DNA is the prime genetic molecule carrying all the hereditary information within chromosomes.
The most important feature of DNA is that it is usually composed of two polynucleotide chains twisted around each other in the form of right handed double helix. These two strands are complementary to each other.
However, since each strand has a both a free 5′ hydroxyl group at one end and a free 3′ hydroxyl group at the other, each strands has a polarity or directionality. The polarity of these two strands of macromolecule are in opposite directions, and thus DNA is described as an ‘anti-parallel‘ structure.
These macro molecule structures are composed of regular repeating polymers formed from nucleotides. These are the basic building blocks of nucleic acids. The nucleotides are derived from nucleosides that are composed of two elements; a five-membered pentose sugar, known as 2′-deoxyribose and a nitrogenous base. The sugar is called 2′-deoxyribose because there is no hydroxyl at position 2′. (just two hydrogen). The carbon atom of the sugar are designated ‘prime’ (1′,2′,3′,…5′) to distinguish them from the carbon atoms of nitrogenous bases.
A nucleotide or nucleoside phosphate is fromed by the attachment of a phosphate to the 5′ position of a nucloside by an ester linkage. Such nuclotides can be joined together by the formation of a second ester bond by reaction between the terminal phosphate group of one nucleotide and the 3′ hydroxyl of another, thus generating a 5′ to 3′ phophodiester bond between adjacent sugars; this process can be repeated indefinitely to give long polynucleotide molecule.
The bases in DNA falls in to two classes; purines and pyrimidines. The purines are adenine (A) and Guanine (G) and the pyrimidines are cytosin (C) and thymine (T). The purines are derived from the double-ringed structure but with different groups attached. The pyrimidines are single-ringed structures. The bases are attached to the deoxyribose by Glucosidic linkages at N1 of the pyrimidines or N9 of the purines.
The sequence of bases at one strand is complementary to that in the other. A purine base attached to a sugar residue on one strand is always hydrogen bonded to a sugar residue on the other strand. Adenine always pairs with thymine, via two hydrogen bonds, and guanine always pairs with cytosin by three hydrogen bonds. This is called the specificity of base pairing.
These bases exists in two alternative tautomeric states. The nitrogen atoms attached to the purines and pyrimidine rings are in amino form in the predominant state and only rarely assume the imino configuration. Likewise, the oxygen atoms attached to the guanine and thymine normally have the keto form and only rarely take on the enol configuration.
The high degree of thermodynamic stability of DNA double helices result in part from the large number of hydrogen bonds between base-pairs and in part from the hydrophobic bonding (or “staking force“) between staked base-pairs.
An organic molecule in aqueous solution has all its hydrogen bonding properties satisfied with by water molecules, that comes on and off very rapidly. This means for every hydrogen bond formed requires breaking of H-bond with water molecule that was there before the base pair formed. However, when the polynucleotide chains are seperated, water molecules are lined up on the bases. when strands come together in the double helix, the water molecules are displaced from the bases. This creates disorder and increase entropy, thereby stabilizing the double helix.
DNA double helix is also stabilized by the stacking interactions between the bases. The bases are flat, relatively insoluble molecules, and they stack above each other roughly perpendicular to direction of double helix. Electron cloud interaction (Pi-Pi) between bases in the helical stacks contribute significantly to the stability of the double helix.
Hydrogen bonding is also important for the specificity of the base pairing. Suppose we tried to pair an Adenine with a Cytosine, then they have a hydrogen acceptor (N3 of cytosine) lying opposite a H-Bond acceptor (N1 of Adenine) with no room to put a water molecule in between to satisfy the two acceptors. And like wise two hydrogen bond donor opposite each other. Thus an A:C base pair is unstable in forming H-Bond.