Self-assembly Of Building Blocks Research Articles

Nanomechanics of self-assembled DNA building blocks

DNA has become a powerful platform to design functional nanodevices. DNA nanodevices are often composed of self-assembled DNA building blocks that differ significantly from the structure of native DNA. In this study, we present Flow Force Microscopy as a massively parallel approach to study the nanomechanics of DNA self-assemblies on the single-molecular level. The high-throughput experiments performed in a simple microfluidic channel enable statistically meaningful studies with nanometer scale precision in a time frame of several minutes. A surprisingly high flexibility was observed for a typical construct used in DNA origami, reflected in a persistence length of 10.2 nm, a factor of five smaller than for native DNA. The enhanced flexibility is attributed to the discontinuous backbone of DNA self-assemblies that facilitate base pair opening by thermal fluctuations at the end of hybridized oligomers. We believe that the results will contribute to the fundamental understanding of DNA nanomechanics and help to improve the design of DNA nanodevices with applications in biological analysis and clinical research.

Flexible Alkyl Tails Help Shape Matching and Close Packing in Self-Assembly of Supramolecular Structure

Due to the flexibility and bowl-shaped cavity, C-alkylpyrogallol[4]arenes (PgCx, where x represents the length of alkyl chains) have garnered much attention over the past decade in supramolecular chemistry. Such cyclic polyphenolic compounds have been shown to be an excellent molecular building block for self-assembly of a variety of crystalline materials and have been applied in many frontier research areas ranging from ion transport to gas absorption/separation and biomedicine. In this work, we demonstrate that the long flexible alkyl tails play a critical role in the self-assembly of PgCx. It is found that they help the shape matching between the self-assembled building blocks and improve the packing density, thus promoting formation of an unprecedented “tails-driven” supramolecular structure. The successful demonstration of this work paves a new route to self-assembly materials by tuning the functional alkyl tails of the building blocks.

A Matter of Size and Placement: Varying the Patch Size of Anisotropic Patchy Colloids.

Non-spherical colloids provided with well-defined bonding sites—often referred to as patches—are increasingly attracting the attention of materials scientists due to their ability to spontaneously assemble into tunable surface structures. The emergence of two-dimensional patterns with well-defined architectures is often controlled by the properties of the self-assembling building blocks, which can be either colloidal particles at the nano- and micro-scale or even molecules and macromolecules. In particular, the interplay between the particle shape and the patch topology gives rise to a plethora of tilings, from close-packed to porous monolayers with pores of tunable shapes and sizes. The control over the resulting surface structures is provided by the directionality of the bonding mechanism, which mostly relies on the selective nature of the patches. In the present contribution, we investigate the effect of the patch size on the assembly of a class of anisotropic patchy colloids—namely, rhombic platelets with four identical patches placed in different arrangements along the particle edges. Larger patches are expected to enhance the bond flexibility, while simultaneously reducing the bond selectivity as the single bond per patch condition—which would guarantee a straightforward mapping between local bonding arrangements and long-range pattern formation—is not always enforced. We find that the non-trivial interplay between the patch size and the patch position can either promote a parallel particle arrangement with respect to a non-parallel bonding scenario or give rise to a variety a bonded patterns, which destroy the order of the tilings. We rationalize the occurrence of these two different regimes in terms of single versus multiple bonds between pairs of particles and/or patches.

DNA-π Amphiphiles: A Unique Building Block for the Crafting of DNA-Decorated Unilamellar Nanostructures.

