Eric Kool, Chemical Biologist and Research Leader in RNA Mapping and DNA Repair

In the late 1980s and early 1990s, Peter Dervan was leading a revolution which helped to create a new field called Chemical Biology. Dervan saw the profound possibilities in taking a chemical approach to biological problems, and his lab attracted top graduate students and postdoctoral scholars who recognized the exciting research to pursue in merging the chemists' toolbox with the wonders, even the messiness, of biology and the molecular basis of life. In the discussion below, Eric Kool recounts his attraction to join the Dervan Lab from Columbia, and he describes the centrality of DNA synthesis in exploring how DNA bases could be designed. Following his initial faculty appointment at the University of Rochester, Kool reports that he is still happily modifying DNA and RNA at Stanford. Kool's experiences reflect a truism in science: sometimes new ideas and new approaches are so forward-thinking, and are so detached from convention, that one can simultaneously advance the field while still pursuing the same basic questions, even over the span of thirty-plus years.

DAVID ZIERLER: This is David Zierler, Director of the Caltech Heritage Project. It's Monday, September 18, 2023. I'm very happy to be here with Professor Eric Kool. Eric, it's very nice to be with you. Thank you for joining me today.

ERIC KOOL: You're welcome.

ZIERLER: To start, please tell me your title and institutional affiliation.

KOOL: I'm the George and Hilda Daubert Professor of Chemistry at Stanford University.

The Evolution of Chemical Biology

ZIERLER: I want to start just at a very basic level. What does the term chemical biology mean to you? How does it differ from, for example, biochemistry?

KOOL: That's an interesting question. And I think early on in the field–and this was less clear–it's become more clear over time as people have begun to define themselves differently, I think. And I'd say in my years at Caltech, the field of chemical biology didn't really exist but was in its kind of fledgling state and hadn't even been named at that time. I was there in the end of the 1980s. Chemical biology, I now define as the application of chemical tools to the study of biology and the practitioners spend most of their time either A, developing new chemical tools, or B, applying them to specific biological problems. Chemical biologists are proficient in organic chemistry, at least to some extent, and proficient in cellular, potentially organismal, biology to some extent. And that conjunction of abilities, of proficiencies, didn't really exist back in the 1980s and 90s to any really big extent.

ZIERLER: Is this to say that the development of the field, at least in the span of your career, is really premised on technological advances?

KOOL: I think that's a lot of it. Biology has changed incredibly over this time, more than chemistry has. Biology's become much more molecular. Methodologies have become much more accessible through things like kits, through technologies like sequencing, through the addition of genetic databases, and things like that. I think they have really made biology much more accessible to chemists. And this has helped to lower the barrier to the entry of chemists into biology. The fields of organic chemistry and molecular biology have kind of grown together such that there is really no seam between them anymore. It's really a seamless transition, and some chemists dabble slightly in biology, some chemists dive headfirst into biology and only use a little chemistry. And, I would say, there are some biologists who are now calling themselves biologists but are also doing chemical biology. There's a huge blend now of people across the entire discipline.

There was a field called biochemistry, and there are still people who call themselves biochemists. And back in the 1990s, biochemistry was almost foreign to organic chemists and was seen as scary, at least to me as an organic chemist, [Laugh] and to some of my colleagues. And they published in different journals, there were fewer molecular techniques available to them. Biochemists typically would not synthesize organic molecules. They would not design and synthesize organic molecules but would simply apply known organic molecules to biological or biochemical questions. What's really changed is that, in chemical biology, chemists are not afraid to design and synthesize new molecules and then also do the biological part. Back then, if we wanted to solve a biological problem, organic chemists would make a molecule and then ship it off to biologists, and biologists would take it and do some experiments with it, knowing very little about the chemistry, and the chemists would know very little about the day-to-day methods that the biologists used.

The Merging of Disciplines

ZIERLER: Another question about trends. So far as I can tell, people who belong in the club, the chemical biology club, by and large, are in departments of chemistry. Now, the merging that you're talking about, is that to say that this is now itself becoming fuzzier along administrative lines?

KOOL: I think it is. I haven't done a survey of biology departments, but I can tell you for sure that in medical schools, many biological departments are hiring chemical biologists, who are still not ashamed to say that they're doing chemical biology. Here at Stanford, there are at least as many people practicing chemical biology in our medical school outside the chemistry program as there are in the chemistry department itself.

ZIERLER: Is there a program at Stanford in chemical biology? Do you have a degree in chemical biology?

