Self-assembly of biological structures

Hierarchical Self-Organization and Disorganization of Helical Supramolecular Columns Mediated by H-Bonding and Shape Complementarity

H-bonding, shape complementarity, and quasi-equivalence are widely accepted as some of the most influential molecular recognition events mediating biological and synthetic self-organizations. H-bonds are weaker than ionic but stronger than van der Waals forces. However, the directionality of H-bonds makes them the most powerful among all nonbonding interactions. Here, we selected two taper-shaped self-assembling dendrons, one flexible and one rigid, and equipped them with -CO2CH3, -CH2OH, and -COOH at their apex. They demonstrated the hierarchical way in which shape-complementarity in the presence of -CO2CH3 mediated highly ordered helical self-organization for the case of the rigid building block and less ordered helical arrays for the flexible one. Weak H-bonding by -CH2OH unwound the helix from the rigid dendron, yielding a porous column. Due to its quasi-equivalence, the flexible dendron tolerated better the H-bonding by -CH2OH self-organizing a different helical column. The rigid and the flexible dendrons yielded only disorganized nonhelical columns in the presence of -COOH at the apex. This balance between rigidity, flexibility, and tolerance or lack of it to diverse H-bonding architectures indicates that mechanistic elucidation of the self-organization process helps endow it with the same building block, both helical organizations approaching biological precision, and disorganized nonhelical arrangements.

Specialized structure and function of the apical extracellular matrix at sense organs

Apical extracellular matrix (aECM) covers every surface of the body and exhibits tissue-specific structures that carry out specialized functions. This is particularly striking at sense organs, where aECM forms the interface between sensory neurons and the environment, and thus plays critical roles in how sensory stimuli are received. Here, we review the extraordinary adaptations of aECM across sense organs and discuss how differences in protein composition and matrix structure assist in sensing mechanical forces (tactile hairs, campaniform sensilla, and the tectorial membrane of the cochlea); tastes and smells (uniporous gustatory sensilla and multiporous olfactory sensilla in insects, and salivary and olfactory mucus in vertebrates); and light (cuticle-derived lenses in arthropods and mollusks). We summarize the power of using C. elegans, in which defined sense organs associate with distinct aECM, as a model for understanding the tissue-specific structural and functional specializations of aECM. Finally, we synthesize results from recent studies in C. elegans and Drosophila into a conceptual framework for aECM patterning, including mechanisms that involve transient cellular or matrix scaffolds, mechanical pulling or pushing forces, and localized secretion or endocytosis.

Seeing the Supracolloidal Assemblies in 3D: Unraveling High-Resolution Structures Using Electron Tomography

Transmission electron microscopy (TEM) imaging has revolutionized modern materials science, nanotechnology, and structural biology. Its ability to provide information about materials' structure, composition, and properties at atomic-level resolution has enabled groundbreaking discoveries and the development of innovative materials with precision and accuracy. Electron tomography, single particle reconstruction, and microcrystal electron diffraction techniques have paved the way for the three-dimensional (3D) reconstruction of biological samples, synthetic materials, and hybrid nanostructures at near atomic-level resolution. TEM tomography using a series of two-dimensional (2D) projections has been used extensively in biological science, but in recent years it has become an important method in synthetic nanomaterials and soft matter research. TEM tomography offers unprecedented morphological details of 3D objects, internal structures, packing patterns, growth mechanisms, and self-assembly pathways of self-assembled colloidal systems. It complements other analytical tools, including small-angle X-ray scattering, and provides valuable data for computational simulations for predictive design and reverse engineering of nanomaterials with the desired structure and properties. In this perspective, I will discuss the importance of TEM tomography in the structural understanding and engineering of self-assembled nanostructures with specific emphasis on colloidal capsids, composite cages, biohybrid superlattices with complex geometries, polymer assemblies, and self-assembled protein-based superstructures.

Precision nanoengineering for functional self-assemblies across length scales

As nanotechnology continues to push the boundaries across disciplines, there is an increasing need for engineering nanomaterials with atomic-level precision for self-assembly across length scales, i.e., from the nanoscale to the macroscale. Although molecular self-assembly allows atomic precision, extending it beyond certain length scales presents a challenge. Therefore, the attention has turned to size and shape-controlled metal nanoparticles as building blocks for multifunctional colloidal self-assemblies. However, traditionally, metal nanoparticles suffer from polydispersity, uncontrolled aggregation, and inhomogeneous ligand distribution, resulting in heterogeneous end products. In this feature article, I will discuss how virus capsids provide clues for designing subunit-based, precise, efficient, and error-free self-assembly of colloidal molecules. The atomically precise nanoscale proteinic subunits of capsids display rigidity (conformational and structural) and patchy distribution of interacting sites. Recent experimental evidence suggests that atomically precise noble metal nanoclusters display an anisotropic distribution of ligands and patchy ligand bundles. This enables symmetry breaking, consequently offering a facile route for two-dimensional colloidal crystals, bilayers, and elastic monolayer membranes. Furthermore, inter-nanocluster interactions mediated via the ligand functional groups are versatile, offering routes for discrete supracolloidal capsids, composite cages, toroids, and macroscopic hierarchically porous frameworks. Therefore, engineered nanoparticles with atomically precise structures have the potential to overcome the limitations of molecular self-assembly and large colloidal particles. Self-assembly allows the emergence of new optical properties, mechanical strength, photothermal stability, catalytic efficiency, quantum yield, and biological properties. The self-assembled structures allow reproducible optoelectronic properties, mechanical performance, and accurate sensing. More importantly, the intrinsic properties of individual nanoclusters are retained across length scales. The atomically precise nanoparticles offer enormous potential for next-generation functional materials, optoelectronics, precision sensors, and photonic devices.

