Nucleic Acids Research, Vol 24, Issue 24 4910-4917, Copyright © 1996 by Oxford University Press
K Hellendoorn, PJ Michiels, R Buitenhuis and CW Pleij
The secondary structures of the 5'-untranslated region (5'-UTR) of five
different tymoviruses have been determined by structure probing, computer
prediction and sequence comparison. Despite large sequence differences,
there are remarkable similarities in the secondary structure. In all
viruses two or four hairpins are found, most of which contain a symmetrical
internal loop consisting of adjacent C-C or C-A mismatches. Since it is
known that such mismatches can be protonated and protonated cytosines play
an important role in RNA-protein interactions in tymoviral virions, the
influence of pH on the conformation of the internal loop was studied. UV
melting experiments and 1-dimensional proton NMR at varying pH values and
salt concentrations confirm that the hairpins can be protonated under
relatively mild conditions. The hairpin found in the 5'-UTR of erysimum
latent virus, which has an asymmetrical internal loop consisting of
cytosines and uridines, shows comparable behaviour. It is concluded that
all tymoviral RNAs contain protonatable hairpins in the 5'-UTR. Binding
experiments with empty viral capsids, however, do not yet establish a role
in capsid protein binding.
ARTICLES
Protonatable hairpins are conserved in the 5'-untranslated region of tymovirus RNAs
Leiden Institute of Chemistry, Leiden University, The Netherlands.
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