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Reexpansion of charged nanoparticle assemblies in concentrated electrolytes
Electrostatic forces in solutions are highly relevant to a variety of fields, ranging from electrochemical energy storage to biology. However, their manifestation in concentrated electrolytes is not fully understood, as exemplified by counterintuitive observations of colloidal stability and long-ranged repulsions in molten salts. Highly charged biomolecules, such as DNA, respond sensitively to ions in dilute solutions. Here, we use non-base-pairing DNA-coated nanoparticles (DNA-NP) to analyze electrostatic interactions in concentrated salt solutions. Despite their negative charge, these conjugates form colloidal crystals in solutions of sufficient divalent cation concentration. We utilize small-angle X-ray scattering (SAXS) to study such DNA-NP assemblies across the full accessible concentration ranges of aqueous CaCl 2 , MgCl 2 , and SrCl 2 solutions. SAXS shows that the crystallinity and phases of the assembled structures vary with cation type. For all tested salts, the aggregates contract with added ions at low salinities and then begin expanding above a cation-dependent threshold salt concentration. Wide-angle X-ray scattering (WAXS) reveals enhanced positional correlations between ions in the solution at high salt concentrations. Complementary molecular dynamics simulations show that these ion–ion interactions reduce the favorability of dense ion configurations within the DNA brushes below that of the bulk solution. Measurements in solutions with lowered permittivity demonstrate a simultaneous increase in ion coupling and decrease in the concentration at which aggregate expansion begins, thus confirming the connection between these phenomena. Our work demonstrates that interactions between charged objects continue to evolve considerably into the high-concentration regime, where classical theories project electrostatics to be of negligible consequence.
Data and code associated with the publication: A DNA-encoded recipe to direct multi-stage colloidal assembly
Raw data for Figure 2 is located in: /Experiments/Fig2_delayed_aggregation Raw data for Figures 3 and 4 can be found at: /Experiments/Fig3_4_Core_shell The analysis code is available at: /Experiments/Code Raw data for the Figure 5 simulation is locate in: /Simulation/Raw_data/Fig5_Structural_features_of_cluster
Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro
Abstract Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter “nicking” and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.
Light-Modulated Self-Assembly of Synthetic Nanotubes
Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, in this work, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.
Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. In this paper, we use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
DNA Crystals as a Template for Patterned Functional Materials
DNA nanotechnology offers a wide toolkit of molecular functionalities and scales, including intricate motifs less than 10 nm and periodic structures exceeding 100 µm. At larger scales, however, there are often significant tradeoffs for DNA structures, namely stability and mechanical strength. This work describes the design, synthesis, and characterization of a functionalized DNA crystal. Using a ligated DNA crystal grants significant freedom for various functional materials to be applied, in this case, semiconducting cadmium sulfide and palladium metal. Properties investigated in this study include stability, mechanical strength, and optoelectronic properties such as photoluminescence (PL) and electric conductivity. Significant changes are observed based on the functional material applied to DNA crystals. The Young's modulus of the crystal varies by about five orders of magnitude when functionalized with palladium. PL and semiconductive behaviors were observed when cadmium sulfide was attached. These crystals represent an expansion of the capabilities of DNA structures at these length scales, and additionally a platform for future studies exchanging the materials or altering the ligation scheme.
The Interaction of Positively-charged Ions with Nucleic Acid Systems
The successful development of extremely low background sample cells for x-ray scattering studies has enabled experiments designed to elucidate some of the fundamental physical interactions involved in macromolecular folding. Microfabrication techniques were used to fabricate low volume (50 micro-liter) sample cells with silicon nitride membranes (sub micron in thickness) as x-ray windows. Scientifically, these studies focus on the interaction of negatively charged nucleic acid systems, RNA and DNA, with their surrounding (positively charged) ion atmospheres. Understanding the structure of the ion atmosphere and its influence on the shape/conformation of the macromolecule will help reveal the underlying physical forces employed by nature in the self-assembly of these important molecules.
Advanced Colloids Experiment (ACE) Science Overview
The Advanced Colloids Experiment is being conducted on the International Space Station (ISS) using the Light Microscopy Module (LMM) in the Fluids Integrated Rack (FIR). Work to date will be discussed and future plans and opportunities will be highlighted. The LMM is a microscope facility designed to allow scientists to process, manipulate, and characterize colloidal samples in micro-gravity where the absence of gravitational settling and particle jamming enables scientists to study such things as:a.The role that disordered and ordered-packing of spheres play in the phase diagram and equation of state of hard sphere systems,b.crystal nucleation and growth, growth instabilities, and the glass transition, c.gelation and phase separation of colloid polymer mixtures,d.crystallization of colloidal binary alloys,e.competition between crystallization and phase separation,f.effects of anisotropy and specific interactions on packing, aggregation, frustration and crystallization,g.effects of specific reversible and irreversible interactions mediated in the first case by hybridization of complementary DNA strands attached to separate colloidal particles,h.Lock and key interactions between colloids with dimples and spheres which match the size and shape of the dimples,i.finding the phase diagrams of isotropic and interacting particles,j.new techniques for complex self-assembly including scenarios for self-replication, k.critical Casimir forces,l.biology (real and model systems) in microgravity,m.etc. By adding additional microscopy capabilities to the existing LMM, NASA will increase the tools available for scientists that fly experiments on the ISS enabling scientists to observe directly what is happening at the particle level. Presently, theories are needed to bridge the gap between what is being observed (at a macroscopic level when photographing samples) with what is happening at a particle (or microscopic) level. What is happening at a microscopic level will be directly accessible with the availability of the Light Microscopy Module (LMM) on ISS. To meet these goals, the ACE experiment is being built-up in stages, with the availability of confocal microscopy being the ultimate objective. Supported by NASAs Physical Sciences Research Program, ESAESTEC, and the authors respective governments.
