In the spring of 2002, I was in my first year of graduate school and joined Drew Endy’s lab, who had just started as a fellow on the sixth floor of the biology building (building 68). Our floor then included several senior faculty included Khorana and Boris Magasanik. When I was started, I had no idea who they were and they just seemed to be old people that I tried to avoid. I still remember my first meeting with Khorana, which in retrospect was mortifying.
I was working at the computer, in a basically empty lab space, and a slight, old man with a gigantic cup of hot tea held in both hands walked by slowly taking a long look. Then he walked by again going the other way, and then back again, each time peering in looking curious. I kind of thought it was one of those Indian things where the older Indian generation still seemed shocked every time they see another Indian person in America. I’m thinking mostly that I should probably say hi and help him move along:
Me: Hi, my name is Sri, can I help you?
Khorana: Hi, I’m Khorana
Khorana: I like seeing new labs start. What are you working on?
I had no idea who he was. I just saw a nice old man that at the time I thought was wasting my time. I was working on a simulator for gene expression, to build a model for a simple virus that infects E. coli called bacteriophage T7. I didn’t really want to discuss with him what I was working on, because I didn’t know where to begin, and I was 22 and pretty confident I had nothing to learn from him. I was luckily rescued by Drew, who brought him into his office.
In the ensuing years, I began diving a lot deeper in the biology of T7 and models of gene expression, which led me to many papers that were published in the Cold Spring Harbor Symposia series on Quantitative Biology that were organized by Demerec (who also first isolated T7). It was really amazing reading the history of your field through these symposia, and how people thought about the emergence of molecular biology. There was an especially eventful symposium, 1961 on regulatory mechanisms, where many of the luminaries like Jacob and Monod, Brenner, Crick and others were formulating early ideas around the central dogma. I could not find them online, nor in the library, and for some reason that day I knocked on Boris Magasanik’s office. I asked if he had a copy of a particular paper from that issue. He said, sure, he was there, and pulled out the book. I was pretty stunned. We talked for something like 3 hours in his office that day about the symposium and what people were talking about. I ended up having many talks with him, and took his course on bacterial physiology (which I loved). I dove deeper into the symposia, as Boris had most of them, and came upon the famous 1966 meeting, where I ran first ran into Khorana’s work. Around the same time, I began reading the Eighth Day of Creation, where I read more about the excitement around that time and Khorana’s formidable accomplishments. Over the next several years, I talked with Boris, and Gobind, but also Maury Fox, Vernon Ingram and others. I feel both blessed to have experienced that, but also regretful that I didn’t spend more time talking with all of them, especially Khorana.
Our lab’s work today is deeply inspired by Khorana’s work and approaches to use nucleic acid synthesis and gene assembly to explore important aspects of biology. It didn’t matter that he was solving the genetic code using unnatural sequences, in the end it was still the genetic code. Moreover, it turned out to be easier to break this code by using synthesis, rather than by genetics or inference from natural sequences. These are concepts that have taken me a while to understand, but Khorana clearly understood it decades before I was born, and doggedly pursued those goals producing spectacular work that changed the world.
My explorations of Khorana’s works were really fun. For example, there is the synthesis of the first artificial gene, a yeast tRNA, with the interesting title: “Studies on polynucleotides. 103. Total synthesis of the structural gene for an alanine transfer ribonucleic acid from yeast.” That 103 is amazing. It’s actually the 103rd paper with the same title, starting from the first in 1958, to some of the last ones I could find that end in 1976 at 143. He did this a lot apparently. Another great example is the synthesis of the second gene, published in a numbered series of 17 back-to-back papers entitled: “Total synthesis of the structural gene for the precursor of a tyrosine suppressor transfer RNA from Escherichia coli”. Back to the first series, Ian Molineux was on my thesis committee, and worked for Khorana as a postdoc. He pointed me to one that he was an author on, #96, entitled “Studies on polynucleotides: XCVI. Repair replication of short synthetic DNA's as catalyzed by DNA polymerases.” It basically describes PCR, and according to Ian, the method was routinely run a full decade prior to it’s invention by Mullis, but they didn’t think it was worth publishing. Read the final paragraph for instance:
“The principles for extensive synthesis of the duplexed tRNA genes which emerge from the present work are the following. The DNA duplex would be denatured to form single strands. This denaturation step would be carried out in the presence of a sufficiently large excess of the two appropriate primers. Upon cooling, one would hope to obtain two structures, each containing the full length of the template strand appropriately complexed with the primer. DNA polymerase will be added to complete the process of repair replication. Two molecules of the original duplex should result. The whole cycle could be repeated, there being added every time a fresh dose of the enzyme.”
Anyways, Khorana continued to be the only person building synthetic genes for a while, and it spawned an entire generation of people and an approach to biology that is still alive today. Part of the reason I cringe when people refer to me as a synthetic biologist, is because it seems to erase a history that is as old as molecular biology itself. It is very weird to me that I worked down the hall from him, as much of what he did seems to be from antiquity. I wish I had a chance to talk with him again, but at least I still have many chapters of Studies of Polynucleotides to get through.