Hydrogen-1 and phosphorus-31 nuclear magnetic resonance study of the solution structure of Bacillus licheniformis 5S ribonucleic acid.

Abstract

The conformation of Bacillus licheniformis 5S RNA in solution has been studied by using 360-MHz 1H NMR and 40.5-MHz 31P NMR spectroscopy. The 1H NMR spectra, which are well resolved, have been compared with theoretical spectra derived by ring-current shift calculations for various models proposed in the literature for the secondary structure of 5S RNA. The total amount of base pairs is estimated to be around 36. NMR melting experiments indicate that both the molecular stalk and the prokaryotic loop [Fox, G. E., & Woese, C. R. (1975) Nature (London) 256, 505] are present in the solution structure. On this basis, some models proposed for the secondary structure of 5S RNA not containing these structural features can be rejected. Several resonances are observed around 10.7 ppm that can be ascribed to protons involved in non-Watson-Crick base pairing most likely present in tertiary interactions in the 5S RNA molecule or to ring N protons of nonpaired bases which as a result of the molecular folding are shielded from the solvent. Under our solution conditions, these structural features disappear at physiological temperature, the process being uncoupled from the collapse of the secondary structure. Using 31P NMR, we demonstrate that the number of phosphate conformations in the sugar phosphate backbone of 5S RNA, deviating from the g-,g- conformation normally found in double helices, is far les than in tRNA.