DNA Packaging

Introduction

Watson and Crick gave the DNA structure. According to their model DNA is a double-helical structure with two polynucleotide strands that run antiparallel. Due to phosphate groups in the DNA backbone, this double helix is negatively charged. The cell produces histone proteins that bind to the DNA to counteract the negative charge. These histone proteins have a role in the packaging of DNA. Continue reading to learn more about DNA packaging definition and why it’s necessary.

What is DNA Packaging, and how does it work?

Have you ever wondered how a DNA molecule can exist in a nucleus that is a fraction of its size? The mechanism of DNA packaging helps explain this.

DNA is a complex organic molecular structure that may be found in both prokaryotic and eukaryotic cells and many viruses. It is a hereditary substance located in the cell nucleus primarily responsible for conveying genetic information.

DNA structure characteristics

• The DNA strands are helically wound, with each strand forming a right-handed coil. 
• Each helix has a 3.32 nm pitch, and one turn is made up of around 10 nucleotides.
• The distance between two base pairs is 0.34 nanometers.
• A DNA’s overall length is determined by the distance between two successive base pairs and the product of the total number of base pairs.
• An average strand of DNA is about 2.2 metres long, significantly longer than a nucleus.
• The absence of a well-defined nucleus distinguishes prokaryotic cells from eukaryotic ones. On the other hand, their negatively charged DNA is structured in a nucleoid. They appear as a positively-charged protein molecule wrapped in a loop.
• The DNA is contained in a well-defined nucleus in all eukaryotes. DNA is a negatively charged polymer that is tightly packed into chromatin around the positively charged histone proteins.
• The nucleosome is formed when an octamer of histone proteins is wrapped around a DNA helix. The nucleosomes coil, even more, resulting in the development of chromatin fibres. Nucleosomes are beads that sit on top of chromatin fibres, dyed thread-like structures. During mitosis, these chromatin fibres condense to produce chromosomes.

Histones

Histones can be defined as the proteins that help fill DNA into chromatin fibres. Histone proteins are positively charged proteins that attach to negatively charged DNA with arginine and lysine amino acids. Histones are divided into two categories:

• Core Histones
• Linker Histones

The core histones are H2A, H2B, H3, and H4. An octamer is made up of two H3, H4 dimers and two H2A, H2B dimers.

The DNA is locked in place on the nucleosome by linker histones, which can be released for transcription.

Histones can be manipulated to modify how much DNA is packaged. The addition of a methyl group to histones improves their hydrophobicity. This leads to very tight DNA packaging.

Acetylation and phosphorylation loosen DNA packaging by making it more negatively charged.

Histone methyltransferases are enzymes that add methyl groups to histones. Histone acetyltransferases are enzymes that add acetyl groups to histones, while histone deacetylases remove them.

Why are nucleosomes regarded as the most important component of DNA packaging?

A nucleosome is a DNA helix made up of 200 base pairs. Nucleosomes are the thread-like stained (coloured) entities present in the nucleus that are repetitive units of chromatin. Nucleosomes in chromatin look like beads on a string when examined under an electron microscope (EM). During the metaphase stage of cell division, the beads-on-string arrangement of chromatin is bundled to form chromatin fibres, which are then coiled and condensed to form chromosomes.

For packing of chromatin at a higher level, an extra set of proteins, known as Non-histone Chromosomal (NHC) proteins, is required. Euchromatin refers to chromatin areas in a normal nucleus that is loosely packed (and stain light). Heterochromatin is the chromatin that is more densely packed and stained black. Heterochromatin is inactive and has no transcriptional activity, whereas euchromatin is active.

Why is DNA packaging important?

The DNA is around 3 metres long and must fit inside the nucleus, only a few micrometres across. To fit into the nucleus, the DNA molecules must be bundled into chromatin, a highly condensed and compact shape.

During the earliest packaging phases, the DNA is reduced to an 11 nm fibre, which represents approximately 5-6 folds of compaction. Wrapping nucleosomes in a precise order accomplishes this.

The DNA packaging classification includes: 

• The nucleosome is the initial stage in DNA packing.
• Solenoid fibre is the second step in DNA packing.
• Scaffold loop Chromatids Chromosome is the third tier of DNA packaging.

One of the benefits of DNA packaging is that it can be separated into what we use frequently and what we don’t. Certain portions of DNA are only required at specific periods. The loosely packed portion of the genome that is largely required for protein production is known as euchromatin. This facilitates the entry of DNA and the production of RNA. Heterochromatin Is densely packed DNA is rarely required.

We’ve discussed DNA packaging, the relevance of DNA packaging, DNA packaging classification, histones and many other topics. Take a look at these top frequently asked questions to expand your knowledge on DNA packaging classification.