Energetics of order/order transitions in nucleic acids

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Abstract
Besides the temperature induced canonical helix to random coil transition, which serves as a prototype of an order/disorder transition, there is a second group of conformational changes in helical polynucleotides, which will be termed order/order transitions. Depending on the environmental conditions and the sequence of the polynucleotides involved, there are four alternative reaction schemes: (i) The inversion of the helical handedness from a right-handed to a left-handed conformation, (ii) the disproportionation of a double helix into a single strand and a triple helix, (iii) the addition of a single strand to a double helix, and (iv) the single/double strand displacement reactions, that is, the displacement of one of the two strands of the helix by a matching single-stranded polynucleotide or the mutual exchange of one strand each between two helical structures. The first three reactions are considered reversible while the last reaction is irreversible; that is, one cannot regain the initial state by inversing the course of the change, here the change in temperature. Both ribo and deoxyribo polynucleotides can undergo these reactions. In the following paper at least one example is given for each of these reactions.