Structural analysis of two plant 5S rRNA species and fragments thereof by lead-induced hydrolysis

Abstract

The structure of plant 5S rRNA species from lupin and wheat germ as well as the structure of two RNA fragments that represent domains β and γ of lupin 5S rRNA have been probed by Pb(II)-induced hydrolysis. The lead digestion patterns of 5S rRNA species show that the secondary and tertiary structures of the molecules are very similar. The data suggests that two potential base pairs at the bottom of helix E are destabilized and this causes an enlargement of the hairpin loop e. On the other hand, nucleotides from loop c seem to be involved in the formation of some kind of higher order structure. A comparison of the distribution of cleavages induced in RNA fragments to those in the corresponding regions of the entire 5S rRNA shows that under conditions applied in our studies the structural domains β and γ are not involved in formation of any tertiary interaction within 5S rRNA structure.