Vesicles, fibres, films and crystals: A low-molecular-weight-gelator [Au(6-thioguanosine)2]Cl which exhibits a co-operative anion-induced transition from vesicles to a fibrous metallo-hydrogel

We describe a simple coordination compound of Au(I) and 6-thioguanosine, [Au(6-tGH)2]Cl, that has a rich self-assembly chemistry. In aqueous solution, the discrete complex assembles into a supramolecular fibre and forms a luminescent hydrogel at concentrations above about 1 mM. Below this concentration, the macromolecular structure is a vesicle. Through appropriate control of the solvent polarity, the gel can be turned into a lamellar film or crystallised. The molecular structure of [Au(6-tGH)2]Cl was determined using single crystal X-ray diffraction, which showed bis-6-thioguanosine linearly coordinated through the thione moiety to a central Au(I) ion. In the vesicles, the photoluminescence spectrum shows a broad, weak band at 550 nm owing to aurophilic interactions. Co-operative self-assembly from vesicle to fibre is made possible through halogen hydrogen bonding interactions and the aurophilic interactions are lost, resulting in a strong photoluminescence band at 490 nm with vibronic structure typical of an intraligand transition. The vesicle-fibre transition is also revealed by a large increase of ellipticity in the circular dichroism spectrum with a prominent peak near 390 nm owing to the helical structure of the fibres. Atomic force microscopy shows that at the same time as fibres form, the sample gels. Imaging near the vesicle-fibre transition shows that the fibres form between vesicles and a mechanism for the transition based on vesicle collisions is proposed.

Geometric Transformations Afforded by Rotational Freedom in Aramid Amphiphile Nanostructures

Molecular self-assembly in water leads to nanostructure geometries that can be tuned owing to the highly dynamic nature of amphiphiles. There is growing interest in strongly interacting amphiphiles with suppressed dynamics, as they exhibit ultrastability in extreme environments. However, such amphiphiles tend to assume a limited range of geometries upon self-assembly due to the specific spatial packing induced by their strong intermolecular interactions. To overcome this limitation while maintaining structural robustness, we incorporate rotational freedom into the aramid amphiphile molecular design by introducing a diacetylene moiety between two aramid units, resulting in diacetylene aramid amphiphiles (D-AAs). This design strategy enables rotations along the carbon-carbon sp hybridized bonds of an otherwise fixed aramid domain. We show that varying concentrations and equilibration temperatures of D-AA in water lead to self-assembly into four different nanoribbon geometries: short, extended, helical, and twisted nanoribbons, all while maintaining robust structure with thermodynamic stability. We use advanced microscopy, X-ray scattering, spectroscopic techniques, and two-dimensional (2D) NMR to understand the relationship between conformational freedom within strongly interacting amphiphiles and their self-assembly pathways.

A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization

The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.

Self-Organization of Iron Sulfide Nanoparticles into Complex Multicompartment Supraparticles

Self-assembled compartments from nanoscale components are found in all life forms. Their characteristic dimensions are in 50-1000 nm scale, typically assembled from a variety of bioorganic "building blocks". Among the various functions that these mesoscale compartments carry out, protection of the content from the environment is central. Finding synthetic pathways to similarly complex and functional particles from technologically friendly inorganic nanoparticles (NPs) is needed for a multitude of biomedical, biochemical, and biotechnological processes. Here, it is shown that FeS2 NPs stabilized by l-cysteine self-assemble into multicompartment supraparticles (mSPs). The NPs initially produce ≈55 nm concave assemblies that reconfigure into ≈75 nm closed mSPs with ≈340 interconnected compartments with an average size of ≈5 nm. The intercompartmental partitions and mSP surface are formed primarily from FeS2 and Fe2 O3 NPs, respectively. The intermediate formation of cup-like particles enables encapsulation of biological cargo. This capability is demonstrated by loading mSPs with DNA and subsequent transfection of mammalian cells. Also it is found that the temperature stability of the DNA cargo is enhanced compared to the traditional delivery vehicles. These findings demonstrate that biomimetic compartmentalized particles can be used to successfully encapsulate and enhance temperature stability of the nucleic acid cargo for a variety of bioapplications.

Theoretical and computational methodologies for understanding coordination self-assembly complexes

This perspective highlights three theoretical and computational methods to capture the coordination self-assembly processes at the molecular level: quantum chemical modeling, molecular dynamics, and reaction network analysis. These methods cover the different scales from the metal-ligand bond to a more global aspect, and approaches that are best suited to understand the coordination self-assembly from different perspectives are introduced. Theoretical and numerical researches based on these methods are not merely ways of interpreting the experimental studies but complementary to them.

Soft Functionally Gradient Materials and Structures - Natural and Manmade: A Review

Functionally gradient materials (FGM) have gradual variations in their properties along one or more dimensions due to local compositional or structural distinctions by design. Traditionally, hard materials (e.g., metals, ceramics) are used to design and fabricate FGMs; however, there is increasing interest in polymer-based soft and compliant FGMs mainly because of their potential application in the human environment. Soft FGMs are ideally suitable to manage interfacial problems in dissimilar materials used in many emerging devices and systems for human interaction, such as soft robotics and electronic textiles and beyond. Soft systems are ubiquitous in everyday lives; they are resilient and can easily deform, absorb energy, and adapt to changing environments. Here, the basic design and functional principles of biological FGMs and their manmade counterparts are discussed using representative examples. The remarkable multifunctional properties of natural FGMs resulting from their sophisticated hierarchical structures, built from a relatively limited choice of materials, offer a rich source of new design paradigms and manufacturing strategies for manmade materials and systems for emerging technological needs. Finally, the challenges and potential pathways are highlighted to leverage soft materials' facile processability and unique properties toward functional FGMs.

