DNA Catalysis of a Normally Disfavored RNA Hydrolysis
Reaction
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Abstract
We recently used in vitro selection
to identify many deoxyribozymes
that catalyze DNA phosphodiester bond hydrolysis and create 5′-phosphate
and 3′-hydroxyl termini. Alternatively, numerous deoxyribozymes
have been identified for catalysis of RNA cleavage by 2′-hydroxyl
transesterification, forming 2′,3′-cyclic phosphate
and 5′-hydroxyl termini. In this study, we investigated the
ability of DNA to catalyze RNA cleavage by hydrolysis rather than
transesterification, although normally the hydrolysis reaction is
substantially disfavored relative to transesterification. Via a series
of in vitro selection experiments, we found that reselection of a
DNA-hydrolyzing deoxyribozyme leads either to transesterification
or hydrolysis, depending on exclusion or inclusion of a stringent
selection pressure for hydrolysis. An entirely new selection starting
from a random DNA pool, using an all-RNA substrate and imposing the
same selection pressure, also leads to RNA hydrolysis. Collectively,
these results establish experimentally that small DNA sequences have
the catalytic ability to direct a chemical reaction down a disfavored
pathway, even when a more favorable mechanism is readily available.
Our view of DNA catalysis is therefore expanded beyond merely increasing
the rates of reactions that would have occurred more slowly without
the catalyst