Features News from Chemical Engineering Alumni Relations Faculty Highlights When the Double Helix hit the Scientific Community College and Campus News
|
50 Years After the Discovery of the Double Helix DNA Research in the College
"We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest" - James Watson and Francis Crick, Nature, 25 April 1953 And with these words, a revolution was launched. DNA held the key to the genetic code. Only 50 years have passed since the discoverers of the double helix hinted at what this unassuming biological molecule possessed: unlimited possibilities. We now know just how similar we are to every other organism on this planet; we can screen for mutations in cancer that can direct a physician towards a novel targeted treatment; we can even work towards the cure of neurological nightmares such as Alzheimer's or Parkinson's diseases. The revolution of biotech has opened doors only dreamed of-if that even-50 years ago.
The research community at Berkeley, especially in the College of Chemistry, has played a noteworthy role in establishing our scientific knowledge of these molecules. The discovery of topoisomerase, the utilization of DNA crosslinking, the refining of the structure of tRNA and the development of key technology for the Human Genome Project all took place here in the college (see related story). Current research includes bioengineering and gene therapy, structural studies of the ribosome and DNA polymerase, and use of DNA in innovative analytical methods that promise to make medical dreams a reality. A significant contribution of the college to the nucleic acid research community that does not appear in publications is the fact that many talented students have been trained here in biophysics and have gone on to become leaders in the field, both in the academic and the industrial setting, as noted by numerous professors. STRUCTURAL BIOLOGY PLAYS A PROMINENT ROLE Even though DNA takes the form of a double helix, with each of the four bases pairing up with an unchanging partner, there is still much left to learn about the interactions that govern its function. Professor David Wemmer, a biophysical chemist, and his group are studying these interactions, including those that stabilize particular conformations of the DNA molecule, as well as those that cause different molecules to come together and form specific complexes in order to function.
"This was a big accomplishment because the differences in DNA structure at different sequences is small, particularly from the minor groove viewpoint, and many thought that it would not be possible to 'read' the sequence as we showed was possible," he continued. "The molecules can bind DNA tightly, and compete with proteins for binding sites, which in turn can change the level of gene expression. Such compounds are being investigated as possible drugs, though understanding their actions in the complex environment inside cells where they must act is bringing new challenges." "It has been great fun to have a project move from spectroscopic studies all the way to biology in the cell," Wemmer concluded. DNA REPLICATION BRINGS CHALLENGES
"I became interested in studying DNA polymerase when it was pointed out to me that this enzyme complex moved at high speed along DNA without dissociating from it," Kuriyan continued. "In the bacteria E. coli, the polymerase spins around the DNA at an amazing rate of 100 times per second. How does nature deal with the topological problems that would result?" he asked. "One part of the answer is that ring shaped proteins, known as sliding clamps, are attached to DNA. The polymerase is tethered to the sliding clamp and the DNA is threaded through the ring. The polymerase can then detach from the DNA but remain tethered via the clamps. My group was the first to solve the structure of the sliding clamp protein and the clamp-loader machines that load them onto DNA. We are now working on understanding the integrated process of DNA replication, and we hope to visualize the whole replication assembly by using electron microscopy and X-ray crystallography." MAPPING THE NUCLEIC ACID STRUCTURE UNIVERSE
"This is a very conceptual method. We get a global view of what kind of structural space nucleic acids can occupy. It can also help scientists studying the structural transitions of DNA and RNA among various different conformational states and substrates, since the molecules can change forms depending on the environment," Kim added. "This approach has been very exciting. We got very exciting and revealing results using it to map the protein structure universe, which implicated how protein structures may have evolved. Nucleic acids are a very different animal," he said. SEQUENCING DNA "FASTER, BETTER AND
CHEAPER"
"We are also very excited about microfabricating a fully automated DNA sequencing factory on a chip," continued Mathies. His group's goal is to develop a system that could resequence the majority of a single person's genome for ~$10,000. "If we can resequence the genomes of a large portion of the population, we can understand our genetic differences and polymorphisms and better understand their role in disease. "This microfluidic technology has a multitude of exciting possibilities," said Mathies. GENE THERAPY COMING OF AGE "We work with genetic medicine," said David Schaffer. "The common method to discover a new drug is to determine which protein is involved in the disease and develop a small molecule to target that protein. However, direct genetic modification is a very powerful alternative."
