Chemical Nature of DNA

The DNA is found in all plants, animals, prokaryotes and some viruses. In eukaryotes it is present inside the nucleus, chloroplast and mitochondria, whereas in prokaryotes it is dispersed in cytoplasm. In plants, animals and some viruses the genetic material is double stranded (ds) DNA molecule except some viruses such as ΦX174. In TMV, influenza virus poliomyelitis virus and bacteriophages the genetic material is single stranded (ss) RNA molecule (Table 1). The entire genetic message that controls the chemistry of every cell of the body acting in a specific way is actually written in the language of four nitrogenous bases of DNA i.e. purines and pyrimidines. The defined sequence of the four bases constitutes a 'gene' which may be a few or several hundred base pairs long. Genes are the structures of the blue prints called proteins which control the infinite variety of life.

Chemical Composition
Purified DNA isolated from a variety of plants, animals, bacteria and viruses has shown a complex form of polymeric compounds containing four monomers known as deoxyribonucleotide monomers or deoxyribotids (Fig.1). Each deoxyribonucleotide consists of pentose sugar (deoxyribose), a phosphate group and a nitrogenous base (either purine or pyrimidine). Purines bases (adenine and guanine) are heterocyclic and two ringed bases and the pyrimidines (thymine and cytosine) are one ringed bases. The following components of deoxyribonucleotide have been described:

(i) A five carbon ring. Deoxyribose is a pentose sugar consisting of five carbon atoms. Four carbon atoms (1', 2', 3', 4') of this sugar combine with one oxygen atom and form a ring. The fifth atom (5') forms -CH₂ group which is present outside this ring. Three -OH groups are attached at position 1', 3' and 5' and the hydrogen atoms combine at position 1', 2', 3' and 4' of carbon atoms (Fig.1). In ribonucleotides, the pentose sugar is ribose which is similar to deoxyribose except that there is an -OH group instead of -H at 2' carbon atom. The absence of -OH group in DNA makes it chemically more stable than the RNA.

(ii) Nitrogenous base. There are two nitrogenous bases, purines and pyrimidines. The purines are double ring compounds that consists of 5-membered imidazole ring with nitrogen at 1', 3', T and 9' position. The pyrimidmes are single ring compounds, the nitrogen being at position 1'and 3' in 6- membered benzene ring. A single base is attached to 1'-carbon atom of pentose sugar by N-glycosidic bond. Purines are of two types, adenine (A) and guanine (G), and pyrimidines are also of two types, thymine (T) and cytosine (C). Uracil (U) is a third pyrimidine (Fig.2). A, G and C are common in both DNA and RNA. U is found only in RNA.

Table 1. Nature of genetic material. Nucleosides and nucleotides
The nitrogenous bases combined with pentose sugar are called nucleosides. A nucleoside linked with phosphate forms a nucleotide (Fig.1).
Nucleoside = pentose sugar + nitrogenous base
Nucleotide = nucleoside + phosphate

On the basis of different nitrogenous bases the deoxynucleotides are of following types :
(i) Adenine (A) = deoxyadenosine-3'/5'-monophosphate (3'/5'-d AMP)
(ii) Guanine (G) = deoxyguanosine -5'-monophosphate (5'-d GMP)
(iii) Thymine (T) = deoxythymidine -5'-monophosphate (5'-d TMP)
(iv) Cytosine (C) = deoxycytidine -5'-monophosphate (5'-d CMP)

In addition to the presence of nucleosides in DNA helix, these are also present in nucleoplasm and cytoplasm in the form of deoxyribonucleotide phosphates e.g. deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate (dCTP), deoxythymidine triphosphate (dTTP). The advantage of these four deoxyribonucleotide in triphosphate form is that the DNA polymerase acts only on triphosphates of nucleotides during DNA replication.



Similarly, the ribonucleotides contain ribose sugar, nitrogenous bases and phosphate. Except sugar, the other components are similar. However, uracil (U) is found in RNA instead of thymine. Generally, RNA molecule is single stranded besides some exceptions.

Polynucleotide
The nucleotides undergo the process of polymerization to form a long chain of polynucleotide. The nucleotides are designated by prefixing 'poly' to each repeating unit such as poly A (polyadenylic acid), poly T (polythymidilic acid), poly G (polyguanidylic acid), poly C (polycytidilic acid) and poly U (poly uridylic acid). The polynucleotides that consists of the same repeating unit are called homopolynucleotides such as poly A, poly T, poly G, poly C and poly U.

Chargaff-equivalence Rule
By 1948, a chemist Erwin Chargaff started using paper chromatography to analyze the base composition of DNA from a number of studies. In 1950, Chargaff discovered that in the DNA of different types of organisms the total amount of purines is equal to the total amount of pyrimidines i.e. the total number of A is equal to the total number of T (A-T), and the total number of G is equal to the total number of C (G-C). It means that A/T = G/C i.e. A+T/G+C = 1. In the DNA molecules isolated from several organisms regularity exists in the base composition.

The DNA molecule of each species comprises of base composition which is not influenced either by environmental conditions or growth stages or age. The molar ratio i.e. [A] + [T]/[G]+[C] represents a characteristic composition of DNA of each species. However, in higher plants and animals A-T composition was found generally high and G-C content low, whereas the DNA molecules isolated from lower plants and animals, and bacteria and viruses was generally rich in G-C and poor in A-T contents (Table 2). The two closely related species will have very similar molar % G+C values and vice versa. Thus, the use of base composition has much significance in establishing relationship between two species and in taxonomy and phylogeny of species.

Table 2. Relative amount of nitrogenous bases in DNA isolated from different organisms.