Preparation-sensitive conformations in ribosomal RNAs

Abstract

A METHOD has already been described for isolating RNA from the small subunit of the E. coli ribosome which had altered conformation by the following criteria: additional protein binding sites^1,2, sensitivity to T₁ RNase³ and mobility on polyacrylamide–Agarose electrophoresis³. We also showed that it was possible to detect the conformational difference by electron microscopy⁴. Even though the details of the structure were either below the resolution of the electron microscope, or not sufficiently homogeneous to describe in detail, length measurements of the molecules gave a statistically significant description of the structure. Previously, the only significant ribosomal RNA structure that could be resolved in the electron microscope was the characteristic secondary structure of RNA of the large subunit of eukaryotic ribosomes, or the precursor to eukaryote rRNA⁵. We wished to find out whether, generally, in rRNAs other than the 16S of E. coli, one could detect additional structure in the electron microscope, the details of which may be beyond the resolving power, and whether there are preparation-sensitive conformations in ribosomal RNA. The two preparation procedures used correspond to those described¹, acetic acid-urea extraction (rRNA^a) and the conventional phenol extraction (rRNA^p). We show here that there are in fact previously unrecognised structural elements in a variety of ribosomal RNAs.