The structural ensemble of a Holliday junction determined by X-ray scattering interference

Abstract The DNA four-way (Holliday) junction is the central intermediate of genetic recombination, yet key aspects of its conformational and thermodynamic properties remain unclear. While multiple experimental approaches have been used to characterize the canonical X-shape conformers under specific ionic conditions, the complete conformational ensemble of this motif, especially at low ionic conditions, remains largely undetermined. In line with previous studies, our single-molecule Förster resonance energy transfer (smFRET) measurements of junction dynamics revealed transitions between two states under high salt conditions, but smFRET could not determine whether there are fast and unresolvable transitions between distinct conformations or a broad ensemble of related states under low and intermediate salt conditions. We therefore used an emerging technique, X-ray scattering interferometry (XSI), to directly probe the conformational ensemble of the Holliday junction across a wide range of ionic conditions. Our results demonstrated that the four-way junction adopts an out-of-plane geometry under low ionic conditions and revealed a conformational state at intermediate ionic conditions previously undetected by other methods. Our results provide critical information to build toward a full description of the conformational landscape of the Holliday junction and underscore the utility of XSI for probing conformational ensembles under a wide range of solution conditions.

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Synthesis and Advanced Characterization of Polymer-Protein Core-Shell Nanoparticles

Catalysts ◽

10.3390/catal11060730 ◽

2021 ◽

Vol 11 (6) ◽

pp. 730

Author(s):

Erik Sarnello ◽

Tao Li

Keyword(s):

Particle Size ◽

Small Angle ◽

Core Shell ◽

Assembly Process ◽

Shell Nanoparticles ◽

X Ray ◽

X Ray Scattering ◽

Wide Range ◽

Core Shell Nanoparticles ◽

Ray Scattering

Enzyme immobilization techniques are widely researched due to their wide range of applications. Polymer–protein core–shell nanoparticles (CSNPs) have emerged as a promising technique for enzyme/protein immobilization via a self-assembly process. Based on the desired application, different sizes and distribution of the polymer–protein CSNPs may be required. This work systematically studies the assembly process of poly(4-vinyl pyridine) and bovine serum albumin CSNPs. Average particle size was controlled by varying the concentrations of each reagent. Particle size and size distributions were monitored by dynamic light scattering, ultra-small-angle X-ray scattering, small-angle X-ray scattering and transmission electron microscopy. Results showed a wide range of CSNPs could be assembled ranging from an average radius as small as 52.3 nm, to particles above 1 µm by adjusting reagent concentrations. In situ X-ray scattering techniques monitored particle assembly as a function of time showing the initial particle growth followed by a decrease in particle size as they reach equilibrium. The results outline a general strategy that can be applied to other CSNP systems to better control particle size and distribution for various applications.

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Towards a methodology for the characterisation of the fabric of wet clays using X-ray scattering

E3S Web of Conferences ◽

10.1051/e3sconf/20199201005 ◽

2019 ◽

Vol 92 ◽

pp. 01005

Author(s):

Georgios Birmpilis ◽

Reza Ahmadi-Naghadeh ◽

Jelke Dijkstra

Keyword(s):

Materials Science ◽

Measurement Techniques ◽

Invasive Technique ◽

Colloidal Systems ◽

Characteristic Distance ◽

X Ray ◽

Hydrophobic Coating ◽

X Ray Scattering ◽

Wide Range ◽

Ray Scattering

X-ray scattering is a promising non-invasive technique to study evolving nano- and micromechanics in clays. This study discusses the experimental considerations and a successful method to enable X-ray scattering to study clay samples at two extreme stages of consolidation. It is shown that the proposed sample environment comprising flat capillaries with a hydrophobic coating can be used for a wide range of voids ratios ranging from a clay suspension to consolidated clay samples, that are cut from larger specimens of reconstituted or natural clay. The initial X-ray scattering results using a laboratory instrument indicate that valuable information on, in principal evolving, clay fabric can be measured. Features such as characteristic distance between structural units and particle orientations are obtained for a slurry and a consolidated sample of kaolinite. Combined with other promising measurement techniques from Materials Science the proposed method will help advance the contemporary understanding on the behaviour of dense colloidal systems of clay, as it does not require detrimental sample preparation

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Fast in-situ X-ray scattering reveals stress sensitivity of gypsum dehydration kinetics

Communications Materials ◽

10.1038/s43246-021-00156-9 ◽

2021 ◽

Vol 2 (1) ◽

Author(s):

Christoph Eckart Schrank ◽

Oliver Gaede ◽

Tomasz Blach ◽

Katherine Carmen Michelle Gioseffi ◽

Stephen Mudie ◽

...

