Structure and composition of DNA

The remarkable properties of the nucleic acids, which qualify these substances to serve as the carriers of genetic information, have claimed the attention of many investigators. The groundwork was laid by pioneer biochemists who found that nucleic acids are long chainlike molecules, the backbones of which consist of repeated sequences of phosphate and sugar linkages—ribose sugar in RNA and deoxyribose sugar in DNA. Attached to the sugar links in the backbone are two kinds of nitrogenous bases: purines and pyrimidines. The purines are adenine (A) and guanine (G) in both DNA and RNA; the pyrimidines are cytosine (C) and thymine (T) in DNA and cytosine (C) and uracil (U) in RNA. A single purine or pyrimidine is attached to each sugar, and the entire phosphate-sugar-base subunit is called a nucleotide. The nucleic acids extracted from different species of animals and plants have different proportions of the four nucleotides. Some are relatively richer in adenine and thymine, while others have more guanine and cytosine. However, it was found by biochemist Erwin Chargaff that the amount of A is always equal to T, and the amount of G is always equal to C.

With the general acceptance of DNA as the chemical basis of heredity in the early 1950s, many scientists turned their attention to determining how the nitrogenous bases fit together to make up a threadlike molecule. The structure of DNA was determined by American geneticist James Watson and British biophysicist Francis Crick in 1953. Watson and Crick based their model largely on the research of British physicists Rosalind Franklin and Maurice Wilkins, who analyzed X-ray diffraction patterns to show that DNA is a double helix. The findings of Chargaff suggested to Watson and Crick that adenine was somehow paired with thymine and that guanine was paired with cytosine.

Using this information, Watson and Crick came up with their now-famous model showing DNA as a double helix composed of two intertwined chains of nucleotides, in which the adenines of one chain are linked to the thymines of the other, and the guanines in one chain are linked to the cytosines of the other. The structure resembles a ladder that has been twisted into a spiral shape: the sides of the ladder are composed of sugar and phosphate groups, and the rungs are made up of the paired nitrogenous bases. By making a wire model of the structure, it became clear that the only way the model could conform to the requirements of the molecular dimensions of DNA was if A always paired with T and G with C; in fact, the A-T and G-C pairs showed a satisfying lock-and-key fit. Although most of the bonds in DNA are strong covalent bonds, the A-T and G-C bonds are weak hydrogen bonds. However, multiple hydrogen bonds along the centre of the molecule confer enough stability to hold the two strands together.

The two strands of Watson and Crick’s double helix were antiparallel; that is, the nucleotides were arranged in opposite orientation. This can be visualized if the L shape of a nucleotide is imagined to be a sock: the neck of the sock is the nitrogenous base, the toe is the phosphate group, and the heel is the sugar group. The nucleotide chain would then be a string of socks attached heel to toe, with the necks pointing inward toward the centre of the DNA molecule. In one strand the arrangement of the sugar-phosphate backbone would be toe-heel-toe-heel and so on, and in the other strand in the same direction the arrangement would be heel-toe-heel-toe. Chemically, the heel is the 3′-hydroxyl end and the toe is the 5′-phosphate end. (These names are derived from the carbon atoms through which the sugar-phosphate linkage is made.) Therefore, one DNA strand runs from 5′ → 3′ (five prime to three prime), whereas the other runs from 3′ → 5′.

Watson and Crick noted that their proposed DNA structure fulfilled two necessary features of a hereditary molecule. First, a hereditary molecule must be capable of replication so that the information can be passed on to the next generation; therefore, Watson and Crick hypothesized that, if the two halves of the double helix could separate, they could act as templates for the synthesis of two identical double helices. Second, a hereditary molecule must contain information to guide the development of a complete organism; therefore, Watson and Crick speculated that the sequence of nucleotides might represent coded information of this sort. Subsequent research showed that their speculations on both points were correct.

DNA replication

The Watson-Crick model of the structure of DNA suggested at least three different ways that DNA might self-replicate. The experiments of Matthew Meselson and Franklin Stahl on the bacterium Escherichia coli in 1958 suggested that DNA replicates semiconservatively. Meselson and Stahl grew bacterial cells in the presence of ¹⁵N, a heavy isotope of nitrogen, so that the DNA of the cells contained ¹⁵N. These cells were then transferred to a medium containing the normal isotope of nitrogen, ¹⁴N, and allowed to go through cell division. The researchers were able to demonstrate that, in the DNA molecules of the daughter cells, one strand contained only ¹⁵N, and the other strand contained ¹⁴N. This is precisely what is expected by the semiconservative mode of replication, in which the original DNA molecules should separate into two template strands containing ¹⁵N, and the newly aligned nucleotides should all contain ¹⁴N.

The hooking together of free nucleotides in the newly synthesized strand takes place one nucleotide at a time in the 5′ → 3′ direction. An incoming free nucleotide pairs with the complementary nucleotide on the template strand, and then the 5′ end of the free nucleotide is covalently joined to the 3′ end of a nucleotide already in place. The process is then repeated. The result is a nucleotide chain, referred to chemically as a nucleotide polymer or a polynucleotide. Of course the polymer is not a random polymer; its nucleotide sequence has been directed by the nucleotide sequence of the template strand. It is this templating process that enables hereditary information to be replicated accurately and passed down through the generations. In a very real way, human DNA has been replicated in a direct line of descent from the first vertebrates that evolved hundreds of millions of years ago.

DNA replication starts at a site on the DNA called the origin of replication. In higher organisms, replication begins at multiple origins of replication and moves along the DNA in both directions outward from each origin, creating two replication “forks.” The events at both replication forks are identical. In order for DNA to replicate, however, the two strands of the double helix first must be unwound from each other. A class of enzymes called DNA topoisomerases removes helical twists by cutting a DNA strand and then resealing the cut. Enzymes called helicases then separate the two strands of the double helix, exposing two template surfaces for the alignment of free nucleotides. Beginning at the origin of replication, a complex enzyme called DNA polymerase moves along the DNA molecule, pairing nucleotides on each template strand with free complementary nucleotides. Because of the antiparallel nature of the DNA strands, new strand synthesis is different on each template. On the 3′ → 5′ template strand, polymerization proceeds in the 5′ → 3′ direction, and this growing strand is called the leading strand. However, polymerization must be carried out differently on the 5′ → 3′ template strand because nucleotides cannot be assembled in the 3′ → 5′ direction. Here short sequences of RNA are polymerized on the template. These sequences act as primers to which the DNA polymerase can add nucleotides in the 5′ → 3′ direction but in the opposite direction in which synthesis is proceeding on the lagging strand. The DNA polymerase hence makes short segments of DNA called Okazaki fragments in the “wrong” direction. For this reason the strand synthesized on the 5′ → 3′ template strand is called the lagging strand. Later, the RNA primers are removed and the Okazaki fragments are joined. This RNA priming system cannot be used to synthesize the very end of the 3′ → 5′ strand; once the last RNA primer is removed, synthesis cannot continue over the remaining gap. To overcome this obstacle, the enzyme telomerase adds multiple copies of a nucleotide sequence to the end of the DNA strand to allow completion of replication. Despite the peculiar events on the lagging strand, the entire DNA strand is eventually polymerized, and the two daughter DNA molecules thus produced are identical.