Thermodynamic analysis of transfer RNA unfolding

Abstract

The results of calorimetric studies of specific transfer RNAs (tRNA Val, tRNA Phe, tRNA t Met, tRNA Ile, tRNA Ser, tRNA Asp) are summarized and analyzed thermodynamically. It is shown that the overall melting enthalpies are larger and do not depend significantly on temperature and ionic conditions, as was previously thought. In all cases the melting curves are very complicated and cannot be approximated by a function for the two-state transition. The apparent reason for the discrepancy is the large breadth of transition over the temperature scale in magnesium-free solutions, which complicates the determination of the heat effect. The presence of magnesium ions sharpens the transition, but also induces the degradation of polynucleotides at elevated temperatures, which is observed as a large increase in heat capacity. It is shown that the unfolding process can be represented as a sequence of independent two-state transitions. The steps of unfolding were identified by using the known experimental facts and by comparing the experimentally obtained thermodyriamic characteristics of the steps with the calculated values for the different parts of the structure. According to the received ascription, the first two steps of unfolding correspond to disruption of tertiary structure and the dhU branch, i.e. the disruption of the tRNA core, after which it unfolds into a topologically flat structure with separate branches. This explains the experimentally observed independence of the steps involved in the unfolding and folding of the tRNA native structure. It is suggested that this property is important for the folding of various tRNA polynucleotide chains into a unified three-dimensional structure.