Double Helical Structure of DNA | Watson and Crick Model | Structure of nucleotides

DNA is an important biomolecule. It stores genetic information and transfers it from one generation to another generation, thus plays important role in the sustainability of life on earth. DNA is present in the nucleus of a cell, coiled in the form of chromosomes. 

The number of chromosomes varies in different species and thus the information stored in DNA also varies. In a human cell, 46 chromosomes are present that carry all the information about the structure and function of a human body. The structure of DNA makes it suitable to store such a large amount of information.

What is the structure of DNA?

The DNA is made up of small repeating units called nucleotides. Nucleotides arrange themselves in a specific sequence which is important for the sequence of amino acids in proteins.

Before we study the structure of DNA, knowledge about the nucleotide structure is necessary.

Structure of nucleotide

The structure of nucleotide is made up of three components:

  1. Nitrogenous (nitrogen-containing) base
  2. Pentose sugar
  3. Phosphate group
structure of nucleotide
Structure of a nucleotide.

Note: If the phosphate group is removed from the nucleotide then it is called nucleoside.

1. Nitrogenous base

The nitrogenous base is a nitrogen-containing molecule that has the chemical properties of a base. They are derivatives of two-parent compounds i.e., pyrimidine and purine.

Pyrimidine is a single ring structure. The major pyrimidines are cytosine (C), thymine (T), and uracil (U). While purine contains two rings. The two major purine bases are adenine (A) and guanine (G).

Note: The adenine (A) and guanine and cytosine (C) are present in both DNA and RNA molecules, however, thymine is present only in DNA, and uracil (U) is found only in RNA.

2. Pentose sugar

Pentose sugar contains 5 carbon atoms. The carbon atoms in pentose sugar form a close structure and carbon atoms are numbered.

The DNA molecule contains 2'-deoxyribose as pentose sugar. Deoxyribose sugar has hydrogen present at the 2’ position.

Note: The carbon in pentose sugars of nucleotides and nucleosides are numbered by giving a prime (') designation to distinguish them from the numbered atoms of the nitrogenous bases.

3. Phosphate group

The third component is the Phosphate group (PO43-). When phosphate is attached to a molecule containing carbon, it is called a phosphate group.

It is found not only found in DNA, but also present in RNA, and in adenosine triphosphate (ATP) that provide energy to cells.

In nucleotide, if one phosphate group is present then it is called monophosphate, the presence of two makes diphosphate. And triphosphate contains three phosphate groups.

Note: Instead of full name, symbols are used to represent nucleotides. For example, A for nucleotide having adenine, G for guanine containing nucleotide, C for cytosine containing nucleotide, and T for thymine containing nucleotide.

Structure of DNA

Nucleotides are organized in a specific manner to form the structure of DNA.

what is the structure of DNA
Organization of nucleotides to form structure of DNA.

Phosphodiester linkage

The successive nucleotides of DNA are linked covalently through phosphate-group by forming bridges. The bridge is formed when the 5'-phosphate group of one nucleotide unit is joined to the 3'-hydroxyl group of the next nucleotide, creating a phosphodiester linkage.

The oxygen from the hydroxyl group of pentose sugar makes a covalent bond with the phosphorous of the phosphate group resulting in the formation of a phosphodiester bond and one water molecule is eliminated during this process. Here, diester means that two ester bonds are formed.

The alternating phosphate and pentose residues make the covalent backbone of DNA, and the nitrogenous bases may be regarded as side groups joined to the backbone at regular intervals.

DNA strand has distinct 5' and 3' ends. By definition, the 5' end lacks a nucleotide at the 5' position and the 3' end lacks a nucleotide at the 3' position.

Note: The sequence of a singles strand of nucleic acid is always written with the 5' end at the left and the 3' end at the right-that is, in the 5’to 3’ direction.

Interactions between bases

The stable DNA structure is maintained by two-mode of interactions i.e., hydrogen bonding and hydrophobic stacking interactions.

1. Hydrogen bonding

The functional groups of pyrimidine and purines contain ring nitrogen, exocyclic amino group, and carbonyl groups. Hydrogen bonds are developed between the amino and carbonyl groups of two complementary strands of nucleic acid. Double bonds are formed between A and T, while triple bonds are formed between G and C as shown in above figure.

2. Hydrophobic stacking interactions

In these interactions, two or more bases are positioned with the planes of their rings parallel just like a stack of coins. The van der Waals and dipole-dipole interactions are involved in the interaction between the bases.

The two complementary strands of DNA are coiled around each other to form a stable double-helical structure of DNA.

Structure of DNA based on hierarchical levels of complexity 

The structure of DNA makes different hierarchical levels of complexity (primary, secondary, tertiary) just like protein.

1. Primary structure

The nucleotides (Guanine, cytosine, Adenine, and Thymine) arrangement by covalent bonding into long chains of a specific sequence is called primary structure.

2. Secondary structure

The base-pairing interaction between two polymer chains (nucleotide chains) forms a secondary structure. The nucleotide Guanine makes the bond with Cytosine, while bonds are formed between Adenine and Thymine in a secondary structure of a DNA.

3. Tertiary structure

Two polymer chains are coiled to form a stable helical structure referred to as tertiary structure.

4. Quaternary structure

The complex folding of DNA molecules with proteins to form chromosome structure is called a quaternary structure.

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Double helical structure of DNA

In 1953, Watson and Crick discovered the structure of DNA as a significant event in science, an event that led to completely new fields and affected the direction of many existing ones. Double helical structure of DNA is also called Watson and Crick model. 

DNA contains two strands that wound around the same axis to form a right-handed double helical structure. The detailed structure of double helical structure of DNA is discussed below.

double helical structure of DNA
The diagram of double helical structure of DNA.

Arrangement of sugar, bases and phosphate

In a double helical structure, sugar (deoxyribose) and phosphate groups are arranged on the outside forming hydrophilic backbones. While the nitrogenous bases (purine and pyrimidine) are stacked inside the double helix. These bases with their nearly planar ring structures and hydrophobic nature and organized very close to each other and perpendicular to the long axis.

Major and minor grooves

Major groove and minor groove on the surface of the duplex are formed by the pairing of the two strands. Each nucleotide base of one strand is paired with the base of the other strand in the same plane.

Hydrogen bonding

Three hydrogen bonds are formed between Guanine and Cytosine (G ≡ C), however, only two bonds are made between Adenine and Thymine (A = T). The strong binding between Guanine and Cytosine makes the separation of two paired DNA strands difficult if the ratio of GC is higher than AT in DNA.

double helical structure of DNA
Hydrogen bonding between nitrogenous bases.

Distances between bases

Inside the double helix, the vertically stacked bases would be 0.34nm away from each other, while, each complete turn of the double helix would have a repeat distance of about 3.4nm. There are 10 base pairs present in each complete turn of the double helix.

Antiparallel strands of DNA

The two DNA strands run antiparallel to each other. One strand will run from 5’ to 3’ while the other will run from 3’ to 5’.

DNA has two complementary strands

The composition and base sequence of two antiparallel strands of double-helical DNA are not identical to each other, but rather complementary to each other. Wherever adenine exists in one chain, thymine is present in the other. Similarly, cytosine is found in one chain, guanine is found in another chain.

Interaction forces

Lastly, a double helical structure of DNA is held together by two forces i.e., hydrogen bonding between complementary base pairs and base-stacking interactions.

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