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Bacteriophages, parasitic viral particles that invade and destroy bacteria, played an historic role in the development of molecular biology. Extensive experiments during the 1940s showed how genes operate in these elementary organisms. A generation later, experiments with phages led to another crucial discovery—the restriction enzymes. These "molecular scissors", used by bacteria for protection, could be appropriated for research. They furnished a much-needed toolkit for probing and manipulating DNA, and provided the chemical key to the development of genetic engineering.

Hamilton O. Smith Courtesy Marty Katz

The discovery of restriction enzymes took place over the course of a decade or more, and demonstrated that bacteria have evolved defenses against their phage invaders. Bacteriophages that flourish naturally in one strain of bacteria are likely to fare poorly if incubated with another strain—but the few phages that do survive will prosper. This phenomenon of "host-controlled restriction" was first described in the 1950s. Werner Arber, a Swiss microbiologist, subsequently advanced a molecular explanation. He suggested that bacteria cope with phages by "restriction-modification"—genetically-controlled enzymatic reactions.

Once inside bacteria, bacteriophages consist of nothing but naked DNA. A "restriction" enzyme that degraded phages implied that it recognized a specific series of nucleotides, and cut the DNA apart at that point. At the same time, another "modification" enzyme protected the same sequence of DNA where it appeared in the host.

Most notable were the specificity of such reactions, and biochemists were excited by the potential value of restriction enzymes if they could be characterized and purified. While Arber worked with E. coli, other researchers demonstrated the same phenomenon in other species of bacteria. Hopes dimmed for a time in the late 1960s, after the first restriction enzymes to be purified would cleave stretches of DNA randomly, not at specific base sequences.

In a series of landmark papers, beginning in 1970, Hamilton Smith, a molecular biologist at Johns Hopkins University School of Medicine, outlined the results of work with Haemophilus influenzae Rd and phage P22, which naturally infects Salmonella bacteria. In 1972, he purified the first site-specific "Type II" restriction enzyme, known as Hind II. The crucial discovery came by chance: Incubating bacteria and phage together, Smith happened to notice that the phage DNA degraded over time. He and his colleagues were successful in purifying the enzyme at work, and went on to identify the short sequence of 6 base pairs in phage P22 that Hind II recognized and cut apart—always at the same location, in exactly the same way.

Building on Smith's methods, researchers soon discovered other Type II restriction enzymes. Each cleaved DNA at a specific site, from four to eight nucleotides long. Restriction enzymes enabled researchers to identify base sequences and, in combination with other tools, to manipulate DNA—and hence, genes—as never before. Perhaps the most celebrated early continuation of Smith's experiments was Daniel Nathan's work with SV40, a much-studied monkey virus. This became the starting point for Paul Berg's famous experiments, in 1972, that laid the basis for recombinant DNA research. Both genomics and the entire biotechnology industry owe, in great measure, to the discovery of restriction enzymes.

Today, more than 3,000 restriction enzymes (often called, more precisely, restriction endonucleases) have been identified. For his discovery Hamilton Smith shared the Nobel Prize in physiology or medicine in 1978, with Werner Arber, Daniel Nathans.

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