As a graduate student, Eric Greene imagined building a microscope that would allow him to watch molecules react with each other. “I have always been a visual learner, and for me actually seeing biochemical interactions would make them easier to understand,” he says.
During a postdoc at the National Institutes of Health in 1998, Greene used a specially designed microscope to observe a 48-kilobase piece of DNA as it interacted with various proteins. The technique he used—called total internal reflection fluorescence microscopy (TIRFM)—was not new, says Greene, but “no one had tried to look at a molecule this long using TIRFM.”
After starting his own laboratory at Columbia University, Greene patented a method for visualizing thousands of individual DNA molecules and proteins at once. The major limitation of the TIRFM technique, he says, was that it allowed you to observe only a single molecular interaction at a time, when you might need to watch hundreds of interactions to have enough statistical power to draw a meaningful conclusion.
Greene devised a nanoscale platform upon which he could line up many identical molecules of DNA and observe them all at the same time. “We actually line up DNA molecules into patterns that we call DNA curtains, because they really do look like the curtains you might have on your living room windows,” he says. “What we’ve done, that no one else in the world can do right now, is to combine several different technologies all into a single experimental platform that lets us literally look at 1,000 DNA molecules all at once.”
As to the benefits of this approach, Greene says, “Imagine how difficult it would be if you had to make one trip to the grocery store for every item in your kitchen. This is what single molecule imaging was like when I first began in the field. What we have done is the equivalent of allowing you to buy all of your groceries at once. This makes the experiments easier, and any time you make an experiment easier you also make it possible to tackle more challenging problems.”
Greene and his laboratory members are beginning to apply this technology to problems that affect several aspects of eukaryotic DNA metabolism. They are trying to understand how DNA repair proteins navigate the genome to fix errors in the genetic code, and what happens when two or more proteins collide with one another as they move along DNA. That’s key, he says, because any working protein will encounter thousands, if not millions, of other proteins inside of living cells, but traditional laboratory experiments involve “naked DNA” and don’t take these interactions into account. Inside cells, no interaction between molecules actually occurs in such isolated conditions.
“These are exciting times in the laboratory, because the experiments I could only imagine as a graduate student are actually working,” he says.
The roots of Greene’s success, he says, lie in his childhood. His grandfather bought him books about science, medicine, and engineering, and at an early age Greene developed a keen ability to take things apart and put them back together. Once he got a first taste of laboratory science as a senior in college, he was hooked. “I was thrown into the fire with no oversight and had to figure out how to ask questions, and find help from people and the scientific literature. It was an absolutely perfect situation for me,” he says.