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Active materials are hierarchically assembled, starting from extensile microtubule bundles, to form emulsions with unexpected collective biomimetic properties such as autonomous motility. Self-driven active matter Autonomous motion is a characteristic of living organisms; by consuming energy, cells and their components can generate motion without the need for externally applied force. This paper reports the creation of polymer gels, liquid crystals and emulsions that mimic this behaviour using biological molecules as building blocks. The authors assemble microtubules into hierarchical bundles and then into percolating networks. In the presence of ATP as the chemical energy source and the molecular motor protein kinesin, spatiotemporally chaotic flows are generated by creating hydrodynamic instabilities and enhanced fluid transport. When confined to the surface of emulsion droplets, the microtubule networks form two-dimensional active liquid crystals that impart autonomous motility to the emulsion droplets. This work raises the exciting possibility that chaotic behaviour of this type could be engineered to be tunable and controllable. With remarkable precision and reproducibility, cells orchestrate the cooperative action of thousands of nanometre-sized molecular motors to carry out mechanical tasks at much larger length scales, such as cell motility, division and replication 1 . Besides their biological importance, such inherently non-equilibrium processes suggest approaches for developing biomimetic active materials from microscopic components that consume energy to generate continuous motion 2 , 3 , 4 . Being actively driven, these materials are not constrained by the laws of equilibrium statistical mechanics and can thus exhibit sought-after properties such as autonomous motility, internally generated flows and self-organized beating 5 , 6 , 7 . Here, starting from extensile microtubule bundles, we hierarchically assemble far-from-equilibrium analogues of conventional polymer gels, liquid crystals and emulsions. At high enough concentration, the microtubules form a percolating active network characterized by internally driven chaotic flows, hydrodynamic instabilities, enhanced transport and fluid mixing. When confined to emulsion droplets, three-dimensional networks spontaneously adsorb onto the droplet surfaces to produce highly active two-dimensional nematic liquid crystals whose streaming flows are controlled by internally generated fractures and self-healing, as well as unbinding and annihilation of oppositely charged disclination defects. The resulting active emulsions exhibit unexpected properties, such as autonomous motility, which are not observed in their passive analogues. Taken together, these observations exemplify how assemblages of animate microscopic objects exhibit collective biomimetic properties that are very different from those found in materials assembled from inanimate building blocks, challenging us to develop a theoretical framework that would allow for a systematic engineering of their far-from-equilibrium material properties.

In electron-transfer processes, spin effects normally are seen either in magnetic materials or in systems containing heavy atoms that facilitate spin-orbit coupling. We report spin-selective transmission of electrons through self-assembled monolayers of double-stranded DNA on gold. By directly measuring the spin of the transmitted electrons with a Mott polarimeter, we found spin polarizations exceeding 60% at room temperature. The spin-polarized photoelectrons were observed even when the photoelectrons were generated with unpolarized light. The observed spin selectivity at room temperature was extremely high as compared with other known spin filters. The spin filtration efficiency depended on the length of the DNA in the monolayer and its organization.

Visibility cloak for hidden proteins When proteins associate with larger structures such as polymers, membranes or solid supports, they usually become 'invisible' to the techniques used to visualize them as free molecules in solution. Marius Clore and colleagues have now developed a new technique of solution nuclear magnetic resonance that can probe such exchange phenomena at atomic resolution. Termed dark-state exchange saturation transfer (DEST), the procedure is demonstrated here by following the aggregation of the amyloid-β monomers implicated in Alzheimer's disease. It should also be adaptable to many of the supramolecular systems encountered in biological systems and materials science. Exchange dynamics between molecules free in solution and bound to the surface of a large supramolecular structure, a polymer, a membrane or solid support are important in many phenomena in biology and materials science. Here we present a novel and generally applicable solution NMR technique, known as dark-state exchange saturation transfer (DEST), to probe such exchange phenomena with atomic resolution. This is illustrated by the exchange reaction between amyloid-β (Aβ) monomers and polydisperse, NMR-invisible (‘dark’) protofibrils, a process of significant interest because the accumulation of toxic, aggregated forms of Aβ, from small oligomers to very large assemblies, has been implicated in the aetiology of Alzheimer’s disease 1 , 2 , 3 , 4 , 5 , 6 . The 15 N-DEST experiment imprints with single-residue-resolution dynamic information on the protofibril-bound species in the form of 15 N transverse relaxation rates ( 15 N- R 2 ) and exchange kinetics between monomers and protofibrils onto the easily observed two-dimensional 1 H– 15 N correlation spectrum of the monomer. The exchanging species on the protofibril surface comprise an ensemble of sparsely populated states where each residue is either tethered to (through other residues) or in direct contact with the surface. The first eight residues exist predominantly in a mobile tethered state, whereas the largely hydrophobic central region and part of the carboxy (C)-terminal hydrophobic region are in direct contact with the protofibril surface for a significant proportion of the time. The C-terminal residues of both Aβ40 and Aβ42 display lower affinity for the protofibril surface, indicating that they are likely to be surface exposed rather than buried as in structures of Aβ fibrils 7 , 8 , 9 , 10 , and might therefore comprise the critical nucleus for fibril formation 11 , 12 . The values, however, are significantly larger for the C-terminal residues of Aβ42 than Aβ40, which might explain the former’s higher propensity for rapid aggregation and fibril formation 13 , 14 .