Enzyme-mediated intratumoral self-assembly of nanotheranostics for enhanced imaging and tumor therapy

Enzyme-mediated intratumoral self-assembled (EMISA) nanotheranostics represent a new class of smart agents for combined imaging and therapy of cancer. Cancer cells overexpress various enzymes that are essential for high metabolism, fast proliferation, and tissue invasion and metastasis. By conjugating small molecules that contain an enzyme-specific cleavage site to appropriate chemical linkers, it is possible to induce self-assembly of nanostructures in tumor cells having the target enzyme. This approach of injecting small theranostic molecules that eventually become larger nanotheranostics in situ avoids some of the major limitations that are encountered when injecting larger, pre-assembled nanotheranostics. The advantage of EMISA nanotheranostics include the avoidance of nonspecific uptake and rapid clearance by phagocytic cells, increased cellular accumulation, reduced drug efflux and prolonged cellular exposure time, all of which lead to an amplified imaging signal and therapeutic efficacy. We review here the different approaches that can be used for preparing EMISA-based organic, inorganic, or organic/inorganic hybrid nanotheranostics based on noncovalent interactions and/or covalent bonding. Imaging examples are shown for fluorescence imaging, nuclear imaging, photoacoustic imaging, Raman imaging, computed tomography imaging, bioluminescent imaging, and magnetic resonance imaging. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Biology-Inspired Nanomaterials > Peptide-Based Structures.

Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD

Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method that generates transition pathways between a reactant and product. To sample the transition pathways, PaCS-MD repeats short-time MD simulations from important configurations as conformational resampling cycles. In this study, PaCS-MD was extended to sample ligand binding pathways toward a target protein, which is referred to as LB-PaCS-MD. In a ligand-concentrated environment, where multiple ligand copies are randomly arranged around the target protein, LB-PaCS-MD allows for the frequent sampling of ligand binding pathways. To select the important configurations, we specified the center of mass (COM) distance between each ligand and the relevant binding site of the target protein, where snapshots generated by the short-time MD simulations were ranked by their COM distance values. From each cycle, snapshots with smaller COM distance values were selected as the important configurations to be resampled using the short-time MD simulations. By repeating conformational resampling cycles, the COM distance values gradually decreased and converged to constants, meaning that a set of ligand binding pathways toward the target protein was sampled by LB-PaCS-MD. To demonstrate relative efficiency, LB-PaCS-MD was applied to several proteins, and their ligand binding pathways were sampled more frequently than conventional MD simulations.

Fuel Acid Drives Base Catalysis and Supramolecular Cage-to-Device Transformation under Dissipative Conditions

In State-I, a mixture comprising a DABCO-bridged tris(zinc-porphyrin) double decker and a free biped (=slider), catalysis was OFF. Acid addition (TFA or Di-Stefano fuel acid) to State-I liberated DABCO-H⁺ while generating a highly dynamic slider-on-deck device (State-II). The released DABCO-H⁺ acted as a base organocatalyst for a Knoevenagel reaction (catalysis ON). The system was reversed to State-I (catalysis OFF) by reducing the acidity in the system (by adding DBU or via the fuel-derived base).

Phase transitions in virology

Viruses have established relationships with almost every other living organism on Earth and at all levels of biological organization: from other viruses up to entire ecosystems. In most cases, they peacefully coexist with their hosts, but in most relevant cases, they parasitize them and induce diseases and pandemics, such as the AIDS and the most recent avian influenza and COVID-19 pandemic events, causing a huge impact on health, society, and economy. Viruses play an essential role in shaping the eco-evolutionary dynamics of their hosts, and have been also involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organization, from the molecular mechanisms of genome replication, gene expression and encapsidation, to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as occurs with temperature separating phases in a liquid, define sharp qualitative types of behaviour. Thesephase transitionsare very well known in physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing us to better understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review well-known mathematical models of transition phenomena in virology. We suggest that the advantages of abstract, simplified pictures used in physics are also the key to properly understanding the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across scales and their evolutionary and clinical implications are outlined.

Unexpected Self-Assembly Pathway to a Pd(II) Coordination Square-Based Pyramid and Its Preferential Formation beyond the Boltzmann Distribution

Experimental and theoretical investigations of the self-assembly process of a Pd(II) coordination M₆L₄ square-based pyramid (SP) were conducted. It was found that the probable self-assembly pathway, in which the dimerization of M₂L₂ with two M leads to SP, expected from the connectivity of the building blocks is not a major self-assembly pathway to the M₆L₄ SP. Whether the M₆L₄ SP is assembled or M₂L₂ is trapped is determined by an inter- or intramolecular reaction in a chain-like M₂L₂X, where X is a leaving ligand. The kinetically trapped state where the M₆L₄ SP is produced from M₂L₂ beyond the Boltzmann distribution was realized by a concentration-induced process and was kept for at least 2 months at 298 K.

Self-assembling peptides as vectors for local drug delivery and tissue engineering applications

Molecular self-assembly has forged a new era in the development of advanced biomaterials for local drug delivery and tissue engineering applications. Given their innate biocompatibility and biodegradability, self-assembling peptides (SAPs) have come in the spotlight of such applications. Short and water-soluble SAP biomaterials associated with enhanced pharmacokinetic (PK) and pharmacodynamic (PD) responses after the topical administration of the therapeutic systems, or improved regenerative potential in tissue engineering applications will be the focus of the current review. SAPs are capable of generating supramolecular structures using a boundless array of building blocks, while peptide engineering is an approach commonly pursued to encompass the desired traits to the end composite biomaterials. These two elements combined, expand the spectrum of SAPs multi-functionality, constituting them potent biomaterials for use in various biomedical applications.

