Conserved features of Y RNAs: a comparison of experimentally derived secondary structures

In this study, phylogenetically conserved structural features of the Ro RNP associated Y RNAs were investigated. The human, iguana, and frog Y3 and Y4 RNA sequences have been determined previously and the respective RNAs were subjected to enzymatic and chemical probing to obtain structural informati on, For all of the analyzed RNAs, the probing data were used to compose sec ondary structures, which partly deviate from previously predicted structure s. Our results confirm the existence of two stem structures, which are also found at similar positions in hY1 and hY5 RNA. For the remaining parts of hY3 and hY4 RNA the secondary structures differ from those previously propo sed based upon computer predictions. What might be more important is that c ertain parts of the RNAs appear to be flexible, i.e., to adopt several conf ormations. Another striking feature is that a characteristic pyrimidine-ric h region, present in every Y RNA known, is single-stranded in all secondary structures. This may suggest that this region is readily available for bas e pairing interactions with other cellular nucleic acids, which might be im portant for the as yet unknown function of the RNAs.