Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigating DNA Radiation Damage Using X-Ray Absorption Spectroscopy.

ABSTRACT: The biological influence of radiation on living matter has been studied for years; however, several questions about the detailed mechanism of radiation damage formation remain largely unanswered. Among all biomolecules exposed to radiation, DNA plays an important role because any damage to its molecular structure can affect the whole cell and may lead to chromosomal rearrangements resulting in genomic instability or cell death. To identify and characterize damage induced in the DNA sugar-phosphate backbone, in this work we performed x-ray absorption spectroscopy at the P K-edge on DNA irradiated with either UVA light or protons. By combining the experimental results with theoretical calculations, we were able to establish the types and relative ratio of lesions produced by both UVA and protons around the phosphorus atoms in DNA.

SUBMITTER: Czapla-Masztafiak J

PROVIDER: S-EPMC4816689 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Investigating DNA Radiation Damage Using X-Ray Absorption Spectroscopy.

Czapla-Masztafiak Joanna J Szlachetko Jakub J Milne Christopher J CJ Lipiec Ewelina E Sá Jacinto J Penfold Thomas J TJ Huthwelker Thomas T Borca Camelia C Abela Rafael R Kwiatek Wojciech M WM

Biophysical journal 20160301 6

The biological influence of radiation on living matter has been studied for years; however, several questions about the detailed mechanism of radiation damage formation remain largely unanswered. Among all biomolecules exposed to radiation, DNA plays an important role because any damage to its molecular structure can affect the whole cell and may lead to chromosomal rearrangements resulting in genomic instability or cell death. To identify and characterize damage induced in the DNA sugar-phospha ...[more]

PMID: 27028640

Similar Datasets

X-ray absorption spectroscopy.

Project description:This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn(4)Ca cluster in Photosystem II is presented.

| S-EPMC2777224 | biostudies-other

High-throughput computational X-ray absorption spectroscopy.

Project description:X-ray absorption spectroscopy (XAS) is a widely-used materials characterization technique. In this work we present a database of computed XAS spectra, using the Green's formulation of the multiple scattering theory implemented in the FEFF code. With more than 500,000 K-edge X-ray absorption near edge (XANES) spectra for more than 40,000 unique materials, this database constitutes the largest existing collection of computed XAS spectra to date. The data is openly distributed via the Materials Project, enabling researchers across the world to access it for free and use it for comparisons with experiments and further analysis.

| S-EPMC6067047 | biostudies-literature

X-ray absorption spectroscopy of dinuclear metallohydrolases.

Project description:In this mini-review, we briefly discuss the physical origin of x-ray absorption spectroscopy (XAS) before illustrating its application using dinuclear metallohydrolases as exemplary systems. The systems we have selected for illustrative purposes present a challenging problem for XAS, one that is ideal to demonstrate the potential of this methodology for structure/function studies of metalloenzymes in general. When the metal ion is redox active, XAS provides a sensitive measure of oxidation-state-dependent differences. When the metal ion is zinc, XAS is the only spectroscopic method that will provide easily accessible structural information in solution. In the case of heterodimetallic sites, XAS has the unique ability to interrogate each metal site independently in the same sample. One of the strongest advantages of XAS is its ability to examine metal ion site structures with crystallographic precision, without the need for a crystal. This is key for studying flexible metal ion sites, such as those described in the selected examples, because it allows one to monitor structural changes that occur during substrate turnover.

| S-EPMC4167288 | biostudies-literature

Wiggler radiation at a low-emittance storage ring and its usage for X-ray absorption spectroscopy.

Project description:A wiggler is a high-power insertion device that was used in the past to produce a smooth wide-band X-ray spectrum. It is widely believed that on low-emittance synchrotrons this X-ray source loses its spatial and spectral homogeneity and therefore becomes less ideal than a scanning undulator. In this paper, we report on experimental and computational studies of an in-vacuum wiggler installed on the first fourth-generation synchrotron MAX IV. We investigate how several physical parameters affect the wiggler spectrum and propose a combination of a few of them that results in significant spectral smoothing. We also examine EXAFS spectra for possible distortions originating from the source imperfection. For this purpose, we scrutinize samples of various homogeneity. We conclude that wigglers are still an appropriate class of insertion devices, also on low-emittance synchrotrons.

| S-EPMC8900845 | biostudies-literature

Investigating the High-Temperature Water/MgCl<sub>2</sub> Interface through Ambient Pressure Soft X-ray Absorption Spectroscopy.

