The 3′ splice site of group I introns is
defined, in part, by base pairs between the intron core
and residues just upstream of the splice site, referred
to as P9.0. We have studied the specificity imparted by
P9.0 using the well-characterized L–21 ScaI
ribozyme from Tetrahymena by adding residues to
the 5′ end of the guanosine (G) that functions as
a nucleophile in the oligonucleotide cleavage reaction:
CCCUCUA5 (S) + NNG [lhard ][rharu ] CCCUCU +
NNGA5. UCG, predicted to form two base pairs
in P9.0, reacts with a (kcat/KM)
value ∼10-fold greater than G, consistent with previous
results. Altering the bases that form P9.0 in both the
trinucleotide G analog and the ribozyme affects the specificity
in the manner predicted for base-pairing. Strikingly, oligonucleotides
incapable of forming P9.0 react ∼10-fold more slowly
than G, for which the mispaired residues are simply absent.
The observed specificity is consistent with a model in
which the P9.0 site is sterically restricted such that
an energetic penalty, not present for G, must be overcome
by G analogs with 5′ extensions. Shortening S to
include only one residue 3′ of the cleavage site
(CCCUCUA) eliminates this penalty and uniformly enhances
the reactions of matched and mismatched oligonucleotides
relative to guanosine. These results suggest that the 3′
portion of S occupies the P9.0 site, sterically interfering
with binding of G analogs with 5′ extensions. Similar
steric effects may more generally allow structured RNAs
to avoid formation of incorrect contacts, thereby helping
to avoid kinetic traps during folding and enhancing cooperative
formation of the correct structure.