scholarly journals Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering

2016 ◽  
Vol 30 (08) ◽  
pp. 1650117 ◽  
Author(s):  
Gundolf Schenk ◽  
Brad Krajina ◽  
Andrew Spakowitz ◽  
Sebastian Doniach

In vivo chromosomal behavior is dictated by the organization of genomic DNA at length scales ranging from nanometers to microns. At these disparate scales, the DNA conformation is influenced by a range of proteins that package, twist and disentangle the DNA double helix, leading to a complex hierarchical structure that remains undetermined. Thus, there is a critical need for methods of structural characterization of DNA that can accommodate complex environmental conditions over biologically relevant length scales. Based on multiscale molecular simulations, we report on the possibility of measuring supercoiling in complex environments using angular correlations of scattered X-rays resulting from X-ray free electron laser (xFEL) experiments. We recently demonstrated the observation of structural detail for solutions of randomly oriented metallic nanoparticles [D. Mendez et al., Philos. Trans. R. Soc. B 360 (2014) 20130315]. Here, we argue, based on simulations, that correlated X-ray scattering (CXS) has the potential for measuring the distribution of DNA folds in complex environments, on the scale of a few persistence lengths.

2021 ◽  
Vol 28 (2) ◽  
pp. 518-529
Author(s):  
Andrew Wittmeier ◽  
Chiara Cassini ◽  
Mareike Töpperwien ◽  
Manuela Denz ◽  
Johannes Hagemann ◽  
...  

X-rays are emerging as a complementary probe to visible-light photons and electrons for imaging biological cells. By exploiting their small wavelength and high penetration depth, it is possible to image whole, intact cells and resolve subcellular structures at nanometer resolution. A variety of X-ray methods for cell imaging have been devised for probing different properties of biological matter, opening up various opportunities for fully exploiting different views of the same sample. Here, a combined approach is employed to study cell nuclei of NIH-3T3 fibroblasts. Scanning small-angle X-ray scattering is combined with X-ray holography to quantify length scales, aggregation state, and projected electron and mass densities of the nuclear material. Only by joining all this information is it possible to spatially localize nucleoli, heterochromatin and euchromatin, and physically characterize them. It is thus shown that for complex biological systems, like the cell nucleus, combined imaging approaches are highly valuable.


2012 ◽  
Vol 25 (4) ◽  
pp. 9-15 ◽  
Author(s):  
L. Braicovich ◽  
N. B. Brookes ◽  
G. Ghiringhelli ◽  
M. Minola ◽  
G. Monaco ◽  
...  
Keyword(s):  
X Rays ◽  
X Ray ◽  

2013 ◽  
Vol 46 (5) ◽  
pp. 1508-1512 ◽  
Author(s):  
Byron Freelon ◽  
Kamlesh Suthar ◽  
Jan Ilavsky

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.


2020 ◽  
Vol 61 (6) ◽  
Author(s):  
C E Schrank ◽  
K Gioseffi ◽  
T Blach ◽  
O Gaede ◽  
A Hawley ◽  
...  

Abstract We present a review of a unique non-destructive method for the real-time monitoring of phase transformations and nano-pore evolution in dehydrating rocks: transmission small- and wide-angle synchrotron X-ray scattering (SAXS/WAXS). It is shown how SAXS/WAXS can be applied to investigating rock samples dehydrated in a purpose-built loading cell that allows the coeval application of high temperature, axial confinement, and fluid pressure or flow to the specimen. Because synchrotron sources deliver extremely bright monochromatic X-rays across a wide energy spectrum, they enable the in situ examination of confined rock samples with thicknesses of ≤ 1 mm at a time resolution of order seconds. Hence, fast kinetics with reaction completion times of about hundreds of seconds can be tracked. With beam sizes of order tens to hundreds of micrometres, it is possible to monitor multiple interrogation points in a sample with a lateral extent of a few centimetres, thus resolving potential lateral spatial effects during dehydration and enlarging sample statistics significantly. Therefore, the SAXS/WAXS method offers the opportunity to acquire data on a striking range of length scales: for rock samples with thicknesses of ≤ 10-3 m and widths of 10-2 m, a lateral interrogation-point spacing of ≥ 10-5 m can be achieved. Within each irradiated interrogation-point volume, information concerning pores with sizes between 10-9 and 10-7 m and the crystal lattice on the scale of 10-10 m is acquired in real time. This article presents a summary of the physical principles underpinning transmission X-ray scattering with the aim of providing a guide for the design and interpretation of time-resolved SAXS/WAXS experiments. It is elucidated (1) when and how SAXS data can be used to analyse total porosity, internal surface area, and pore-size distributions in rocks on length scales from ∼1 to 300 nm; (2) how WAXS can be employed to track lattice transformations in situ; and (3) which limitations and complicating factors should be considered during experimental design, data analysis, and interpretation. To illustrate the key capabilities of the SAXS/WAXS method, we present a series of dehydration experiments on a well-studied natural gypsum rock: Volterra alabaster. Our results demonstrate that SAXS/WAXS is excellently suited for the in situ tracking of dehydration kinetics and the associated evolution of nano-pores. The phase transformation from gypsum to bassanite is correlated directly with nano-void growth on length scales between 1 and 11 nm for the first time. A comparison of the SAXS/WAXS kinetic results with literature data emphasises the need for future dehydration experiments on rock specimens because of the impact of rock fabric and the generally heterogeneous and transient nature of dehydration reactions in nature. It is anticipated that the SAXS/WAXS method combined with in situ loading cells will constitute an invaluable tool in the ongoing quest for understanding dehydration and other mineral replacement reactions in rocks quantitatively.


