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Protein-associated DNA occupies about 1/4 of the intracellular volume forming a concentrated viscous phase with liquid crystalline properties, called the nucleoid. Other research also indicated that the genome of bacteria occupies approximately 10-15% of the bacteria's volume. [ 5 ]
The major structures in DNA compaction: DNA, the nucleosome, the 11 nm beads on a string chromatin fibre and the metaphase chromosome. Chromatin is a complex of DNA and protein found in eukaryotic cells. [1] The primary function is to package long DNA molecules into more compact, denser structures.
Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes, this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved.
Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4. DNA must be compacted into nucleosomes to fit within the cell nucleus. [2]
[19] [20] This is accompanied by simultaneous accumulation of RNF8 protein and the DNA repair protein NBS1 which bind to MDC1 as MDC1 attaches to γH2AX. [21] RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4 protein, [ 22 ] a component of the nucleosome remodeling and deacetylase complex NuRD .
[21] [22] Both RNAi and an exosome-dependent RNA degradation process contribute to heterochromatic gene silencing. These mechanisms of Schizosaccharomyces pombe may occur in other eukaryotes. [23] A large RNA structure called RevCen has also been implicated in the production of siRNAs to mediate heterochromatin formation in some fission yeast. [24]
Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits .
The organization of DNA presents a remarkable biological challenge: human DNA can reach 2 meters [1] and is packed into the nucleus with the diameter of 5-20 µm. [2] At the same time, the critical cell processes involve complex processes on highly compacted DNA, such as transcription, replication, recombination, DNA repair, and cell division.