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Effect of cytosine protonation and cation on thermodynamic properties of parallel DNA triplex family.

The conformational and thermodynamic properties of three modified parallel triplexes, which have the same base composition but differ in the orientation of the Hoogsteen third strand with respect to the core duplex, were comparatively discussed. The results show that the intermolecular triplex is unstable relatively to the intramolecular triplex and the thermodynamic properties are slightly dependent on the 3' or/and 5' junctions. Furthermore, mono- and divalent cations compete each other in stabilizing the triple helix structure and a higher concentration of the monovalent cation would shield the effect of divalent cations on the triplex stability.