DNA Structure | Watson and Crick's model of DNA

The structure of DNA was a mystery before the 1950s. It was at the beginning of 1950s, James Watson (American biologist) and Francis Crick (British physicist) after combining the available physical and chemical data and based on their research introduced the double-helix model for DNA. The work of Rosalind Franklin and Maurice Wilkins helped Watson and Crick in their discovery of the double helix structure of DNA. This model for the DNA structure was widely accepted and is known as Watson and Crick's model of DNA.

The three dimensional (3-D) double helix model of DNA as proposed by Watson and Crick including the latest advances in its structure is described below:

• DNA is a two-stranded molecule. It is made of two helical chains or strands that are spirally coiled around a common axis to form a right-handed double helix like a twisted ladder.
  
• Each strand has two ends; 5' end with a phosphate group and 3' end with a hydroxyl group. The DNA strands run in opposite directions which means the 5'end of one chain and 3'end of another chain are on the same side, so they are antiparallel to each other. One strand runs from 5' to 3' direction and is known as sense strand and the opposite strand runs from 3' to 5' direction, which is known as antisense strand.
  
• The diameter of DNA is uniform and is around 2 nm.
• The distance between each turn or the length of each spiral turn is 3.6 nm (earlier 3.4 nm).
• The distance between base pairs or two successive rings is 0.34 nm.
• There are 10.5 nucleotides per turn or in one complete spiral turn or one complete rotation of 360 degrees (earlier 10 nucleotides).
• The spiral arrangement of chains creates major and minor grooves between the two chains or strands. The major groove is large, whereas, the minor groove is small. Major groove occurs when backbones are apart and minor groove occurs when they are close.
• The alternating deoxyribose sugar and phosphate groups are located on the outside of the double helix. So, it makes the backbone of the helix.
• Each DNA strand consists of a long sequence of four bases that include Adenine (A), Cytosine (C), Guanosine (G) and Thymine (T). The bases on one strand are bonded or paired with the complementary bases on the opposite strand.
  
• The pyrimidine (Thymine and Cytosine) and purine (Adenine and Guanine) bases are located inside the double helix.
• A specific purine base is bonded or make pair with a specific pyrimidine base through hydrogen bonds. For example, Adenine (A) pairs with Thymine (T) and Guanine (G) pairs with Cytosine (C).
• Adenine and Thymine are joined through two hydrogen bonds (A=T), whereas, Guanine and Cytosine are joined through three Hydrogen bonds (G≡C).
• The double helix structure is stabilized by hydrogen bonds that are formed between purine and pyrimidine bases.
• These base pairs are known as complementary base pairs and form the steps of the DNA ladder. So, the two DNA strands are complementary to each other. The number of A bases is equal to the number of T bases and, similarly, the number of G bases is equal to C bases. So, the number of purine bases is always equal to the number of pyrimidine bases. This is also suggested by a rule called Chargaff's rule.
• The sides of the helix or strands are made up of alternating sugar and phosphate molecules of nucleotides that are linked by 3'-5' phosphodiester bond. Whereas, the steps of the ladder are made of nitrogen bases that are connected to sugars by glycosidic bonds. If we imagine the double helix structure as a ladder, the sugar and phosphate group can be considered as sides and the bases would be the steps or rungs.

The structure of DNA helped understand the various functions of DNA such as how it is replicated and how the information is carried by it is used to make proteins by the cells.

Molecular Structure of DNA:

DNA is a nucleic acid, which is one of the major groups of biological macromolecules. The DNA molecule has two strands that are tightly packed or coiled into a thread like structure called chromosome and is present in the nucleus of a eukaryotic cell. It is tightly coiled around histone proteins that provide stability to its structure. DNA is visible under a microscope only when the cell is diving as during cell division DNA gets more tightly packed.

Each strand of DNA is made up of nucleotides and has two ends; 5' end and a 3' end. DNA has an antiparallel structure that means the two DNA strands are antiparallel and thus run in opposite directions.

