DNA is the material of which genes are made. This had not not been widely accepted until 1953 when J.D. Watson and F.H, Crick proposed a structure for DNA which accounted for its ability to self--replicate and to direct the synthesis of proteins. The usual configuration of DNA is as following. Two strands of repeated chemical units are coiled together into a double helix. Each strand has a backbone of alternating deoxyribose residues and phosphate groups.
Attached to each sugar residue is one of the four essentially planar nitrogenic organic bases: Adenine A, Cytosine C, Guanine G, Thymine T, The plane of each base is essentially perpendicular to the helix axis. Encoded in the order of the bases along a strand is the hereditary information.
The two strands coil about each other so that all the bases project inward towards the helix axis. The two strands are held together by hydrogen bonds linking each base projecting from one backbone to its complementary base projecting from another backbone. The base A always binds to T and C always binds to G. The order of bases on one strand implies that on the other strand. (The two strands are termed complementary.) This complementary pairing allows DNA to serve as a template for its own replication.
A and G are purines and C and T are pyrimidines. So, we see that purines always pair with pyrimidines. The A-T pair is held together by 2 hydrogen bonds whereas the G-C pair is connected by 3 hydrogen bonds, and so is stronger.
Each strand of DNA is a polymer made up of four repeated units called deoxyribonucleotides, or simply nucleotides. The four nucleotides are regarded as the monomers of DNA because the nucleotides are the units added as a strand of DNA is being synthesized. Each nucleotide is usually designated by the symbol of the base it contains.
Linking any two sugar residues is an -O--P--O-, a phosphate bridge between the 3' carbon atom of one of the sugars and the 5' carbon atom of the other sugar. (The 3' and 5' designations come from standard notation for labeling atoms in organic molecules). When a DNA molecule is broken into pieces, the breaks usually occur at one of the covalent bonds in each bridge.
Note that in solution DNA is negatively charged due to the presence of the phosphate group.
Because deoxyribose has an asymmetric structure, the ends of each strand of a DNA fragment are different. At one end the terminal carbon atom in the backbone is the 5' carbon atom of the terminal sugar (the carbon atom that lies outside the planar portion of the sugar); and at the other end it is the 3' carbon atom (one that lies within the planar portion of the sugar).
The two complementary strands of DNA are antiparallel (i.e, 5' end to 3' end directions for each strand are opposite). Usually, DNA is represented by showing the strand where the left to right direction corresponds to 5' to 3' direction. ( Los Alamos Science,[2])
For instance ACT (or equivalently AGT) notation my be written in equivalent form:
5'-ACT-3' 3'-TGA-5'