Spectral Performance of Multilayer Amorphous Selenium and Selenium–Tellurium Photodetectors
The ability to robustly and with scalability detect single photons in the visible spectrum with wavelength resolution would transform many imaging applications. Theoretical studies propose an array of carbon nanotubes (CNTs) functionalized with semiconductor quantum dots (QDs) as a physical realization of such photon sensors. In this work, we report approaches to synthesize these CNT-QD nanostructures using DNA as a smart glue to connect CNTs to QDs.
High Temperature, Isothermal Growth Promotes Close Packing and Thermal Stability in DNA-Engineered Colloidal Crystals
Here, we report a strategy to accelerate the synthesis and increase the crystallinity of colloidal crystals engineered with DNA. Specifically, by holding the DNA-modified Au particle building blocks above the T m of the individual nanoparticle building blocks, but slightly below the T m of the anticipated colloidal crystal during the assembly process, crystallinity is increased, and enthalpically-favored phases with high degrees of facet registration are observed. We studied the utility of this approach with systems for which the commonly adopted slow-cooling approach yielded primarily amorphous aggregates. In particular, we used it to synthesize high-volume fraction colloidal crystals from large (80 nm) anisotropic nanoparticles (cubes and rhombic dodecahedra) with short (<14 nm) DNA designed to restrict the degrees of freedom for the DNA bonds and maintain the anisotropy of the particle building block. Small-angle X-ray scattering and electron microscopy studies show that the crystalline phases synthesized via this method are more thermally stable than their corresponding aggregate phases, likely due to an increased number of DNA-DNA bonds between particles. Crystal size tunability (between 0.5 and 15 µm edge lengths) and epitaxial growth were demonstrated using this strategy by modulating the NaCl concentration in tandem with previously synthesized colloidal crystal nuclei. Taken together, this isothermal strategy provides a route to deliberately crystallize a wide variety of anisotropic colloidal materials and expands the phase space accessible to nanoparticles modified with DNA.
STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii
Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ~20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.
Nicotinamide-Loaded Peptoid Nanotubes for Energy Regeneration in Acute Brain Injury
Acute brain injuries such as perinatal asphyxia, stroke, and traumatic brain injury result in ischemia, oxidative stress, excitotoxicity, and inflammation, leading to a depletion of ATP. Nicotinamide adenine dinucleotide (NAD+) is crucial for ATP regeneration and DNA repair during postinjury recovery. However, the therapeutic benefits of NAD+ and its precursors, such as nicotinamide (NAM), are limited by challenges in achieving effective cell-specific intracellular delivery. In this study, we use a nanopeptoid delivery strategy to replenish the cellular redox state and increase energy production in the acutely injured brain. By self-assembling peptoids into tubular structures, we created biocompatible NAM-conjugated peptoid nanotubes (NAM-PNTs) that vary in tubular length. NAM-PNTs demonstrated significant therapeutic benefits by enhancing cell viability and replenishing intracellular ATP levels within 24 h of treatment in oxygen–glucose-deprived (OGD) BV-2 cells. In organotypic brain slices, NAM-PNT treatment promoted glial proliferation, reduced proinflammatory cytokines, and increased anti-inflammatory cytokines after OGD, an ex vivo model of hypoxia-ischemia. The effect of NAM-PNTs is associated with their uptake into microglia via fluid-phase phagocytosis and caveolae-mediated endocytosis. A single systemic dose of NAM-PNTs localized in microglia in the injured hemisphere and reduced brain tissue loss and improved neuropathology after hypoxia-ischemia in term-equivalent rats. These findings highlight the therapeutic potential of NAM-PNTs for cell-specific targeted delivery and energy restoration in the acutely injured neonatal brain. In the neonatal brain injury field, this work demonstrates the development of an innovative nanoparticle platform from first-principles design and synthesis to in vitro screening and then demonstration of efficacy in vivo .