Stimuli responsive dynamic transformations in supramolecular gels

Supramolecular gels are formed by the self-assembly of small molecules under the influence of various non-covalent interactions. As the interactions are individually weak and reversible, it is possible to perturb the gels easily, which in turn enables fine tuning of their properties. Synthetic supramolecular gels are kinetically trapped and usually do not show time variable changes in material properties after formation. However, such materials potentially become switchable when exposed to external stimuli like temperature, pH, light, enzyme, redox, and chemical analytes resulting in reconfiguration of gel matrix into a different type of network. Such transformations allow gel-to-gel transitions while the changes in the molecular aggregation result in alteration of physical and chemical properties of the gel with time. Here, we discuss various methods that have been used to achieve gel-to-gel transitions by modifying a pre-formed gel material through external perturbation. We also describe methods that allow time-dependent autonomous switching of gels into different networks enabling synthesis of next generation functional materials. Dynamic modification of gels allows construction of an array of supramolecular gels with various properties from a single material which eventually extend the limit of applications of the gels. In some cases, gel-to-gel transitions lead to materials that cannot be accessed directly. Finally, we point out the necessity and possibility of further exploration of the field.

Revealing Thermodynamics and Kinetics of Lipid Self-Assembly by Markov State Model Analysis

Self-assembly is ubiquitous in the realm of biology and has become an elegant bottom-up approach to fabricate new materials. Although molecular dynamics (MD) simulations can complement experiments by providing the missing atomic details, it still remains a grand challenge to reveal the thermodynamic and kinetic information on a self-assembly system. In this work, we demonstrate for the first time that the Markov state model analysis can be used to delineate the variation of free energy during the self-assembly process of a typical amphiphilic lipid dipalmitoyl-phosphatidylcholine (DPPC). Free energy profiles against the solvent-accessible surface area and the root-mean-square deviation have been derived from extensive MD results of more than five hundred trajectories, which identified a metastable crossing-cylinder (CC) state and a transition state of the distorted bilayer with a free energy barrier of ∼0.02 kJ mol^-1 per DPPC lipid, clarifying a long-standing speculation for 20 years that there exists a free energy barrier during lipid self-assembly. Our simulations also unearth two mesophase structures at the early stage of self-assembly, discovering two assembling pathways to the CC state that have never been reported before. Further thermodynamic analysis derives the contributions from the enthalpy and the entropy terms to the free energy, demonstrating the critical role played by the enthalpy-entropy compensation. Our strategy opens the door to quantitatively understand the self-assembly processes in general and provides new opportunities for identifying common thermodynamic and kinetic patterns in different self-assembly systems and inspiring new ideas for experiments. It may also contribute to the refinement of force field parameters of various self-assembly systems.

A framework for parsing heritable information

Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here, I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.) and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This entity-sensor-property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.

Adaptive Polymeric Assemblies for Applications in Biomimicry and Nanomedicine

Dynamic and adaptive self-assembly systems are able to sense an external or internal (energy or matter) input and respond via chemical or physical property changes. Nanomaterials that show such transient behavior have received increasing interest in the field of nanomedicine due to improved spatiotemporal control of the nanocarrier function. In this regard, much can be learned from the field of systems chemistry and bottom-up synthetic biology, in which complex and intelligent networks of nanomaterials are designed that show transient behavior and function to advance our understanding of the complexity of living systems. In this Perspective, we highlight the recent advancements in adaptive nanomaterials used for nanomedicine and trends in transient responsive self-assembly systems to envisage how these fields can be integrated for the formation of next-generation adaptive stimuli-responsive nanocarriers in nanomedicine.

Magnetic origami creates high performance micro devices

Self-assembly of two-dimensional patterned nanomembranes into three-dimensional micro-architectures has been considered a powerful approach for parallel and scalable manufacturing of the next generation of micro-electronic devices. However, the formation pathway towards the final geometry into which two-dimensional nanomembranes can transform depends on many available degrees of freedom and is plagued by structural inaccuracies. Especially for high-aspect-ratio nanomembranes, the potential energy landscape gives way to a manifold of complex pathways towards misassembly. Therefore, the self-assembly yield and device quality remain low and cannot compete with state-of-the art technologies. Here we present an alternative approach for the assembly of high-aspect-ratio nanomembranes into microelectronic devices with unprecedented control by remotely programming their assembly behavior under the influence of external magnetic fields. This form of magnetic Origami creates micro energy storage devices with excellent performance and high yield unleashing the full potential of magnetic field assisted assembly for on-chip manufacturing processes.

Despite the potential of self-assembly strategies for fabricating 3D micro-electronic devices, technological limitations prohibit widespread industrial adoption. Here, the authors report the magnetic field-assisted Origami-based assembly of high-performance devices with high yield.

Supramolecular copolymers predominated by alternating order: Theory and application

We investigate the copolymerization behavior of a two-component system into quasilinear self-assemblies under conditions that interspecies binding is favored over identical species binding. The theoretical framework is based on a coarse-grained self-assembled Ising model with nearest neighbor interactions. In Ising language, such conditions correspond to the antiferromagnetic case giving rise to copolymers with predominantly alternating configurations. In the strong coupling limit, we show that the maximum fraction of polymerized material and the average length of strictly alternating copolymers depend on the stoichiometric ratio and the activation free energy of the more abundant species. They are substantially reduced when the stoichiometric ratio noticeably differs from unity. Moreover, for stoichiometric ratios close to unity, the copolymerization critical concentration is remarkably lower than the homopolymerization critical concentration of either species. We further analyze the polymerization behavior for a finite and negative coupling constant and characterize the composition of supramolecular copolymers. Our theoretical insights rationalize experimental results of supramolecular polymerization of oppositely charged monomeric species in aqueous solutions.

Temporally-Programmed Transient Supramolecular Gels

In living systems, self-assembly processes are driven by the consumption of chemical fuels. Synthetic adaptation of living systems can be achieved by coupling of competing pathways that drive the assembly and disassembly, respectively, under the influence of chemical fuels. Here, a pH-responsive transient gel system is created by simultaneous incorporation of two triggers, of which one is responsible for the initiation of the self-assembly by increasing the pH and the second trigger drives the disassembly by reducing the pH. This method allows us to prepare transient gels with a high degree of control over the self-assembly lifetime as well as the mechanical properties of the transient gels.

Is the cell really a machine?

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.

