The new small-angle X-ray scattering beamline for materials research at PETRA†III: SAXSMAT beamline P62.

The SAXSMAT beamline P62 (Small-Angle X-ray Scattering beamline for Materials Research) is a new beamline at the high-energy storage ring PETRA III at DESY. This beamline is dedicated to combined small- and wide-angle X-ray scattering (SAXS/WAXS) techniques for both soft and hard condensed matter systems. It works mainly in transmission geometry. The beamline covers an energy range from 3.5 keV to 35.0 keV, which fulfills the requirements of the user community to perform anomalous scattering experiments. Mirrors are used to reduce the intensity of higher harmonics. Furthermore, the mirrors and 2D compound refracting lenses can focus the beam down to a few micrometres at the sample position. This option with the high photon flux enables also SAXS/WAXS tensor tomography experiments to be performed at this new beamline in a relatively short time. The first SAXS/WAXS pattern was collected in August 2021, while the first user experiment was carried out two months later. Since January 2022 the beamline has been in regular user operation mode. In this paper the beamline optics and the SAXS/WAXS instrument are described and two examples are briefly shown.

Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications.

Small-angle X-ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element-specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X-rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.

Accurate Determination of the Quantity and Spatial Distribution of Counterions around a Spherical Macroion.

The accurate distribution of countercations (Rb+ and Sr2+ ) around a rigid, spherical, 2.9-nm size polyoxometalate cluster, {Mo132 }42- , is determined by anomalous small-angle X-ray scattering. Both Rb+ and Sr2+ ions lead to shorter diffuse lengths for {Mo132 } than prediction. Most Rb+ ions are closely associated with {Mo132 } by staying near the skeleton of {Mo132 } or in the Stern layer, whereas more Sr2+ ions loosely associate with {Mo132 } in the diffuse layer. The stronger affinity of Rb+ ions towards {Mo132 } than that of Sr2+ ions explains the anomalous lower critical coagulation concentration of {Mo132 } with Rb+ compared to Sr2+ . The anomalous behavior of {Mo132 } can be attributed to majority of negative charges being located at the inner surface of its cavity. The longer anion-cation distance weakens the Coulomb interaction, making the enthalpy change owing to the breakage of hydration layers of cations more important in regulating the counterion-{Mo132 } interaction.

Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form.

It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and complemented by (31) P NMR. With due consideration for the kinetics of the B-Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5'-d[T-(m(5) C-G)12 -T] 26-mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson-Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369-384, 2016.

Characterization of an in-vacuum PILATUS 1M detector.

A dedicated in-vacuum X-ray detector based on the hybrid pixel PILATUS 1M detector has been installed at the four-crystal monochromator beamline of the PTB at the electron storage ring BESSY II in Berlin, Germany. Owing to its windowless operation, the detector can be used in the entire photon energy range of the beamline from 10 keV down to 1.75 keV for small-angle X-ray scattering (SAXS) experiments and anomalous SAXS at absorption edges of light elements. The radiometric and geometric properties of the detector such as quantum efficiency, pixel pitch and module alignment have been determined with low uncertainties. The first grazing-incidence SAXS results demonstrate the superior resolution in momentum transfer achievable at low photon energies.

Anomalous small-angle X-ray scattering analyses on hierarchical structures of rubber-filler systems.

The hierarchical structures of poly(styrene-ran-butadiene) (SBR) rubber/carbon black (CB) systems vulcanized with sulfur and ZnO have been clarified using anomalous small-angle X-ray scattering (ASAXS) near the Zn absorption edge. In the case of SBR/CB systems vulcanized with peroxide, it has been found previously that the hierarchical structures formed by CB consist of aggregates of primary particles and agglomerates of those aggregates with mass-fractal dimensions. However, to date the hierarchical structures in SBR/CB systems vulcanized with sulfur and ZnO have not been well investigated, despite being commonly used. This is because the strong scattering contrast of Zn prevents the quantitative analyses of the hierarchical structures of CB using X-ray scattering. In this study, the effects of Zn on the scattering intensity were eliminated and the structure factors of CB in SBR/CB systems were obtained using the ASAXS method. By extrapolating to the zero volume fraction of CB, the particle structure factor of the CB aggregates was estimated and it was found that the CB aggregates consist of closely packed CB primary particles. The presence of large particles of ZnO and particles of ZnS on the order of 10 nm in size is confirmed.

Hybrid polymeric micelles stabilized by gallium ions: Structural investigation.

The addition of gallium ions to a solution of a double-hydrophilic block copolymer, i.e. poly(ethylene oxide)-block-poly(acrylic acid), leads to the spontaneous formation of highly monodisperse micelles with a Hybrid PolyIon Complexes (HPICs) core. By combining several techniques, a precise description of the HPIC architecture was achieved. In particular and for the first time, NMR and anomalous small angle X-ray scattering (ASAXS) enable tracking of the inorganic ions in solution and highlighting the co-localization of the gallium and the poly(acrylic acid) blocks in a rigid structure at the core of the micelle. Such a core has a radius of ca 4.3 nm while the complete nano-object with its poly(ethylene oxide) shell has a total radius of ca 11 nm. The aggregation number was also estimated using the ASAXS results. This comprehensive structural characterization of the Ga HPICs corroborates the assumptions made for HPICs based on other inorganic ions and demonstrates the universality of the HPIC structure leading, for example, to new families of contrast agents in medical imaging.