The unparalleled ability of DNA to recognize its complementary strand through Watson and Crick base pairing is one of the most reliable molecular recognition events found in natural systems. This highly specific sequence information encoded in DNA enables it to be a versatile building block for bottom-up self-assembly. Hence, the decoration of functional nanostructures with information-rich DNA is extremely important as this allows the integration of other functional molecules onto the surface of the nanostructures through DNA hybridization in a highly predictable manner. DNA amphiphiles are a class of molecular hybrids where a short hydrophilic DNA is conjugated to a hydrophobic moiety. Since DNA amphiphiles comprise DNA as the hydrophilic segment, their self-assembly in aqueous medium always results in the formation of nanostructures with shell made of DNA. This clearly suggests that self-assembly of DNA amphiphiles is a straightforward strategy for the ultradense decoration of a nanostructure with DNA. However, initial attempts toward the design of DNA amphiphiles were primarily focused on long flexible hydrocarbon chains as the hydrophobic moiety, and it has been demonstrated in several examples that they typically self-assemble into DNA-decorated micelles (spherical or cylindrical). Hence, molecular level control over the self-assembly of DNA amphiphiles and achieving diverse morphologies was extremely challenging and unrealized until recently.In this Account, we summarize our recent efforts in the area of self-assembly of DNA amphiphiles and narrate the remarkable effect of the incorporation of a large π-surface as the hydrophobic domain in the self-assembly of DNA amphiphiles. Self-assembly of DNA amphiphiles with flexible hydrocarbon chains as the hydrophobic moiety is primarily driven by the hydrophobic effect. The morphology of such nanostructures is typically predicted based on the volume ratio of hydrophobic to hydrophilic segments. However, control over the self-assembly and prediction of the morphology become increasingly challenging when the hydrophobic moieties can interact with each other through other noncovalent interactions. In this Account, the unique self-assembly behaviors of DNA-π amphiphiles, where a large π-surface acts as the hydrophobe, are described. Due to the extremely strong π-π stacking in aqueous medium, the assembly of the amphiphile is found to preferably proceed in a lamellar fashion (bilayer) and hence the morphology of the nanostructures can easily be tuned by the structural modification of the π-surface. Design principles for crafting various DNA-decorated lamellar nanostructures including unilamellar vesicles, two-dimensional (2D) nanosheets, and helically twisted nanoribbons by selecting suitable π-surfaces are discussed. Unilamellar vesicular nanostructures were achieved by using linear oligo(phenylene ethynylene) (OPE) as the hydrophobic segment, where lamellar assembly undergoes folding to form unilamellar vesicles. The replacement of OPE with a strongly π-stacking hydrophobe such as hexabenzocoronene (HBC) or tetraphenylethylene (TPE) provides extremely strong π-stacking compared to OPE, which efficiently directed the 2D growth for the lamellar assembly and led to the formation of 2D nanosheets. A helical twist in the lamella was achieved by the replacement of HBC with hexaphenylbenzene (HPB), which is the twisted analogue of HBC, directing the assembly into helically twisted nanoribbons. The most beneficial structural feature of this kind of nanostructure is the extremely dense decoration of their surface with ssDNA, which can further be used for DNA-directed organization of other functional nanomaterials. By exploring this, their potential as a nanoscaffold for predefined assembly of plasmonic nanomaterials into various plasmonic 1D, 2D, and 3D nanostructures through DNA hybridization is discussed. Moreover, the design of pH-responsive DNA-based vesicles and their application as a nanocarrier for payload delivery is also demonstrated.

Chemical engineering of quasicrystal approximants in lanthanide-based coordination solids

Tessellation of self-assembling molecular building blocks is a promising strategy to design metal-organic materials exhibiting geometrical frustration and ensuing frustrated physical properties. Appearing in two-dimensional quasiperiodic phases, tilings consisting of five-vertex nodes are regarded as approximants for quasicrystals. Unfortunately, these structural motifs are exceedingly rare due to the complications of acquiring five-fold coordination confined to the plane. Lanthanide ions display the sufficient coordinative plasticity, and large ionic radii, to allow their incorporation into irregular molecule-based arrays. We herein present the use of ytterbium(II) as a five-vertex node in a two-dimensional coordination solid, YbI2(4,4′-bipyridine)2.5. The semi-regular Archimedean tessellation structure verges on quasicrystallinity and paves the way for lanthanide-based metal-organic materials with interesting photonic and magnetic properties.

Multiscale simulation and kinetic network model analysis of the self-assembly of amphiphilic systems

Amphiphilic building blocks play an important role in fabricating nanomaterials. To achieve the precise control of self-assembled nanostructures, it is important to understand the self-assembly process at both microscopic and mesoscopic scale. Multiscale simulations could simulate the self-assembly process in both microscopic and mesoscopic scale, and get the metastable and equilibrium assembled structures and the corresponding trajectories. Based on these trajectories, we can further build the kinetic network model and obtain the kinetic transition pathway of the self-assembly process. This approach provides the theoretical principles for designing novel self-assembly building blocks and achieving novel self-assembled structures. In this article, we review our recent progress on the study of mechanisms of self-assembly of amphiphilic building blocks, such as small organic molecules, block copolymers and patchy particles by combining multiscale simulation and kinetic network model analysis.

