According to J.D. Watson and F.H.C. Crick (1953) deoxyribonucleic acid has a double helical structure. It consists of two polynucleotide chains connected by hydrogen bonds running in opposite directions.
Deoxyribonucleic acid (DNA) is the fundamental building block of all living cells. It is a polymer consisting of a large repetition of monomer sequences. The monomer units of DNA are nucleotides. Each nucleotide consists of three components, deoxyriose (a 5-carbon sugar), a nitrogen-containing base attached to the sugar, and a phosphate group.
Nucleic acid molecule is a long chain polymer (polynucleotide) composed of monomeric units, termed as nucleotides. Each nucleotide consists of a nucleoside and a phosphate group and each nucleoside in its turn consists of a sugar molecule and a base. The sugar is ribose in case of RNA and deoxyribose in case of DNA.
The bases are of two types namely, pyrimidines and purines. The pyrimidines can be numbered in two different manners. There are three main pyrimidine bases occurring in nucleic acid, namely, thymine, cytosine and uracil. While cytosine and thymine commonly occur in DNA cytosine and uracil commonly occur in RNA. In RNA uracil replaces thymine.
Similarly, there are two main purine bases, adenine and guanine.
A base in combination with the sugar molecule is termed as nucleoside. Following are the four different nucleotides occuring in DNA.
In case of RNA, ribose replaces deoxyribose and uracil replaces thymine. Corresponding nucleosides would therefore be
In a nucleoside, carbon number 1 in sugar links with nitrogen at position number 3 in pyrimidines and at position number 9 in purines.
Nucleotide comes from a nucleoside by the addition of a molecule of phosphoric acid. The phosphate molecule links with sugar molecule at carbon number 5 or at carbon number 3. Correspondingly nucleotides will be termed as 5′ p3′ OH nucleotide and 3′ p5′ OH nucleotide. In case of ribose, the phosphate group may be linked even at carbon number 2 of ribose sugar, because hydroxyl group is available at position number 2 also. However in biological systems nucleotides have phosphate either at 5′ position or at 3′ position. Following are the four nucleotides occurring in DNA
- Deoxycytidylic acid or deoxycytidylate
- Deoxythymidylic acids or deoxythymidylate
- Deoxyadenylic acids or deoxyadenylate
- Deoxyguanylic acids or deoxyguanylate
Following are the four nucleotides occurring in RNA
- Cytidylic acid or cytidylate
- Uridylic acid or uridylate
- Adenylic acid or adenylate
- Guanylic acid or guanylate
A number of nucleotide monomer units may give rise to a polynucleotide chain through the formation of phosphodiester bonds (a diester bond is one which involves two ester bonds). A phosphodiester bond will be formed between any two adjacent nucleotides. A polynucleotide chain would have a direction so that, if it starts from C³, it would end in C5 and if it starts from C5 it would end in C³. Normally, therefore, whether we are referring to a mononucleotide or else to a polynucleotide we should indicate the groups between at C5 end. It could be either a phosphate group or a hydroxyl group. For instance, 5′ p3′ OH dinucleotide could mean that it is a polynucleotide with only two nucleotide units and has phosphate group at the 5′ end and a hydroxyl group at the 3′ end.
Structure of Deoxyribonucleic Acid (DNA)
Following are some of the characteristic feature of double helical structure of DNA
1. Each nucleotide consists of sugar, phosphate and nitrogenous base. Many such nucleotides link by phosphodiester bonds, thus forming a polynucleotide chain or strand.
2. Phosphodiester bonds form between 5’ carbon of sugar of one molecule and 3’ carbon of sugar of the next nucleotide.
3. Nitrogenous base is attached to 1’ carbon of sugar. At this place purine base is attached by its 9’ position and pyrimidine by its 3’ position.
4. Polynucleotide strand is made of backbone of sugar and phosphate thus forming its long axis and bases at right angles to it.
5. Chargaff’s rule that in natural DNAs, the base ratio A/T is always close to unity and the G/C ratio also is always close to unity indicating that A always pairs with T and G pairs with C. A and T, and G and C are therefore complementary base pairs. Thus, if one DNA strand has A, the other would have T and if it has G, the other would have C. Thus, if the base sequence of one strand is CAT TAG GAC, the base sequence of the other strand would be GTA ATC CTG. Hence, the two polynucleotide strands are complementary to one another.
6. Two such complementary strands join with one another by hydrogen bonds between their complementary nitrogenous bases. Thus, there are three hydrogen bonds between cytosine and guanine and two hydrogen bonds between adenine and thymine.
7. The two polynucleotide chains coils helically around the same axis in such a way that these can separate from one another only by uncoiling. Helical coiling is supposed to be right handed. This right handed form of DNA is now termed as B-DNA.
8. The two chains or strands are antiparallel, i.e., they run in opposite direction in relation to their sugar molecules. Thus, their 5’p-3’OH phosphodiester links are in opposite directions.
9. Double stranded DNA molecule has a diameter of 20 angstrom i.e., the distance between two polynucleotide strands is 20 angstrom.
10. The helix makes one complete turn every 34 angstrom along its length. This is also the diameter of the helix. There are 10 nucleotides per turn of helix. Thus the distance between two neighbouring base pairs is 3.4 angstrom (Å).