Conformation and conformational fluctuation of Bacillus stearothermophilus 5S ribosomal RNA

Abstract

To investigate the conformational stability and fluctuation of the thermophilic 5S ribosomal RNA (rRNA), the thermal melting and hydrogen exchange processes of Bacillus stearothermophilus 5S rRNA were studied in Tris and other buffers including K + (or Na +) and/or Mg 2+, and the results were compared with those of other non-thermophilic 5S rRNA. The unfolding of two double helices was observed in differential optical absorption and c.d. melting curves in the absence of Mg 2+ or at low [Mg 2+]. At high [Mg 2+] the melting becomes apparently monophasic and temperature dependence of optical absorption is negative or almost zero, especially at 260 nm, at low temperatures < 40°C. Various physicochemical measurements show that under such conditions the 5S rRNA is in a highly folded and less fluctuating conformation that the other non-thermophilic 5S rRNA. Hydrogen exchange profiles demonstrated differences in the conformational fluctuations between B. stearothermophilus and the other 5S rRNA.