The G[bull ]U pair at the third position in the
acceptor helix of Escherichia coli tRNAAla
is critical for aminoacylation. The features that allow
G[bull ]U recognition are likely to include direct interaction
of alanyl-tRNA synthetase with distinctive atomic groups
and indirect recognition of the structural and stability
information encoded in the sequence of G[bull ]U and its
immediate context. The present work investigates the thermodynamic
stability and acceptor activity for a comprehensive set
of variant RNAs with substitutions of the G[bull ]U pair
of E. coli tRNAAla. The four RNAs with
Watson–Crick substitutions had a lower acceptor activity
and a higher stability relative to the G[bull ]U RNA. On
the other hand, the RNAs with mispair substitutions had
a lower stability, but either a higher or a lower acceptor
activity. Thus, the entire set of variant RNAs does not
exhibit a correlation between thermodynamic stability of
the free, unbound tRNA and its acceptor activity. The substantial
acceptor activity of tRNAs with particular mispair substitutions
may be explained by their ability to assume the conformational
preferences of alanyl–tRNA synthetase. Moreover,
the G[bull ]U pair may provide a point of deformability
for the substrate tRNA to adapt to the enzyme's active
site.