Conformation of the Central, Three-helix Junction of the 5 S Ribosomal RNA of Sulfolobus acidocaldarius

Abstract

The current investigation has focused on the structure of the central, three-helix junction of the 5 S ribosomal RNA from Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium. The 5 S molecule from S. acidocaldarius represents a paradigm for the study of the 5 S junction (and branched RNA structures in general) due to its unusually high degree of predicted secondary structure and stability. In order to study the junction in isolation, a set of three RNA heteroduplex molecules was assembled in which pairs of helices bounding the junction were extended by 70 base-pairs per helix. Since the extended helices comprise more than 95% of the heteroduplex structure, the relative solution conformations of the heteroduplex molecules, in effect, "report" the interhelix (branch) angles bounded by the extended pairs of helices. Examination of these heteroduplex molecule, using a combination of gel electrophoresis and transient electric birefringence measurements, has revealed a tertiary structure for the central branch in which helices I and V are essentially collinear, and in which helix II is relatively free to reorient with respect to the I-V axis.