Theory of thermal transitions in low molecular weight RNA chains

A statistical mechanical theory of thermal transitions in short polynucleotide chains which achieve their secondary structure primarily by intramolecular complementary base-pair interactions is described. Thermal transition profiles for a large class of possible arrangements of base-pairs in short RNA chains can be calculated from the theory, using parameters derived from the thermal denaturation of high molecular weight RNA double-helices. Effects of length, base composition and configuration are discussed quantitatively. The theory is applied to calculating melting curves of three yeast tRNA species, for which experimental data are available. In the case of yeast serine tRNA, close agreement between the profile predicted from the "clover-leaf" structural model is found. The alanine and tyrosine models lead to profiles sharper than those observed, although the data are not so extensive for these later species. Certain quantities of interest apart from those usually measured in thermal denaturation studies can be calculated from the theory.