Keyword(s):

Stress Sensitivity ◽

Water Vapour Pressure ◽

Fast Time ◽

Dehydration Kinetics ◽

Efficient Design ◽

X Ray ◽

Triggered Earthquakes ◽

X Ray Scattering ◽

Wide Range ◽

Ray Scattering

AbstractThe dehydration of gypsum to hemihydrate has been studied for decades because it is an important model reaction for understanding fluid-triggered earthquakes, and due to the global use of plaster of Paris in the construction industry. The dehydration kinetics of gypsum strongly depend on temperature and water vapour pressure. Here, we perform fast, time-resolved synchrotron X-ray scattering on natural alabaster samples, finding that a small elastic load accelerates the dehydration reaction significantly. The mechanical acceleration of the reaction consumes about 10,000 times less energy than that due to heating. We propose that this thermodynamically surprising finding is caused by geometry-energy interactions in the microstructure, which facilitate nucleation and growth of the new crystalline phase. Our results open research avenues on the fundamental thermo-mechanics of crystal hydrates and the interaction of stress and chemical reactions in crystalline solids with a wide range of implications, from understanding dehydration-triggered earthquakes to the energy-efficient design of calcination processes.

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A multi-length-scale USAXS/SAXS facility: 10–50 keV small-angle X-ray scattering instrument

Journal of Applied Crystallography ◽

10.1107/s0021889813021900 ◽

2013 ◽

Vol 46 (5) ◽

pp. 1508-1512 ◽

Cited By ~ 11

Author(s):

Byron Freelon ◽

Kamlesh Suthar ◽

Jan Ilavsky

Keyword(s):

Small Angle ◽

Soft Matter ◽

High Energy ◽

X Rays ◽

X Ray ◽

X Ray Scattering ◽

Wide Range ◽

And Performance ◽

New Facility ◽

Ray Scattering

Coupling small-angle X-ray scattering (SAXS) and ultra-small-angle X-ray scattering (USAXS) provides a powerful system of techniques for determining the structural organization of nanostructured materials that exhibit a wide range of characteristic length scales. A new facility that combines high-energy (HE) SAXS and USAXS has been developed at the Advanced Photon Source (APS). The application of X-rays across a range of energies, from 10 to 50 keV, offers opportunities to probe structural behavior at the nano- and microscale. An X-ray setup that can characterize both soft matter or hard matter and high-Zsamples in the solid or solution forms is described. Recent upgrades to the Sector 15ID beamline allow an extension of the X-ray energy range and improved beam intensity. The function and performance of the dedicated USAXS/HE-SAXS ChemMatCARS-APS facility is described.

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Universal nature of collapsibility in the context of protein folding and evolution

10.1101/461046 ◽

2018 ◽

Cited By ~ 1

Author(s):

D. Thirumalai ◽

Himadri S. Samanta ◽

Hiranmay Maity ◽

Govardhan Reddy

Keyword(s):

Single Molecule ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Saxs Data ◽

X Ray ◽

Model Free ◽

X Ray Scattering ◽

Theoretical Predictions ◽

Helical Proteins ◽

Universal Nature

AbstractTheory and simulations predicted sometime ago that the sizes of unfolded states of globular proteins should decrease continuously as the denaturant concentration is shifted from a high to a low value. However, small angle X-ray scattering (SAXS) data were used to assert the opposite, while interpretation of single molecule Forster resonance energy transfer experiments (FRET) supported the theoretical predictions. The disagreement between the two experiments is the SAXS-FRET controversy. By harnessing recent advances in SAXS and FRET experiments and setting these findings in the context of a general theory and simulations, we establish that compaction of unfolded states is universal. The theory also predicts that proteins rich in β-sheets are more collapsible than α-helical proteins. Because the extent of compaction is small, experiments have to be accurate and their interpretations should be as model free as possible. Theory also suggests that collapsibility itself could be a physical restriction on the evolution of foldable sequences, and provides a physical basis for the origin of multi-domain proteins.

