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The refolding of 5S RNA into its two conformational states has been examined as a function of solvent composition and annealing conditions. The results show that the product distribution depends on the folding pathway. Quick cooling from high temperature produces roughly equal amounts of the two forms, even in the presence of 1 mm Mg++. However annealing by slow cooling to intermediate temperatures (50 degrees--60 degrees C) in Mg++-containing buffers, followed by quick cooling, allows formation of a structure which guides the refolding path to the "native" conformation.  The stability of this structural nucleus for the "native" conformation depends strongly on Mg++ concentration. We conclude that the A ("native") conformation differs from the B conformation not in rate of refolding, but rather in having a lower enthalpy and a also a smaller rate of unfolding for the critical structural nucleus. The order of folding during biosynthesis may be crucial for forming the "native" conformation.

Pathway-dependent refolding of E. coli 5S rRNA