Cytoskeletal actin patterns shape mast cell activation

Activation of immune cells relies on a dynamic actin cytoskeleton. Despite detailed knowledge of molecular actin assembly, the exact processes governing actin organization during activation remain elusive. Using advanced microscopy, we here show that Rat Basophilic Leukemia (RBL) cells, a model mast cell line, employ an orchestrated series of reorganization events within the cortical actin network during activation. In response to IgE antigen-stimulation of FCε receptors (FCεR) at the RBL cell surface, we observed symmetry breaking of the F-actin network and subsequent rapid disassembly of the actin cortex. This was followed by a reassembly process that may be driven by the coordinated transformation of distinct nanoscale F-actin architectures, reminiscent of self-organizing actin patterns. Actin patterns co-localized with zones of Arp2/3 nucleation, while network reassembly was accompanied by myosin-II activity. Strikingly, cortical actin disassembly coincided with zones of granule secretion, suggesting that cytoskeletal actin patterns contribute to orchestrate RBL cell activation.

Huw Colin-York et al. use advanced microscopy techniques to show that the cortical actin network within a model mast cell line undergoes a series of reorganizational events at the basal interface during activation. They find that actin patterns co-localize with zones of Arp2/3 nucleation and myosin-II activity accompanies network reassembly.

pH clock instructed transient supramolecular peptide amphiphile and its vesicular assembly

A pH clock directed transient supramolecular peptide amphiphile and its vesicular assembly using ternary complexation of cucurbit[8]uril is displayed.

Nanoparticles Self-Assembly within Lipid Bilayers

Coarse-grained molecular dynamics simulations are used to model the self-assembly of small hydrophobic nanoparticles (NPs) within the interior of lipid bilayers. The simulation results reveal the conditions under which NPs form clusters and lattices within lipid bilayers of planar and spherical shapes, depending on the NP-lipid coupling strengths. The formation of nanopores within spherical bilayers with self-assembled planar NPs is also described. These observations can provide guidance in the preparation of functional bio-inorganic systems.

Architecture, space and information in constructions built by humans and social insects: a conceptual review

The similarities between the structures built by social insects and by humans have led to a convergence of interests between biologists and architects. This new, de facto interdisciplinary community of scholars needs a common terminology and theoretical framework in which to ground its work. In this conceptually oriented review paper, we review the terms 'information', 'space' and 'architecture' to provide definitions that span biology and architecture. A framework is proposed on which interdisciplinary exchange may be better served, with the view that this will aid better cross-fertilization between disciplines, working in the areas of collective behaviour and analysis of the structures and edifices constructed by non-humans; and to facilitate how this area of study may better contribute to the field of architecture. We then use these definitions to discuss the informational content of constructions built by organisms and the influence these have on behaviour, and vice versa. We review how spatial constraints inform and influence interaction between an organism and its environment, and examine the reciprocity of space and information on construction and the behaviour of humans and social insects.This article is part of the theme issue 'Interdisciplinary approaches for uncovering the impacts of architecture on collective behaviour'.

UsnRNP biogenesis: mechanisms and regulation

Macromolecular complexes composed of proteins or proteins and nucleic acids rather than individual macromolecules mediate many cellular activities. Maintenance of these activities is essential for cell viability and requires the coordinated production of the individual complex components as well as their faithful incorporation into functional entities. Failure of complex assembly may have fatal consequences and can cause severe diseases. While many macromolecular complexes can form spontaneously in vitro, they often require aid from assembly factors including assembly chaperones in the crowded cellular environment. The assembly of RNA protein complexes implicated in the maturation of pre-mRNAs (termed UsnRNPs) has proven to be a paradigm to understand the action of assembly factors and chaperones. UsnRNPs are assembled by factors united in protein arginine methyltransferase 5 (PRMT5)- and survival motor neuron (SMN)-complexes, which act sequentially in the UsnRNP production line. While the PRMT5-complex pre-arranges specific sets of proteins into stable intermediates, the SMN complex displaces assembly factors from these intermediates and unites them with UsnRNA to form the assembled RNP. Despite advanced mechanistic understanding of UsnRNP assembly, our knowledge of regulatory features of this essential and ubiquitous cellular function remains remarkably incomplete. One may argue that the process operates as a default biosynthesis pathway and does not require sophisticated regulatory cues. Simple theoretical considerations and a number of experimental data, however, indicate that regulation of UsnRNP assembly most likely happens at multiple levels. This review will not only summarize how individual components of this assembly line act mechanistically but also why, how, and when the UsnRNP workflow might be regulated by means of posttranslational modification in response to cellular signaling cues.

Self-organizing actin patterns shape cytoskeletal cortex organization

Living systems rely, for biological function, on the spatiotemporal organization of their structures. Cellular order naturally emerges by dissipation of energy. Consequently, energy-consuming processes operating far from thermodynamic equilibrium are a necessary condition to enable biological systems to respond to environmental cues that allow their transitions between different steady-states. Such self-organization was predicted for the actin cytoskeleton in theoretical considerations and has repeatedly been observed in cell-free systems. We now demonstrate in our recent work how self-organizing actin patterns such as vortices, stars, and asters may allow cells to adjust their membrane architecture without affecting their cell mechanical properties.

Self-organizing actin patterns shape membrane architecture but not cell mechanics

Cell-free studies have demonstrated how collective action of actin-associated proteins can organize actin filaments into dynamic patterns, such as vortices, asters and stars. Using complementary microscopic techniques, we here show evidence of such self-organization of the actin cortex in living HeLa cells. During cell adhesion, an active multistage process naturally leads to pattern transitions from actin vortices over stars into asters. This process is primarily driven by Arp2/3 complex nucleation, but not by myosin motors, which is in contrast to what has been theoretically predicted and observed in vitro. Concomitant measurements of mechanics and plasma membrane fluidity demonstrate that changes in actin patterning alter membrane architecture but occur functionally independent of macroscopic cortex elasticity. Consequently, tuning the activity of the Arp2/3 complex to alter filament assembly may thus be a mechanism allowing cells to adjust their membrane architecture without affecting their macroscopic mechanical properties.

