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Naturally Occurring Histone Deacetylase (HDAC) Inhibitors in the Treatment of Cancers
Published in Namrita Lall, Medicinal Plants for Cosmetics, Health and Diseases, 2022
Sujatha Puttalingaiah, Murthy V. Greeshma, Mahadevaswamy G. Kuruburu, Venugopal R. Bovilla, SubbaRao V. Madhunapantula
Each nucleosome bead is separated from the next bead by a 54-base pair linker DNA. The linker DNA contains a single H1 histone protein, which seals off the two complete DNA turns (200 base pairs long) (Hergeth and Schneider, 2015). The addition of one H1 wraps another 20 base pairs, resulting in two full turns around the octamer, and forms a structure called ‘chromatosome.’ Long eukaryotic DNA wrapped around the histone proteins leads to the formation of a compact chromosome (Maeshima and Eltsov, 2008).
Genetics and exercise: an introduction
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Claude Bouchard, Henning Wackerhage
Linearly, the DNA of a diploid cell is about 2 m long and is packaged to fit into the tiny nuclei of our cells. How is this done? First, the linear DNA (primary structure) is twisted to form the double helix where one turn accommodates 10 nucleotides (Figure 3.4, secondary structure). The DNA double helix is then wrapped around protein complexes termed nucleosomes, which makes it appear like beads on a string (tertiary structure). A nucleosome contains 4 pairs of so-called histone (H) proteins (2 × H2A, 2 × H2B, 2 × H3 and 2 × H4) around which are wrapped 146 DNA base pairs of DNA (Figure 3.10). The DNA surrounding one nucleosome is joined to the DNA of the next nucleosome by about 20 linear DNA base pairs, known as linker DNA. Histones are not only the “curlers” of DNA but also regulate whether a stretch of DNA is open for biological interactions or tightly closed (more below on this topic).
Nucleic Acids
Published in Danilo D. Lasic, LIPOSOMES in GENE DELIVERY, 2019
Histones are small positively charged proteins (around 5000 Da) around which DNA is wound. These particles are called nucleosomes and contain octamers of histones which form a short cylinder-like particle around which DNA is wound twice (at 147 bp/nucleosome). They are connected by a linker DNA and form chromatin which in electron micrographs resembles a “bead-on-a-string” structure after higher-order packing is unfolded. Nucleosomes pack into 30-nm-thick fibers which have to be further packed because this condensation decreases the size of a human gene to 1 mm and therefore has to be condensed approximately 100-fold more to fit into the cell nucleus. This allows approximately a centimeter-long molecule to be packed into a relatively small cell nucleus. Nucleosomes can also be used in the preparation of very monodisperse short DNA molecules. Linker DNA can be enzymatically cut, and after separation around 50-nm-long DNA is obtained. Milder lysis followed by separation on a gel chromatographic column can lead to dinucleosomal DNA. Condensation of DNA with histones and its packaging into a chromosome are shown in the scheme which shows the preparation of short fragment DNA (see Figure 3-10).
Molecular radiobiology and the origins of the base excision repair pathway: an historical perspective
Published in International Journal of Radiation Biology, 2023
With my colleague David Pederson, we looked at clustered base damage processing on nucleosomes in order to compare it to processing on naked DNA (Cannan et al. 2014). Overall, nucleosomes suppressed DSB formation in clustered base lesions. The degree of suppression depended on the lesion, the glycosylase, stagger between opposing strand lesions, orientation of the lesions with respect to the histone octamer and the distance between the cluster and the nucleosome edge. These data suggest that DSBs formed from direct attempted damage processing of clustered lesions will most likely occur in linker DNA and in genomic regions associated with elevated rates of nucleosome turnover or remodeling but the excess unrepaired single strand breaks could still result in double strand breaks when encountered by replication forks.
Preanalytical variables that affect the outcome of cell-free DNA measurements
Published in Critical Reviews in Clinical Laboratory Sciences, 2020
Vida Ungerer, Abel J. Bronkhorst, Stefan Holdenrieder
Another study compared four brands of tubes: Streck, PAXgene, Roche, and cf-DNA Preservative tubes (Norgen Biotek Corp., Thorold, Canada). The Norgen tubes performed well regarding cfDNA yield, the Roche tubes performed well regarding integrity/concentration, and there were indications of hemolysis in the Streck tubes. This group also compared the size distribution of cfDNA fragments isolated from the different tubes and found consistent fragment sizes in the range of 168–180 bp from all manufacturers with the exception of the Norgen tubes which had slightly smaller fragment sizes (150 bp range) [175]. The reason for the observed shortening of cfDNA in the Norgen tubes was unclear. However, a fragment size of 150 bp might suggest that the linker DNA segment that connects two nucleosome cores was lost or degraded during storage.
In vitro cytotoxicity of polyphenols from Datura innoxia aqueous leaf-extract on human leukemia K562 cells: DNA and nuclear proteins as targets
Published in Drug and Chemical Toxicology, 2020
Elham Chamani, Roshanak Ebrahimi, Khatereh Khorsandi, Azadeh Meshkini, Asghar Zarban, Gholamreza Sharifzadeh
Studies have shown that DNA is a pharmacological target of many of the drugs currently in clinical use or in advanced clinical trials (Hurley and Boyd 1988, Sirajuddin et al. 2013). In the eukaryotes, nuclear DNA interacts with histone proteins and forms a nucleoprotein complex known as chromatin. Chromatin arranges the nuclear genome into a restricted volume. The first level of chromatin organization consists of DNA-folding around histone proteins to shape the fundamental unit of the chromatin, the nucleosome (Hübner et al. 2013). In a nucleosome, 147 bp of DNA are enfolded in an octamer with two copies of four core histone proteins (H2A, H2B, H3, and H4) (Nair and Kumar 2012). As a linker histone, histone H1 surrounds the chromatosome by protecting the internucleosomal linker DNA near the nucleosome entry-exit point (Dixon et al. 2016, Kalashnikova et al. 2016).