Waste to high performance materials: Self-assembly of short carbon fiber polymer composites

Traditional manufacturing of carbon fiber/polymer composite parts is restricted to non-complex geometries and remains expensive due to costly carbon fiber production, laborious processing steps, and generates 20–30% short fiber waste. We present an inexpensive method of aligning and consolidating short (waste) fibers into needle-like building blocks for composite part manufacturing that capitalizes on the anisotropy of short fibers. The method consists of mixing suspended short fibers with a secondary phase that induces self-assembly of the short fibers into an overlapping needle-like bundle with polymer binder distributed in the interstitial sites. The process can achieve high volume fraction of fiber comparable to that of high-performance composites. These self-assembled building blocks can be consolidated to form large scale parts, and they offer several advantages over traditional continuous fiber manufacturing, such as forming complex geometries, utilizing less expensive short fibers, simplifying processability, and increasing fiber recyclability.

Host-Guest-Mediated Epitope Presentation on Self-Assembled Peptide Amphiphile Hydrogels.

A key feature in biomaterial design is the incorporation of bioactive signals into artificial constructs to stimulate tissue regeneration. Most currently used hydrogel cell culture systems depend on the covalent attachment of extracellular matrix (ECM)-derived peptides to either macromolecular units or smaller self-assembling building blocks, thereby restricting biosignal presentation and adaptability. However, new ways to rationally incorporate adhesion epitopes through noncovalent interactions would offer opportunities to better recreate the dynamic and reversible nature of the native ECM. Here, we report on a noncovalent epitope presentation approach mediated by host-guest interactions. Using peptide amphiphile hydrogels, we demonstrate that the adamantane/β-cyclodextrin pair can be used to anchor RGDS cell adhesion signals onto self-assembled hydrogels via host-guest interactions. We evaluate hydrogel morphological and rheological properties as well as fibroblast attachment, organization, and spreading when cultured atop these scaffolds. This host-guest-mediated epitope display might lead to new self-assembling hydrogels for improved cell culture applications in fields such as tissue engineering and regenerative medicine.

Rational Design and Self-Assembly of Coiled-Coil Linked SasG Protein Fibrils.

Protein engineering is an attractive approach for the self-assembly of nanometer-scale architectures for a range of potential nanotechnologies. Using the versatile chemistry provided by protein folding and assembly, coupled with amino acid side-chain functionality, allows for the construction of precise molecular "protein origami" hierarchical patterned structures for a range of nanoapplications such as stand-alone enzymatic pathways and molecular machines. The Staphyloccocus aureus surface protein SasG is a rigid, rod-like structure shown to have high mechanical strength due to "clamp-like" intradomain features and a stabilizing interface between the G5 and E domains, making it an excellent building block for molecular self-assembly. Here we characterize a new two subunit system composed of the SasG rod protein genetically conjugated with de novo designed coiled-coils, resulting in the self-assembly of fibrils. Circular dichroism (CD) and quartz-crystal microbalance with dissipation (QCM-D) are used to show the specific, alternating binding between the two subunits. Furthermore, we use atomic force microscopy (AFM) to study the extent of subunit polymerization in a liquid environment, demonstrating self-assembly culminating in the formation of linear macromolecular fibrils.

Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures.

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.

Correction to Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks

Correction to Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks

Dissipative Self-Assembly of Dynamic Multicompartmentalized Microsystems with Light-Responsive Behaviors

Summary Living cells are compartmentalized systems operating far from thermodynamic equilibrium and consume energy from the environment to carry out their functions. The construction of biomimetic synthetic compartments has both scientific and technological value. Despite many advances, the assembly of synthetic compartments that present nonequilibrium behaviors based on dissipative (or transient) self-assembly remains a grand challenge. Here, we describe the design and synthesis of multicompartmental systems with an active microstructure and complex behaviors. By including an artificial pathway for energy dissipation, we demonstrate the autonomous generation of active polymeric systems using a strategy based on polymerization-induced self-assembly (PISA), driven by chemical fuel. Remarkably, these self-organized synthetic systems exhibit a dynamic change in their multicompartmental structures when exposed to light. This work introduces a strategy toward the design and construction of synthetic compartments with a dynamic structure and also presents pathways to engineer materials with spatially controllable structures and functionalities.

