To analyze the structure of DNA at the molecular level, imagine being able to magnify a small piece of a gene about 5 million times. What you would see is one of the great marvels of life. The pieces of this molecular puzzle were finally worked out by James Watson and Francis Crick in 1953. They determined that DNA is a giant molecule with two strands bound together into a double helix. The structure of DNA is universal, except in some viruses that contain single-stranded DNA.
The basic unit of DNA structure is a nucleotide, composed of phosphate, deoxyribose sugar, and a nitrogenous base, as shown in this simplified model (figure1):
Fig1. Simplified structure of DNA. Nucleotides stack together to form two opposing strands held together by hydrogen bonds between the base pairs.
Figure 2 lays out the structure of DNA going from general (a,b,c) to specific (d). To make the vertical sugar-phosphate backbones of the molecule, each deoxyribose sugar bonds covalently in a repeating pattern with two phosphates. One of the bonds is to the number 5′ (read “five prime”) carbon on deoxyribose, and the other is to the 3′ (three prime) carbon. This pattern dictates the direction of the strands, which run opposite to each other, as shown in figure 2d.
Fig2. Levels of DNA structure. (a) A space-filling model of DNA shows its basic configuration as a double helix of sugar-phosphate backbones holding the nitrogenous bases between them. (b) The twisted ladder model depicts how the complementary nitrogenous bases (bars) pair with each other across the center of the molecule. (c) A schematic lays out the basic chemical makeup and bonding pattern of the molecule. (d) A more detailed view of the base pairs, hydrogen bonds, and the antiparallel arrangement of the two helices. Note that in one strand, the deoxyribose-phosphate runs in the 5′ to 3′ direction and the other side is oriented from 3′ to 5′
The bases—purines and pyrimidines—attach by covalent bonds at the 1′ position of the sugar (figure 2c, d). When these bases span the center of the molecule and bind with their complementary bases from the opposite strand, they form a double stranded helix. The paired bases are held together by hydrogen bonds, which can be readily broken, allowing the molecule to be “unzipped” into two strands. This feature is of great importance in gaining access to the information encoded in the base sequence. Pairing is not random; it is dictated by the structure of the bases and how they align to form hydrogen bonds. Thus, in DNA, the purine adenine (A) pairs with the pyrimidine thymine (T), and the purine guanine (G) pairs with the pyrimidine cytosine (C). Note that adenine forms two hydrogen bonds with thymine, and cytosine forms three hydrogen bonds with guanine. This difference will influence a number of DNA functions. Like the letters in a book, the sequence of base pairs along the DNA molecule can assume any order, resulting in an infinite number of possible nucleotide sequences.
As mentioned previously, one side of the helix runs in the opposite direction of the other, in what is called an antiparallel arrangement. Using the order of the bond between the carbon on deoxyribose and the phosphates, we see that one helix runs from the 5′ to 3′ direction and the other runs from the 3′ to 5′ direction (figure 2d). This characteristic is a significant factor in DNA syn thesis, transcription, and translation.
