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When the Nobel Prizes were announced in October 1959, Kornberg was beginning his tenure as chair of the new biochemistry department at Stanford University School of Medicine. The medical school had been located in San Francisco rather than at Stanford's Palo Alto campus, but in the mid-1950s plans were made for a new medical school and medical center on the main campus. Stanford had recruited Kornberg in 1957, offering him the unique opportunity to choose his faculty members, establish the curriculum, and help design the space the department would occupy in the medical school's new buildings. Kornberg recruited most of his Washington University faculty and staff, and a number of former postdoctoral fellows for Stanford. He was also instrumental in recruiting leading scientists such as Joshua Lederberg for other departments at the medical school.
In the congenial, tailor-made working environment he was able to create at Stanford, Kornberg continued his efforts to synthesize a genetically active DNA, working with a variety of bacteria. This proved far more difficult than just copying a template DNA; any imperfection in the template doomed the viability of the DNA. And it was almost impossible to avoid damaging the large template DNA molecules while handling them in the lab. Kornberg turned instead to some of the smallest bacterial viruses (phages), such as the phi X174 and M13 viruses of E. coli, for his study. With their comparatively short DNA strands, these viruses are easier to keep intact during handling, and their biological activity is easy to observe. Robert Sinsheimer had found that the phi X 174 virus DNA was a circular single strand, but immediately after entering its host, enzymes converted it to the familiar double helix. That DNA by itself--with no protein coat--could infect another host cell. A similar pattern was found in the M13 virus. Kornberg and his team were able to synthesize both viral DNAs, but not in the circular forms; and the circular form seemed essential for infectivity. Was there an enzyme that could seal the free ends of the synthesized strands together, and also seal any breaks in the DNA? There was: in 1967, five different research groups, including Kornberg's, found the enzyme DNA ligase. By the end of that year, Kornberg had synthesized a phi X174 DNA with the same circular form, composition, sequence, and infectivity of DNA from the natural virus.
To announce this accomplishment, Kornberg and the Stanford news bureau arranged a press conference on December 14, timed to coincide with the publication of the research in the Proceedings of the National Academy of Sciences. They cautioned journalists in advance not to characterize it as "synthesizing life in a test tube." After all, though the DNA synthesis was a biochemical landmark, viral DNA has no life of its own outside a larger system. That same day, President Lyndon B. Johnson was scheduled to speak at the Smithsonian Institution, and his speechwriter asked Stanford for a paragraph on the DNA work. This was supplied, but as Johnson began to read the prepared statement, he abruptly put it aside and told his audience, "Some geniuses at Stanford University have created life in the test tube!" To Kornberg's dismay, all the newspaper stories about his work the next day began with that statement.
Further work with the viral DNA brought more discoveries about the various enzymes involved in its synthesis. Kornberg discovered that DNA polymerase doesn't just assemble DNA molecules, but can also degrade them in some situations, essentially editing out mismatched nucleotides (a rare but serious event) as the chain grows. It also finds small breaks in the sugar-phosphate "backbone" of the DNA template strand, and removes part of the area around the break so it can be filled in properly. It also plays a big role in DNA repair. When damage occurs, another enzyme nicks the backbone of the chain at that spot. DNA polymerase grabs onto that nick, removes the damaged nucleotides, then fills in the area, using the opposite side as a template. The nick in the backbone is then sealed by the ligase enzyme.
Ironically, these discoveries by Kornberg and others about the remarkable repair functions of DNA polymerase led some scientists to question whether Kornberg's enzyme truly was the one responsible for DNA replication. Further doubts came with John Cairns' discovery of an E. coli mutant that could reproduce normally even though it lacked that enzyme. Kornberg was vindicated in 1971 by his son Tom, who found a second DNA polymerase in the Cairns E. coli mutant, quite different in structure, but identical in its ability to synthesize and edit DNA chains. During the following year he found a third polymerase. It was a sensational scientific debut for Tom; a talented cellist studying at the Julliard School, he had only recently taken up laboratory work after a hand injury forced him out of performance.