Enzymatic RNA Molecules and the Structure of 
Chromosome Ends 
Thomas R. Cech, Ph.D. — Investigator 
Dr. Cech is also American Cancer Society Professor at the University of Colorado at Boulder and Professor 
of Biochemistry, Biophysics, and Genetics at the University of Colorado Health Sciences Center, Denver. 
He received his B.A. degree in chemistry from Grinnell College and his Ph.D. degree in chemistry from the 
University of California, Berkeley. His postdoctoral work in biology was conducted in the laboratory of 
Mary Lou Pardue at the Massachusetts Institute of Technology. Dr. Cech is a member of the National 
Academy of Sciences. Among the many honors he has received are the Lasker Award and the 1989 Nobel 
Prize in chemistry. 
A cell must orchestrate thousands of chemical 
reactions in order to live, to grow, and to 
respond to its environment. These chemical reac- 
tions rarely happen spontaneously, but are 
usually catalyzed by macromolecules called en- 
zymes. It was long thought that all enzymes were 
proteins. More recently we and others have found 
that RNA, a form of genetic material, can in some 
cases act as an enzyme. 
The finding of RNA catalysis has several impli- 
cations. First, it means that RNA is not restricted 
to being a passive carrier of genetic information 
but can participate actively in directing cellular 
biochemistry. In particular, many RNA-process- 
ing reactions are at least in part catalyzed by RNA. 
Second, the study of how RNA enzymes work may 
reveal hitherto unknown mechanisms of biologic 
catalysis. Third, RNA enzymes (ribozymes) can 
be used as sequence-specific RNA cleavage agents 
in vitro, providing useful tools for biochemical 
studies of RNA. Finally, on a more speculative 
note, RNA catalysis has the potential of providing 
new therapeutic agents. For example, it has been 
suggested that ribozymes directed against viral 
RNA sequences might be able to cleave and 
thereby inactivate viruses in a living organism. 
Many of our studies of RNA catalysis concern 
the Tetrahymena ribozyme, named for the sin- 
gle-celled animal from which it was originally 
isolated. This RNA enzyme is capable of cleaving 
other RNA molecules (substrates) in a sequence- 
specific manner. One of our objectives is to un- 
derstand the mechanisms by which this RNA mol- 
ecule acts as a catalyst. A second goal, in the area 
of structural biology, is to obtain a detailed pic- 
ture of the active site of this ribozyme. 
In the past year we have demonstrated that this 
ribozyme uses a novel mode of RNA recognition 
to bind its RNA substrate. In addition to the well- 
established mode of binding by formation of base 
pairs (as in the "ladder" of the famous DNA dou- 
ble helix), the ribozyme also binds two of the 
sugar groups that form the "backbone" of the 
RNA substrate chain. We expect that this type of 
recognition will be widespread in biology. In a 
separate study, we used genetic engineering to 
introduce small changes near the active site of the 
ribozyme. We were able to improve greatly both 
the speed with which the ribozyme cleaves RNA 
and its specificity (its ability to cleave the correct 
RNA sequence while leaving others untouched). 
In the structural area, we developed a method 
for monitoring the folding of the RNA chain of the 
ribozyme. This allowed us to understand one of 
the roles of magnesium ions in RNA catalysis. We 
are now using the same technique to explore the 
contributions of individual structural domains 
and even individual units (nucleotides) to the 
folding of the ribozyme. 
Telomere Structure 
Unlike the circular chromosomes of bacteria, 
the chromosomes found in the nuclei of higher 
organisms are linear DNA molecules. The ends of 
linear chromosomes, called telomeres, must be 
protected from degradation, and special features 
are required to ensure their replication. We are 
studying telomere structure and function, with 
special emphasis on the protein that caps off the 
ends of each chromosome. 
Most cells have only a few dozen chromosomes 
and therefore not many telomeres. We chose to 
work with the ciliated protozoan Oxytricha 
nova, because it has 26 million miniature chro- 
mosomes per cell. This gives us a large amount of 
telomeric protein to study. Similarities in the 
DNA sequences of the telomeres of Oxytricha 
and those of higher cells, including human cells, 
give us reason to believe that our findings in Oxy- 
tricha will be of some generality. 
Last year we isolated and sequenced the genes 
encoding the two subunits of the Oxytricha telo- 
mere-binding protein. We have now used genetic 
engineering methods to produce large amounts 
of these protein subunits in bacteria. The protein 
synthesized and purified from bacteria forms the 
same telomeric DNA-protein interaction seen in 
living Oxytricha. Thus we now have a laboratory 
system for studying telomere structure and func- 
tion that is convenient and appears to be faithful 
to the biological system. 
We have also begun to search for proteins with 
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