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Hitchings' and Elion's approach to their work was highly innovative. Contrary to most previous drug developers, who had depended largely on trial-and-error methods, they actively designed drugs based on knowledge of how cells worked. Although Watson and Crick had yet to discover the double-helix structure of DNA, scientists did know that cells need nucleic acids to reproduce. Hitchings theorized that by interfering with the DNA of cancer cells, bacteria, and viruses—which, because they need very large amounts of DNA to reproduce, should be particularly vulnerable to disruptions of their lifecycles - they could prevent the unwanted cells from replicating and thus stop the spread of disease. The goal was a drug that would disable the disease cells without harming normal cells.

Hitchings assigned Elion to work on the purines, two of the four bases that make up DNA. Elion created slightly altered versions of the purines, hoping to make one that would be similar enough to the real base that the disease cell would be fooled into incorporating it but different enough that it would be unable to use it to reproduce. "We used to call it a rubber donut," she said. "It looked like the real thing, but it wouldn't work."

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Even as Elion became immersed in her research, she continued to aspire to the Ph.D. she had as yet been unable to earn. Enrolling at the Brooklyn Polytechnic Institute, she commuted three nights a week from her job in Westchester County, to Brooklyn, and home to the Bronx. After two years, however, the dean demanded that she either work full-time on her doctorate or leave school. Unwilling to give up the exciting job that had been so difficult to get, Elion reluctantly gave up her dreams of a Ph.D.