In vitro models of actin organization show the formation of vortices, asters and stars. Here Fritzsche et al. show that such actin structures form in living cells in a manner dependent on the Arp2/3 complex but not myosin, and such structures influence membrane architecture but not cortex elasticity.

Dissipative self-assembly of vesicular nanoreactors

Dissipative self-assembly is exploited by nature to control important biological functions, such as cell division, motility and signal transduction. The ability to construct synthetic supramolecular assemblies that require the continuous consumption of energy to remain in the functional state is an essential premise for the design of synthetic systems with lifelike properties. Here, we show a new strategy for the dissipative self-assembly of functional supramolecular structures with high structural complexity. It relies on the transient stabilization of vesicles through noncovalent interactions between the surfactants and adenosine triphosphate (ATP), which acts as the chemical fuel. It is shown that the lifetime of the vesicles can be regulated by controlling the hydrolysis rate of ATP. The vesicles sustain a chemical reaction but only as long as chemical fuel is present to keep the system in the out-of-equilibrium state. The lifetime of the vesicles determines the amount of reaction product produced by the system.

Exploiting recognition-mediated assembly and reactivity in [2]rotaxane formation

A small molecular reaction network exploits recognition-mediated reactive processes in order to drive the assembly and formation of both a self-replicating linear template (thread) and a [2]rotaxane, in which the linear template is encircled by a diamide macrocycle. Complementary recognition sites, placed at strategic positions on the reactive building blocks, drive these assembly and replication processes. Template-instructed experiments show that the thread is capable of efficient self-replication and that no cross-catalytic relationships exist between the thread and the [2]rotaxane. The rate of [2]rotaxane formation is insensitive to the addition of a preformed template, however, [2]rotaxane formation does show enhanced diastereoselectivity, most likely originating from its recognition-mediated formation through a ternary reactive complex.

Army ants dynamically adjust living bridges in response to a cost-benefit trade-off

The ability of individual animals to create functional structures by joining together is rare and confined to the social insects. Army ants (Eciton) form collective assemblages out of their own bodies to perform a variety of functions that benefit the entire colony. Here we examine ‟bridges" of linked individuals that are constructed to span gaps in the colony's foraging trail. How these living structures adjust themselves to varied and changing conditions remains poorly understood. Our field experiments show that the ants continuously modify their bridges, such that these structures lengthen, widen, and change position in response to traffic levels and environmental geometry. Ants initiate bridges where their path deviates from their incoming direction and move the bridges over time to create shortcuts over large gaps. The final position of the structure depended on the intensity of the traffic and the extent of path deviation and was influenced by a cost-benefit trade-off at the colony level, where the benefit of increased foraging trail efficiency was balanced by the cost of removing workers from the foraging pool to form the structure. To examine this trade-off, we quantified the geometric relationship between costs and benefits revealed by our experiments. We then constructed a model to determine the bridge location that maximized foraging rate, which qualitatively matched the observed movement of bridges. Our results highlight how animal self-assemblages can be dynamically modified in response to a group-level cost-benefit trade-off, without any individual unit's having information on global benefits or costs.

Biomedical Applications of Untethered Mobile Milli/Microrobots

Untethered robots miniaturized to the length scale of millimeter and below attract growing attention for the prospect of transforming many aspects of health care and bioengineering. As the robot size goes down to the order of a single cell, previously inaccessible body sites would become available for high-resolution in situ and in vivo manipulations. This unprecedented direct access would enable an extensive range of minimally invasive medical operations. Here, we provide a comprehensive review of the current advances in biome dical untethered mobile milli/microrobots. We put a special emphasis on the potential impacts of biomedical microrobots in the near future. Finally, we discuss the existing challenges and emerging concepts associated with designing such a miniaturized robot for operation inside a biological environment for biomedical applications.

Evolution of antimicrobial peptides to self-assembled peptides for biomaterial applications

Biomaterial-related infections are a persistent burden on patient health, recovery, mortality and healthcare budgets. Self-assembled antimicrobial peptides have evolved from the area of antimicrobial peptides. Peptides serve as important weapons in nature, and increasingly medicine, for combating microbial infection and biofilms. Self-assembled peptides harness a "bottom-up" approach, whereby the primary peptide sequence may be modified with natural and unnatural amino acids to produce an inherently antimicrobial hydrogel. Gelation may be tailored to occur in the presence of physiological and infective indicators (e.g. pH, enzymes) and therefore allow local, targeted antimicrobial therapy at the site of infection. Peptides demonstrate inherent biocompatibility, antimicrobial activity, biodegradability and numerous functional groups. They are therefore prime candidates for the production of polymeric molecules that have the potential to be conjugated to biomaterials with precision. Non-native chemistries and functional groups are easily incorporated into the peptide backbone allowing peptide hydrogels to be tailored to specific functional requirements. This article reviews an area of increasing interest, namely self-assembled peptides and their potential therapeutic applications as innovative hydrogels and biomaterials in the prevention of biofilm-related infection.

