Topological techniques are well suited to the study of DNA, because DNA molecules are both long and flexible. The basic structure of duplex DNA consists of two molecular strands that are twisted together in a right-handed helix, while the two strands are joined together by bonds. Figure 7.1 illustrates how the basic structure of duplex DNA resembles a twisted ribbon.

Each strand of duplex DNA is made up of alternating sugars and phosphates, and every sugar has one of four bases attached to it. The bases (illustrated in Figure 7.2) are called adenine, thymine, cytosine, and guanine, and they are normally designated only by the first letters of their names. The letter R on each base indicates where the base is attached to a sugar.

There are bonds that attach each base on one of the strands to a base on the other strand, and thus hold the two strands together. These bonds are formed because one of the hydrogen atoms of an NH or an NH2 on one base bonds with an N or an O, respectively, on the other base. The base A on one strand is always bonded with the base T on the other strand, and the base C on one strand is always bonded with the base G on the other strand. In Figure 7.3 we illustrate the hydrogen bonding between the bases A and T, and between the bases C and G. A pair of bases, which are bonded together, is referred to as a base pair of the molecule.