"With gene therapy, the basic idea is to target a faulty gene directly, by injecting a piece of DNA that can integrate into the chromosome and correct the defective gene," explained Schaffer, an assistant professor of chemical engineering. A carrier molecule called a vector must be used to deliver the therapeutic gene to the patient's target cells. Currently, the most common vector is a virus that has been genetically altered to carry normal human DNA. Viruses have evolved a way of encapsulating and delivering their genes to human cells to serve their own ends. However, scientists have tried to take advantage of this capability and manipulate the virus genome to remove the viral genes and insert therapeutic genes. The Schaffer lab is working to improve viral gene delivery vectors by engineering their properties at the molecular level. "We are working on evolving new properties into viral vectors that will enable them to deliver therapeutic genes more efficiently," Schaffer said. "This work will enable to delivery of therapeutic genes to treat many disorders, including Alzheimer's and Parkinson's Diseases" ENGINEERING IN BIOLOGY Keasling sees a good fit for chemical engineers in the bio-world. "We have been genetically engineering organisms for only 30 years, not a long time. And 30 years ago, there were no chemical engineers in the field; it would have been unheard of. But now chemical engineering is a good discipline to come from when approaching these biological problems. Chemical engineers tend to deal with large complicated processes, such as all of the pieces and parts of a petroleum refinery, and put them together seamlessly to produce a useful product." In the past the Keasling group has done bioremediation work to help clean up the environment. "A lot of pollutants in our ecosystem can be cleaned up using some of these methods. We showed that it is possible to use bacteria to clean up toxic nerve agents and accumulate heavy metals. But now we are working to build new systems that do not cause pollution in the first place," he said. Jean Fréchet is a chemist with an engineer's eye for detail. He is an organic chemist who has synthesized novel conjugates of DNA with polymers known as dendrimers, which are well-defined branched polymers. "The DNA portion self-assembles, taking the shape of a double-helix and dragging along whatever is attached to it, whether a reporter dye, a nanocrystals, or a dendrimer" he said. Researchers in the Fréchet group have prepared DNA dendrimer conjugates and polymerizable DNA for potential use in nanobiotechnology, therapeutics, or the rapid detection of specific DNA strands associated with a particular disease. They have also built a series of unnatural DNA-like building blocks useful in the automated synthesis of DNA hybrid systems. Members of his group are currently involved in novel designs for gene and antisense therapy.
Although only in its first decade of development, DNA computing has come a great distance. Researchers have used strips of DNA to carry out read and write operations with the tools of genetic engineering. More recently, DNA computing was used to solve a six-variable problem, although one that is solvable by hand. More daunting tasks are currently being carried out with this type of technology. Scientific prognosticators believe DNA computing could become more commonplace in the next few decades. PREDICTING THE DNA FUTURE "I think we have a good understanding of many of the fundamentals of structural principles for these nucleic acids. However there are undoubtedly many new 'twists' in how they work that remain to be discovered," said Wemmer. Schaffer is a firm believer in the future of gene therapy. "A lot of the delivery vectors are being perfected and the clinical trials that are ongoing and beginning will bear that out," he said. There are many genetic diseases that can be treated and perhaps even conquered with these types of treatments. And since they affect only the somatic cells, the genetic changes cannot be passed down, hopefully avoiding much of the public fear that bioengineering can sometimes bring about. According
to John Hearst, professor emeritus of chemistry, the understanding
of DNA and RNA will be a major part of the future-not only of medicine,
but also of human understanding of life and of the long-term survival
of life on Earth. "I remain convinced that there are no subjects
more important to civilization than nucleic acid chemistry, or perhaps
more generally molecular biology."
Related sites: |
 © 2003 UC Regents |
|
| College
of Chemistry UC
Berkeley |
|
DNA
and RNA, its versatile relative, have captured the public's imagination.
As biological molecules, they have found applications in numerous fields:
physical chemists study their structure and pull them apart to see what
happens, synthetic chemists use them as a scaffold for new compounds,
engineers chop DNA up and swap it around in bacteria to produce novel
drugs, scientists and engineers are trying to make DNA-based computers.
Nucleic acids serve as biological ambassadors to many fields.
One
of Wemmer's first extended projects after arriving at Berkeley in the
mid-80s was to understand how a natural product bound to DNA specifically
at runs of A-T base pairs (adenine and thymine). Various molecules can
bind to DNA at specific nucleic acid sequences and can alter the structure
and function of the DNA. The DNA helix has two "grooves," a
major groove and a minor groove. "By studying its complexes using
nuclear magnetic resonance spectroscopy, we confirmed previous suggestions
that the natural product bound in the minor groove of the helix. But then
we found something surprising, a new type of complex in which two molecules
bound together to DNA rather than on their own," said Wemmer. This
finding was the first of its kind, as most molecules bind on their own
to DNA. "We used this to change the sequence specificity, that is
to design and build a ligand that would target almost any specific sequence
of interest, including those with G-C base pairs (guanine-cytosine).
"It
turns out, however, that DNA replication is a very complicated process
because the two template strands run in different directions, yet DNA
polymerase, the protein complex that copies DNA, works in only one direction,"
he noted. "One strand is copied continuously while the other is replicated
in discontinuous loops, with both strands being handled simultaneously
by a polymerase machine containing a dozen or more protein subunits.
"Structure
of nucleic acids is dictated by the smallest unit. Depending on the conformation
of the dinucleotide phosphate, nucleic acids adopt a different structure,
either the A, B or Z form," said Kim. Using mathematical multidimensional
scaling and presenting how the forms distribute, Kim and his graduate
student Gregory Sims showed that the nucleic acid universe is composed
of nine primary clusters ("conformational galaxies") representing
all the substrates of A, B, and Z forms-and five secondary clusters.
"Our
work today continues in the direction of miniaturization of analytical
separations using advanced microfabrication techniques. We want to use
low volumes for fast separation and high sensitivity detection,"
he explained. "Some of our techniques are leading to 'point-of-care'
technologies that would allow a person's genome to be probed in a matter
of minutes. We can also use this technology to sequence the DNA in tumor
cells. This information could then be used to tailor medical treatment.
Future exciting applications also involve development of a portable DNA
analyzer for pathogen and infectious disease detection. 
Genes
are specific sequences of bases that encode instructions on how to make
proteins. Although genes get a lot of attention, it's the proteins that
perform most life functions and even make up the majority of cellular
structures. When genes are altered so that the encoded proteins are unable
to carry out their normal functions, genetic disorders can result.