Even before the structure of DNA was elucidated, genetic studies indicated that the hereditary material must have three key properties:

Consider the discovery of the double-helical structure of DNA by Watson and Crick as the solution to a complicated three-dimensional puzzle. To solve this puzzle, Watson and Crick used a process called “model building” in which they assembled the results of earlier and ongoing experiments (the puzzle pieces) to form the three-dimensional puzzle (the double-helix model). To understand how they did so, we first need to know what pieces of the puzzle were available to Watson and Crick in 1953.

The building blocks of DNA The first piece of the puzzle was knowledge of the basic building blocks of DNA. As a chemical, DNA is quite simple. It contains three types of chemical components: (1) phosphate, (2) a sugar called deoxyribose, and (3) four nitrogenous bases—adenine, guanine, cytosine, and thymine. The sugar in DNA is called “deoxyribose” because it has only a hydrogen atom (H) at the 2′-carbon atom, unlike ribose (a component of RNA), which has a hydroxyl (OH) group at that position. Two of the bases, adenine and guanine, have a double-ring structure characteristic of a type of chemical called a purine. The other two bases, cytosine and thymine, have a single-ring structure of a type called a pyrimidine.

The carbon atoms in the bases are assigned numbers for ease of reference. The carbon atoms in the sugar group also are assigned numbers—in this case, the number is followed by a prime (1′, 2′, and so forth).

The chemical components of DNA are arranged into groups called nucleotides, each composed of a phosphate group, a deoxyribose sugar molecule, and any one of the four bases (Figure 7-5). It is convenient to refer to each nucleotide by the first letter of the name of its base: A, G, C, or T. The nucleotide with the adenine base is called deoxyadenosine 5′-monophosphate, where the 5′ refers to the position of the carbon atom in the sugar ring to which the single (mono) phosphate group is attached.

265

Chargaff’s rules of base composition The second piece of the puzzle used by Watson and Crick came from work done several years earlier by Erwin Chargaff. Studying a large selection of DNAs from different organisms (Table 7-1), Chargaff established certain empirical rules about the amounts of each type of nucleotide found in DNA:

266

X-ray diffraction analysis of DNA The third and most controversial piece of the puzzle came from X-ray diffraction data on DNA structure that were collected by Rosalind Franklin when she was in the laboratory of Maurice Wilkins (Figure 7-6). In such experiments, X rays are fired at DNA fibers, and the scatter of the rays from the fibers is observed by catching the rays on photographic film, on which the X rays produce spots. The angle of scatter represented by each spot on the film gives information about the position of an atom or certain groups of atoms in the DNA molecule. This procedure is not simple to carry out (or to explain), and the interpretation of the spot patterns requires complex mathematical treatment that is beyond the scope of this text. The available data suggested that DNA is long and skinny and that it has two similar parts that are parallel to each other and run along the length of the molecule. The X-ray data showed the molecule to be helical (spiral-like). Unknown to Rosalind Franklin, her best X-ray picture was shown to Watson and Crick by Maurice Wilkins, and it was this crucial piece of the puzzle that allowed them to deduce the three-dimensional structure that could account for the X-ray spot patterns.

267

A 1953 paper by Watson and Crick in the journal Nature began with two sentences that ushered in a new age of biology: “We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.”¹ The structure of DNA had been a subject of great debate since the experiments of Avery and co-workers in 1944. As we have seen, the general composition of DNA was known, but how the parts fit together was not known. The structure had to fulfill the main requirements for a hereditary molecule: the ability to store information, the ability to be replicated, and the ability to mutate.

The three-dimensional structure derived by Watson and Crick is composed of two side-by-side chains (“strands”) of nucleotides twisted into the shape of a double helix (Figure 7-7). The two nucleotide strands are held together by hydrogen bonds between the bases of each strand, forming a structure like a spiral staircase (Figure 7-8a). The backbone of each strand is formed of alternating phosphate and deoxyribose sugar units that are connected by phosphodiester linkages (Figure 7-8b). We can use these linkages to describe how a nucleotide chain is organized. As already mentioned, the carbon atoms of the sugar groups are numbered 1′ through 5′. A phosphodiester linkage connects the 5′-carbon atom of one deoxyribose to the 3′-carbon atom of the adjacent deoxyribose. Thus, each sugar–phosphate backbone is said to have a 5′-to-3′ polarity, or direction, and understanding this polarity is essential in understanding how DNA fulfills its roles. In the double-stranded DNA molecule, the two backbones are in opposite, or antiparallel, orientation (see Figure 7-8b).

Each base is attached to the 1′-carbon atom of a deoxyribose sugar in the backbone of each strand and faces inward toward a base on the other strand. Hydrogen bonds between pairs of bases hold the two strands of the DNA molecule together. The hydrogen bonds are indicated by dashed lines in Figure 7-8b.

Two complementary nucleotide strands paired in an antiparallel manner automatically assume a double-helical conformation (Figure 7-9), mainly through the interaction of the base pairs. The base pairs, which are flat planar structures, stack on top of one another at the center of the double helix (see Figure 7-9a). Stacking adds to the stability of the DNA molecule by excluding water molecules from the spaces between the base pairs. The most stable form that results from base stacking is a double helix with two distinct sizes of grooves running in a spiral: the major groove and the minor groove, which can be seen in both the ribbon and the space-filling models of Figure 7-9a and 7-9b. Most DNA–protein associations are in major grooves. A single strand of nucleotides has no helical structure; the helical shape of DNA depends entirely on the pairing and stacking of the bases in the antiparallel strands. DNA is a right-handed helix; in other words, it has the same structure as that of a screw that would be screwed into place by using a clockwise turning motion.

The double helix accounted nicely for the X-ray data and successfully accounted for Chargaff’s data. By studying models that they made of the structure, Watson and Crick realized that the observed radius of the double helix (known from the X-ray data) would be explained if a purine base always pairs (by hydrogen bonding) with a pyrimidine base (Figure 7-10). Such pairing would account for the (A + G) = (T + C) regularity observed by Chargaff, but it would predict four possible pairings: T A, T···G, C A, and C···G. Chargaff’s data, however, indicate that T pairs only with A, and C pairs only with G. Watson and Crick concluded that each base pair consists of one purine base and one pyrimidine base, paired according to the following rule: G pairs with C, and A pairs with T.

268

Note that the G–C pair has three hydrogen bonds, whereas the A–T pair has only two (see Figure 7-8b). We would predict that DNA containing many G–C pairs would be more stable than DNA containing many A–T pairs. In fact, this prediction is confirmed. Heat causes the two strands of DNA double helix to separate (a process called DNA melting or DNA denaturation); DNAs with higher G + C content can be shown to require higher temperatures to melt because of the greater attraction of the G–C pairing.

269

Watson and Crick’s discovery of the structure of DNA is considered by some to be the most important biological discovery of the twentieth century and led to their being awarded the Nobel Prize with Maurice Wilkins in 1962 (Rosalind Franklin died of cancer in 1958 and the prize is not awarded posthumously). The reason that this discovery is considered so important is that the double helix model, in addition to being consistent with earlier data about DNA structure, fulfilled the three requirements for a hereditary substance:

270