Multiple states in macromolecules II. Entropic behaviour of tRNA degraded by polynucleotide phosphorylase

Abstract

Degradation of tRNA by polynucleotide phosphorylase has been shown to be very different from the degradation of other tRNAs (for review, see [ 1 ] ); this was supposedly due to the peculiar structural features of transfer RNA [2]. A theoretical model for single nucleation process in macromolecules has been described in a previous article [3] and we shall try to use it on the special case of tRNA, with as few thermodynamic parameters as possible, and then to relate them to known features of the tRNA molecule. The characteristic degradation path of polynucleotide phosphorylase is the following reversible reaction: intact. Therefore, when we say n% of phosphorolysis, it means that n% of the molecules have been destroyed (arid not fragments of n% from all the molecules). Polynucleotide phosphorylase will thus be used here as the experimental means for separating the tRNA population [3] . It is worth emphasizing again that the reaction stops before complete phosphorolysis of the total tRNA population is achieved, not because the enzyme has become inactive, but because the limiting factor resides in the tRNA itself. We shall sum up the experimental facts and correlate them to the single nucleation model to finally obtain values of the thermodynamic parameters involved.