Tailoring DNA Self-assembly to Build Hydrogels.

DNA hydrogels are crosslinked polymeric networks in which DNA is used as the backbone or the crosslinker. These hydrogels are novel biofunctional materials that possess the biological character of DNA and the framed structure of hydrogels. Compared with other kinds of hydrogels, DNA hydrogels exhibit not only high mechanical strength and controllable morphologies but also good recognition ability, designable responsiveness, and programmability. The DNA used in this type of hydrogel acts as a building block for self-assembly or as a responsive element due to its sequence recognition ability and switchable structural transitions, respectively. In this review, we describe recent developments in the field of DNA hydrogels and discuss the role played by DNA in these hydrogels. Various synthetic strategies for and a range of applications of DNA hydrogels are detailed.

Devising Synthetic Reaction Cycles for Dissipative Nonequilibrium Self-Assembly.

Fuel-driven reaction cycles are found in biological systems to control the assembly and disassembly of supramolecular materials such as the cytoskeleton. Fuel molecules can bind noncovalently to a self-assembling building block or they can react with it, resulting in covalent modifications. Overall the fuel can either switch the self-assembly process on or off. Here, a closer look is taken at artificial systems that mimic biological systems by making and breaking covalent bonds in a self-assembling motif. The different chemistries used so far are highlighted in chronological order and the pros and cons of each system are discussed. Moreover, the desired traits of future reaction cycles, their fuels, and waste management are outlined, and two chemistries that have not been explored up to now in chemically fueled dissipative self-assembly are suggested.

Self-assembly of anisotropic nanoparticles into functional superstructures.

Self-assembly of colloidal nanoparticles (NPs) into superstructures offers a flexible and promising pathway to manipulate the nanometer-sized particles and thus make full use of their unique properties. This bottom-up strategy builds a bridge between the NP regime and a new class of transformative materials across multiple length scales for technological applications. In this field, anisotropic NPs with size- and shape-dependent physical properties as self-assembly building blocks have long fascinated scientists. Self-assembly of anisotropic NPs not only opens up exciting opportunities to engineer a variety of intriguing and complex superlattice architectures, but also provides access to discover emergent collective properties that stem from their ordered arrangement. Thus, this has stimulated enormous research interests in both fundamental science and technological applications. This present review comprehensively summarizes the latest advances in this area, and highlights their rich packing behaviors from the viewpoint of NP shape. We provide the basics of the experimental techniques to produce NP superstructures and structural characterization tools, and detail the delicate assembled structures. Then the current understanding of the assembly dynamics is discussed with the assistance of in situ studies, followed by emergent collective properties from these NP assemblies. Finally, we end this article with the remaining challenges and outlook, hoping to encourage further research in this field.

A molecular model for self-assembly of the synaptonemal complex protein SYCE3

The synaptonemal complex (SC) is a supramolecular protein assembly that mediates homologous chromosome synapsis during meiosis. This zipper-like structure assembles in a continuous manner between homologous chromosome axes, enforcing a 100-nm separation along their entire length and providing the necessary three-dimensional framework for cross-over formation. The mammalian SC comprises eight components—synaptonemal complex protein 1–3 (SYCP1–3), synaptonemal complex central element protein 1–3 (SYCE1–3), testis-expressed 12 (TEX12), and six6 opposite strand transcript 1 (SIX6OS1)—arranged in transverse and longitudinal structures. These largely α-helical, coiled-coil proteins undergo heterotypic interactions, coupled with recursive self-assembly of SYCP1, SYCE2–TEX12, and SYCP2–SYCP3, to achieve the vast supramolecular SC structure. Here, we report a novel self-assembly mechanism of the SC central element component SYCE3, identified through multi-angle light scattering and small-angle X-ray scattering (SAXS) experiments. These analyses revealed that SYCE3 adopts a dimeric four-helical bundle structure that acts as the building block for concentration-dependent self-assembly into a series of discrete higher-order oligomers. We observed that this is achieved through staggered lateral interactions between self-assembly surfaces of SYCE3 dimers and through end-on interactions that likely occur through intermolecular domain swapping between dimer folds. These mechanisms are combined to achieve potentially limitless SYCE3 assembly, particularly favoring formation of dodecamers of three laterally associated end-on tetramers. Our findings extend the family of self-assembling proteins within the SC and reveal additional means for structural stabilization of the SC central element.

