DNA is the most important nucleic acids present in our body. It stores all the information regarding various processes performed by a cell. The genetic information is also transferred to the next generation of cells via DNA. After the development of the latest technology, DNA is used in various non-biological processes for the welfare of mankind. It is now being used in labs for diagnosis of a disease or genetic disorder, to identify a criminal, to settle the disputes of paternity, etc. 

The structure of DNA can be studied at different levels:

• DNA double helix
• Nucleosomes
• Chromatin fibres
• Chromosomes

In this section of notes, we will study the structure of DNA at all these levels in detail. 

Read more about DNA Replication

DNA Double Helix

The double-helical structure of DNA was introduced to the world by Watson and Crick, and was identified by the use the X-ray diffraction techniques to find out the three-dimensional structure of DNA. Although the globally accepted structure is known as the Watson and Crick model of DNA structure, one important person left out of the historical teaching of DNA’s discovery is Rosalind Franklin. The data of this female British biophysicist was critical to Watson, Crick and Wilson’s work, which would earn them a Nobel Prize for the discovery. Franklin was not eligible for the prize firstly because she died before the nomination (which is not given posthumously), and secondly because during this time it was not uncommon for women to be overlooked in the sciences and not have their contributions duly credited and recognised. Indeed, their discovery hinged on an x-ray that Franklin had taken and Crick later wrote in a letter that “the data which really helped us to obtain the structure was mainly obtained by Rosalind Franklin”.

The various postulates of this model are discussed below.

1. DNA is made of two polynucleotide chains

DNA is a polymer of nucleotides. These nucleotides are arranged in the form of two chains. 

The nucleotides present in DNA are deoxyribonucleotides. They are made up of 

• Deoxyribose sugar
• A nitrogenous base 
• One phosphate group

One of the following four bases is present in DNA nucleotides.

• Alanine
• Guanine
• Cytosine
• Thymine

Thousands of these nucleotides are linked via phosphodiester bonds two form two polynucleotide chains. 

Each of these two chains have a 3’ end and a 5’ end.

The end of the polynucleotide chain having a free hydroxyl group at the third carbon of deoxyribose sugar is called the 3’end.

The other end of the chain containing the free phosphate group attached to the fifth carbon of the deoxyribose sugar is called the 5’ end.  

2. Two polynucleotide chains are coiled around each other 

A helix is a spiral-shaped structure. The two polynucleotide chains in DNA are coiled around one another to form a DNA double helix. It is called double helix because, in the three-dimensional model, DNA molecule was seen to have a spiral or helical structure made up of two polynucleotide chains. This helical structure was made when the two polynucleotide chains are wound around each other. 

3. The polynucleotide chains are coiled anti-parallel 

This means that in DNA double helix, the two polynucleotide chains are arranged opposite to each other. If one chain is arranged in 3’ to 5’ direction with its sugar and phosphate molecules directed upwards, the other chain is in 5’ to 3’ direction with the sugar and phosphate molecules facing downwards. 

4. DNA double helix has Phosphate-sugar backbone

The backbone of DNA double helix is made by the sugar and phosphate molecules. The polynucleotide chains in DNA are arranged in such a way that the sugar and phosphate molecules are arranged on the outer side of the double helix with the nitrogenous bases facing inwards. 

5. The two chains are held together by hydrogen bonds

The two polynucleotide chains in DNA double helix are held together by hydrogen bonds between their nitrogenous bases. The purines of one chain pair with the pyrimidines of the other chain via these hydrogen bonds. 

Alanine always pairs with Thymine, while Guanine always pairs with Cytosine. 

There are two hydrogen bonds between Alanine and Thymine, while there are three hydrogen bonds between Guanine and Cytosine. 

6. The ratio of purines and pyrimidines in DNA are equal

As mentioned above, the double helix is held together by hydrogen bonds between purine and pyrimidine bases. Adenine in DNA always pairs with Thymine, while Guanine in DNA always pairs with cytosine. This means that the amount of Adenine in DNA is equal to the amount of Thymine, and the amount of Guanine is equal to that of Cytosine. Thus, purines and pyrimidines are always present in equal ratio within a molecule of DNA. 

