Luria and Delbrück remained friends and colleagues, although they took different research paths after the "fluctuation test" work. Luria continued to investigate mutations, and in 1944 discovered that phages mutate too, often to forms capable of attacking resistant bacteria. Delbrück pursued phage replication, particularly the phenomenon of mutual exclusion. The new field of bacterial genetics would grow explosively during the next decade, in the wake of a series of discoveries. In 1944, Oswald Avery demonstrated that the "transforming agent" in his pneumococcus cultures was DNA. In 1946, Edward Tatum and Joshua Lederberg discovered that bacteria can reproduce sexually. By 1952, Hershey and his colleague Martha Chase had demonstrated the transforming agent in viruses was also DNA: viral protein shells were left outside when viruses attacked bacterial cells; i.e., it was the DNA or RNA that entered, multiplied, and produced more phage. (Though Luria was an early believer that DNA was the transforming principle in bacteria, he rashly suggested that the genetic material of phage was in the protein component until Hershey and Chase proved him wrong. His autobiography described this as "a scientific gaffe that sometimes still gives me a pang of shame like the memory of some rude or gauche behavior.")
In 1945, Luria married Zella Hurwitz, a psychology graduate student. They spent the first year of their marriage at Cold Spring Harbor Laboratory, where Luria, on leave from Indiana University, directed a government research project on bacterial resistance to antibiotics. Back at Indiana the next year, Luria resumed his work on mutation in phage, following up on some irregularities in phage cultures killed by ultraviolet light. According to earlier assumptions, the number of phage killed should relate directly to the amount of light used, but sometimes the correlation wasn't exact. What Luria found was that when two or more "dead" phage entered the same bacterial cell, they often became alive again and produced normal live progeny. This, he noted, was the first example of reactivation of organisms that had been damaged by radiation. He interpreted this as the result of recombination: two or more phages, if they were damaged in different genes, could reconstitute an undamaged, normal phage by genetic exchanges. He assigned his first graduate student, James Watson, the task of repeating the experiments using x-rays instead of ultraviolet light, and this problem was the basis of Watson's doctoral thesis. Watson found the work unsatisfying, however, and within a few years Luria arranged for him to work with biochemists in Europe and England, where he met Francis Crick and began unraveling the structure of DNA.
The University of Illinois at Urbana offered Luria a position as professor of bacteriology in 1950, which he accepted (Indiana University did not try to match the Illinois offer, according to Luria, because of his political activities with the 1948 Progressive party campaign and the university workers' union.) His laboratory there explored many aspects of phage genetics, the most important of which was the phenomenon of restriction and modification. It was becoming clear that phages take over in bacterial cells in a process whereby the phage DNA produces enzymes that break up the bacterial DNA; the pieces of bacterial DNA are then used to build more phage DNA. While studying that phenomenon in 1952, Luria found that phage that grew in some mutant E. coli bacterial cells produced unexpected results when they attacked a new culture of E. coli; though apparently killed by the phage, the new E. coli didn't seem to produce new phage. What had happened to the phage? One day, when he had no E. coli cultures available to work with, Luria borrowed a culture of Shigella bacteria to use, and added the phage from the mutant E. coli. The phage attacked the Shigella and produced new phage within a day. Luria realized then that the E. coli phage had been modified by the E. coli mutant so that it could no longer grow in that species, but could grow in a different one, e.g., Shigella. Later researchers would show that each strain of bacteria produces enzymes--specific to that bacteria--that can recognize specific short nucleotide sequences and cut DNA strands at those sites. The DNA of Luria's E. coli phage had been modified in just this manner by the mutant E. coli. These are now called "restriction enzymes" and have become the main tool for recombinant DNA technology.
During the late 1950s, Luria worked with Japanese bacteriologist Hisao Uetake on Salmonella phages, and found that certain phages caused the bacteria to lose some of their antigen (the specific polysaccharide on the cell surface that stimulated antibodies in an infected person's immune system) and acquire new ones. Luria and Uetake concluded that, since the antigenic polysaccharides are normally synthesized by bacterial enzymes, the entering phage DNA was either making some new enzymes or activating some latent enzymes of the bacterium. Because these antigen-converting bacteriophages allowed most of the bacterial cells to survive, the phage DNA remained present and functional and converted the bacteria to a new antigenic type.
Interested in expanding their biology department, the Massachusetts Institute of Technology (MIT) invited Luria to spend the 1958-59 academic year in Cambridge to help plan a new microbiology program, and subsequently offered him a permanent position as program chair. At about this time, Luria's research moved away from phage studies--he felt that the field was getting too crowded, and the research pace too frantic. Also, as he later noted, molecular biology had reached a point where the "new" work consisted in "putting together little pieces of a large puzzle whose overall features were already evident." Luria did not want to do genetic analysis, and was looking for "unplowed fields" to dig in.
The unplowed field he chose was that of cell membranes. Researchers at the time were only beginning to understand the complexities of membranes, which mediate the many biochemical operations that allow cells and tissues to function. Biochemist Phillips Robbins (who joined Luria's faculty at MIT in 1959) did further work on the phage enzymes that converted bacterial antigens, and in the process, he also solved the problem of how the complex polysaccharides of cell membranes are built step-by-step by enzymes located within the bacterial membrane itself. This intrigued Luria, who wondered how enzymes got into the membranes, and how they worked there. Since membranes have a lipid layer in them, he reasoned, the enzymes must be proteins that operate well in that situation. With Robbins, Luria organized series of international seminars (dubbed the Microdermatology Project) for researchers working on bacterial cell surfaces, partly to gather the extant knowledge in the field.
Luria chose to focus on colicins, water-soluble proteins produced by certain types of bacteria which kill bacteria of similar kinds. They had been discovered in the 1920s; in 1963 Mayasano Nomura showed that there are three types of colicins, each of which kills bacteria in a different way, probably by damaging the membrane of the cell. Luria's initial question was how did a water-soluble colicin get into or through the fatty layers of the membrane, and once there, what chemical action did it perform?
Luria went to Paris on sabbatical in 1963 and worked in Jacques Monod's department at the Institut Pasteur. He knew that colicin E1 stopped essential synthetic processes in bacteria, and that one colicin molecule was enough to kill one cell. Where did the cell membrane come in? All cells need to pump necessary substances in from outside; the pumping is done by proteins in the membrane. Luria found that colicin somehow blocked the function of transport proteins in the membrane. Back at MIT, he and his research fellows spent the next several years investigating colicin's action, and found that a colicin molecule stops the flow of energy that allows membrane proteins to transport food into the cell. Specifically, it destroys the electrical charge difference (electrical potential) between the inside and outside of the cell. Even more specifically, colicin makes channels in the membrane, through which ions (e.g. sodium and potassium) and small molecules can move. Since certain concentrations of ions on each side of the membrane are needed to maintain the electrical charge difference across the membrane, the channels destroy the electrical potential that powers the membrane proteins.
In 1969, Luria's pioneering work in microbial genetics was recognized several times: he and Delbrück were awarded Columbia University's Louisa Horowitz prize, and, one month later, shared the Nobel Prize in Physiology or Medicine with Alfred Hershey, for their "discoveries concerning the replication mechanism and the genetic structure of viruses." Not long after the Nobel Prize announcement, Luria received further publicity when he was included in a National Institutes of Health research grants "blacklist" due to his ongoing political activism.