2009 ◽  
Vol 103 (23) ◽  
Author(s):  
Robert H. Coridan ◽  
Nathan W. Schmidt ◽  
Ghee Hwee Lai ◽  
Rahul Godawat ◽  
Michael Krisch ◽  
...  

1984 ◽  
Vol 17 (5) ◽  
pp. 337-343 ◽  
Author(s):  
O. Yoda

A high-resolution small-angle X-ray scattering camera has been built, which has the following features. (i) The point collimation optics employed allows the scattering cross section of the sample to be directly measured without corrections for desmearing. (ii) A small-angle resolution better than 0.5 mrad is achieved with a camera length of 1.6 m. (iii) A high photon flux of 0.9 photons μs−1 is obtained on the sample with the rotating-anode X-ray generator operated at 40 kV–30 mA. (iv) Incident X-rays are monochromated by a bent quartz crystal, which makes the determination of the incident X-ray intensity simple and unambiguous. (v) By rotation of the position-sensitive proportional counter around the direct beam, anisotropic scattering patterns can be observed without adjusting the sample. Details of the design and performance are presented with some applications.


2016 ◽  
Vol 23 (4) ◽  
pp. 880-886 ◽  
Author(s):  
Jungho Kim ◽  
Xianbo Shi ◽  
Diego Casa ◽  
Jun Qian ◽  
XianRong Huang ◽  
...  

Advances in resonant inelastic X-ray scattering (RIXS) have come in lockstep with improvements in energy resolution. Currently, the best energy resolution at the IrL3-edge stands at ∼25 meV, which is achieved using a diced Si(844) spherical crystal analyzer. However, spherical analyzers are limited by their intrinsic reflection width. A novel analyzer system using multiple flat crystals provides a promising way to overcome this limitation. For the present design, an energy resolution at or below 10 meV was selected. Recognizing that the angular acceptance of flat crystals is severely limited, a collimating element is essential to achieve the necessary solid-angle acceptance. For this purpose, a laterally graded, parabolic, multilayer Montel mirror was designed for use at the IrL3-absorption edge. It provides an acceptance larger than 10 mrad, collimating the reflected X-ray beam to smaller than 100 µrad, in both vertical and horizontal directions. The performance of this mirror was studied at beamline 27-ID at the Advanced Photon Source. X-rays from a diamond (111) monochromator illuminated a scattering source of diameter 5 µm, generating an incident beam on the mirror with a well determined divergence of 40 mrad. A flat Si(111) crystal after the mirror served as the divergence analyzer. From X-ray measurements, ray-tracing simulations and optical metrology results, it was established that the Montel mirror satisfied the specifications of angular acceptance and collimation quality necessary for a high-resolution RIXS multi-crystal analyzer system.


1997 ◽  
Vol 30 (1) ◽  
pp. 49-54 ◽  
Author(s):  
J.-M. Dubuisson ◽  
T. Decamps ◽  
P. Vachette

An evacuated, temperature-controlled cell has been built for use on the small-angle X-ray scattering instrument D24 at the synchrotron radiation facility LURE. The sample is placed in a quartz capillary sealed in a stainless-steel holder using a vacuum-tight glue. Several O rings provide a vacuum path upstream and downstream from the cell, so that the X-ray beam only meets the capillary walls and the solution under study between the slits and the beam stop, while the sample is maintained under atmospheric pressure. The cell temperature is controlled via a water circulation through a copper sheath in tight contact with the steel holder. The use of this cell results in a marked reduction of the background, as observed in two series of parallel experiments using a conventional cell and this evacuated cell. The decrease ranges from a factor of 2 at s 1 values larger than 0.008 Å−1 to more than 15 at s = 0.00116 Å−1, where s is the modulus of the scattering vector (s = 2sin θ/λ, 2θ is the scattering angle and λ is the wavelength of the X-rays).


2012 ◽  
Vol 208 (1) ◽  
pp. 231-244 ◽  
Author(s):  
P. Andreazza ◽  
H. Khelfane ◽  
O. Lyon ◽  
C. Andreazza-Vignolle ◽  
A. Y. Ramos ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document