Equilibrium and kinetics of the thermal unfolding of yeast 5S ribosomal RNA.

The equilibrium and kinetics of thermal unfolding of yeast 5S ribosomal RNA have been studied by optical methods, in a low ionic strength environment without Mg2+, to follow the disruption of the secondary structure base pairs in the molecule. The equilibrium results demonstrated that all of the helical regions melted simultaneously, and the kinetics of the thermal unfolding were first order. These findings suggest the validity of the two-state approximation for the unfolding reaction under the present conditions. The total number of secondary structure base pairs estimated from our experiment was consistent with that contained in the conformational model based on the Raman spectrum rather than that in the one derived by the enzymic digestion method. Taking our results on the kinetic behavior of the thermal unfolding overall, we propose that the 5S RNA has a partly melted secondary structure under the solvent conditions used.