7. Each turn of helix is made of ten base pairs

According to the Watson and Crick model, each turn of DNA double helix has ten base pairs in it. It was found through the X-ray diffraction technique that one turn of helix measure around 34 Angstrom units (1 Angstrom= 10^-10) or 3.4 nm. Thus, in DNA double helix each base pair is 3.4 Angstrom units or 0.34 nm apart. 

DNA double helix has two grooves

The two polynucleotide chains are not symmetrical. When the two strands are wound around each other, spaces are left behind in the form of grooves. Two types of grooves are present in the DNA double helix.

• Major Groove: It is the widest groove measuring around 22 Angstrom units. 
• Minor Grooves: The width of this groove is less than that of the major groove. It measures around 12 Angstrom units. 

These grooves in DNA double helix provide space for the attachment of enzymes and transcription factors, etc. 

Nucleosomes

The DNA in living organism is not present in the form of straight fibers made up of double helix. Rather, it is tightly packed so that it can be enclosed in such a tiny nucleus. It is known that the DNA of a single human cell is so long that if stretched, it would make a 3 meters long rope. Such a long DNA is kept inside the nucleus only by tightly pacing it with proteins.

Nucleosome is a structure formed when DNA is packed around proteins. It has a core around which the DNA fiber is wound in turns. 

Histone proteins are rich in basic amino acids like arginine and lysine. These amino acids carry positive charges. Because of the basic amino acids, histones are also sometimes called basic proteins. The core of a nucleosome is made up of eight histone proteins. 

In a nucleosome, DNA double helix is wound around the core 1.67 times.

The positive charges of amino acids in histone proteins enable the tight packing of DNA. These amino acids make strong ionic bonds with the phosphate groups of DNA carrying negative charges. 

There is another histone protein that is associated with the nucleosome. It is called H1 protein. This protein is not present inside the core of the nucleosome. Rather, the H1 protein holds the DNA around the core.

The DNA fiber between the two nucleosomes is called linker DNA. The length of linker DNA depends on the extent of packing. In the case of humans, it varies from 8 to 151 base pairs. 

Chromatin fibers

The next level in DNA packaging is chromatin fibers. The nucleosomes and the linker DNA resemble beads on a string.  These nucleosomes undergo further coiling to form a 30 nanometers long fiber, known as chromatin fiber. The chromatin can be of two types.

• Euchromatin: In this type of chromatin, the nucleosomes are arranged distant apart. The length of the linker DNA is large. It shows less compact DNA packing. The linker DNA in this type of chromatin can be transcribed into RNA. 
• Heterochromatin: It is a type of chromatin that shows extensive packing of DNA. The nucleosomes are very tightly packed. The linker DNA is also very short. The DNA that is packed in the form of heterochromatin cannot be transcribed. 

These 30 nm chromatin fibers make loops known as chromatin loops.

Chromosome

Chromosomes represent the final stage of DNA packaging within a cell. In a non-dividing cell, DNA is present in the nucleus in the form of chromatin fibers. Just before the beginning of cell division, these chromatin fibers arrange themselves in the form of chromosomes. 

The chromatin loops created by 30 nm fibers are held together by scaffold proteins to form a rosette-like structure. Thousands of these rosettes are linked together resulting in the formation of a chromosome. 

Each chromosome is made up of two sister chromatids. These sister chromatids are held together by a constriction known as the centromere. 

The number of chromosomes in an individual depends on the amount of nuclear material or DNA in its nucleus. It is species-specific. All the individuals of a species have an equal number of chromosomes in their nucleus. 

Humans have 46 chromosomes that are arranged in the form of pairs. The chromosomes of one pair are called homologous chromosomes. 

