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We are investigating the mechanism of catalysis
in a class of molecules known as ribozymes. The main
focus is on two self-cleaving RNA sequence found in
a human pathogen, hepatitis delta virus (HDV). HDV is
an unusual viral pathogen in that it is a satellite
of hepatitis B virus and contains a small circular RNA
genome. We are investigating both the structure and
function of the self-cleaving ribozymes in the RNA;
a key element in the replication of the virus that is
responsible for processing replication products into
viral size genomes. Initial work established the conditions
required for cleavage and led us to propose a novel
secondary structure for the HDV RNA sequence required
for self-cleavage. This secondary structure correctly
describes most, but not all, of the essential Watson-Crick
interactions of the ribozyme and has revealed a key
region of the RNA that may be involved in formation
of the catalytic center. Currently, biochemical approaches
are applied to the study of the role of metal ions and
nucleobases in the mechanism of catalysis. In addition,
we are interested in the process of folding and the
importance of both alternative secondary structure and
more subtle conformational changes to catalysis and
regulation. Due to the small size and inherent stability
of the HDV ribozymes, they have turned out to be excellent
model systems for studying these questions.
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