Principles of Biochemistry, Volume 3 - A. Lehninger 1985

Molecular Mechanisms of Genetic Information Transfer
DNA: Structure of Chromosomes and Genes
Watson and Crick postulated the double helix model of DNA

We have already seen how the Introduction/13.html">Structure of Fibrous and Globular Proteins was elucidated (Chapters 7 and 8) using the highly effective method of X-Ray Diffraction Analysis based on the scattering of X-rays. Using X-ray diffraction of DNA fibers, Rosalind Franklin and Maurice Wilkins obtained a characteristic diffraction pattern (Fig. 27-8). Based on this X-ray photograph, it was concluded that DNA polymer chains exhibit Two Types of periodicity along their long axis: 0.34 and 3.4 nm. The challenge was to construct a three-dimensional model of the DNA molecule that could account not only for the presence of these periodicities, but also for the specific base ratios discovered by Chargaff (A = T and G = C).

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Fig. 27-8. X-ray diffraction pattern of DNA. The X-shaped arrangement of reflections indicates the helical STRUCTURE OF THE molecule. The heavily darkened regions at the top and bottom of the photograph correspond to adjacent DNA bases.

Fig. 27-9. Watson and Crick with one of their DNA models (photographed in 1953).

Fig. 27-10. The model of DNA Structure proposed by Watson and Crick. A. Wire-frame model. B. Space-filling model representing atomic volumes.

In 1953, American geneticist James Watson and English physicist Francis Crick, As a result of their work at the University of Cambridge, proposed a three-dimensional model of DNA that accounted for both the X-ray diffraction data and the characteristic base pairing of DNA (Fig. 27-10). The model consists of two DNA chains coiled right-handedly around the same axis to form a double helix. The two chains in this helix are antiparallel, meaning their 5', 3'-internucleotide phosphodiester bridges run in opposite directions. The hydrophilic backbones of the chains, composed of alternating deoxyribose residues and negatively charged phosphate groups, are located on the outside of The Double Helix, facing the surrounding Water. The hydrophobic purine and pyrimidine bases of both chains are stacked inside the double helix, so that the nearly flat base molecules are closely spaced and oriented perpendicular to the long axis of the double helix. The spatial arrangement of the chains results in The formation of Major and minor grooves. The bases of one chain are paired with the bases lying in the same plane in the other chain. Within this structure, only specific Base Pairs fit precisely. These complementary pairs are always purine-pyrmidine pairs, specifically A–T and G–C pairs—the very pairs formed by the bases found in equivalent amounts in DNA preparations, as demonstrated by Chargaff (Table 27-3). Moreover, the bases of each pair are close enough for Hydrogen Bonds to form between them. How hydrogen bonds form between adenine and thymine, and between guanine and cytosine, is shown in Fig. 27-11. It is important to note that three Hydrogen bonds are formed between G and C (G≡C), whereas only two are formed between A and T (A=T). Other base pairs do not fit into The structure of the double helix. A base pair composed of two Purines (A and G) is too large to fit inside a helix of these parameters, while the bases in a C–T pair are too far apart to form stable hydrogen bonds. Furthermore, while maintaining its position in the helix, A cannot form hydrogen bonds with C, nor G with T.

Fig. 27-11. Scale structural formulas and space-filling models of hydrogen-bonded base pairs in adenine-thymine and guanine-cytosine. The first pair is formed by two hydrogen bonds, and the second by three hydrogen bonds. G–C pairs are packed somewhat more compactly in space than A–T pairs.

To account for the periodicities observed in X-ray diffraction analysis, Watson and Crick demonstrated using molecular models that the bases stacked inside the double helix must be spaced 0.34 nm apart. These models also showed that the other periodicity of 3.4 nm can be explained by the fact that there are about 10 nucleotide residues per complete turn of the double helix (Fig. 27-10). The diameter of the double helix is approximately 2 nm. It is crucial to note that the two antiparallel polynucleotide chains of the DNA double helix are identical neither in base sequence nor in nucleotide composition, as can be seen in Fig. 27-12. However, they are complementary to each other. Wherever adenine appears in one chain, thymine is invariably found opposite it in the other chain; likewise, if guanine is in one chain, cytosine is invariably present opposite it in the other.

The chains forming the DNA double helix (or duplex, as the double helix is often called) are held together by hydrogen bonds between complementary bases (Fig. 27-11) and by hydrophobic interactions, which largely shield the stacked bases inside the double helix and protect them from water, while the highly polar backbones of the polymer chains are located on the outside, exposed to water. Hydrophobic interactions make the primary contribution to maintaining the Stability of the double helix, much like in the tertiary Structure of Globular proteins (Section 8.6). Note that at pH 7, all phosphate groups in the polar backbones of the double helix are ionized and negatively charged, making DNA a strong acid.

Fig. 27-12. Schematic representation of complementary antiparallel DNA chains According to the Watson-Crick model. Note that the chains differ in base composition as well as in sequence when each chain is read in the 5'→3' direction. Also note that the equalities A = T and G = C are satisfied.

Extensive evidence—both chemical and biological—indicates that the double-helix model of DNA is essentially correct. Let us now examine how this structure ensures the accurate Replication of Genetic information.