The secondary structure of the p5abc
subdomain (a 56-nucleotide RNA) of the tetrahymena thermophyla group I
intron has been determined by NMR. Its secondary structure in aqueous solution
is significantly different from the subdomain in a crystal as part of the
P4-P6 domain. It is also different from the secondary structure obtained
by phylogenetic analysis of group I introns, but it is consistent with
thermodynamic predictions. In the presence of magnesium, p5abc subdomain
folds into a tertiary structure with a secondary structure consistent with
the crystal secondary structure, but completely different from the one
in the absence of magnesium. Magnesium-mediated RNA tertiary folding causes
significant secondary structure rearrangement. The common assumption that
RNA folds by first forming secondary structure, then forming tertiary interactions
from unpaired bases, is not always correct. |
