Solenoid Model

introduction image

The solenoid model illustrates the packaging or folding of DNA within the eukaryotic cell nucleus. It was first introduced by the scientist’s named John Finch and Aaron Klug in the year 1976. In eukaryotes, the DNA is organized compactly by the association of bead-like histone octamer and linker histone, while in prokaryotes the DNA content is dispersed throughout the cell.

The solenoid model is a one-start helix arrangement of nucleosome cores in such a way that each lie parallel to each other along the same helix. Through electron microscopy and X-ray diffraction, the pattern of DNA packaging inside the eukaryotic cell nucleus can be easily studied.

Content: Solenoil Model

  1. Definition
  2. Important Terms
  3. Overview
  4. Formation
  5. Conclusion

Definition of Solenoid Model

The solenoid model represents the nucleosomes organization within the 30 nm wide chromatin fibre. A term solenoid itself defines the winding of the DNA-helix. In eukaryotes, the DNA is compressed into the chromatin fibres by the association of DNA-linking histone proteins.

The protein complex (histone octamer) attached to the core DNA is termed as a nucleosome. Then, the H1 protein seals the wrapped DNA around the core protein. In this way, multiple nucleosomes can polymerize to form oligonucleosome. The nucleosome cores attach through a 35-58 bp long segment of linker DNA, which colloquially known as chromatosome.

Important Terms

While studying the solenoid model, we will go through some important terms that we must know.

DNA

It is an acronym for the term deoxyribose sugar. DNA is the hereditary material that is the fundamental unit of a chromosome. It is composed of nucleosides (a combination of nitrogenous bases and ribose sugar) and a phosphate backbone. The DNA has a complete set of information that plays a humongous role in deciding what a cell should do, how it should look like etc.

Gene

It is the smallest section of DNA found in the chromosome, which contains a specific DNA sequence and encodes specific enzymes that regulate the genetic attributes, cell’s physiology, cell metabolism, and cell replication etc.

Chromatin

It is the less condensed form of DNA. Chromatin is a macromolecule, in which the free eukaryotic DNA twists around the histone octamer that looks like the beads on a string. Within the cell nucleus, the DNA is condensed into the chromatin fibres (30 nm wide) after the DNA packaging around the repeating units of nucleosome cores (10 nm wide). A scientist named Roger Kornberg stated that the chromatin fibre appears as a result of  the coiling between the core DNA (200 bp) and the repeating units of a core protein complex.

Nucleosome

It is the structural unit of chromatin that can define as the repeating globular units around the core DNA. A nucleosome complex consists of 146 bp of nucleosomal DNA and core histone complex (possess eight histone proteins). It appears as a spherical mass that is 11 nm wide with a height of 5.5 nm.

Chromatosome

It can define as the binding of nucleosome to the chromatin, and consists of a nucleosome, DNA-linker and H-1 histone protein. It possesses nine histone proteins, including H1 protein.

Chromosome

It is the highly condensed form of DNA that is visible during the metaphase cell cycle when the cell gets ready to divide. It results after the scaffolding of the chromatin fibre (30 nm diameter).

There are some scaffold attachment regions (A+T rich regions), where the scaffold proteins attach and result into supercoiling of the chromatin fibre with a diameter of 300 nm. Later, the fibre gets more condensed into the 700 nm wide chromatids.

The degree of compaction gradually increases with the leading stages of the cell cycle. During metaphase, the chromatids become highly condensed to form chromosomes that are having a diameter of 1400 nm.

Overview of Solenoid Model

The solenoid model explains the compaction of the eukaryotic genome within the small spherical nucleus. Firstly, the free DNA condenses into less-compressed chromatin fibres. A chromatin fibre holds the DNA-helix by the repeating globular units or histone proteins. Later, the chromatin fibres condense to a higher degree and transform into highly compressed structure called chromosome.

solenoid model of DNA folding

Finally, when the cell is ready to divide then the chromosome separates the DNA content equally between the two dividing cells. Through the X-ray diffraction method, the DNA organization in the eukaryotic nucleus gives explicit information about the folding of DNA, degree of compactness and the DNA-linking proteins.

Due to the considerable amount of DNA, the DNA must be fixed in such a way that it can reside in the small nucleus. Through the solenoid model, we can look into the consecutive stacking of nucleosomes that results into the formation of coiled loop that comprises six nucleosomes per turn. A term solenoid represents the coiling of ds-DNA in the form of coiled loop.
formation of solenoid loop during DNA packaging

Formation

Solenoid model represents the formation of helical loop, in which the nucleosomes are assembled one by one in a left-handed fashion around the DNA-helix. The linker DNA is slightly bent, which connects the nucleosome core to the solenoid or DNA-helix to form a long chromatin fibre.

Histone octamer forms by the association of two subunits each of H2A, H2B, H3 and H4. The organization of histone proteins is illustrated in the diagram given below.

arrangement of histone proteins in a nucleosome

The histone proteins are organized in a way, so as to produce steric hindrance repulsion force. Histone subunits are attached via two factors, namely stereo-specific bond and anionic nucleoplasmin protein. Therefore, these two factors stabilize the core histone complex.

Then, the DNA (147 bp) coils around the core protein particle by 1.75 times, i.e. a DNA takes one full turn and then a 3/4th turn to form a single nucleosome. Finally, the nucleosome units are sealed off by the H1 linker proteins.

Multiple nucleosomes then join linearly, which can ultimately form an 11nm wide nucleosomal fibre that looks like “beads on a string“. The nucleosomes cores are attached via a 20-60 base pairs long segment of linker DNA.

Oligonucleosomes (multiple nucleosomes) combine to form a long nucleosomal fibre of width 10nm, in which the H1 proteins are located centrally. As a result, H1 proteins interact with each other that cause H1-H1 proteins repulsion and an electrostatic attraction between the DNA and H1 protein.

nucleosome solenoid model

DNA is negatively charged (due to phosphate ions), by which it gets attracted to the positively charged H1 protein (due to presence of arginine, histidine and lysine residues). There were two models given for the DNA packaging, namely solenoid and zigzag.

In both the models, the formation of 30 nm helical fibre from the secondary folding of the 11 nm fibre is common. But, the arrangement of nucleosomes around the helix and the position of linker DNA differs in both the models. The solenoid model for DNA packaging was widely accepted by many scientists, and still in use to represent the chromatin organization.

Conclusion

In the solenoid model, a 10 nm wide nucleosomal fibre transforms into a 30 nm wide chromatin fibre. Therefore, we can conclude that the nucleosomes are the structural units of chromatin that fix the free DNA into much precise or condense form within the cell nucleus.

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