Organization, Replication, and Types of DNA in Vivo 



309 



common patterns showed, besides the 3.4 A 

 repetition, other repeat units which would be 

 explained only if DNA usually does not occur 

 as a single strand. (On the other hand, X-ray 

 diffraction studies show that RNA is usually 

 single stranded.) Here, then, was a clear 

 demonstration that there is a secondary 

 structure to DNA which was hitherto un- 

 expected, and there was every reason to 

 believe this was the organization normally 

 found in the chromosome. The simplest 

 explanation consistent with the diffraction 

 results was proposed by J. D. Watson and 

 F. H. C. Crick (see the 1953a reference to 

 them at the end of this Chapter). They 

 hypothesized that DNA is normally two- 

 stranded (see Figure 34-3). Each strand is a 

 polynucleotide, and the two strands are coiled 

 around each other in such a manner that they 

 cannot be separated unless the ends are per- 

 mitted to revolve. This kind of coiling is 

 plectonemic (as is found in the strands of a 

 rope) and can be contrasted with paranemic 

 coiling in which two coils can be separated 

 without their ends revolving (just as two 

 bedsprings pushed together can be sepa- 

 rated). 



The Watson-Crick model for the secondary 

 organization of DNA macromolecules in- 

 volves a double helix in which each strand is 

 coiled right-handedly (i.e., clockwise). This is 

 the same direction of coil as is found in the 

 secondary structure of polypeptides (see p. 

 286). The model shows the pentose and 

 phosphate backbone of each strand on the 

 outside of the spiral, while the relatively flat 

 bases which project into the center lie perpen- 

 dicular to the long axis of the fiber. The 

 backbone completes a turn each 34 A. Since 

 each nucleotide occupies 3.4 A along the 

 length of a strand, there are 10 nucleotides 

 per complete turn and each nucleotide has a 

 pitch of 36° relative to the long axis (so that 

 10 nucleotides complete the 360° required for 

 a complete turn). 



The two helices are held together by chemi- 



cal bonds between bases on different strands. 

 It has been found that the two strands can 

 form a regular double helix, whose diam- 

 eter is uniformly 20 A, only if the bases on 

 different strands join in pairs, each of which 

 is composed of one pyrimidine and one 

 purine. Two pyrimidines together (being 

 single rings) would be too short to bridge the 

 gap between backbones, while two purines 

 (being double rings) would take up too much 

 space. Moreover, the pyrimidine-purine pair- 

 ing must be either between C and G or be- 

 tween T and A, for only in this way is the 

 maximum number of stabilizing bondages 

 between them produced. The type of stabiliz- 

 ing bond holding the members of a base pair 

 together is called a hydrogen bond or "//" 

 bond."" The base pairs, with their H bonds 

 shown as dotted lines, are diagrammed in 

 Figure 34-4. (All these diagrams really 

 should be at a 36° tilt from the horizontal.) 

 The top half of the Figure shows the C-G 

 (and G-C) arrangements. Note, in the C-G 

 pair, that cytosine has been turned over (from 

 left to right) relative to the way it was dia- 

 grammed in Figure 33-3. Three H bonds 

 are formed. Two occur between NH2 and O 

 (the 6— NH2 of C with the 6— O of G; the 

 2—0 of C with the 2— NH, of G), and one 

 occurs between the 1 — N of C and the 

 1 NH of G. The G;C pair is identical to 

 C;G, as shown, except that, in this case, the 

 base turned over is guanine. 



The bottom half of Figure 34-4 shows the 

 other type of base pair (T:A or A:T, in 

 which T and A, respectively, have been 

 turned over relative to the way they were 

 shown in Figures 33-3 and 33-4). In this 

 pair only two H bonds are formed, one be- 

 tween the 6 — O of T and the 6 — NH2 of A, 

 and the other between the 1 — NH of T and 

 the 1 — N of A. Although the H bond is a 

 weak electrostatic bond (requiring only about 

 5 kcal of energy to break the H bond in 

 N — H . . . O, whereas a regular C — C bond 

 would require 50-100 kcal for breakage), there 