Odd or even? Monolayer domain size depends on diyne position in alkadiynylanthracenes

1,5-(Alkadiynyl)anthracenes self-assemble single component and multicomponent monolayers at the solution-HOPG interface. An alkadiynyl chain's kinked shape constrains the molecular structures with which it can close-pack. This affords rudimentary molecular recognition that has been used to direct self-assembly of 1-D patterned, multicomponent monolayers. The unit cell building blocks of single- and multicomponent alkadiynylanthracene monolayers repeat with high fidelity for 100s of nanometers along the side chain direction. Unit cell repeat fidelity along the orthogonal, anthracene column direction of the monolayer depends on diyne location within the side chain; even-position diyne side chains produce high fidelity of unit cell repeats and wider domain widths along the anthracene columns, whereas odd-position diyne side chains produce more frequent domain interfaces that disrupt the anthracene columns. Alkadiynylanthracene monolayers may be viewed as stacks of 1-D molecular tapes. 1-D tape molecular composition, sequence, and intratape side chain alignment are dictated by shape complementarity of the kinked alkadiynyl side chains. Stacking alignments of adjacent 1-D tapes are controlled by shape matching of tape peripheries and determine repeat fidelity along the anthracene columns. Tapes stacked with a constant intertape alignment comprise crystalline domains that repeat along the anthracene columns. The 1-D tapes formed by anthracenes with odd-position diynes have triangle wave peripheries that close-pack in multiple stacking alignments. This reduces unit cell repeat fidelity and decreases the widths of crystalline domains along the anthracene columns. Even-position diyne side chains form 1-D tapes with trapezoid wave peripheries that close-pack in only one stacking alignment. This generates higher stacking fidelity, larger domain widths, and fewer domain interfaces along the anthracene columns of even-position diyne monolayers. Even- and odd-position diyne monolayers exhibit comparable densities of interfaces between enantiotopic domains and between domains aligned along different graphite symmetry axes. These interfaces likely arise through collisions of independently nucleated/growing domains and persist for lack of kinetically competent pathways that interconvert or merge the domains.

Stability and responsiveness in a self-organized living architecture

Robustness and adaptability are central to the functioning of biological systems, from gene networks to animal societies. Yet the mechanisms by which living organisms achieve both stability to perturbations and sensitivity to input are poorly understood. Here, we present an integrated study of a living architecture in which army ants interconnect their bodies to span gaps. We demonstrate that these self-assembled bridges are a highly effective means of maintaining traffic flow over unpredictable terrain. The individual-level rules responsible depend only on locally-estimated traffic intensity and the number of neighbours to which ants are attached within the structure. We employ a parameterized computational model to reveal that bridges are tuned to be maximally stable in the face of regular, periodic fluctuations in traffic. However analysis of the model also suggests that interactions among ants give rise to feedback processes that result in bridges being highly responsive to sudden interruptions in traffic. Subsequent field experiments confirm this prediction and thus the dual nature of stability and flexibility in living bridges. Our study demonstrates the importance of robust and adaptive modular architecture to efficient traffic organisation and reveals general principles regarding the regulation of form in biological self-assemblies.

While migrating, the nomadic army ant Eciton burchellii forms long trails of workers that can extend over hundreds of meters in the rain forest. To facilitate the movement of sometimes millions of individuals on uneven and unpredictable terrains, part of the ant workers link together their legs and bodies to form temporary bridges over gaps along the trails. In this work we showed that these bridges were formed readily when the flow of ants hit an unspanned gap and were dismantled very quickly after traffic has ceased on the trail. However, we also observed that the bridges were formed and remained stable under a large spectrum of the traffic intensities on the trail. Using field experiments and computer simulations we discovered the construction rules used by the ants to create these living structures that are capable of enduring variations of the traffic while remaining highly responsive to its interruption. These results offer important insights about the mechanisms that regulate biological self-assemblies and they have potential applications in swarm robotics and swarm intelligence.

Viral information

Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be to reinterpreted in light of viral knowledge or we need to develop new theory from the viral point-of-view. Here we briefly introduce our viral planet and then address a major outstanding question in biology: why is most of life viral? A key insight is that during an infection cycle the original virus is completely broken down and only the associated information is passed on to the next generation. This is different for cellular organisms, which must pass on some physical part of themselves from generation to generation. Based on this premise, it is proposed that the thermodynamic consequences of physical information (e.g., Landauer's principle) are observed in natural viral populations. This link between physical and genetic information is then used to develop the Viral Information Hypothesis, which states that genetic information replicates itself to the detriment of system energy efficiency (i.e., is viral in nature). Finally, we show how viral information can be tested, and illustrate how this novel view can explain existing ecological and evolutionary theories from more fundamental principles.

Selective association between nucleosomes with identical DNA sequences

Self-assembly is the autonomous organization of constituents into higher order structures or assemblages and is a fundamental mechanism in biological systems. There has been an unfounded idea that self-assembly may be used in the sensing and pairing of homologous chromosomes or chromatin, including meiotic chromosome pairing, polytene chromosome formation in Diptera and transvection. Recent studies proved that double-stranded DNA molecules have a sequence-sensing property and can self-assemble, which may play a role in the above phenomena. However, to explain these processes in terms of self-assembly, it first must be proved that nucleosomes retain a DNA sequence-sensing property and can self-assemble. Here, using atomic force microscopy (AFM)-based analyses and a quantitative interaction assay, we show that nucleosomes with identical DNA sequences preferentially associate with each other in the presence of Mg(2+) ions. Using Xenopus borealis 5S rDNA nucleosome-positioning sequence and 601 and 603 sequences, homomeric or heteromeric octa- or tetranucleosomes were reconstituted in vitro and induced to form weak intracondensates by MgCl(2). AFM clearly showed that DNA sequence-based selective association occurs between nucleosomes with identical DNA sequences. Selective association was also detected between mononucleosomes. We propose that nucleosome self-assembly and DNA self-assembly constitute the mechanism underlying sensing and pairing of homologous chromosomes or chromatin.

Reductionistic and holistic science

A reductionistic approach to science, epitomized by molecular biology, is often contrasted with the holistic approach of systems biology. However, molecular biology and systems biology are actually interdependent and complementary ways in which to study and make sense of complex phenomena.

L-tyrosine on Ag(111): universality of the amino acid 2D zwitterionic bonding scheme?

