In this work we report a thermodynamic characterization of stability and melting behaviour of two 24-mer DNA triplexes. The
third strand, that binds the Watson-Crick double helix with Hoogsteen hydrogen bonds, contains 3′-3′ phosphodiester junction
that determines the polarity inversion. The target double helix is composed of adjacent and alternate fragments of oligopurine-oligopyrimidine
tracts. The two helices differ from the substitution of the cytosine, involved in the junction, with the thymine. Calorimetric
data reported here provide a quantitative measure of the influence of pH and base modification on the stability of a DNA triplex.