Comparison of eubacterial and eukaryotic 5S RNA structures: a chemical modification study

Abstract

The 5S RNA from Bacillus stearothermophilus and Saccharomyces cerevisiae were probed by nucleotide-specific reagents, with a view to compare and contrast their higher order structures. The progressive unfolding of the RNA during heating, in the presence and absence of Mg was monitored. Evidence was provided for the double-helical segments which occur in the secondary structural models of both RNA. The results also placed constraints on the possible structuring of the remainder of the RNA and yielded some insight into ways of folding up the molecule. Together with the data from earlier studies employing RNase, these results provide a detailed picture of the structuring and topography of the 5S RNA. The main structural differences between the eubacterial and eukaryotic RNA occur throughout the loop D/helix IV/loop E/helix V arm; in particular strong evidence is provided for loop D of the eukaryotic RNA being involved in a tertiary interaction.