Enhanced Nanoassembly-Incorporated Antibacterial Composite Materials

The rapid advancement of peptide- and amino-acid-based nanotechnology offers new approaches for the development of biomedical materials. The utilization of fluorenylmethyloxycarbonyl (Fmoc)-decorated self-assembling building blocks for antibacterial and anti-inflammatory purposes represents promising advancements in this field. Here, we present the antibacterial capabilities of the nanoassemblies formed by Fmoc-pentafluoro-l-phenylalanine-OH, their substantial effect on bacterial morphology, as well as new methods developed for the functional incorporation of these nanoassemblies within resin-based composites. These amalgamated materials inhibit and hinder bacterial growth and viability and are not cytotoxic toward mammalian cell lines. Importantly, due to the low dosage required to confer antibacterial activity, the integration of the nanoassemblies does not affect their mechanical and optical properties. This approach expands on the growing number of accounts on the intrinsic antibacterial capabilities of self-assembling building blocks and serves as a basis for further design and development of enhanced composite materials for biomedical applications.

Chiral Recognition of Hexahelicene on a Surface via the Forming of Asymmetric Heterochiral Trimers.

Chiral recognition among helical molecules is of essential importance in many chemical and biochemical processes. The complexity necessitates investigating manageable model systems for unveiling the fundamental principles of chiral recognition at the molecular level. Here, we reported chiral recognition in the self-assembly of enantiopure and racemic hexahelicene on a Au(111) surface. Combing scanning tunneling microscopy (STM) and atomic force microscopy (AFM) measurements, the asymmetric heterochiral trimers were observed as a new type of building block in racemic helicene self-assembly on Au(111). The intermolecular recognition of the heterochiral trimer was investigated upon manual separation so that the absolute configuration of each helicene molecule was unambiguously determined one by one, thus confirming that the trimer was “2+1” in handedness. These heterochiral trimers showed strong stability upon different coverages, which was also supported by theoretical calculations. Our results provide valuable insights for understanding the intermolecular recognition of helical molecules.

Highly efficient dicyano-phenylenevinylene fluorophore as polymer dopant or zinc-driven self-assembling building block

From a diamino dicyano-phenylenevinylene skeleton a symmetrically di-salen dye was obtained and employed both as a dopant in non-emissive polymer matrixes and as building blocks in the preparation of a zinc self-assembly polymer. The new fluorophore C1 belongs to the class of the luminescent liquid crystals (LLCs). The molecule produces red emission in the crystalline phase and yellow luminescence in the nematic phase, which dramatically decreases in on-off switch mode after LC order was lost. Both C1 and its self-assembly zinc-based coordination polymer suffers a lot aggregation caused quench effect (ACQ). Conversely, thin films obtained by dispersion in polystyrene (PS) and poly(9-vinylcarbazole) (PVK) show remarkably enhanced fluorescence, reaching the noteworthy value of 77% Photoluminescence Quantum Yield (PLQY) for the PVK doped sample.

Ultra-dense (~20 Tdot/in2) nanoparticle array from an ordered supramolecular dendrimer containing a metal precursor

The fabrication of an ultra-dense, highly periodic nanoparticle array from a soft template is one of the most important issues in the fields of material science and nanotechnology. To date, block copolymer (BCP) structures have been primarily used as templates for fabricating highly periodic nanoparticle arrays with high areal densities. Herein, we demonstrate for the first time the use of a supramolecular dendrimer assembly for the formation of a highly ordered nanoparticle array with a high areal density of ~20 Tdot/in2, four times larger than that of the currently reported BCP-based nanoparticle arrays. By the simple thermal annealing of a dendrimers containing a metal precursor between two flat, solid substrates, a hexagonal array of small gold nanoparticles (with a diameter of ~1.6 nm and center-to-center distance of ~5.3 nm), oriented normal to the bottom, was achieved. Density functional theory calculations demonstrated that the gold cation strongly bound to the head group of the dendrimer. This structure served as a building block for self-assembly into a stable cylindrical structure. We anticipate that this study will lead to the creation of a large family of supramolecular dendrimers that can be utilized as soft templates for creating periodic, ultra-dense nanoparticle arrays.