Folding of yeast 5S ribosomal RNA induced by magnesium binding

The magnesium-induced conformational changes of yeast 5S ribosomal RNA have been studied by means of difference absorption spectroscopy and circular dichroism. A hypochromic difference absorption spectrum with a trough at approximately 260 nm was observed together with a slight increase and blue shift of the peak at 265 nm and a significant increase of the absolute magnitude of the trough at 208 nm in the circular dichroism spectrum. The magnesium concentration dependence of the difference absorption gave a Hill coefficient of 2.0 +/- 0.2. All of the equilibrium data indicate that magnesium ions produce a more ordered form of the molecule. Transient kinetic studies using a magnesium concentration-jump were carried out. The kinetic curves were biphasic, each phase being associated with a relatively slow unimolecular conformational change induced by magnesium binding. A simple scheme was able to accommodate all of the equilibrium and kinetic data, and the kinetic parameters were calculated. Activation parameters for the unimolecular steps suggest that the conformational changes of the 5S RNA involved the breaking of several base pairs and tertiary folding.