The collective phenomena exhibited by artificial active matter systems present novel routes to fabricating out‐of‐equilibrium microscale assemblies. Here, the crystallization of passive silica ...colloids into well‐controlled 2D assemblies is shown, which is directed by a small number of self‐propelled active colloids. The active colloids are titania–silica Janus particles that are propelled when illuminated by UV light. The strength of the attractive interaction and thus the extent of the assembled clusters can be regulated by the light intensity. A remarkably small number of the active colloids is sufficient to induce the assembly of the dynamic crystals. The approach produces rationally designed colloidal clusters and crystals with controllable sizes, shapes, and symmetries. This multicomponent active matter system offers the possibility of obtaining structures and assemblies that cannot be found in equilibrium systems.
Non‐equilibrium assembly of mixtures of active and passive colloids is shown to form 2D structures. The active self‐propelled colloids are light driven, so the clustering can be externally triggered and is completely reversible. The shape and size of individual small clusters, as well as the lattice symmetry and order of larger assemblies, can be changed easily by controlling the light intensity and size ratio of active to passive particles.
The lanthanide ions possess long lived excited states, which can be populated by sensitizing antennae, and emit at long wavelengths in the visible and the near infrared (NIR) regions. These are ...particularly desirable features for: (a) sensing as it overcomes drawbacks such as light scattering and auto fluorescence associated with short wavelength emitting sensors and (b) for probing metal directed synthesis of large supramolecular systems often formed between f–f or f–d metal ions. This review article focuses on some of the recent work published in the areas of lanthanide luminescent sensing of ions and molecules, and the formation of self-assembly structures. These examples are based on the use of structurally defined organic (or coordination) ligands which complement (either as a single ligands or through metal-directed self-assembly formation between several ligands) the coordination requirements of lanthanide ions. Examples of ligands that can either in a step-wise manner or simultaneously bind lanthanide and transition metal ions will also be discussed.
Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling ...genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat‐rich and GC‐rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long‐read, linked‐read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC‐rich microchromosomes and the repeat‐rich W chromosome. Telomere‐to‐telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
The fabrication of nanowire (NW)‐based flexible electronics including wearable energy storage devices, flexible displays, electrical sensors, and health monitors has received great attention both in ...fundamental research and market requirements in our daily lives. Other than a disordered state after synthesis, NWs with designed and hierarchical structures would not only optimize the intrinsic performance, but also create new physical and chemical properties, and integration of individual NWs into well‐defined structures over large areas is one of the most promising strategies to optimize the performance of NW‐based flexible electronics. Here, the recent developments and achievements made in the field of flexible electronics composed of integrated NW structures are presented. The different assembly strategies for the construction of 1D, 2D, and 3D NW assemblies, especially the NW coassembly process for 2D NW assemblies, are comprehensively discussed. The improvements of different NW assemblies on flexible electronics structure and performance are described in detail to elucidate the advantages of well‐defined NW assemblies. Finally, a short summary and outlook for future challenges and perspectives in this field are presented.
Directional assembly of nanowires into 1D, 2D, and 3D assemblies toward flexible electronic devices benefits many potential applications. 1D assemblies with fiber structures can be used as flexible electronics for textiles, 2D assemblies can be used as transparent electrodes or units for logic circuits, and 3D assemblies can be used in the fabrication of pressure sensors or high‐performance energy‐storage devices.
Stabilizing liquids based on supramolecular assembly (non‐covalent intermolecular interactions) has attracted significant interest, due to the increasing demand for soft, liquid‐based devices where ...the shape of the liquid is far from the equilibrium spherical shape. The components comprising these interfacial assemblies must have sufficient binding energies to the interface to prevent their ejection from the interface when the assemblies are compressed. Here, we highlight recent advances in structuring liquids based on non‐covalent intermolecular interactions. We describe some of the progress made that reveals structure–property relationships. In addition to treating advances, we discuss some of the limitations and provide a perspective on future directions to inspire further studies on structured liquids based on supramolecular assembly.
Stabilizing liquids based on supramolecular assembly (non‐covalent intermolecular interactions) has attracted significant interest, due to the increasing demand for soft, liquid‐based devices. Recent advances in structuring liquids based on non‐covalent intermolecular interactions are highlighted and a perspective is provided on future directions to inspire further studies on structured liquids based on supramolecular assembly.
Abstract
Background
Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. ...Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes.
Results
In this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble.
Conclusions
Without using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from:
http://bioinfolab.unl.edu/emlab/consemble/
.
Biomolecular self‐assembly is a powerful approach for fabricating supramolecular architectures. Over the past decade, a myriad of biomolecular assemblies, such as self‐assembly proteins, lipids, and ...DNA nanostructures, have been used in a wide range of applications, from nano‐optics to nanoelectronics and drug delivery. The method of controlling when and where the self‐assembly starts is essential for assembly dynamics and functionalization. Here, train‐shaped DNA nanostructures are actively self‐assembled using DNA tiles as artificial “carriages,” hairpin structures as “couplers,” and initiators of catalytic hairpin assembly (CHA) reactions as “wrenches.” The initiator wrench can selectively open the hairpin couplers to couple the DNA tile carriages with high product yield. As such, DNA nanotrains are actively prepared with two, three, four, or more carriages. Furthermore, by flexibly modifying the carriages with “biotin seats” (biotin‐modified DNA tiles), streptavidin “passengers” are precisely arranged in corresponding seats. The applications of the CHA‐triggered self‐assembly mechanism are also extended for assembling the large DNA origami dimer. With the creation of 1D architectures established, it is thought that this CHA‐triggered self‐assembly mechanism may provide a new element of control for complex autonomous assemblies from a variety of starting materials with specific sites and times.
The train‐shaped DNA nanostructure is assembled by integrating the catalytic hairpin assembly reactions with DNA tiles self‐assembly. Furthermore, by flexibly modifying the carriages with biotin‐seats (biotin modified DNA tiles), the passengers (streptavidin) are precisely arranged in corresponding seats.
Protein Assembly by Design Zhu, Jie; Avakyan, Nicole; Kakkis, Albert ...
Chemical reviews,
11/2021, Volume:
121, Issue:
22
Journal Article
Peer reviewed
Open access
Proteins are nature’s primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase ...that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
Controlling the self‐assembly morphology of π‐conjugated block copolymer is of great interesting. Herein, amphiphilic poly(3‐hexylthiophene)‐block‐poly(phenyl isocyanide)s (P3HT‐b‐PPI) copolymers ...composed of π‐conjugated P3HT and optically active helical PPI segments were readily prepared. Taking advantage of the crystallizable nature of P3HT and the chirality of the helical PPI segment, crystallization‐driven asymmetric self‐assembly (CDASA) of the block copolymers lead to the formation of single‐handed helical nanofibers with controlled length, narrow dispersity, and well‐defined helicity. During the self‐assembly process, the chirality of helical PPI was transferred to the supramolecular assemblies, giving the helical assemblies large optical activity. The single‐handed helical assemblies of the block copolymers exhibited interesting white‐light emission and circularly polarized luminescence (CPL). The handedness and dissymmetric factor of the induced CPL can be finely tuned through the variation on the helicity and length of the helical nanofibers.
One hand makes light work: The crystallization‐driven asymmetric self‐assembly (CDASA) of the block copolymers leads to the formation of single‐handed helical nanofibers with controlled length, narrow dispersity, and well‐defined helicity. The helical assembly of the block copolymer induced white‐light emission and intense circularly polarized luminescence (CPL).
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