How Restriction Enzymes Changed Biology

In the early 1970s, researchers reported that restriction enzymes cleave DNA at specific sites, producing individual fragments that are distinguishable using gel electrophoresis.^1,2 This timely discovery opened a new window for understanding and manipulating DNA, but for 1993 Nobel laureate and chief scientific officer at New England Biolabs, Sir Richard Roberts, it began a lifelong passion for restriction enzymes and their potential.³

Scientists first observed the biological phenomenon of restriction and modification in the 1950s, but they did not identify and isolate restriction enzymes until the late 1960s.³ In 1970, Hamilton Smith and Kent Wilcox from Johns Hopkins University discovered “endonuclease R” (later named HindII), a restriction enzyme isolated from Hemophilus influenza.¹ A year later, Kathleen Danna and Daniel Nathans, also from Johns Hopkins University, found that endonuclease R produced specific fragments of simian virus 40 and that gel electrophoresis could distinguish these fragments from each other.

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Richards first encountered endonuclease R during his postdoctoral fellowship at Harvard University in 1972 when he attended a talk by Nathans. “In the early days, you couldn’t do much with DNA because it was a very large molecule,” Roberts recalled. “As soon as the Type II restriction enzymes were discovered—and HindII in particular—it was obvious that you could take a fairly large DNA and cut it into smaller pieces. And that offered you the opportunity to look and see what was going on.”

Later that same year, Roberts joined James Watson’s team at the Cold Spring Harbor Laboratory and immediately began isolating endonuclease R and other restriction enzymes. “Every time we opened up a new bug, there was a restriction enzyme with a new specificity,” Roberts said. “People used to bring test tubes with DNA samples to meetings, and they’d step out and ask if we had any enzymes that would cut their DNA.”

While Roberts pursued new restriction enzymes, others used them to sequence, map, clone, and manipulate genes. At the start of his tenure with Cold Spring Harbor Laboratory, Roberts originally intended to focus on using restriction enzymes to sequence DNA, echoing the RNA sequencing techniques developed by Frederick Sanger half a decade prior. “One of the reasons that [sequencing] methods had been developed for RNA research was because there were small molecules to practice on. Restriction enzymes gave the opportunity to do likewise for DNA,” said Roberts. However, he and his team soon found restriction enzymes themselves to be so interesting that they abandoned their foray into sequencing. Eventually, Roberts’ team sent restriction enzymes to Sanger, helping him develop the DNA sequencing technique that bears his name today.

As soon as the Type II restriction enzymes were discovered—and HindII in particular—it was obvious that you could take a fairly large DNA and cut it into smaller pieces. And that offered you the opportunity to look and see what was going on.

—Sir Richard Roberts, New England Biolabs

Roberts’ team characterized or discovered three-quarters of the world’s first restriction enzymes.⁴ In the absence of commercial sources, scientists purified restriction enzymes in their own labs—or came knocking at Roberts’ door. As worldwide demand increased, Roberts encouraged Cold Spring Harbor Laboratory to commercialize restriction enzyme production for the benefit of the scientific community, but he encountered opposition from Watson, who did not see potential for profit in it. Fortunately, Roberts crossed paths with Donald Comb, a previous faculty member at Harvard University Medical School who had just started a small company called New England Biolabs (NEB),⁵ in 1974. At the time, Comb intended to sell HindII through Miles Laboratories. This naturally piqued Roberts’ interest, and he contacted Comb and convinced him to sell restriction enzymes directly using NEB instead. A relationship formed, and Roberts quickly became the chief consultant for the fledgling company that he now calls home.

“At the start, restriction enzymes were very important in isolating DNA fragments. These days, they’re more often used to diagnose whether you made the recombinant DNA properly or not,” Roberts said. “There was a time when PCR came along that people thought that the market for restriction enzymes was going to disappear, but what they failed to realize was that PCR just meant that there was going to be a lot more DNA around. All of a sudden, as people sought to check their sequences for accuracy, the market changed, but demand went up.”