Project description:Magnesium chloride is a prototypical deliquescent material whose surface properties, although central for Ziegler-Natta cataysis, have so far remained elusive to experimental characterization. In this work, we use surface-selective X-ray absorption spectroscopy (XAS) at ambient pressure in combination with multivariate curve resolution, molecular dynamics, and XAS theoretical methods to track in real time and accurately describe the interaction between water vapor and the MgCl2 surface. By exposing MgCl2 to water vapor at temperatures between 595 and 391 K, we show that water is preferentially adsorbed on five-coordinated Mg2+ sites in an octahedral configuration, confirming previous theoretical predictions, and find that MgCl2 is capable of retaining a significant amount of adsorbed water even under prolonged heating to 595 K. As a consequence, our work provides first experimental insights into the unique surface affinity of MgCl2 for atmospheric water. The developed technique is proven highly sensitive to the modifications induced by adsorbates on a given low-Z metal based surface and may be useful in the toolbox required to disentangle the mechanisms of interfacial chemical processes.

| S-EPMC10236435 | biostudies-literature

Simultaneous two-color X-ray absorption spectroscopy using Laue crystals at an inverse-compton scattering X-ray facility.

Project description:X-ray absorption spectroscopy (XAS) is an element-selective technique that provides electronic and structural information of materials and reveals the essential mechanisms of the reactions involved. However, the technique is typically conducted at synchrotrons and usually only probes one element at a time. In this paper, a simultaneous two-color XAS setup at a laboratory-scale synchrotron facility is proposed based on inverse Compton scattering (ICS) at the Munich Compact Light Source (MuCLS), which is based on inverse Compton scattering (ICS). The setup utilizes two silicon crystals in a Laue geometry. A proof-of-principle experiment is presented where both silver (Ag) and palladium (Pd) K-edge X-ray absorption near-edge structure spectra were simultaneously measured. The simplicity of the setup facilitates its migration to other ICS facilities or maybe to other X-ray sources (e.g. a bending-magnet beamline). Such a setup has the potential to study reaction mechanisms and synergistic effects of chemical systems containing multiple elements of interest, such as a bimetallic catalyst system.

| S-EPMC8570203 | biostudies-literature

Single-shot X-ray absorption spectroscopy at X-ray free electron lasers.

Project description:X-ray Absorption Spectroscopy (XAS) is a widely used X-ray diagnostic method for studying electronic and structural properties of matter. At first glance, the relatively narrow bandwidth and the highly fluctuating spectral structure of X-ray Free Electron Lasers (XFEL) sources seem to require accumulation over many shots to achieve high data quality. To date the best approach to implementing XAS at XFEL facilities has been using monochromators to scan the photon energy across the desired spectral range. While this is possible for easily reproducible samples such as liquids, it is incompatible with many important systems. Here, we demonstrate collection of single-shot XAS spectra over 10s of eV using an XFEL source, with error bars of only a few percent. We additionally show how to extend this technique over wider spectral ranges towards Extended X-ray Absorption Fine Structure measurements, by concatenating a few tens of single-shot measurements. Our results pave the way for future XAS studies at XFELs, in particular those in the femtosecond regime. This advance is envisioned to be especially important for many transient processes that can only be initiated at lower repetition rates, for difficult to reproduce excitation conditions, or for rare samples, such as those encountered in high-energy density physics.

| S-EPMC10598033 | biostudies-literature

L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser.

Project description:L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

| S-EPMC3901369 | biostudies-literature

Following the Formation of Silver Nanoparticles Using <i>In Situ</i> X-ray Absorption Spectroscopy.

Project description:The formation of silver and Au@Ag core@shell nanoparticles via reduction of AgNO3 by trisodium citrate was followed using in situ X-ray absorption near-edge structure (XANES) spectroscopy and time-resolved UV-visible (UV-vis) spectroscopy. The XANES data were analyzed through linear combination fitting, and the reaction kinetics were found to be consistent with first-order behavior with respect to silver cations. For the Au@Ag nanoparticles, the UV-vis data of a lab-scale reaction showed a gradual shift in dominance between the gold- and silver-localized surface plasmon absorbance bands. Notably, throughout much of the reaction, distinct gold and silver contributions to the UV-vis spectra were observed; however, in the final product, the contributions were not distinct.

| S-EPMC7301364 | biostudies-literature

The chemical forms of mercury in human hair: a study using X-ray absorption spectroscopy.

Project description:Human hair is frequently used as a bioindicator of mercury exposure. We have used X-ray absorption spectroscopy to examine the chemical forms of mercury in human hair samples taken from individuals with high fish consumption and concomitant exposure to methylmercury. The mercury is found to be predominantly methylmercury-cysteine or closely related species, comprising approximately 80% of the total mercury, with the remainder an inorganic thiolate-coordinated mercuric species. No appreciable role was found for selenium in coordinating mercury in hair.

| S-EPMC3887512 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data