one of many possible stereochemical outcomes selectively.     

Discrete fracture patterns of virus shells reveal mechanical building blocks

Viral shells are self-assembled protein nanocontainers with remarkable material properties. They combine simplicity of construction with toughness and complex functionality. These properties make them interesting for bionanotechnology. To date we know little about how virus structure determines assembly pathways and shell mechanics. We have here used atomic force microscopy to study structural failure of the shells of the bacteriophage Φ29. We observed rigidity patterns following the symmetry of the capsid proteins. Under prolonged force exertion, we observed fracture along well-defined lines of the 2D crystal lattice. The mechanically most stable building block of the shells was a trimer. Our approach of “reverse engineering” the virus shells thus made it possible to identify stable structural intermediates. Such stable intermediates point to a hierarchy of interactions among equal building blocks correlated with distinct next-neighbor interactions. The results also demonstrate that concepts from macroscopic materials science, such as fracture, can be usefully employed in molecular engineering.     

Toward the development of peptide nanofilaments and nanoropes as smart materials

Protein design studies using coiled coils have illustrated the potential of engineering simple peptides to self-associate into polymers and networks. Although basic aspects of self-assembly in protein systems have been demonstrated, it remains a major challenge to create materials whose large-scale structures are well determined from design of local protein-protein interactions. Here, we show the design and characterization of a helical peptide, which uses phased hydrophobic interactions to drive assembly into nanofilaments and fibrils ("nanoropes"). Using the hydrophobic effect to drive self-assembly circumvents problems of uncontrolled self-assembly seen in previous approaches that used electrostatics as a mode for self-assembly. The nanostructures designed here are characterized by biophysical methods including analytical ultracentrifugation, dynamic light scattering, and circular dichroism to measure their solution properties, and atomic force microscopy to study their behavior on surfaces. Additionally, the assembly of such structures can be predictably regulated by using various environmental factors, such as pH, salt, other molecular crowding reagents, and specifically designed "capping" peptides. This ability to regulate self-assembly is a critical feature in creating smart peptide biomaterials.     

Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains

The fundamental fracture mechanisms of biological protein materials remain largely unknown, in part, because of a lack of understanding of how individual protein building blocks respond to mechanical load. For instance, it remains controversial whether the free energy landscape of the unfolding behavior of proteins consists of multiple, discrete transition states or the location of the transition state changes continuously with the pulling velocity. This lack in understanding has thus far prevented us from developing predictive strength models of protein materials. Here, we report direct atomistic simulation that over four orders of magnitude in time scales of the unfolding behavior of alpha-helical (AH) and beta-sheet (BS) domains, the key building blocks of hair, hoof, and wool as well as spider silk, amyloids, and titin. We find that two discrete transition states corresponding to two fracture mechanisms exist. Whereas the unfolding mechanism at fast pulling rates is sequential rupture of individual hydrogen bonds (HBs), unfolding at slow pulling rates proceeds by simultaneous rupture of several HBs. We derive the hierarchical Bell model, a theory that explicitly considers the hierarchical architecture of proteins, providing a rigorous structure-property relationship. We exemplify our model in a study of AHs, and show that 3-4 parallel HBs per turn are favorable in light of the protein's mechanical and thermodynamical stability, in agreement with experimental findings that AHs feature 3.6 HBs per turn. Our results provide evidence that the molecular structure of AHs maximizes its robustness at minimal use of building materials.     

Supramolecular chemistry: functional structures on the mesoscale

Supramolecular chemistry deals with the chemistry and collective behavior of organized ensembles of molecules. In this so-called mesoscale regime, molecular building blocks are organized into longer-range order and higher-order functional structures via comparatively weak forces. As one of the modern frontiers in chemistry, supramolecular chemistry heralds many promises that range from biocompatible materials and biomimetic catalysts to sensors and nanoscale fabrication of electronic devices.     

Targeting an antimicrobial effector function in insect immunity as a pest control strategy

Insect pests such as termites cause damages to crops and man-made structures estimated at over $30 billion per year, imposing a global challenge for the human economy. Here, we report a strategy for compromising insect immunity that might lead to the development of nontoxic, sustainable pest control methods. Gram-negative bacteria binding proteins (GNBPs) are critical for sensing pathogenic infection and triggering effector responses. We report that termite GNBP-2 (tGNBP-2) shows β(1,3)-glucanase effector activity previously unknown in animal immunity and is a pleiotropic pattern recognition receptor and an antimicrobial effector protein. Termites incorporate this protein into the nest building material, where it functions as a nest-embedded sensor that cleaves and releases pathogenic components, priming termites for improved antimicrobial defense. By means of rational design, we present an inexpensive, nontoxic small molecule glycomimetic that blocks tGNBP-2, thus exposing termites in vivo to accelerated infection and death from specific and opportunistic pathogens. Such a molecule, introduced into building materials and agricultural methods, could protect valuable assets from insect pests.     

Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape

Here, we depict the anatomy of protein structures in terms of the protein folding process. Via an iterative, top-down dissecting procedure, tertiary structures are spliced down to reveal their anatomy: first, to produce domains (defined by visual three-dimensional inspection criteria); then, hydrophobic folding units (HFU); and, at the end of a multilevel process, a set of building blocks. The resulting anatomy tree organization not only clearly depicts the organization of a one-dimensional polypeptide chain in three-dimensional space but also straightforwardly describes the most likely folding pathway(s). Comparison of the tree with the formation of the hydrophobic folding units through combinatorial assembly of the building blocks illustrates how the chain folds in a sequential or a complex folding pathway. Further, the tree points to the kinetics of the folding, whether the chain is a fast or a slow folder, and the probability of misfolding. Our ability to successfully dissect the protein into an anatomy tree illustrates that protein folding is a hierarchical process and further validates a building blocks protein folding model.     

Dynamic assembly of surface structures in living cells

Although the dynamics of cell membranes and associated structures is vital for cell function, little is known due to lack of suitable methods. We found, using scanning ion conductance microscopy, that microvilli, membrane projections supported by internal actin bundles, undergo a life cycle: fast height-dependent growth, relatively short steady state, and slow height-independent retraction. The microvilli can aggregate into relatively stable structures where the steady state is extended. We suggest that the intrinsic dynamics of microvilli, combined with their ability to make stable structures, allows them to act as elementary "building blocks" for the assembly of specialized structures on the cell surface.     

Maintenance and Inspection of Fiber-Reinforced Polymer (FRP) Bridges: A Review of Methods

Fiber-reinforced polymers (FRPs) are materials that comprise high-strength continuous fibers and resin polymer, and the resins comprise a matrix in which the fibers are embedded. As the technique of FRP production has advanced, FRPs have attained many incomparable advantages over traditional building materials such as concrete and steel, and thus they play a significant role in the strengthening and retrofitting of concrete structures. Bridges that are built out of FRPs have been widely used in overpasses of highways, railways and streets. However, damages in FRP bridges are inevitable due to long-term static and dynamic loads. The health of these bridges is important. Here, we review the maintenance and inspection methods for FRP structures of bridges and analyze the advantages, shortcomings and costs of these methods. The results show that two categories of methods should be used sequentially. First, simple methods such as visual inspection, knock and dragging-chain methods are used to determine the potential damage, and then radiation, modal analysis and load experiments are used to determine the damage mode and degree. The application of FRP is far beyond the refurbishment, consolidation and construction of bridges, and these methods should be effective to maintain and inspect the other FRP structures.