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Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

Science ◽

10.1126/science.aar7101 ◽

2018 ◽

Vol 361 (6405) ◽

pp. eaar7101 ◽

Cited By ~ 23

Author(s):

Robert B. Best ◽

Wenwei Zheng ◽

Alessandro Borgia ◽

Karin Buholzer ◽

Madeleine B. Borgia ◽

...

Keyword(s):

Energy Transfer ◽

Small Angle ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Disordered Proteins ◽

Förster Resonance Energy Transfer ◽

Unfolded Proteins ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

Riback et al. (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Förster resonance energy transfer (FRET) experiments. There is thus no “contradiction” between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.

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Development of combined microstructure and structure characterization facility forin situandoperandostudies at the Advanced Photon Source

Journal of Applied Crystallography ◽

10.1107/s160057671800643x ◽

2018 ◽

Vol 51 (3) ◽

pp. 867-882 ◽

Cited By ~ 48

Author(s):

Jan Ilavsky ◽

Fan Zhang ◽

Ross N. Andrews ◽

Ivan Kuzmenko ◽

Pete R. Jemian ◽

...

Keyword(s):

Small Angle ◽

National Laboratory ◽

Argonne National Laboratory ◽

Incident Beam ◽

Evolutionary Development ◽

X Ray ◽

X Ray Scattering ◽

Wide Range ◽

Photon Source ◽

Ray Scattering

Following many years of evolutionary development, first at the National Synchrotron Light Source, Brookhaven National Laboratory, and then at the Advanced Photon Source (APS), Argonne National Laboratory, the APS ultra-small-angle X-ray scattering (USAXS) facility has been transformed by several new developments. These comprise a conversion to higher-order crystal optics and higher X-ray energies as the standard operating mode, rapid fly scan measurements also as a standard operational mode, automated contiguous pinhole small-angle X-ray scattering (SAXS) measurements at intermediate scattering vectors, and associated rapid wide-angle X-ray scattering (WAXS) measurements for X-ray diffraction without disturbing the sample geometry. With each mode using the USAXS incident beam optics upstream of the sample, USAXS/SAXS/WAXS measurements can now be made within 5 min, allowingin situandoperandomeasurement capabilities with great flexibility under a wide range of sample conditions. These developments are described, together with examples of their application to investigate materials phenomena of technological importance. Developments of two novel USAXS applications, USAXS-based X-ray photon correlation spectroscopy and USAXS imaging, are also briefly reviewed.

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High-Energy Small- and Wide-Angle X-Ray Scattering: A Versatile Tool for Materials Analysis

X-Rays in Mechanical Engineering Applications ◽

10.1115/imece2004-62458 ◽

2004 ◽

Author(s):

Jonathan Almer

Keyword(s):

High Energy ◽

Real Space ◽

Wide Angle ◽

X Ray ◽

Study Materials ◽

X Ray Scattering ◽

Angle Scattering ◽

Wide Range ◽

Versatile Tool ◽

Ray Scattering

Acquisition of microstructural information during realistic service conditions is an ongoing need for fundamental materials insight and computational input. In addition, for engineering applications it is often important to be able to study materials over a wide range of penetration depths, from the surface to bulk. In this presentation we discuss developments at the Sector 1-ID beamline of the Advanced Photon Source (APS) to utilize high-energy x-ray scattering for such studies. The use of high-energies (~80 keV) provides a highly penetrating probe, with sampling depths up to several mm in most materials. Through the development and use of high-energy optics, we can perform both small- and wide-angle scattering (SAXS/WAXS), to probe a large range of sample dimensions in reciprocal space (ranging from Angstroms to hundreds of nanometers), with real space resolutions ranging from microns to mm.

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