The discovery that DNA is the prime genetic molecule, carrying all the hereditary information within chromosomes, immediately focused attention on its structure. It was hoped that knowledge of the structure would reveal how DNA carries the genetic messages that are replicated when chromosomes divide to produce two identical copies of themselves. During the late 1940s and early 1950s, several research groups in the United States and in Europe engaged in serious efforts—both cooperative and rival—to understand how the atoms of DNA are linked together by covalent bonds and how the resulting molecules are arranged in three-dimensional space. Not surprisingly, there initially were fears that DNA might have very complicated and perhaps bizarre structures that differed radically from one gene to another. Great relief, if not general elation, was thus expressed when the fundamental DNA structure was found to be the double helix. It told us that all genes have roughly the same three-dimensional form and that the differences between two genes reside in the order and number of their four nucleotide building blocks along the complementary strands.

ow, some 50 years after the discovery of the double helix, this simple description of the genetic material remains true and has not had to be appreciably altered to accommodate new findings. Nevertheless, we have come to realize that the structure of DNA is not quite as uniform as was first thought. For example, the chromosome of some small viruses have single-stranded, not double-stranded, molecules. Moreover, the precise orientation of the base pairs varies slightly from base pair to base pair in a manner that is influenced by the local DNA sequence. Some DNA sequences even permit the double helix to twist in the left-handed sense, as opposed to the right-handed sense originally formulated for DNA’s general structure. And while some DNA molecules are linear, others are circular. Still additional complexity comes from the supercoiling (further twisting) of the double helix, often around cores of DNA-binding proteins.

Likewise, we now realize that RNA, which at first glance appears to be very similar to DNA, has its own distinctive structural features. It is principally found as a single-stranded molecule. Yet by means of intra-strand base pairing, RNA exhibits extensive double-helical character and is capable of folding into a wealth of diverse tertiary structures. These structures are full of surprises, such as non-classical base pairs, base-backbone interactions, and knot-like configurations. Most remarkable of all, and of profound evolutionary significance, some RNA molecules are enzymes that carry out reactions that are at the core of information transfer from nucleic acid to protein. Clearly, the structures of DNA and RNA are richer and more intricate than was at first appreciated. Indeed, there is no one generic structure for DNA and RNA. As we shall see in this chapter, there are in fact variations on common themes of structure that arise from the unique physical, chemical, and topological properties of the polynucleotide chain.

DNA Is Composed of Polynucleotide Chains

The most important feature of DNA is that it is usually composed of two polynucleotide chains twisted around each other in the form of a double helix (Figure 6-1). The upper part of the figure (a) presents the structure of the double helix shown in a schematic form. Note that if inverted 180° (for example, by turning this book upside-down), the double helix looks superficially the same, due to the complementary nature of the two DNA strands. The space-filling model of the double helix, in the lower part of the figure (b), shows the components of the DNA molecule and their relative positions in the helical structure. The backbone of each strand of the helix is composed of alternating sugar and phosphate residues; the bases project inward but are accessible through the major and minor grooves.

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