[A comparative computer analysis of thermodynamic parameters of transport RNA secondary structure]

Thermodynamic parameters of the cloverleaf secondary structure of tRNAs of several major taxons (archaebacteria, eubacteria, eukaryotes, chloroplasts, and mitochondria) were subjected to computer analysis. The distribution of free-energy values was close to normal in all groups (except for the mitochondrial tRNA). In the organisms existing under extreme environmental conditions, the stability of the tRNA secondary structure was higher. Comparative analysis of teh frequency of ¿quasi-complementary¿ GU pairs in stems of randomly generated and real sequences demonstrated preferential fixation of such pairs in the contexts with the most favorable thermodynamics parameters. Noncanonic pairs in tRNA stems set limits on the presence of highly mutable CG dinucleotides. Moreover, the effect of noncanonic pairs other than GU on the frequency of such dinucleotides is far more pronounced than that of GU pairs.