The Future of Bio-technology
Hosts of technologies, most notably in electronics, have been on the path of miniaturization for decades and in 2005 they have crossed the threshold of the nano-scale. Crossing the nano-scale threshold is a milestone in miniaturization, setting impressive new standards for component-packing densities. It also brings technology to a scale at which quantum effects and fault tolerance play significant roles and approaches the feasible physical limit form many conventional "top-down" manufacturing methods. I will suggest that the most formidable manufacturing problems in nanotechnology will be overcome and major breakthroughs will occur in a host of technologies, when nanotechnology converges with bio-technology; i.e. I will argue that the future of bio-technology is in nanotechnology. In 2005, methods in molecular biology, microscopy, bioinformatics, biochemistry, and genetic engineering have focused considerable attention on the nano-scale. On this scale, biology is a kind of recursive chemistry in which molecular recognition, self-assembly, self-organization and self-referencing context-control lead to the emergence of the complexity of structures and processes that are fundamental to all life forms. While we are still far from understanding this complexity, we are on the threshold of being able to use at least some of these biological properties for .technology. I will discuss the use of biomolecules, such as DNA, RNA, and proteins as "tools" for the bio-technologist of the future. More specifically, I will present in some detail an example of how we are using a genetically engineered 60-kDa protein (HSP60) from an organism living in near boiling sulfuric acid to build nano-scale templates for arranging metallic nanoparticles. These "extremophile" HSP60s self-assemble into robust double-ring structures called "chaperonins," which further assemble into filaments and arrays with nanometer accuracy. I will discuss our efforts to use chaperonins to organize quantum dots, electronic and magnetic nano-particles for electronic and photonic applications.
Structural and compositional complexities of hierarchical self-assembly: A hypergraph approach
Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. In this work, we introduce a hypergraph-based formalism, Blocks & Bonds (B&B), which generalizes classical chemical graph theory by incorporating directed and multicolored interactions, internal symmetries, and hierarchical organization. Within this framework, we develop the Structure Code (SC), a compact and versatile language for describing self-assembled architectures. We define a Kolmogorov-style structural complexity as the total information content of SC, obtained through its tokenization and Shannon information assignment. Complementing this encoding-based measure, we introduce a much simpler quantity, the compositional complexity, which depends only on the number and cumulative usage of block and bond types in the construction set. A central result of this work is a strong empirical correlation between the token-based structural complexity and the compositional complexity across all examined systems. Owing to this agreement, the compositional complexity emerges as the most practical and broadly applicable measure: it is easy to compute, requires no explicit encoding, and yet closely tracks the actual information content of structurally diverse architectures. Applications to molecular systems (ethylene glycol and glucose), DNA-origami lattices, and crystalline assemblies show that B&B hypergraphs provide a unified, scalable, and information-efficient representation of structural organization, naturally capturing symmetry, modularity, and stereochemistry. This framework establishes a quantitative foundation for complexity-aware classification and inverse design of programmable matter.
Organic Modulators Enable Morphological Diversity in Colloidal Crystals Engineered with DNA
Colloidal crystal engineering with DNA is a powerful way of generating a wide variety of crystals spanning over 90 different symmetries. However, in many cases, crystals with well-defined habits are difficult, if not impossible, to make, in part due to rapid crystal defect formation and propagation. This is especially true in the case of face-centered cubic (FCC) structures. Herein, we report a strategy that uses formamide as a chemical modulator to slow down colloidal crystal growth, which decreases defect formation and yields higher-quality crystals. Formamide forms hydrogen bonds with DNA bases and destabilizes the DNA duplex; in the context of colloidal crystallization, formamide leads to the disassembly of undercoordinated particles (defect architectures) and facilitates their reassembly into structures with the maximum number of nearest-neighbor contacts and DNA bonds. Here, when targeting an FCC lattice comprised of DNA-modified spherical 20 nm particles, formamide promotes the formation of its Wulff polyhedron (a truncated octahedron), never observed before in colloidal crystal engineering with DNA. Importantly, kinetic habits, including tetrahedra, octahedra, icosahedra, and decahedra, are also observed depending on formamide concentration.
Hopping and crawling DNA-coated colloids
Understanding the motion of particles with multivalent ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or roll, depending on the study. We shed light on this problem by observing DNA-coated colloids diffusing near surfaces coated with complementary strands for a wide array of coating designs. We find colloids rapidly switch between 2 modes: They hop—with long and fast steps—and crawl—with short and slow steps. Both modes occur at all temperatures around the melting point and over various designs. The particles become increasingly subdiffusive as temperature decreases, in line with subsequent velocity steps becoming increasingly anticorrelated, corresponding to switchbacks in the trajectories. Overall, crawling (or hopping) phases are more predominant at low (or high) temperatures; crawling is also more efficient at low temperatures than hopping to cover large distances. We rationalize this behavior within a simple model: At lower temperatures, the number of bound strands increases, and detachment of all bonds is unlikely, hence, hopping is prevented and crawling favored. We thus reveal the mechanism behind a common design rule relying on increased strand density for long-range self-assembly: Dense strands on surfaces are required to enable crawling, possibly facilitating particle rearrangements.
Arbitrary Design of DNA-Programmable 3D Crystals through Symmetry Mapping
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