Abstract Chromatin structure is dictated by nucleosome assembly and internucleosomal interactions. The tight wrapping of nucleosomes inhibits gene expression, but modifications to histone tails modulate chromatin structure, allowing for proper genetic function. The histone H4 tail is thought to play a large role in regulating chromatin structure. Here we investigated the structure of nucleosomes assembled with a tail-truncated H4 histone using Atomic Force Microscopy. We assembled tail-truncated H4 nucleosomes on DNA templates allowing for the assembly of mononucleosomes or dinucleosomes. Mononucleosomes assembled on nonspecific DNA led to decreased DNA wrapping efficiency. This effect is less pronounced for nucleosomes assembled on positioning motifs. Dinucleosome studies resulted in the discovery of two effects- truncation of the H4 tail does not diminish the preferential positioning observed in full-length nucleosomes, and internucleosomal interaction eliminates the DNA unwrapping effect. These findings provide insight on the role of histone H4 in chromatin structure and stability.
more »
« less
X-ray photoemission studies of the interaction of metals and metal ions with DNA
Abstract X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.
more »
« less
- PAR ID:
- 10328047
- Date Published:
- Journal Name:
- Zeitschrift für Physikalische Chemie
- Volume:
- 236
- Issue:
- 4
- ISSN:
- 0942-9352
- Page Range / eLocation ID:
- 439 to 480
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The chemical structures of Co oxynitrides – in particular, interactions among N and O atoms bonded to the same cobalt – are of great importance for an array of catalytic and materials applications. X-ray diffraction (XRD), core and valence band X-ray photoelectron spectroscopy (XPS) and plane wave density functional theory (DFT) calculations are used to probe chemical and electronic interactions of nitrogen-rich CoO1-xNx (x > 0.7) films deposited on Si(100) using NH3 or N2 plasma-based sputter deposition or surface nitridation. Total energy calculations indicate that the zincblende (ZB) structure is energetically favored over the rocksalt (RS) structure for x > ~ 0.2, with an energy minimum observed in the ZB structure for x ~ 0.8 - 0.9. This is in close agreement with XPS-derived film compositions when corrected for surface oxide/hydroxide layers. XRD data indicate that films deposited on Si (100) at room temperature display either a preferred (220) orientation or no diffraction pattern, and are consistent with either rocksalt (RS) or zincblende (ZB) structure. Comparison between experimental and calculated X-ray excited valence band densities of states – also similar for all films synthesized herein – demonstrates a close agreement with a ZB, but not an RS structure. Core level XPS spectra exhibit systematic differences between films deposited in NH3 vs N2 plasma environments. Films deposited by N2 plasma magnetron sputtering exhibit greater O content as evidenced by systematic shifts in N 1s binding energies. Excellent agreement with experiment for core level binding energies is obtained for DFT calculations based on the ZB structure, but not for the RS structure. The agreement between theory and experiment demonstrates that these N-rich Co oxynitride films exhibit the ZB structure, and forms the basis of a predictive model for understanding how N and O interactions impact the electronic, magnetic and catalytic properties of these materials.more » « less
-
In eukaryotic nuclei, DNA is wrapped around an octamer of core histones to form nucleosomes. H1 binds to the linker DNA of nucleosome to form the chromatosome, the next structural unit of chromatin. Structural features on individual chromatosomes contribute to chromatin structure, but not fully characterized. In addition to canonical nucleosomes composed of two copies each of histones H2A, H2B, H3, and H4 (H3 nucleosomes), centromeres chromatin contain nucleosomes in which H3 is replaced with its analog CENP-A, changing structural properties of CENP-A nucleosomes. Nothing is known about the interaction of H1 with CENP-A nucleosomes. Here we filled this gap and characterized the interaction of H1 histone with both types of nucleosomes. H1 does bind both types of the nucleosomes forming more compact chromosome particles with elevated affinity to H3 nucleosomes. H1 binding significantly increases the stability of chromatosomes preventing their spontaneous dissociation. In addition to binding to the entry-exit position of the DNA arms identified earlier, H1 is capable of bridging of distant DNA segments. H1 binding leads to the assembly of mononucleosomes in aggregates, stabilized by internucleosome interactions as well as bridging of the DNA arms of chromatosomes. Contribution of these finding to the chromatin structure and functions are discussed.more » « less
-
null (Ed.)In this study, we show how strong metal–support interaction (SMSI) oxides in Pt–Nb/SiO 2 and Pt–Ti/SiO 2 affect the electronic, geometric and catalytic properties for propane dehydrogenation. Transmission electron microscopy (TEM), CO chemisorption, and decrease in the catalytic rates per gram Pt confirm that the Pt nanoparticles were partially covered by the SMSI oxides. X-ray absorption near edge structure (XANES), in situ X-ray photoelectron spectroscopy (XPS), and resonant inelastic X-ray scattering (RIXS) showed little change in the energy of Pt valence orbitals upon interaction with SMSI oxides. The catalytic activity per mol of Pt for ethylene hydrogenation and propane dehydrogenation was lower due to fewer exposed Pt sites, while turnover rates were similar. The SMSI oxides, however, significantly increase the propylene selectivity for the latter reaction compared to Pt/SiO 2 . In the SMSI catalysts, the higher olefin selectivity is suggested to be due to the smaller exposed Pt ensemble sites, which result in suppression of the alkane hydrogenolysis reaction; while the exposed atoms remain active for dehydrogenation.more » « less
-
This paper describes the identification of specific host–guest interactions between basic gases (NH3, CD3CN, and pyridine) and four topologically similar 2-dimensional (2D) metal–organic frameworks (MOFs) comprising copper and nickel bis(diimine) and bis(dioxolene) linkages of triphenylene-based ligands using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), electron paramagnetic resonance spectroscopy (EPR), and powder X-ray diffraction (PXRD). This contribution demonstrates that synthetic bottom-up control over surface chemistry of layered MOFs can be used to impart Lewis acidity or a mixture of Brønsted and Lewis acidities, through the choice of organic ligand and metal cation. This work also distinguishes differences in redox activity within this class of MOFs that contribute to their ability to promote electronic transduction of intermolecular interactions. Future design of structure–function relationships within multifunctional 2D MOFs will benefit from the insights this work provides.more » « less
An official website of the United States government

