A deoxyribonucleic acid (DNA) molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. The chains run antiparallel to each other, and hydrogen bonds between the base portions of the nucleotides hold the two chains together (Figure 4–3). As we saw in Chapter 2 (Panel 2–6, pp. 100–101), nucleotides are composed of a five-carbon sugar to which are attached one or more phosphate groups and a nitrogen-containing base. In the case of the nucleotides in DNA, the sugar is deoxyribose attached to a single phosphate group (hence the name deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “backbone” of alternating sugar–phosphate–sugar–phosphate. Because only the base differs in each of the four types of nucleotide subunit, each polynucleotide chain in DNA is analogous to a sugar-phosphate necklace (the backbone), from which hang the four types of beads (the bases A, C, G, and T). These same symbols (A, C, G, and T) are commonly used to denote either the four bases or the four entire nucleotides—that is, the bases with their attached sugar and phosphate groups.
The way in which the nucleotides are linked together gives a DNA strand a chemical polarity. If we think of each sugar as a block with a protruding knob (the 5ʹ phosphate) on one side and a hole (the 3ʹ hydroxyl) on the other (see Figure 4–3), each completed chain, formed by interlocking knobs with holes, will have all of its subunits lined up in the same orientation. Moreover, the two ends of the chain will be easily distinguishable, as one has a hole (the 3ʹ hydroxyl) and the other a knob (the 5ʹ phosphate) at its terminus. This polarity in a DNA chain is indicated by referring to one end as the 3ʹ end and the other as the 5ʹ end, names derived from the orientation of the deoxyribose sugar. With respect to DNA’s building blocks of DNA DNA strand information-carrying capacity, the chain of nucleotides in a DNA strand, being both directional and linear, can be read in much the same way as the letters on this page.
The three-dimensional structure of DNA—the DNA double helix—arises from the chemical and structural features of its two polynucleotide chains. Because these two chains are held together by hydrogen-bonding between the bases on the different strands, all the bases are on the inside of the double helix, and the sugar-phosphate backbones are on the outside (see Figure 4–3). In each case, a bulkier two-ring base (a purine; see Panel 2–6, pp. 100–101) is paired with a single-ring base (a pyrimidine): A always pairs with T, and G with C (Figure 4–4). This complementary base-pairing enables the base pairs to be packed in the energetically most favorable arrangement in the interior of the double helix. In this arrangement, each base pair is of similar width, thus holding the sugar-phosphate backbones a constant distance apart along the DNA molecule. To maximize the efficiency of base-pair packing, the two sugar-phosphate backbones wind around each other to form a right-handed double helix, with one complete turn every ten base pairs (Figure 4–5).