Steven Weigand

DNA-programmable nanoparticle crystallization

It was first shown more than ten years ago that DNA oligonucleotides can be attached to gold nanoparticles rationally to direct the formation of larger assemblies. Since then, oligonucleotide-functionalized nanoparticles have been developed into powerful diagnostic tools for nucleic acids and proteins, and into intracellular probes and gene regulators. In contrast, the conceptually simple yet powerful idea that functionalized nanoparticles might serve as basic building blocks that can be rationally assembled through programmable base-pairing interactions into highly ordered macroscopic materials remains poorly developed. So far, the approach has mainly resulted in polymerization, with modest control over the placement of, the periodicity in, and the distance between particles within the assembled material. That is, most of the materials obtained thus far are best classified as amorphous polymers, although a few examples of colloidal crystal formation exist. Here, we demonstrate that DNA can be used to control the crystallization of nanoparticle–oligonucleotide conjugates to the extent that different DNA sequences guide the assembly of the same type of inorganic nanoparticle into different crystalline states. We show that the choice of DNA sequences attached to the nanoparticle building blocks, the DNA linking molecules and the absence or presence of a non-bonding single-base flexor can be adjusted so that gold nanoparticles assemble into micrometre-sized face-centred-cubic or body-centred-cubic crystal structures. Our findings thus clearly demonstrate that synthetically programmable colloidal crystallization is possible, and that a single-component system can be directed to form different structures.

Controlled Growth of Platinum Nanoparticles on Strontium Titanate Nanocubes by Atomic Layer Deposition

With an eye toward using surface morphology to enhance heterogeneous catalysis, Pt nanoparticles are grown by atomic layer deposition (ALD) on the surfaces of SrTiO(3) nanocubes. The size, dispersion, and chemical state of the Pt nanoparticles are controlled by the number of ALD growth cycles. The SrTiO(3) nanocubes average 60 nm on a side with {001} faces. The Pt loading increases linearly with Pt ALD cycles to a value of 1.1 x 10(-6) g cm(-2) after five cycles. Scanning electron microscopy images reveal discrete, well-dispersed Pt nanoparticles. Small- and wide-angle X-ray scattering show that the Pt nanoparticle spacing and size increase as the number of ALD cycles increases. X-ray absorption spectroscopy shows a progression from platinum(II) oxide to metallic platinum and a decrease in Pt--O bonding with an increase in Pt--Pt bonding as the number of ALD cycles increases.

Spontaneous and x-ray-triggered crystallization at long range in self-assembling filament networks.

X-rays to Order Self-assembly of molecules is often irreversible. Cui et al. (p. 555, published online 17 December; see the Perspective by Safinya and Li) examined the ordering of a short peptide sequence (Ala6Glu3) terminated with an alkyl chain. Aqueous solutions of this molecule could form hexagonally ordered filaments, but more dilute solutions were disordered. However, prolonged x-ray exposure caused these arrays to become ordered. These arrays were stable for several hours but eventually returned to a disordered state; the addition of salts slowed the ordering processes. It is possible that during the ordering process, X-ray–induced charging affected the repulsive forces that balance tension within the filament. Dilute solutions of alkyl-terminated peptide filaments can undergo ordering upon x-ray exposure. We report here crystallization at long range in networks of like-charge supramolecular peptide filaments mediated by repulsive forces. The crystallization is spontaneous beyond a given concentration of the molecules that form the filaments but can be triggered by x-rays at lower concentrations. The crystalline domains formed by x-ray irradiation, with interfilament separations of up to 320 angstroms, can be stable for hours after the beam is turned off, and ions that screen charges on the filaments suppress ordering. We hypothesize that the stability of crystalline domains emerges from a balance of repulsive tensions linked to native or x-ray–induced charges and the mechanical compressive entrapment of filaments within a network. Similar phenomena may occur naturally in the cytoskeleton of cells and, if induced externally in biological or artificial systems, lead to possible biomedical and lithographic functions.

In vitro synthesis and stabilization of amorphous calcium carbonate (ACC) nanoparticles within liposomes

We show that amorphous calcium carbonate (ACC) can be synthesized in phospholipid bilayer vesicles (liposomes). Liposome-encapsulated ACC nanoparticles are stable against aggregation, do not crystallize for at least 20 h, and are ideally suited to investigate the influence of lipid chemistry, particle size, and soluble additives on ACC in situ.

Combined SAXS/EM Based Models of the S. elongatus Post-Translational Circadian Oscillator and its Interactions with the Output His-Kinase SasA

The circadian clock in the cyanobacterium Synechococcus elongatus is composed of a post-translational oscillator (PTO) that can be reconstituted in vitro from three different proteins in the presence of ATP and a transcription-translation feedback loop (TTFL). The homo-hexameric KaiC kinase, phosphatase and ATPase alternates between hypo- and hyper-phosphorylated states over the 24-h cycle, with KaiA enhancing phosphorylation, and KaiB antagonizing KaiA and promoting KaiC subunit exchange. SasA is a His kinase that relays output signals from the PTO formed by the three Kai proteins to the TTFL. Although the crystal structures for all three Kai proteins are known, atomic resolution structures of Kai and Kai/SasA protein complexes have remained elusive. Here, we present models of the KaiAC and KaiBC complexes derived from solution small angle X-ray scattering (SAXS), which are consistent with previous EM based models. We also present a combined SAXS/EM model of the KaiC/SasA complex, which has two N-terminal SasA sensory domains occupying positions on the C-terminal KaiC ring reminiscent of the orientations adopted by KaiB dimers. Using EM we demonstrate that KaiB and SasA compete for similar binding sites on KaiC. We also propose an EM based model of the ternary KaiABC complex that is consistent with the sequestering of KaiA by KaiB on KaiC during the PTO dephosphorylation phase. This work provides the first 3D-catalogue of protein-protein interactions in the KaiABC PTO and the output pathway mediated by SasA.