KOOL: Yes, there's a department called Chemical and Systems Biology, and it's existed for, I don't know, at least a decade. And there are kind of multidisciplinary chemical biology programs that cross over multiple departments. Again, I'm just speaking for Stanford. If you go and see what's happening at Harvard, you might find a similar thing. But there are lots of people doing chemical biology in medical schools. A good example is Sloan Kettering in New York. And Rockefeller - it's not really a medical school, but it's certainly a big-time biology place hiring people who do chemical biology. It's a burgeoning discipline in medical schools. Whether hardcore biology departments, ones that just call themselves biology departments, are also hiring in this area, I haven't done a survey recently. But I would be surprised if it were not starting to happen.

ZIERLER: Is that to say, if this is being embraced in medical schools, that chemical biology has already crossed the rubicon from basic science to translational science?

KOOL: Yes. Oh, absolutely. 100%. Yeah, it's in fact seen as one of the most promising translational fields of all. Super-hot in venture capital, in new startups, which are obviously aiming translational, and in medical programs, which are really pushing translational science these days. Chemical biology is one of the hottest fields.

From Columbia to the Dervan Lab

ZIERLER: Let's establish some history to get the context of your time at Caltech. At Columbia, was your dissertation in organic chemistry?

KOOL: Yeah, it was, although our laboratory called ourselves bio-organic chemists. But it was certainly not what we call chemical biology today because we were not handling any cells or any materials from cells, even. We were simply inspired by biochemistry and biology. That was kind of where I started. We were interested in how enzymes functioned, and there was a lot of discussion about whether enzymes were special molecules. What made them such good catalysts, was the big question of the day. This was super-hot back in the 60s, 70s. People were saying, "What is special about enzymes? Why do they do their job so well as catalysts?" When chemists were struggling to find catalysts that would speed a reaction by a factor of 10, enzymes were doing it at six orders of magnitude. Organic chemists were wringing their hands, saying, "What can we do to make better catalysts that even compete?" There was this big question, and that's what we were studying as organic chemists during my PhD. We were making a lot of catalysts inspired by enzymes and doing a relatively poor job of it. [Laugh]

ZIERLER: In retrospect, should it not be surprising that evolution would be capable of producing something so much more efficient than what people can synthesize?

KOOL: I think that's a pretty broad question. Looking back on it, I think we better understand how enzymes work, and we also understand the power of evolution, given that we can actually do evolution now in the laboratory. We know that you can explore so much more chemical space through evolution than you can in the old one-at-a-time, make-a-molecule-and-test-it model. We understand better the power of evolution and why it could lead to such good outcomes.

ZIERLER: What was the overall research question or science objective of your dissertation? What were you after?

KOOL: I studied two different enzyme classes. I had a two-part thesis, two different projects. We studied two different classes of enzymes to see if we could mimic some of the behavior of those enzymes. One was an enzyme that uses a B-family vitamin as a cofactor, and the other was ribonuclease, and that was kind of my first introduction into thinking about enzymes that handle RNA and DNA.

ZIERLER: How did Caltech get on your radar? What attracted you to come to Caltech?

KOOL: I saw a talk at Columbia by Peter Dervan, and it just blew me and some of my colleagues away. We were going, "Wow, this is the future that I want to be a part of." And thinking of DNA, again, it was kind of foreign. These big biomolecules were scary, and we didn't even think of them as organic chemistry, really. It was a bizarre kind of disconnect. But because we couldn't make them, we had a hard time thinking of them as organic. And they were in water, which was another anathema to organic chemists. We had a hard time even thinking of them together. And yet, Dervan brought the two together. He brought organic chemistry to DNA. And I just loved the idea. That's what inspired me, seeing him talk at Columbia, and I was really eager to go and learn from him.

The Relevance of DNA Synthesis

ZIERLER: Do you remember any of the specifics of the talk? You said it was the wave of the future. What about it seemed so future-oriented?

KOOL: That he was not afraid to work with this really big, water-soluble molecule and to even chemically modify it. Around that time was the birth of the DNA synthesizer, which revolutionized biotechnology and medicine, and it was organic chemistry. If we understood the organic chemistry of how to build DNA, we could then modify it as well. I just loved this idea that you could make modified DNA, and that's what I did when I joined the Dervan lab. I designed and modified DNA bases. It's what I did as part of my tenure-winning work, when I went off to start my own lab at Rochester. I just loved the combination of synthetic organic chemistry, molecular design brought to the "biological world," although we were not working with cells or living systems. we were working with a big complex molecule of nature and looking at its properties in water. That was new.

ZIERLER: In his talk or his lab, did Dervan use the term chemical biology when you were a post-doc?

KOOL: No. I don't know who used the term first, but it might've been Stuart Schreiber, and that, I believe, was in the mid-90s. Again, we weren't really doing biology. Except for with collaborators, we were not studying cells at all, and we didn't really feel like we had the tools to do that or even the desire at the time. It was such a leap just to work with and analyze DNA and use all the new tools that were associated with DNA. It didn't even occur to us at the time, at least not to me, to start doing things in cells.

