When Nathans decided at last to pursue a career in medical science rather than clinical medicine, he received two attractive job offers: Oliver Lowry at WUSM offered him a position in the pharmacology department, and W. Barry Wood, formerly of WUSM, offered one in the microbiology department at JHU. In 1962, Nathans accepted Wood's offer, which would provide an opportunity to work and to recruit others in the exciting new area of molecular biology. Wood was an exemplary department chief and role model for Nathans, placing a high value on teaching but also taking pride in his faculty's research accomplishments and making sure they had the facilities, time, and collegial setting for creative research.

In his first years at JHU, Nathans continued work on several protein synthesis projects that he had begun at the Rockefeller Institute. First he continued his investigation (begun with Amos Neidle) of how the antibiotic puromycin blocks protein synthesis in cells. Nathans and other researchers had used puromycin and other early antibiotics to inhibit protein synthesis in their cell-free experiments, without knowing their exact mechanism of action. By the early 1960s, biochemists had learned that synthesis began with activation of amino acids and their attachment to tRNA molecules. These aminoacyl-tRNA complexes then go to the ribosomes, where the amino acids are assembled sequentially into protein chains (according to the "code" of the messenger RNA), and the tRNA molecules are released. Michael Yarmolinsky had found that puromycin blocked protein synthesis at a specific point, where tRNA drops off the amino acid at the ribosome. He also noted that the structure of puromycin was analogous to the amino-acid bearing end of tRNA. Nathans' research demonstrated that puromycin matches tRNA structure closely enough to substitute for it in the protein "assembly line," but though it bonds to the growing peptide chain, its free end isn't configured properly for attachment of subsequent amino acids. That is, puromycin can attach itself to the growing chain of amino acids, but can't accept any further links, so the chain is terminated at that point.

Nathans also continued to explore problems raised in his work on RNA viruses with Norton Zinder. Their protein synthesis experiment with f2 RNA had generated mostly the virus coat protein; however, they had detected other substances, such as the amino acid histidine, which wasn't a component of the coat protein. Working with a related RNA virus, MS2, Nathans and his colleagues used radioactively labeled amino acids to find out what other products the virus RNA was generating. Besides the virus coat protein, they also found small amounts of RNA synthetase (the enzyme needed for RNA replication) and another protein (later called the "maturation" or "A" protein) also required for replication. In later MS2 studies they analyzed the proteins synthesized by intact and mutated forms of the virus, and fragments of the viral RNA under various conditions. These experiments enabled them to infer which parts of the RNA coded for which proteins, and how the protein production was regulated. The methods and techniques that Nathans used here--analyzing fragments of RNA for activity--would transfer nicely to the next phase of his work.

Nathans' research interests began turning in a new direction during the mid-1960s, when all the virologists in his department moved on to more senior positions, and the remaining faculty had to pick up their courses until replacements arrived. Wood asked him to give a series of lectures on tumor viruses, an area Nathans knew little about. Reading up on the topic in preparation for the lectures, Nathans became intrigued: "It was quite clear that tumor viruses, like the phages that had been so well studied, were beautiful models of genetic mechanisms in mammalian cells. . . and [thus would be useful] for studying such mechanisms with the techniques that were so successful with phages." He was also impressed with the wondrous things that such viruses could do to the growth of animal cells in culture--it suggested that tumor viruses would be a relatively simple model system for understanding cell growth, growth controls, and tumor genesis. He decided to pursue this line of inquiry, and in 1969 arranged for a six-month sabbatical at Israel's Weizmann Institute to learn more about cell-culture techniques and tumor viruses.

At the Weizmann Institute, Nathans worked closely with Ernest Winocour and Leo Sachs, who were doing innovative research on tumor viruses. Like several other researchers, including Paul Berg and Sol Spiegelman, he chose to study SV40, a DNA virus, because of its simplicity and small size. As he was starting to plan how to approach the genetics of SV40 in a combined genetic and chemical way, his colleague Hamilton Smith wrote to him, describing an interesting enzyme he'd found in Haemophilus influenzae bacteria that degraded the DNA of bacterial viruses. It had the biochemical properties of a restriction enzyme [see exhibit section "Restriction Enzymes and the New Genetics,"] and he and Thomas Kelly had determined that it cut non-Haemophilus DNA at a specific site, i.e., there was a specific sequence at the ends of the cut DNA. Exploring the extant literature on restriction enzymes, Nathans realized that he might be able to use them to digest DNA molecules into specific fragments for analysis, just as he had used the enzymes trypsin and chymotrypsin to break up protein molecules at specific sites in his earlier work. If he could isolate individual pieces of the SV40 genome, he might be able to determine which parts of the DNA were responsible for its various activities. He started planning the SV40 experiments that would introduce restriction enzymes as the primary tool for genetic analysis and mapping, and earn him the Nobel Prize.