A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules

Antisolvent controls the shape and size of anisotropic lead halide perovskite nanocrystals

Colloidal lead halide perovskite nanocrystals have potential for lighting applications due to their optical properties. Precise control of the nanocrystal dimensions and composition is a prerequisite for establishing practical applications. However, the rapid nature of their synthesis precludes a detailed understanding of the synthetic pathways, thereby limiting the optimisation. Here, we deduce the formation mechanisms of anisotropic lead halide perovskite nanocrystals, 1D nanorods and 2D nanoplatelets, by combining in situ X-ray scattering and photoluminescence spectroscopy. In both cases, emissive prolate nanoclusters form when the two precursor solutions are mixed. The ensuing antisolvent addition induces the divergent anisotropy: The intermediate nanoclusters are driven into a dense hexagonal mesophase, fusing to form nanorods. Contrastingly, nanoplatelets grow freely dispersed from dissolving nanoclusters, stacking subsequently in lamellar superstructures. Shape and size control of the nanocrystals are determined primarily by the antisolvent's dipole moment and Hansen hydrogen bonding parameter. Exploiting the interplay of antisolvent and organic ligands could enable more complex nanocrystal geometries in the future.

In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification

Silicification of DNA origami structures increases their stability and provides chemical protection. Yet, it is unclear whether the whole DNA framework is embedded or if silica just forms an outer shell and how silicification affects the origami's internal structure. Employing in situ small-angle X-ray scattering (SAXS), we show that addition of silica precursors induces substantial condensation of the DNA origami at early reaction times by almost 10 %. Subsequently, the overall size of the silicified DNA origami increases again due to increasing silica deposition. We further identify the SAXS Porod invariant as a reliable, model-free parameter for the evaluation of the amount of silica formation at a given time. Contrast matching of the DNA double helix Lorentzian peak reveals silica growth also inside the origami. The less polar silica forming within the origami structure, replacing more than 40 % of the internal hydration water, causes a hydrophobic effect: condensation. DNA origami objects with flat surfaces show a strong tendency towards aggregation during silicification, presumably driven by the same entropic forces causing condensation. Maximally condensed origami displayed thermal stability up to 60 °C. Our studies provide insights into the silicification reaction allowing for the formulation of optimized reaction protocols.

3D-printed SAXS chamber for controlled in situ dialysis and optical characterization

3D printing changes the scope of how samples can be mounted for small-angle X-ray scattering (SAXS). In this paper a 3D-printed X-ray chamber, which allows for in situ exchange of buffer and in situ optical transmission spectroscopy, is presented. The chamber is made of cyclic olefin copolymers (COC), including COC X-ray windows providing ultra-low SAXS background. The design integrates a membrane insert for in situ dialysis of the 100 µl sample volume against a reservoir, which enables measurements of the same sample under multiple conditions using an in-house X-ray setup equipped with a 17.4 keV molybdenum source. The design's capabilities are demonstrated by measuring reversible structural changes in lipid and polymer systems as a function of salt concentration and pH. In the same chambers optical light transmission spectroscopy was carried out measuring the optical turbidity of the mesophases and local pH values using pH-responsive dyes. Microfluidic exchange and optical spectroscopy combined with in situ X-ray scattering enables vast applications for the study of responsive materials.

SAXS measurements of azobenzene lipid vesicles reveal buffer-dependent photoswitching and quantitative Z→E isomerisation by X-rays

Photoresponsive materials feature properties that can be adjusted by light near-instantaneously, reversibly, and with high spatiotemporal precision. There is considerable interest in maximising the degree of photoswitching, and in measuring this degree during illumination in complex environments. We study the switching of photoresponsive lipid membranes that allow for precise and reversible manipulation of membrane shape, permeability, and fluidity. Though these macroscopic responses are clear, it is unclear how large the changes of trans/cis ratio are, and whether they can be improved. Here, we used small-angle X-ray scattering to measure the thickness of photoswitchable lipid membranes, and we correlate lipid bilayer thickness to trans/cis ratios. This reveals an unexpected dependency of photoswitching ratio upon aqueous phase composition. In buffer with ionic strength, we observe thickness variations twice as large as previously observed. Furthermore, soft X-rays can quantitatively isomerise photolipid membranes to the all-trans state; enabling X-ray-based membrane control. High energy X-rays do not influence the state of the photoswitches, presumably because they deposit less dose in the sample.

X-ray studies bridge the molecular and macro length scales during the emergence of CoO assemblies

The key to fabricating complex, hierarchical materials is the control of chemical reactions at various length scales. To this end, the classical model of nucleation and growth fails to provide sufficient information. Here, we illustrate how modern X-ray spectroscopic and scattering in situ studies bridge the molecular- and macro- length scales for assemblies of polyhedrally shaped CoO nanocrystals. Utilizing high energy-resolution fluorescence-detected X-ray absorption spectroscopy, we directly access the molecular level of the nanomaterial synthesis. We reveal that initially Co(acac)3 rapidly reduces to square-planar Co(acac)2 and coordinates to two solvent molecules. Combining atomic pair distribution functions and small-angle X-ray scattering we observe that, unlike a classical nucleation and growth mechanism, nuclei as small as 2 nm assemble into superstructures of 20 nm. The individual nanoparticles and assemblies continue growing at a similar pace. The final spherical assemblies are smaller than 100 nm, while the nanoparticles reach a size of 6 nm and adopt various polyhedral, edgy shapes. Our work thus provides a comprehensive perspective on the emergence of nano-assemblies in solution.

