Higher-order structure of the 5.8 S rRNA sequence within the yeast 35 S precursor ribosomal RNA synthesized in vitro

Dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluene-sulfonate, RNase T₁ and RNase V₁ have been used as structure-sensitive probes to examine the higher-order structure of the 5.8 S rRNA sequence within the yeast 35 S precursor ribosomal RNA molecule. Data produced have been used to evaluate several theoretical structure models for the 5.8 S rRNA sequence within the precursor rRNA. These models are generated by minimum free energy calculations. A model is proposed that accommodates 83% of the residues experimentally shown to be in either base-paired or single-stranded structure in the correct configuration. Several alternative suboptimal secondary structures have been evaluated. Moreover, the chemical reactivities of several residues within the 5.8 S rRNA sequence in the precursor rRNA molecule differ from those of the corresponding residues in the mature rRNA molecule. This finding provides experimental evidence to support the notion that the 5.8 S rRNA sequence within the precursor rRNA undergoes structural reorganization following rRNA processing.