Abstract：
: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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hellendoorn K,Michiels PJ,Buitenhuis R,Pleij CWdoi
10.1093/nar/24.24.4910subject
Has Abstractpub_date
1996-12-15 00:00:00pages
4910-7issue
24eissn
0305-1048issn
1362-4962pii
6b0253journal_volume
24pub_type
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journal_title：Nucleic acids research
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