ZIERLER: What aspects of your post-doc research did you see as a continuation of your dissertation, and what was really brand new for you?

KOOL: Very little was a continuation. It was simply just the idea that there were interesting problems around DNA and RNA, and potentially interesting technologies that could come out of it. And it was really this technological side that was driving everybody in the 90s. Synthetic DNA was thought of as the all-encompassing answer to all medical problems. [Laugh] That was the idea. Basically, it was the magic bullet, like antibodies. Back when monoclonal antibodies were discovered, people were saying, "This is the magic bullet. It will cure all disease." And we now know that while they don't cure all diseases, they are very, very powerful. The same was thought to be true once we could synthesize DNA back in the late 80s, early 90s. People thought, "We can actually turn these into drugs." And while, again, that ended up being true over decades of work, it hasn't solved all of medicine's problems. But it has led to hundreds of important medical technologies and biomedical technologies. That was really the driving force, the idea that there would be some technologically and medically important things that might come out of this. And Dervan was very aware of the idea that we could use DNA as a drug.

ZIERLER: What was the instrumentation in the Dervan lab when you were a post-doc? What were you using?

KOOL: I was learning all this new equipment. I was learning how to separate and analyze DNA by gel electrophoresis, something that only biologists or maybe the occasional biochemist would've done before then. I remember running through the lab with my first gel and going, "Look, look, I ran a gel. I'm a real DNA chemist now." [Laugh] And the DNA synthesizer was a really simple one back then. He had an early prototype or one of the first early commercially available ones. Playing with that machine was really interesting. I learned a lot from it, and I was trying to modify the machine to make it do what I wanted it to do.

ZIERLER: How big was Dervan's lab when you were there?

KOOL: Oh, boy. I'm going to guess 20, 25 people, somewhere in that range.

ZIERLER: Pretty big by Caltech standards, I think.

KOOL: Yeah, I think it was big. He was one of the hottest people to work for back then, and rightly so. He was a true pioneer and a great communicator of exciting ideas.

ZIERLER: What was his style like as a mentor? Was he in the lab? Was he hands-on? Would you communicate with him frequently?

KOOL: As a post-doc, he was not super hands-on. We would make an appointment with his secretary to go talk to him. I would maybe have a conversation with him once every two to four weeks, something like that, just giving him a little bit of update. In that respect, he was pretty hands-off, and I loved it because I just was free to run with my ideas. We had a general framework around what our goal was, and it was up to me to find a way to solve it. I really liked that.

Designing DNA Bases

ZIERLER: What was the goal, the big project?

KOOL: My goal was to make designer DNA bases that would help a strand of DNA bind to double-stranded DNA of any sequence. And that is still impossible today, but it is easier than it once was. Back then, it was early triple-helix DNA days. The idea was that we could control gene expression by binding to double-stranded DNA with another strand of DNA.

ZIERLER: In retrospect, what is impossible about combining single- and double-stranded DNA?

KOOL: It works, it just doesn't work for all possible sequences. And that's just because of the chemical structure of double-stranded DNA. There are limitations to how another strand of DNA can interact with that existing strand of DNA. It put restrictions on what sequences we could target, and that made it not as broadly applicable as we would've liked it to be.

ZIERLER: When you joined the faculty at Rochester, would you have considered yourself a chemical biologist?

KOOL: No. And it's interesting, for a while, I think, in the early to mid-90s, when Schreiber introduced the term chemical biology, there was some resistance. There were maybe two schools. There was the bio-organic chemistry school, which said, "That name is already fine. We don't need more names," and then the chemical biology school, which started with Stuart Schreiber and his acolytes. Over time, I think the chemical biology term has won out, mainly because biology has become so much more accessible that we're no longer afraid to call ourselves biologists. We can actually do some biology. The barrier broke down by just chemists moving more and more into biology.

ZIERLER: What was your research plan as an assistant professor?

KOOL: I wanted to make modifications to DNA that would alter both its chemical and potentially biological properties. My first project involved taking a synthetic piece of DNA and forming it into a ring of circular DNA. That ended up being a good idea. [Laugh] Good enough to win me tenure, anyway. Also, it's now used in DNA sequencing pretty much around the world.

ZIERLER: This argument over terminology starting with Schreiber, where did you fall in on those debates?

KOOL: Because I was not a Schreiber acolyte, I started off in the organic chemistry community, and it took me a while before I started saying I do chemical biology. It took a decade or more.

Translating Basic Science from Numerous Disciplines

ZIERLER: Did you have translational interests of your own? Did that develop over time for you?

