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Nucleic Acids Research, 2000, Vol. 28, No. 2 610-619
© 2000 Oxford University Press

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

Sander W. M. Teunissen, Martijn J. M. Kruithof, A. Darise Farris1, John B. Harley1, Walther J. van Venrooij and Ger J. M. Pruijn*

Department of Biochemistry, University of Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands and 1Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA

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 information. For all of the analyzed RNAs, the probing data were used to compose secondary structures, which partly deviate from previously predicted structures. 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 proposed based upon computer predictions. What might be more important is that certain parts of the RNAs appear to be flexible, i.e., to adopt several conformations. Another striking feature is that a characteristic pyrimidine-rich region, present in every Y RNA known, is single-stranded in all secondary structures. This may suggest that this region is readily available for base pairing inter­actions with other cellular nucleic acids, which might be important for the as yet unknown function of the RNAs.

* To whom correspondence should be addressed. Tel: +31 24 3616847; Fax: +31 24 3540525; Email: g.pruijn@bioch.kun.nl


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