We describe a simple and robust method to construct complex three-dimensional (3D) structures by using short synthetic DNA strands that we call \"DNA bricks.\" In one-step annealing reactions, bricks with hundreds of distinct sequences self-assemble into prescribed 3D shapes. Each 32-nucleotide brick is a modular component; it binds to four local neighbors and can be removed or added independently. Each 8-base pair interaction between bricks defines a voxel with dimensions of 2.5 by 2.5 by 2.7 nanometers, and a master brick collection defines a \"molecular canvas\" with dimensions of 10 by 10 by 10 voxels. By selecting subsets of bricks from this canvas, we constructed a panel of 102 distinct shapes exhibiting sophisticated surface features, as well as intricate interior cavities and tunnels.

Nanoscale view of cell membrane lipids Cholesterol-mediated lipid interactions, such as nanodomain formation, are considered vital in a cell, but because of the lack of suitable detection techniques, their spatiotemporal range remained highly controversial. Here, Eggeling et al . use subdiffraction-resolution STED (stimulated emission depletion) fluorescence microscopy to detect the diffusion of single lipids or glycosylphosphatidylinositol (GPI)-anchored proteins on the plasma membrane of a living cell. Tuning the probing spot area up to about 70-fold below that of a confocal microscope reveals that unlike phosphoglycerolipids, sphingolipids and GPI-anchored proteins are trapped for about 10 ms in cholesterol-mediated complexes within less than 20 nm space. Optical probing in nanosized areas is a powerful new approach to study biomolecular function. Here, subdiffraction-resolution STED fluorescence microscopy is used to detect the diffusion of single lipids or GPI-anchored proteins on the plasma membrane of a living cell. Tuning the probing spot area ∼70-fold below that of a confocal microscope reveals that unlike phosphoglycerolipids, sphingolipids and GPI-anchored proteins are trapped for ∼10 ms in cholesterol-mediated complexes within <20 nm space. Cholesterol-mediated lipid interactions are thought to have a functional role in many membrane-associated processes such as signalling events 1 , 2 , 3 , 4 , 5 . Although several experiments indicate their existence, lipid nanodomains (‘rafts’) remain controversial owing to the lack of suitable detection techniques in living cells 4 , 6 , 7 , 8 , 9 . The controversy is reflected in their putative size of 5–200 nm, spanning the range between the extent of a protein complex and the resolution limit of optical microscopy. Here we demonstrate the ability of stimulated emission depletion (STED) far-field fluorescence nanoscopy 10 to detect single diffusing (lipid) molecules in nanosized areas in the plasma membrane of living cells. Tuning of the probed area to spot sizes ∼70-fold below the diffraction barrier reveals that unlike phosphoglycerolipids, sphingolipids and glycosylphosphatidylinositol-anchored proteins are transiently (∼10–20 ms) trapped in cholesterol-mediated molecular complexes dwelling within <20-nm diameter areas. The non-invasive optical recording of molecular time traces and fluctuation data in tunable nanoscale domains is a powerful new approach to study the dynamics of biomolecules in living cells.

The mechanisms by which the ångström-scale molecular properties of cells are translated to micrometre-scale macroscopic properties have not been well understood, but this study shows that when multivalent proteins interact with each other, they undergo a switch-like phase separation, which is concomitant with a transition from small complexes to huge polymeric assemblies, as the concentration increases. Cell organization scales up The translation of molecular-scale structures into the macroscopic world of organelles and tissues is a little-understood aspect of cellular organization. Here, Michael Rosen and colleagues show that when multivalent proteins interact with each other, they undergo a switch-like phase transition from small complexes to huge polymeric assemblies as concentration increases. At the same time, they undergo a macroscopic liquid–liquid phase separation. This produces micrometre-sized suspended liquid droplets that resemble cellular structures such as P bodies, P granules and Cajal bodies. Such switch-like phase separations and transitions from small complexes to large assemblies may be a general feature of interactions between multivalent molecules. Cells are organized on length scales ranging from ångström to micrometres. However, the mechanisms by which ångström-scale molecular properties are translated to micrometre-scale macroscopic properties are not well understood. Here we show that interactions between diverse synthetic, multivalent macromolecules (including multi-domain proteins and RNA) produce sharp liquid–liquid-demixing phase separations, generating micrometre-sized liquid droplets in aqueous solution. This macroscopic transition corresponds to a molecular transition between small complexes and large, dynamic supramolecular polymers. The concentrations needed for phase transition are directly related to the valency of the interacting species. In the case of the actin-regulatory protein called neural Wiskott–Aldrich syndrome protein (N-WASP) interacting with its established biological partners NCK and phosphorylated nephrin 1 , the phase transition corresponds to a sharp increase in activity towards an actin nucleation factor, the Arp2/3 complex. The transition is governed by the degree of phosphorylation of nephrin, explaining how this property of the system can be controlled to regulatory effect by kinases. The widespread occurrence of multivalent systems suggests that phase transitions may be used to spatially organize and biochemically regulate information throughout biology.