KOOL: I was interested in finding translational opportunities. I wouldn't have done them myself. I was collaborating with people in medical schools or people at drug companies to test translational applications of what I was doing. Again, early on, I was not doing any biology. I don't think we grew a cell until 2000, 2002, something like that. For a long time, I was not doing really any biology, and I would collaborate with people who could do it.

ZIERLER: To bring the story closer to the present, what are you working on currently, and where are those intellectual roots back to your work at Caltech?

KOOL: Well, I'm still happily studying DNA and RNA. I'm still happily modifying DNA and RNA. Those roots grew a big tree that's now several decades old. [Laugh] I'm still very happy with the field. Over and over again, I keep getting shocked about how broad the field of DNA and RNA science is, and there are still so many corners remaining unexplored. That's given me a whole career for a long time.

ZIERLER: mRNA, of course, became very famous with the COVID vaccines. Is there a chemical biology aspect to the mRNA discovery?

KOOL: Arguably, yes. I don't know if they would've called themselves chemical biologists, but mRNA vaccines contain chemically modified nucleotides. I would say that's arguably a chemical biology solution to the vaccine problem. But I can say there are many more modifications coming, and there are card-carrying chemical biologists who are now working in the field. I'm one of them. But I'm also collaborating with vaccine companies directly. There are a lot of opportunities there. I think the early founders would've called themselves just pure biologists because they weren't really using many chemical tools to solve the problem. But now, there are lots of people making modified lipids to help deliver them, lipid nanoparticles. And I and some others are modifying RNAs using clearly chemical tools that require new chemical development to make them work.

ZIERLER: A question that's on everyone's minds these days, artificial intelligence and machine learning. Are you embracing these technologies, either as a research tool or as a way to analyze copious amounts of data?

KOOL: I am not yet. I'm certainly open to that possibility, I'm just too busy with everything else we're doing to learn yet another technology. Because I've moved into biology and medicine over my career, I've continually had to learn new things. That's still on my to-do list, to learn more about AI and machine learning. Right now, I don't think we have a strong push to do it. But in cases where you are developing big databases to learn from, I think there are some real opportunities there. I think chemistry and chemical biology, so far, are so complex that it's going to take a long learning curve to make real inroads in AI, to make real reliable databases that I think AI can turn useful. But I'm very open to it, and I'm certain it's coming in the future.

ZIERLER: A generational question. With you on the other side of the professor student divide, the students who come to you, graduate students and post-docs, what are some of the dominant academic paths they have taken to get to you? Have they come with specific chemical biology backgrounds?

KOOL: More and more, that is happening. I would say 20 years ago, I had almost exclusively people with chemical backgrounds, and then we would train them in biological methods. Now, it's much more frequent that students come in with chemical biology training, so I don't have to train them on how to culture cells, or how to do flow cytometry, methods that biologists would have used in the past. We're certainly getting more and more students who want to do chemical biology and in fact, already as undergraduates, have had chemical biology training.

ZIERLER: Two last questions to wrap up this most useful conversation. In historical perspective, where do you see Caltech and perhaps specifically Peter Dervan in the development of chemical biology? How would you place both Caltech institutionally and Peter in the development of this field?

KOOL: Caltech is a leading institution, and obviously there are really important people doing chemical biology there. But looking back, although we didn't call ourselves chemical biologists, he really helped us cross an important barrier towards biology by taking a big, complex biomolecule and saying, "We can do things with this chemically. We can make it chemically, and we can modify it chemically, and we can borrow some of the tools that biologists used to exclusively use in order to help study what our molecules do." To me, that was an important barrier that led us toward chemical biology. Again, we weren't calling it chemical biology then, but in retrospect, I think that was a really important line to cross, and one of the most important lines to cross.

ZIERLER: It sounds like what you're saying is he helped define the field before it had a definition.

KOOL: I think that's true. He certainly broke down barriers that made the field possible.

ZIERLER: Finally, looking to the future, the theme of the merging of disciplines. Do you think ultimately that's going to render all of these different terms sort of not as useful as they might be? Is there something more inclusive so that the emphasis is on just how inclusive all of these different areas of research are?

KOOL: People like labels, and I think labels are going to continue. I think there will be blending of people across departments, for example, but we will still refer to chemical biology tools or will refer to other kinds of tools that help us get work done. I don't see that such labels are going to go away for a while. It's important in academic science that young academicians point out what their field is, what their niche is. You need labels to help define those niches, so I think they'll continue. But I think the fields will certainly continue to blend, even more broadly than they have now.

ZIERLER: Eric, this has been a very useful conversation for me. I want to thank you so much for spending the time.

[END]