Features

Dean's Desk

News from Chemical Engineering

News from Chemistry

Alumni Relations

Alumni Association News

Class Notes

Alumnus Profile: Tom Cech

Alumni Questionnaire

Faculty Highlights

DNA Research in the College

When the Double Helix hit the Scientific Community

Faculty Profile: Jay Keasling

College and Campus News

University Updates

Berkeley Newscenter

credits

all NewsJournals

When the Double Helix hit the Scientific Community

When the double helix was first proposed in 1953, the finding caused a ripple of excitement in chemistry circles. "A lot of scientists were very excited about the double helix. The physical chemists wanted to evaluate these early findings and see if nucleic acids could indeed hydrogen bond in aqueous solution," said chemistry professor Ignacio Tinoco.

In his 47th year as a Berkeley faculty member, Tinoco has watched first-hand as nucleic acids slowly ingratiated themselves in the research of chemists.

After Alex Rich at MIT used organic solvents to show how nucleic acids did indeed pair up in solution, "all of the chemists were convinced that this could indeed happen in the cell," said Tinoco. Joining the chemistry department in 1956, Tinoco and his group began to study nucleic acids from the ground up. "We started with dinucleotides and then trinucleotides, hydrolyzing RNA into oligomers and working from there," said Tinoco.

"When I first came to Berkeley, I published a paper using theoretical calculations to explain why the double helix formed, calculating the forces involved in the DNA structure. I also calculated that DNA absorbance would increase 30-40 percent in intensity when the DNA denatured, which was very useful for physical chemists to know."

Tinoco was the first biophysicist hired by the department to work with nucleic acids. "At the time that I joined, Wendell Stanley's group in virology was the main group on campus studying nucleic acids; they were working with the tobacco mosaic RNA (for which Stanley won the Nobel Prize in Chemistry in 1946). The Molecular and Cell Biology department did not exist," said Tinoco.

Many chemists at Cal (and other institutions) at that time were skeptical of the importance of studying DNA. "I was introduced to Stanley back in 1957. When I told him that I was going to study the structure of DNA, he replied, 'Hasn't that already been done?'" said Tinoco with a smile.

The Early Days
Two more nucleic acid pioneers, John Hearst and James Wang, both joined the chemistry faculty in the 1960s. "I found it interesting that the Cal chemistry department faculty were largely unaware and uninterested in the emergence of modern molecular biology," Hearst said. This was true for both the physical chemists and the organic chemists. "I recall a renowned senior physical chemist in our department telling me that DNA was 'a flash in the pan'. The implication was that DNA should not be of fundamental importance to the career of a Berkeley professor of chemistry," remembered Hearst, now professor emeritus.

Along with a background in molecular biology, Hearst came to Berkeley with a strong interest in nucleic acid physical chemistry. "In particular, I developed a theory for the hydrodynamic properties of DNA solutions using polymer statistical mechanics during my post-doctoral training. We developed the "worm-like coil" model for DNA. In Berkeley, I extended these interests in DNA polymer theory, and for the years from 1963 to 1968 had a very fruitful and happy collaboration with Robert Harris, a fellow assistant professor in our department at that time and a wonderful mathematician, better known for his contributions to quantum chemistry than to the theory of the hydrodynamic properties of DNA solutions."

"During the few years when James Wang was still in our department, he, Ignacio, and I had a most interesting and intense effort going on in molecular biology. I felt at the time that it competed successfully with the activities in the biology departments on campus."

Discovering Topoisomerase
The late 1960s were an interesting time to work on campus, according to Wang, a professor of chemistry at Berkeley from 1966-1977, and currently a professor of molecular and cell biology at Harvard. "There were frequent demonstrations on campus, and once the campus was tear-gassed by a helicopter. For weeks a 'stink bomb' left a repugnant smell in our elevator, and one day a band of demonstrators snaked through the chemistry buildings to look for 'military lasers' that never existed," he recalled in Reflections on an accidental discovery.

Wang discovered topoisomerase while at Berkeley in 1971. His finding attracted a lot of attention because scientists now had a way to separate isomers of DNA that differed only topologically. "Because of my physicochemical background, all enzymes seemed rather mysterious and would better be left to others with the right aptitude for messier systems. Therefore, shortly after my arrival in Berkeley, I decided to try a chemical approach of using a reagent carbodiimide for the desired water splitting. I failed miserably in that expedition.

"The finding of topoisomerase was completely accidental. I was studying negative supercoiling of DNA and had one single cell preparation that was not in agreement with the others. In experimental sciences, a common dictum is 'repeat the experiment if the result makes no sense.' Is a strange observation reproducible to allow rigorous scrutiny by the methods of science?

"When I went back to my notebook to see what was different about this one sample, I noticed that I had spun the cell lysate in the centrifuge for much longer than usual and at a higher temperature. The longer time was due to the fact that I suddenly had to take my daughter to the hospital and had set the machine on 'hold'. The increased temperature was most likely due to the fact that I didn't set the temperature correctly-centrifuges were very bulky and demanding back then-as I rushed off to the hospital."

This single sample lacked negative supercoiling, and it was reasonable for Wang to assume that an activity in the cell, at this incubation, was capable of removing the supercoiling. "After months with the chromatography columns in the cold room, I isolated the active fraction and found that it could indeed relax DNA.

"The manuscript was held up for quite some time as the journal's reviewers took their time to 'believe' the results. I can imagine their bewilderment with this strange report of an unprecedented enzyme by someone with no track record in enzymology. For one whole year, I would wonder whether one day the whole thing would turn out to be an artifact. After one year, however, I myself was fully convinced. It probably took many others a few more years to accept the findings," Wang said.

Crosslinking of DNA
Shortly after, in 1973, Hearst began his studies on psoralens. "Thomas Cech, who was then studying as a graduate student with me, had encountered the compounds in a biochemistry class taught by Professor Stuart Linn and had started using them in order to investigate cruciforms in mouse DNA with the electron microscope. He understood the value of a method for cross-linking DNA structure in vivo under spatial and temporal control.

"I became enamored with the potential application of this photochemistry as a tool for revealing significant aspects of the dynamics of replication and transcription. Before psoralen photochemistry could become a reliable laboratory tool for basic studies in molecular biology, however, the photochemical efficiency of the naturally available psoralens such as 8-methoxypsoralen and trioxsalen needed to be dramatically improved," said Hearst.

"I realized the potential importance of having a collaborator in synthetic chemistry within the department and gravitated to Henry Rapoport, both because I was very impressed with him as a scientist and teacher and also because we shared some features of our cultural backgrounds," Hearst recalled. "I asked him if he would collaborate with me in the synthesis of more effective psoralens, and he responded immediately and positively." This conversation initiated a valuable collaboration that lasted 27 years and has recently led to a method of purifying blood by using psoralens to crosslink nucleic acids, thus preventing the replication of pathogens.

Tinoco, Wang and Hearst laid the chemical biology foundation in nucleic acids that still endures today in the college. All three scientists are still making discoveries about the nature of biological molecules, and have left an impressive structure for others to build upon.