On the helix–coil equilibrium in two‐ and three‐stranded complexes involving complementary poly‐ and oligonucleotides

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Abstract
The helix–coil equilibrium in molecular complexes formed between long homopoly‐nucleotides and short complementary oligonucleotides is discussed. Each oligomer is allowed to bind to polymer(s) in an all‐or‐none fashion. The formal treatment of Lifson and Zimm is used as a basis for derivations. Approximations for long polymer(s) yield simple formulae describing the transition. The theory is applied to both a two‐stranded complex (i.e., a complex, one strand of which is a long polymer and the other of which consists of a number of short oligomers) and to a three‐stranded complex (i.e., a complex, two strands of which are long polymers and the third of which consists of a number of short oligomers). For the two‐stranded complex, simple expressions result for average quantities when the interruption constant is much smaller than unity. For the three‐stranded complex the matching and the mismatching models are considered in the case where the non‐bonded segments of polymer chains may form closed loops, and it is shown that true phase transitions occur under certain conditions. For a highly cooperative transition the slope of the melting curve is shown to be independent of the cooperativity parameter, provided that residue molar concentrations of the polymer and oligomer are of comparable magnitude. It is thus possible to obtain the enthalpy of the transition directly from the slopes of the melting curves. Some experimental results on two‐ and three‐stranded complexes are compared with the theory and yield the enthalpy and the entropy for the formation of base pairs and triplets.