Characterization of correlated line edge roughness of nanoscale line gratings using small angle x-ray scattering

To meet the challenges in dimensional metrology as the minimum feature size in semiconductor devices approaches sub-35 nm length scales, we have been developing a nondestructive method using x rays termed critical dimension small angle x-ray scattering (SAXS). Its capacity to quantify the dimension of linewidth, pitch, line height, and sidewall angle of line gratings has been demonstrated. In this work, we have further extended its capabilities to quantify the correlated line-edge roughness (LER) and linewidth roughness (LWR). Model line grating patterns with controlled LER and LWR were prepared and measured using x ray, their results were analyzed with model calculations. The magnitude of LER/LWR deduced from x-ray results compares favorably with the scanning electron microscopy results obtained from the same samples. An apparent Debye–Waller factor, which can be deduced from the SAXS data without any detailed model-based calculations, is found to be a convenient parameter to quantify the amplitude of LE...

Solution structures of DNA-bound gyrase

The DNA gyrase negative supercoiling mechanism involves the assembly of a large gyrase/DNA complex and conformational rearrangements coupled to ATP hydrolysis. To establish the complex arrangement that directs the reaction towards negative supercoiling, bacterial gyrase complexes bound to 137- or 217-bp DNA fragments representing the starting conformational state of the catalytic cycle were characterized by sedimentation velocity and small-angle X-ray scattering (SAXS) experiments. The experiments revealed elongated complexes with hydrodynamic radii of 70–80 Å. Molecular envelopes calculated from these SAXS data show 2-fold symmetric molecules with the C-terminal domain (CTD) of the A subunit and the ATPase domain of the B subunit at opposite ends of the complexes. The proposed gyrase model, with the DNA binding along the sides of the molecule and wrapping around the CTDs located near the exit gate of the protein, adds new information on the mechanism of DNA negative supercoiling.

Hyperuniformity in amorphous silicon based on the measurement of the infinite-wavelength limit of the structure factor

We report the results of highly sensitive transmission X-ray scattering measurements performed at the Advanced Photon Source, Argonne National Laboratory, on nearly fully dense high-purity amorphous-silicon (a-Si) samples for the purpose of determining their degree of hyperuniformity. A perfectly hyperuniform structure has complete suppression of infinite-wavelength density fluctuations, or, equivalently, the structure factor S(q→0) = 0; the smaller the value of S(0), the higher the degree of hyperuniformity. Annealing was observed to increase the degree of hyperuniformity in a-Si where we found S(0) = 0.0075 (±0.0005), which is significantly below the computationally determined lower bound recently suggested by de Graff and Thorpe [de Graff AMR, Thorpe MF (2010) Acta Crystallogr A 66(Pt 1):22–31] based on studies of continuous random network models, but consistent with the recently proposed nearly hyperuniform network picture of a-Si. Increasing hyperuniformity is correlated with narrowing of the first diffraction peak and extension of the range of oscillations in the pair distribution function.

Facile directed assembly of hollow polymer nanocapsules within spontaneously formed catanionic surfactant vesicles.

Surfactant vesicles containing monomers in the interior of the bilayer were used to template hollow polymer nanocapsules. This study investigated the formation of surfactant/monomer assemblies by two loading methods, concurrent loading and diffusion loading. The assembly process and the resulting aggregates were investigated with dynamic light scattering, small angle neutron scattering, and small-angle X-ray scattering. Acrylic monomers formed vesicles with a mixture of cationic and anionic surfactants in a broad range of surfactant ratios. Regions with predominant formation of vesicles were broader for compositions containing acrylic monomers compared with blank surfactants. This observation supports the stabilization of the vesicular structure by acrylic monomers. Diffusion loading produced monomer-loaded vesicles unless vesicles were composed from surfactants at the ratios close to the boundary of a vesicular phase region on a phase diagram. Both concurrent-loaded and diffusion-loaded surfactant/monomer vesicles produced hollow polymer nanocapsules upon the polymerization of monomers in the bilayer followed by removal of surfactant scaffolds.

Precipitation of ACC in liposomes—a model for biomineralization in confined volumes

Biomineralizing organisms frequently precipitate minerals in small phospholipid bilayer-delineated compartments. We have established an in vitro model system to investigate the effect of confinement in attoliter to femtoliter volumes on the precipitation of calcium carbonate. In particular, we analyze the growth and stabilization of liposome-encapsulated amorphous calcium carbonate (ACC) nanoparticles using a combination of in situ techniques, cryo-transmission electron microscopy (Cryo-TEM), and small angle X-ray scattering (SAXS). Herein, we discuss ACC nanoparticle growth rate as a function of liposome size, carbon dioxide flux across the liposome membrane, pH, and osmotic pressure. Based on these experiments, we argue that the stabilization of ACC nanoparticles in liposomes is a consequence of a low nucleation rate (high activation barrier) of crystalline polymorphs of calcium carbonate.