Studies on ribosomal RNA structure: II. Secondary structures in solution of rRNA and crystallizable fragments

Abstract

1. 1. Parallel studies on the secondary structures in solution of rRNA and crystallizable fragments of rRNA by means of ultraviolet and infrared absorption spectroscopy are described. Fragmented and intact rRNA, which are obtained from yeast ribosomes, exhibit qualitatively similar melting properties in the ultraviolet, either in the presence or absence of formaldehyde, a denaturant of base pairing. Deuterium oxide solutions of both types of RNA also give rise to closely similar infrared absorption spectra in the 1550–1750 cm −1 region. 2. 2. The spectroscopic results show that fragmented and intact rRNA have secondary structures containing comparable and extensive amounts of hydrogen-bonded base pairs. The infrared results show further that at 30°, assuming only Watson-Crick pairing, the fragments have 66±6% bases paired ( 32±3% AU pairs, 34±3% GC pairs) while intact rRNA has 64±6% bases paired ( 29±3% AU, 35±3% GC). At 5°, the proportions of paired bases are increased to 76±7% and 69±7%, respectively, for fragments and intact rRNA. The thermal rupture of inter-base hydrogen bonds is essentially complete at 80°. 3. 3. The existence of ordered double helical regions in aqueous RNA fragments is consistent with the results of previous X-ray diffraction studies on crystalline fibers of this material which gave evidence for such structure in the solid state. Base pairing is therefore considered an integral part of the secondary structure of these fragments, rather than something arising from the process of crystallization. The extensive base pairing in yeast rRNA is in agreement with estimates of the double helicity of tobacco mosaic virus RNA, reticulocyte rRNA, 5-S RNA and tRNA.