So, DNA is made up of nucleotides just like a protein is made up of amino acids. It is a bunch of nucleotides that are joined one after another to form spirally coiled DNA strands or chromosome. There are four different nucleotides in DNA. These nucleotides are Adenine, Cytosine, Thymine and Guanine (A, C, T and G). Each nucleotide comprises three simple molecular parts that are a 5-carbon sugar, a phosphate group, and a nitrogenous base.

In a nucleotide, the phosphate group and a nitrogenous base are bonded to a sugar molecule to form the nucleotide. The sugar of all four nucleotides is called deoxyribose sugar, which is a cyclical molecule made of one oxygen and four carbons arranged in a ring structure. However, a fifth carbon atom is attached to the fourth carbon of this ring. All nitrogenous bases have the tendency to have multiple nitrogen atoms due to this they are termed as nitrogenous bases.

The phosphate group comprises a phosphorus atom that is attached to or bonded with four oxygen atoms. This phosphorus atom tends to bond with other oxygen atoms for example oxygen atom of the deoxyribose sugar of another nucleotide.

The four nucleotides of a DNA differ from each other in terms of their nitrogenous bases. Each nucleotide has a different nitrogenous base attached to its deoxyribose sugar and accordingly, they are named as described below:

• Adenine nucleotide contains adenine
• Thymine nucleotide contains thymine
• Guanine nucleotide contains guanine
• Cytosine nucleotide contains cytosine

How nucleotides in DNA are connected to each other?

It is the phosphodiester bond that connects the nucleotide monomers in a DNA molecule. This bond always connects the 3' carbon of a nucleotide to the 5' carbon of the next nucleotide.

In this bonding, a covalent bond is formed between the oxygen at the 3' carbon of a nucleotide and the phosphorus atom in the phosphate group that is connected at the 5' carbon of the other nucleotide. So, it is called 3'-5' phosphodiester bond. When a nucleotide joins another nucleotide a water molecule is released and this process is known as dehydration synthesis. This process usually happens when polymers are formed.

How DNA strands are connected to each other?

DNA strands are connected by noncovalent hydrogen bonds between two strands. These bonds strongly connect the two strands to each other and are formed between specific hydrogen atoms on one base (hydrogen bond donors) and specific oxygen or nitrogen atoms (hydrogen bond acceptors) on the other base located on the opposite side on the opposite strand.

Both Adenine and Thymine nucleotides have one donor and one acceptor. Cytosine nucleotide has one donor and two acceptors, and Guanine has one acceptor and two donors.

The A nucleotides are always connected to T nucleotides through H bonds. Whereas, Cytosine nucleotides are always connected to Guanine nucleotides through H bonds. This type of selective bonding is known as a complementary base pairing that provides stability to the sequence of nucleotides of two DNA strands. The arrows are pointing towards hydrogen (h) bonds; two hydrogen bonds between Thymine and Adenine and three between Cytosine and Guanine.

Chargaff's rule:

Erwin Chargaff in the 1950s discovered that the quantities of nitrogenous bases of nucleotides (A, T, C and G) were not equal. However, it was found that quantity of A was equal to the amount of T and the amount of C was always equal to the quantity of G. This discovery was very beneficial for understanding the model of the DNA double helix and bonding between bases.

Till now, we have understood that two long DNA strands are joined together or spiral to form the double helix structure. Furthermore, DNA can be divided into short segments that are called genes. Gene is a short section or segment of DNA. As DNA molecule is a double-stranded molecule that contains a sequence of bases; A, T, G and C. So, we can say that a gene is a specific sequence of bases.

Each gene can be divided into three-nucleotide sub-segments called codons. So, we can say that a codon is a segment or piece of DNA Strand that is three nucleotides long or made of three nucleotides. A gene can be thought of as a string of codons.

As there are four nucleotides, there could be 64 different ways in which the four nucleotides of DNA can be arranged. The order or sequence of bases determines DNA's instructions or genetic code. Besides this, DNA strands or molecules are very long. They cannot fit inside the cells without the right packaging. So, they are coiled tightly along with histone proteins to form chromosomes.