ASAXS measurements on ferritin and apoferritin at the bioSAXS beamline P12 (PETRA III, DESY).

Small-angle X-ray scattering is widely utilized to study biological macromol-ecules in solution. For samples containing specific (e.g. metal) atoms, additional information can be obtained using anomalous scattering. Here, measuring samples at different energies close to the absorption edges of relevant elements provides specific structural details. However, anomalous small-angle X-ray scattering (ASAXS) applications to dilute macromolecular solutions are challenging owing to the overall low anomalous scattering effect. Here, pilot ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin are reported. These samples were investigated near the resonance X-ray K edges of Fe and Co, respectively, at the EMBL P12 bioSAXS beamline at PETRA III, DESY. Thanks to the high brilliance of the P12 beamline, ASAXS experiments are feasible on dilute protein solutions, allowing one to extract the Fe- or Co-specific anomalous dispersion terms from the ASAXS data. The data were subsequently used to determine the spatial distribution of either iron or cobalt atoms incorporated into the ferritin/apoferritin protein cages.

Experimental approaches for investigating ion atmospheres around nucleic acids and proteins.

Ionic interactions are crucial to biological functions of DNA, RNA, and proteins. Experimental research on how ions behave around biological macromolecules has lagged behind corresponding theoretical and computational research. In the 21st century, quantitative experimental approaches for investigating ionic interactions of biomolecules have become available and greatly facilitated examinations of theoretical electrostatic models. These approaches utilize anomalous small-angle X-ray scattering, atomic emission spectroscopy, mass spectrometry, or nuclear magnetic resonance (NMR) spectroscopy. We provide an overview on the experimental methodologies that can quantify and characterize ions within the ion atmospheres around nucleic acids, proteins, and their complexes.

Systematic Limitations in Concentration Analysis via Anomalous Small-Angle X-ray Scattering in the Small Structure Limit.

Anomalous small angle scattering measurements have been applied to diluted solutions of anionic polyacrylates decorated by specifically-interacting Pb2+ cations, revealing partial collapse of the polyacrylate into pearl-like subdomains with a size on the order of a few nanometers. From the pure-resonant scattering contribution of the Pb2+ cations, and from subsequent analysis of the resonant-invariant, the amount of Pb2+ cations condensed onto the polyanions with respect to the total amount of Pb2+ cations in the solvent was estimated. In order to scrutinize systematic limitations in the determination of the chemical concentrations of resonant scattering counterions in the collapsed phase, Monte Carlo simulations have been performed. The simulations are based on structural confinements at variable size in the range of few nanometers, which represent the collapsed subdomains in the polyanions. These confinements were gradually filled to a high degree of the volume fraction with resonant scattering counterions giving access to a resonant-invariant at a variable degree of filling. The simulations revealed in the limit of small structures a significant underestimation of the true degree of filling of the collapsed subdomains when determining chemical concentrations of Pb2+ cations from the resonant invariant.

Small Angle X-ray and Neutron Scattering: Powerful Tools for Studying the Structure of Drug-Loaded Liposomes.

Nanovectors, such as liposomes, micelles and lipid nanoparticles, are recognized as efficient platforms for delivering therapeutic agents, especially those with low solubility in water. Besides being safe and non-toxic, drug carriers with improved performance should meet the requirements of (i) appropriate size and shape and (ii) cargo upload/release with unmodified properties. Structural issues are of primary importance to control the mechanism of action of loaded vectors. Overall properties, such as mean diameter and surface charge, can be obtained using bench instruments (Dynamic Light Scattering and Zeta potential). However, techniques with higher space and time resolution are needed for in-depth structural characterization. Small-angle X-ray (SAXS) and neutron (SANS) scattering techniques provide information at the nanoscale and have therefore been largely used to investigate nanovectors loaded with drugs or other biologically relevant molecules. Here we revise recent applications of these complementary scattering techniques in the field of drug delivery in pharmaceutics and medicine with a focus to liposomal carriers. In particular, we highlight those aspects that can be more commonly accessed by the interested users.

Anomalous small-angle X-ray scattering: analyzing correlations and fluctuations in polyelectrolytes.

We review recent structural investigations done by anomalous small-angle X-ray scattering (ASAXS). ASAXS uses the dependence of the scattering length of a given element if the energy of the incident X-ray beam is near the absorption edge of this element. The analysis of the ASAXS data leads to three partial intensities. We show that the comparison of these three partial intensities leads to valuable information in fluctuating systems. This has been demonstrated from data derived from recent molecular dynamics simulations of charged colloidal spheres. Moreover, it is shown that the three partial intensities can be obtained from experimental ASAXS data indeed. As an example for this analysis, we discuss recent ASAXS data referring to rod-like polyelectrolytes. These polyelectrolytes consist of a stiff poly(p-phenylene) backbone with attached charged groups that are balanced by bromine counterions. The three partial intensities can be determined experimentally and compared to the prediction of the Poisson-Boltzmann cell model. Quantitative agreement is found demonstrating the strong correlation of the counterions to the rod-like macroion. ASAXS is thus shown to furnish information not available by the conventional small-angle scattering experiment.