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 his many honors are the Lasker Award and the 1989 Nobel Prize in chemistry. 
THE nucleic acids, DNA and RNA, are best 
known as the information-carrying molecules 
of a living cell. For example, a molecule of DNA 
or RNA might carry the instructions to build myo- 
sin, a protein involved in muscle movement, 
or pepsin, a protein enzyme that helps digest 
food. Our laboratory is investigating the non- 
informational roles of nucleic acids, situations in 
which a nucleic acid molecule has an important 
cellular function other than encoding a protein. 
In the area of RNA catalysis, we wish to under- 
stand how a folded RNA structure can have enzy- 
matic activity. In the area of chromosome func- 
tion, we are characterizing the DNA and 
associated protein necessary for proper mainte- 
nance of a chromosome end. In both projects, 
chemical and biological approaches are com- 
bined for fuller analysis of a biochemical 
problem. 
RNA Catalysis 
A cell must orchestrate thousands of chemical 
reactions in order to live, grow, and respond to its 
environment. These chemical reactions, rarely 
spontaneous, are usually catalyzed by macromole- 
cules called enzymes. It was long thought that all 
enzymes were proteins. More recently we and 
others have found that a nucleic acid, RNA, 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 partly catalyzed by RNA. 
Second, the study of RNA enzymes, called ribo- 
zymes, may reveal hitherto unknown mecha- 
nisms of biologic catalysis. Third, ribozymes can 
be used as sequence-specific RNA cleavage agents 
in vitro, providing useful tools for study of RNA 
biochemically. Finally, on a more speculative 
note, RNA catalysis has the potential of providing 
new therapeutic agents. For example, ribozymes 
efficiently cleave and thereby destroy viral RNAs 
under controlled laboratory conditions, suggest- 
ing that they might be able to 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. 
Last year we 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 DNA double helix), the ribo- 
zyme also binds two of the sugar groups that form 
the "backbone" of the RNA substrate chain. We 
have now located the other partner in this inter- 
action, a specific adenine base within the RNA's 
catalytic core. In addition to support from HHMI, 
a grant from the National Institutes of Health 
supported a graduate student working on this 
project. 
In a separate study, nucleic acid chemistry was 
used to change individual oxygen atoms to sulfur 
atoms near the cleavage site in the RNA substrate. 
With one of the sulfur-substituted RNAs, we ob- 
served a change in metal-ion specificity in the 
cleavage reaction. Thus we believe we have lo- 
cated one of the long-postulated active-site metal 
ions and have established that this RNA, like some 
protein enzymes, is a metalloenzyme. 
In the structural area, we have developed a 
new technique for identifying parts of the folded 
RNA molecule that are in proximity to some 
known site. We attach a controllable agent of de- 
struction to a small molecule known to dock in 
the ribozyme's active site, allow it to bind, initi- 
ate the chemical reaction, and map the sites of 
damage. The method has revealed convincing in- 
formation about the higher-order folding of this 
RNA catalyst. 
Telomere Structure 
Unlike the circular chromosomes of bacteria, 
the chromosomes found in the nuclei of higher 
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