OBJECTIVES: A concerted series of site-selective physical measurements on ribosomal RNA's grown and isolated from both eukaryotic and prokaryotic organisms is designed to identify specific secondary and tertiary architectural features of 5S RNA and 5.8S RNA in solution. The results will be used to test the validity of proposed prior (and our own new "cloverleaf") RNa structural models, with the object of establishing a general secondary structure adaptable to all known 5S RNA and 5.8S RNA nucleotide sequences. This universal secondary structure could then form a basis for tracing phylogenetic pathways over an extremely long evolutionary time scale, since the presence and function of the 5S RNA molecule is so highly conserved between all organisms from which it has been isolated. METHODS: Optical techniques (u.V. and circular dichroism spectra; Raman scattering) will provide specific constraints upon the base-stacking and base-pairing of various RNA nucleotides. NMR spectra will establish: the number of sharp bends in the polynucleotide chain (31P NMR); the proportion of surface and buried uracils (19F NMR of 5-fluorouracil 5S RNA); local flexibility at each uracil (19FNMR); number and type (G:C, A;U, G;U) of base pairs, with direct comparison between chemical shifts observed experimentally and calculated from a given theoretical secondary structural model (1H NMR). EPR spectra from "spin-labeled" RNA will report the flexibility at two or more "exposed" sites. Finally, all methods will be applied to 5S RNA isolated from both eukaryotic and prokaryotic 5S RNA, in order to secure the widest generality for any structural conclusions.