A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the molecule into six major structural domains containing over 100 individual helices in all. Regions containing the sites of interaction with several ribosomal proteins and 5S RNA have been located. Segments of the 23S RNA structure corresponding to eucaryotic 5.8S and 25 RNA have been identified, and base paired interactions in the model suggest how they are attached to 28S RNA. Functionally important regions, including possible sites of contact with 30S ribosomal subunits, the peptidyl transferase center and locations of intervening sequences in various organisms are discussed. Models for molecular 'switching' of RNA molecules based on coaxial stacking of helices are presented, including a scheme for tRNA-23S RNA interaction.

We have derived a secondary structure model for 16S ribosomal RNA on the basis of comparative sequence analysis, chemical modification studies and nuclease susceptibility data. Nucleotide sequences of the E. coli and B. brevis 16S rRNA chains, and of RNAse T1 oligomer catalogs from 16S rRNAs of over 100 species of eubacteria were used for phylogenetic comparison. Chemical modification of G by glyoxal, A by m-chloroperbenzoic acid and C by bisulfite in naked 16S rRNA, and G by kethoxal in active and inactive 30S ribosomal subunits was taken as an indication of single stranded structure. Further support for the structure was obtained from susceptibility to RNases A and T1. These three approaches are in excellent agreement. The structure contains fifty helical elements organized into four major domains, in which 46 percent of the nucleotides of 16S rRNA are involved in base pairing. Phylogenetic comparison shows that highly conserved sequences are found principally in unpaired regions of the molecule. No knots are created by the structure.

A 23S ribosomal (rRNA) gene from Bacillus stearothermophilus has been cloned in pBR322, and its nucleotide sequence determined. The corresponding mature 23S rRNA is predicted to contain 2928 nucleotides. We compare the primary and secondary structures of 23S rRNA from Escherichia coli and B. stearothermophilus, and discuss their potential contributions to thermal stability.

Exon shuffled I-A beta genes transfected into the B lymphoma cell line A20-2J were used to localize the epitope recognized by the monoclonal antibody 10.2.16 to the carboxy terminal portion of the beta 1 domain. In addition, several T helper cell hybrids were tested against these novel I-A molecules and the following observations were made: the beta 1 domain of A beta plays a dominant role in the restricted recognition by T helper cells; there appear to be multiple restriction epitopes on the I-A molecule; these epitopes can consist of conformational epitopes created by specific alpha and beta chains or consist of the polymorphic determinants encoded on the beta chain alone, and these novel I-A molecules serve as restriction elements in the antigen-specific recognition by T cells and in one case stimulate an alloreaction in the absence of antigen.