Modification of 18 S rRNA in the 40 S ribosomal subunit of yeast with dimethyl sulfate

Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor

“…The secondary structure models proposed by others are not entirely applicable to every eukaryotic srRNA molecule. Our model comes closest to that proposed by Ellis and co-workers [3] [5,6,8,10] adopt a similar topology for the secondary structure of eukaryotic and prokaryotic srRNAs in this area. Others [l-3,7,9] advocate a eukaryote-specific topology for this region.…”

“…Several authors [l-11] have proposed secondary structure models for srRNAs. Some of these models [5,6,8,10] imply that the molecule is folded essentially in the same way in prokaryotes and eukaryotes, while others [l-3,7,9] assume a different folding in certain areas. In addition, these models must account for variability in primary and secondary structure in several areas of eukaryotic srRNAs that have no equivalent in prokaryotic srRNAs.…”

The rDNA ofC. elegans: sequence and structure

“…This creates the possibility of a series of tightly stacked helices at the 5' end of the molecule. However, cytosine methylation and kethoxal reaction studies indicate that the base pairing in helix 1 may be weak (24,25).…”

Structure of Ribosomal Rna

“…Among the more useful single strand-specific chemical probes are kethoxal (G-specific) (72,95), diethyl pyrocarbonate (A-and G-specific) (96), bisulfite (C-and V-specific) (79), dimethyl sulfate (C-specific as a single strand probe ; G-specific as a "major groove" or tertiary-structure probe at 7N) (96)(97), and m-chloroperbenzoate (79) and monoperphthalate (98) (both A-specific). The reliability of chemical modification in obtaining detailed structural information has been verified in several cases by studies on tRNA, where results can be compared with a known structure (96,99).…”

“…It must remain a possibility that the oligomers themselves inay help to convert the rRNA to the open fo rm, by virtue of their ability to bind the single-stranded fo rm.The latter experiments are examples of a few specific instances where phylogenetically established helices are reproducibly fo und to be sus ceptible to single strand-specific probes under certain conditions. These include the 9-13/2 1-25 and 17-20/9 15-918 helices and the 1050-1067/1189-1204 and 1410-1 490 regions of the 16S-like rRNAs(72,79,97,133, 135), and the 2063-2103 region of 23S-like rRNAs(78,134,136). Whether these results are mere reflections of the inherent instability of these structures under experimental conditions or clues to structural dynamics of rRNA is an open question at the present time.…”