The patterns of life Pattern formation in complex systems made up of many individual self-propelled components is a ubiquitous phenomenon, seen in systems as diverse as flocks of birds, colonies of microorganisms and in the cytoskeleton of living cells. Progress towards a unifying explanation of its mechanisms has been slow because of the lack of a sufficiently simple model, but now there is a candidate for the role. The new experimental system involves filaments of the protein actin propelled by motor proteins immobilized on a surface. Above a critical density the filaments self-organize to form coherently moving structures with persistent density modulations such as clusters, swirls and interconnected bands. Experimental observations combined with simulations reveal a variety of mechanisms underling assembly and disassembly of the ordered structures and show that weak and local alignment interactions are essential for pattern formation. The system's controllability and scope for extension to more complex interactions should make it well suited to studying the emergence of macroscopic order from microscopic interactions. Collective motion is a ubiquitous self-organization phenomenon that can be observed in systems ranging from flocks of animals to the cytoskeleton. Similarities between these systems suggest that there are universal underlying principles. This idea can be tested with 'active' or 'driven' fluids, but so far such systems have offered limited parameter control. Here, an active fluid is studied that contains only a few components — actin filaments and molecular motors — allowing the control of all relevant system parameters. The emergence of collective motion exhibited by systems ranging from flocks of animals to self-propelled microorganisms to the cytoskeleton is a ubiquitous and fascinating self-organization phenomenon 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 . Similarities between these systems, such as the inherent polarity of the constituents, a density-dependent transition to ordered phases or the existence of very large density fluctuations 13 , 14 , 15 , 16 , suggest universal principles underlying pattern formation. This idea is followed by theoretical models at all levels of description: micro- or mesoscopic models directly map local forces and interactions using only a few, preferably simple, interaction rules 12 , 17 , 18 , 19 , 20 , 21 , and more macroscopic approaches in the hydrodynamic limit rely on the systems’ generic symmetries 8 , 22 , 23 . All these models characteristically have a broad parameter space with a manifold of possible patterns, most of which have not yet been experimentally verified. The complexity of interactions and the limited parameter control of existing experimental systems are major obstacles to our understanding of the underlying ordering principles 13 . Here we demonstrate the emergence of collective motion in a high-density motility assay that consists of highly concentrated actin filaments propelled by immobilized molecular motors in a planar geometry. Above a critical density, the filaments self-organize to form coherently moving structures with persistent density modulations, such as clusters, swirls and interconnected bands. These polar nematic structures are long lived and can span length scales orders of magnitudes larger than their constituents. Our experimental approach, which offers control of all relevant system parameters, complemented by agent-based simulations, allows backtracking of the assembly and disassembly pathways to the underlying local interactions. We identify weak and local alignment interactions to be essential for the observed formation of patterns and their dynamics. The presented minimal polar-pattern-forming system may thus provide new insight into emerging order in the broad class of active fluids 8 , 23 , 24 and self-propelled particles 17 , 25 .

We present an analytical treatment of a set of coupled kinetic equations that governs the self-assembly of filamentous molecular structures. Application to the case of protein aggregation demonstrates that the kinetics of amyloid growth can often be dominated by secondary rather than by primary nucleation events. Our results further reveal a range of general features of the growth kinetics of fragmenting filamentous structures, including the existence of generic scaling laws that provide mechanistic information in contexts ranging from in vitro amyloid growth to the in vivo development of mammalian prion diseases.

Key Points Chromatin immunoprecipitation followed by sequencing (ChIP–seq) detects protein–DNA binding events and chemical modifications of histone proteins. Recent technological advances in the ChIP–seq protocol have enabled assaying samples with limited cells, increased precision of the genomic location of binding events, and assaying multiple binding events. However, technical and analytical challenges remain. Open chromatin assays — such as DNase–seq, formaldehyde-assisted identification of regulatory elements (FAIRE–seq) and DNaseI footprinting — offer complementary methods to identify genomic regions bound by regulatory proteins. Chromatin conformation capture (3C) and chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) experiments detect three-dimensional chromatin interactions between bound proteins. Protein binding efficiency varies across sites within a single genome due to differences in the underlying genomic sequences and chromatin state. These differences affect the functionality of transcription factors within cells. SNPs in protein–DNA binding sites can affect binding efficiency across individuals and can be detected by allelic biases in sequences produced from high-throughput sequencing assays. This Review discusses recent improvements to ChIP–seq and a range of complementary techniques, such as DNaseI hypersensitivity mapping, for studying protein–DNA interactions. Functional characterization of protein binding can be improved by methods analysing chromatin conformation or allele-specific binding. Chromatin immunoprecipitation experiments followed by sequencing (ChIP–seq) detect protein–DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP–seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches — for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins — provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.