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Helical Symmetry
Published in Mihai V. Putz, New Frontiers in Nanochemistry, 2020
The DNA chain is left-handed and has 1.67 superhelical turns inside the nucleosome core particle. Furthermore, the superhelix is strongly screwed around the nucleohistone protein fixed by several salt-bridges (Schalchet al., 2005) between the negatively charged PO4 groups of the DNA backbone and the positively charged (protonated) lysine and arginine amino acids of the protein chains. It was shown (Ladiket al., 1960) that in the case DNA base pairs, the one-dimensional helix symmetry can induce similar structures of electronic bands as in the case of a three-dimensional solid with translational symmetry. The semiconductor behavior of a doublestranded DNA chain was for the first time experimentally proven by Eley & Spivey (1962). Since then, a huge number of scientific papers have been published considering both theoretical and experimental techniques.
Epigenetic Landscape–Modifying Nanoparticles
Published in Pradipta Ranjan Rauta, Yugal Kishore Mohanta, Debasis Nayak, Nanotechnology in Biology and Medicine, 2019
In eukaryotic cells, DNA is packed in a regularly repeated structure which is commonly known as the nucleosomes. These nucleosomes are composed of repeated, 147-base pair (bp)-long units of DNA that are wrapped around histone octamers comprised of two copies of each histone, namely, H2A, H2B, H3, and H4 (Natoli 2010) (Deb, Kar et al. 2014). The hierarchical structure of nucleosome is a stable fundamental construction capable of expression and repression of genes by regulating the activities of enzymes that requires direct access to the DNA template, thereby regulating DNA replication, transcription, and translation that form the primary foundation of a cellular function. Depending on cell condition and stage along with DNA methylation of their cytosine bases within CpG repeats, histones are subject to numerous modifications in their random coil N-terminal tails, more than in their C-terminal tails and globular domains, which determine the access of different enzymes to the DNA template for multiple operations like replication, repair, and transcription.
Assembly
Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
The first level of organized storage of DNA is the nucleosome. The core unit of the nucleosome is a positively charged protein (histone) octamer of about 8-nm diameter, around which the DNA wraps about 2 times, about 150 base pairs of DNA (Figure 17.14). The patches of sealing “tape” seen in the figure are histone linker proteins, H1, which lock the DNA into place and facilitate formation of higher-order structure. This structure appears to be a 10-nm fiber of beads on a string, with 10–80 base pairs of DNA separating adjacent beads. Higher order structures include the 30-nm fiber (forming an irregular zigzag) and 100-nm fiber as often observed in cells. Figure 17.15 shows a nucleosome core structure as determined from X-ray crystallography, confirming that the cartoon is not too far off.
Benzo[a]pyrene osteotoxicity and the regulatory roles of genetic and epigenetic factors: A review
Published in Critical Reviews in Environmental Science and Technology, 2022
Jiezhang Mo, Doris Wai-Ting Au, Jiahua Guo, Christoph Winkler, Richard Yuen-Chong Kong, Frauke Seemann
Histone modification can also regulate gene expression epigenetically. Notably, DNA is complexed with histones, which results in its compaction and assembly into nucleosomes of the chromatin. Histone modifications are heavily involved in the regulation of gene transcription, DNA replication and DNA repair, and modifications that occur on accessible histone tails, which regulate the chromatin structure (Bártová et al., 2008). In addition to well-characterized histone modifications, including acetylation, methylation, phosphorylation, and ubiquitylation modification (Lennartsson & Ekwall, 2009), recent studies have identified new types of histone modifications, such as propionylation, butyrylation, malonylation and glycosylation (Wang et al., 2019). Specifically, histone acetyltransferases (HATs) and histone deacetylases (HDACs) are responsible for the acetylation and deacetylation of histones, respectively (Lennartsson & Ekwall, 2009). The deacetylation of histones (hyperacetylated histones) leads to uncompressed chromatin and increased accessibility of DNA binding, which facilitates gene transcription. In contrast, the acetylation of histones (hypoacetylated histones) results in condensed chromatin and transcription repression. Additionally, the methylation and demethylation of histones are catalyzed by lysine methyltransferases and arginine methyltransferases, respectively (Bártová et al., 2008).
Direct and cost-effective method for histone isolation from cultured mammalian cells
Published in Preparative Biochemistry & Biotechnology, 2023
Anja Batel, Mirjana Polović, Mateo Glumac, Andrea Gelemanović, Matilda Šprung, Ivana Marinović Terzić
The nuclear chromatin is a dynamic structure involved in a variety of cellular functions.[1] It undergoes structural reorganizations during cell cycle progression, DNA replication, transcription, repair, and recombination.[2] The main element of the structural organization of chromatin in eukaryotic cells is called a nucleosome and is composed of a DNA molecule wrapped around the core of histone proteins. Core canonical histones (H2A, H2B, H3, and H4) represent one of the most evolutionary conserved protein groups.[3]