We present a combined study of the adsorption and ordering of the l-tyrosine amino acid on the close-packed Ag(111) noble-metal surface in ultrahigh vacuum by means of low-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. On this substrate the biomolecules self-assemble at temperatures exceeding 320 K into linear structures primarily following specific crystallographic directions and evolve with larger molecular coverage into two-dimensional nanoribbons which are commensurate with the underlying atomic lattice. Our high resolution topographical STM data reveal noncovalent molecular dimerization within the highly ordered one-dimensional nanostructures, which recalls the geometrical pattern already seen in the l-methionine/Ag(111) system and supports a universal bonding scheme for amino acids on smooth and unreactive metal surfaces. The molecules desorb for temperatures above 350 K, indicating a relatively weak interaction between the molecules and the substrate. XPS measurements reveal a zwitterionic adsorption, whereas NEXAFS experiments show a tilted adsorption configuration of the phenol moiety. This enables the interdigitation between aromatic side chains of adjacent molecules via parallel-displaced pi-pi interactions which, together with the hydrogen-bonding capability of the hydroxyl functionality, presumably mediates the emergence of the self-assembled supramolecular nanoribbons.

Construction of multifunctional cuboctahedra via coordination-driven self-assembly

We present a general strategy for the synthesis of stable, multifunctional cuboctahedral complexes in which coordination-driven self-assembly allows for precise control over positioning of either ferrocene or crown ether functionalities. The appropriate stoichiometric combination of functionalized 120 degree diplatinum acceptor units with tritopic donor units afforded supramolecular cuboctahedra with covalently linked functional groups. The compounds are characterized by multinuclear NMR spectroscopy, electrospray ionization mass spectrometry, and electrochemistry.

Coordination-driven self-assembly of cavity-cored multiple crown ether derivatives and poly[2]pseudorotaxanes

The synthesis of a new 120 degree diplatinum(II) acceptor unit and the self-assembly of a series of two-dimensional metallacyclic polypseudorotaxanes that utilize both metal-ligand and crown ether-dialkylammonium noncovalent interactions are described. Judiciously combining complementary diplatinum(II) acceptors with bispyridyl donor building blocks, with an acceptor and/or donor possessing a pendant dibenzo[24]crown-8 (DB24C8) moiety, allows for the formation of three new rhomboidal bis-DB24C8, one new hexagonal tris-DB24C8, and four new hexakis-DB24C8 metallacyclic polygons in quantitative yields. The size and shape of each assembly, as well as the location and stoichiometry of the DB24C8 macrocycle, can be precisely controlled. Each polygon is able to complex two, three, or six dibenzylammonium ions without disrupting the underlying metallacyclic polygons, thus producing eight different poly[2]pseudorotaxanes and demonstrating the utility and scope of this orthogonal self-assembly technique. The assemblies are characterized with one-dimensional multinuclear ((1)H and (31)P) and two-dimensional ((1)H-(1)H COSY and NOESY) NMR spectroscopy as well as mass spectrometry (ESI-MS). Further analysis of the size and shape of each assembly is obtained through molecular force-field simulations. (1)H NMR titration experiments are used to establish thermodynamic binding constants and poly[2]pseudorotaxane/dibenzylammonium stoichiometries. Factors influencing the efficiency of poly[2]pseudorotaxane formation are discussed.

Preformed cell structure and cell heredity

This review will first recall the phenomena of "cortical inheritance" observed and genetically demonstrated in Paramecium 40 years ago, and later in other ciliates (Tetrahymena, Oxytricha, Paraurostyla), and will analyze the deduced concept of "cytotaxis" or "structural memory." The significance of these phenomena, all related (but not strictly restricted) to the properties of ciliary basal bodies and their mode of duplication, will be interpreted in the light of present knowledge on the mechanism and control of basal body/centriole duplication. Then other phenomena described in a variety of organisms will be analyzed or mentioned which show the relevance of the concept of cytotaxis to other cellular processes, mainly (1) cytoskeleton assembly and organization with examples on ciliates, trypanosome, mammalian cells and plants, and (2) transmission of polarities with examples on yeast, trypanosome and metazoa. Finally, I will discuss some aspects of this particular type of non-DNA inheritance: (1) why so few documented examples if structural memory is a basic parameter in cell heredity, and (2) how are these phenomena (which all rely on protein/protein interactions, and imply a formatting role of preexisting proteinic complexes on neo-formed proteins and their assembly) related to prions?

Molecular architectonic on metal surfaces

The engineering of highly organized systems from instructed molecular building blocks opens up new vistas for the control of matter and the exploration of nanodevice concepts. Recent investigations demonstrate that well-defined surfaces provide versatile platforms for steering and monitoring the assembly of molecular nanoarchitectures in exquisite detail. This review delineates the principles of noncovalent synthesis on metal substrates under ultrahigh vacuum conditions and briefly assesses the pertaining terminology-self-assembly, self-organization, and self-organized growth. It presents exemplary scanning-tunneling-microscopy observations, providing atomistic insight into the self-assembly of organic clusters, chains, and superlattices, and the metal-directed assembly of low-dimensional coordination architectures. This review also describes hierarchic-assembly protocols leading to intricate multilevel order. Molecular architectonic on metal surfaces represents a versatile rationale to realize structurally complex nanosystems with specific shape, composition, and functional properties, which bear promise for technological applications.

Self-assembly of double-stranded DNA molecules at nanomolar concentrations

Some proteins have the property of self-assembly, known to be an important mechanism in constructing supramolecular architectures for cellular functions. However, as yet, the ability of double-stranded (ds) DNA molecules to self-assemble has not been established. Here we report that dsDNA molecules also have a property of self-assembly in aqueous solutions containing physiological concentrations of Mg2+. We show that DNA molecules preferentially interact with molecules with an identical sequence and length even in a solution composed of heterogeneous DNA species. Curved DNA and DNA with an unusual conformation and property also exhibit this phenomenon, indicating that it is not specific to usual B-form DNA. Atomic force microscopy (AFM) directly reveals the assembled DNA molecules formed at concentrations of 10 nM but rarely at 1 nM. The self-assembly is concentration-dependent. We suggest that the attractive force causing DNA self-assembly may function in biological processes such as folding of repetitive DNA, recombination between homologous sequences, and synapsis in meiosis.