X-ray-Based Techniques to Study the Nano-Bio Interface

X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.

Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument

Coupling of size-exclusion chromatography with biological solution small-angle X-ray scattering (SEC-SAXS) on dedicated synchrotron beamlines enables structural analysis of challenging samples such as labile proteins and low-affinity complexes. For this reason, the approach has gained increased popularity during the past decade. Transportation of perishable samples to synchrotrons might, however, compromise the experiments, and the limited availability of synchrotron beamtime renders iterative sample optimization tedious and lengthy. Here, the successful setup of laboratory-based SEC-SAXS is described in a proof-of-concept study. It is demonstrated that sufficient quality data can be obtained on a laboratory instrument with small sample consumption, comparable to typical synchrotron SEC-SAXS demands. UV/vis measurements directly on the SAXS exposure cell ensure accurate concentration determination, crucial for direct molecular weight determination from the scattering data. The absence of radiation damage implies that the sample can be fractionated and subjected to complementary analysis available at the home institution after SEC-SAXS. Laboratory-based SEC-SAXS opens the field for analysis of biological samples at the home institution, thus increasing productivity of biostructural research. It may further ensure that synchrotron beamtime is used primarily for the most suitable and optimized samples.

3D DNA Origami Crystals

3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1.83 × 10⁵ nm³ , which would also suffice to accommodate ribosome-sized macromolecules. The accurate assembly of the DNA origami lattice itself, as well as the precise incorporation of gold particles, is validated by electron microscopy and small-angle X-ray scattering experiments. The results show that it is possible to create DNA building blocks that assemble into lattices with customized geometry. Site-specific hosting of nano objects in the optically transparent DNA lattice sets the stage for metamaterial and structural biology applications.

The triolein/aqueous interface and lipase activity studied by spectroscopic ellipsometry and coarse grained simulations

In spite of the importance of the triglyceride aqueous interface for processes like emulsification, surfactant interactions and lipase activity, relatively little is known about this interface compared to that between alkanes and water. Here, the contact between triolein and water was investigated in terms of water inclusion in the oil phase and orientation of the molecules at the interface. Coarse grained models of triglycerides in contact with water were constructed and correlated with experimental results of the changes in thickness and refractive index, obtained using spectroscopic ellipsometry of spin-coated triolein films. The topography of the layer was revealed by atomic force microscopy. Dry triolein and a triolein sample after equilibration with water were also compared structurally using small-angle X-ray scattering. Additionally, the kinetics of adsorption/activity of three different variants of the Thermomyces lanuginosus lipase (TLL) were investigated. The results show that uptake of water in the triolein phase leads to increase in thickness of the layer. The observed increase of thickness was further enhanced by an active lipase but reduced when an inactive mutant of the enzyme was applied.

Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements

A model is presented for the errors in small-angle X-ray scattering profiles that takes into account the physics of the measurement process. The model agrees quantitatively with the variations observed in experimental measurements and provides a straightforward prescription to add realistic errors to simulated scattering profiles.

A new model is proposed for the measurement errors incurred in typical small-angle X-ray scattering (SAXS) experiments, which takes into account the setup geometry and physics of the measurement process. The model accurately captures the experimentally determined errors from a large range of synchrotron and in-house anode-based measurements. Its most general formulation gives for the variance of the buffer-subtracted SAXS intensity σ²(q) = [I(q) + const.]/(kq), where I(q) is the scattering intensity as a function of the momentum transfer q; k and const. are fitting parameters that are characteristic of the experimental setup. The model gives a concrete procedure for calculating realistic measurement errors for simulated SAXS profiles. In addition, the results provide guidelines for optimizing SAXS measurements, which are in line with established procedures for SAXS experiments, and enable a quantitative evaluation of measurement errors.

Shape and Interhelical Spacing of DNA Origami Nanostructures Studied by Small-Angle X-ray Scattering

Scaffolded DNA origami nanostructures enable the self-assembly of arbitrarily shaped objects with unprecedented accuracy. Yet, varying physiological conditions are prone to induce slight structural changes in the nanoscale architecture. Here, we report on high precision measurements of overall shape and interhelical distance of three prototypic DNA origami structures in solution using synchrotron small-angle X-ray scattering. Sheet-, brick-, and cylinder-shaped DNA constructs were assembled and the shape factors determined with angstrom resolution from fits to the scattering profiles. With decreasing MgCl2 concentration electrostatic swelling of both shape cross section and interhelical DNA spacing of the DNA origami structures is observed. The structures tolerate up to 10% interhelical expansion before they disintegrate. In contrast, with increasing temperature, the cylinder-shaped structures show no thermal expansion in a wide temperature window before they abruptly melt above 50 °C. Details on molecular structure of DNA origami can also be obtained using in-house X-ray scattering equipment and, hence, allow for routine folding and stability testing of DNA-based agents that are designed to operate under varying salt conditions.