Out of the 23 pairs in humans, 22 pairs are identical in both the sexes and are called autosomes. 

The 23^rd pair is different in males and females. These chromosomes are called sex-chromosome. 

• In males, the 23^rd pair contains one X and one Y chromosome
• In females, the 23^rd pair contains two X chromosomes.

One half of the chromosomes i.e.23 chromosomes come from the mother while the other half of chromosomes comes from the father. 

This is the structure and arrangement of DNA in eukaryotic cells. In bacterial cells and viruses, the structure of DNA is the same as in eukaryotic cells, but it differs in its arrangement. 

DNA in Bacterial cells

Bacterial cells are prokaryotic cells and thus, lack a nucleus. In these cells, DNA is not arranged in the form of nucleosomes and chromosomes. Rather, DNA in bacteria is present in the form of a single large circular molecule within the center of the cell.

The double-stranded DNA molecule in bacteria is compactly packed by supercoiling. In this process, the DNA double helix is wound onto itself again and again like a rubber band.

The supercoiled DNA along with proteins and RNA together makes the nucleoid. Nucleoid is present in the center of most of the bacterial cells. 

When the bacteria divided, the DNA supercoils are opened and DNA is replicated to create daughter DNA. This daughter DNA is then sent to the next generation of bacteria. 

Plasmid

Plasmids are the circular DNA molecules present in bacteria outside the nucleoid. These DNA molecules are capable of self-replication. They carry genes for antibiotic resistance. Bacteria can transfer plasmids to other bacterial cells even without cell division by the process of conjugation or transformation. 

DNA in viruses

DNA viruses are only made up of DNA and proteins. They have a very short DNA molecule. The double-stranded DNA molecule in viruses is present in unpacked form within a coat made by proteins. This coat is known as a capsid. 

Summary 

DNA is the most important nucleic acid present in living organisms. 

The structure of DNA was best explained by Watson and Crick model. According to this model,

• DNA is made up of two polynucleotide chains that are wound around each other in an anti-parallel fashion to form a double helix. 
• The two chains are held together by hydrogen bonds between the nitrogenous bases. 
• One turn of helix contains 10 base pairs and measures around 34 Angstrom units
• The double helix is wound in such a way that it has two grooves, a major groove and a minor groove.

In eukaryotic cells, this DNA double helix is compactly packed within the nucleus.

DNA molecule winds around a core of histone proteins to make nucleosome.

The nucleosomes thus formed resemble the ‘beads on a string’ with DNA between them known as linker DNA.

They arrange themselves in the form of 30 nm fibers known as chromatin fibers.

These chromatin fibers make loops that are arranged to form chromosomes. 

Within the nucleus, DNA is present in the form of chromatin fibers until the beginning of cell division. When the cell begins to divide, the chromosomes start appearing inside the nucleus.

The number of chromosomes varies from species to species. Humans have 46 chromosomes in the form of 23 pairs. 

In bacterial cells, DNA is packed by supercoiling. Bacteria have two types of DNA;

• Chromosomal DNA in the center
• Plasmids

In viruses, DNA is a small double-stranded molecule that is packed inside a protein core. 

Frequently Asked Questions

In which shape DNA is mostly found?

DNA is mostly found in the form of a double-stranded helix. Two stands of DNA are twisted upon each other.

Which nitrogenous bases are present in DNA?

The nitrogenous bases present in the DNA are adenine, thiamine, guanine, and cytosine.

What is the structural unit of DNA?

The structural unit of DNA is a deoxyribonucleotide. It consists of deoxyribose sugar, a nitrogenous base, and a phosphate group.

Which bond is present between two nucleotides in DNA?

A phosphodiester bond is present between two adjacent nucleotides in DNA. This bond is formed between the phosphate group of one nucleotide and the sugar of another nucleotide.

References

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7. Conlon, Anne Marie. Rosalind Franklin, 25 July 1920 – 16 April 1958, Chemist who helped to discover the DNA double helix. New Scientist