Thermal denaturation profiles of deoxypolynucleotide-destabilizer ligand complexes: semiempirical studies

In this paper, we study the dependence of the Tm (melting temperature) of complexes formed between double-stranded deoxypolynucleotides and pure destabilizer nonspecific ligands on Kc (intrinsic association constant), nc (apparent site size), and wc (cooperativity constant). Using the Sequence Generating Function (SGF) method, we have found a simple, analytical relationship between the Tm and these interaction parameters. The validity of this relationship depends strongly on the sigma value (sigma being the nucleation parameter of the deoxypolynucleotide). Through the equation so obtained, it is possible to evaluate Kc, nc, and wc from the melting temperature of three experimental thermal denaturation profiles at different r (ligand/deoxypolynucleotide ratio) values. However, when wc greater than 100, a degeneration in the wc and Kc values appears, and the study of the free deoxypolynucleotide region in the melting profile is necessary in order to accurately evaluate these two parameters. The method has been checked using complexes formed with poly(d(A-T].poly(d(A-T] and both bovine pancreatic ribonuclease and protein GP32 of phage T4 as experimental models. The applicability of the method here developed is discussed in relation to the nature of the ligands and the sigma and wc values.