A triple helix obtained by specific recognition of all 4 bases in duplex DNA can adopt a collapsed or an extended form.

It has been proposed that during homologous recombination promoted by RecA DNA triple helices can be formed between a Watson Crick duplex and a homologous third strand without any sequence constraint. A triple helix, obtained by targeting the d(AGTTAGCATG) sequence containing all 4 bases, in which both homologous strands are oriented in a parallel direction with respect to each other, stabilized by addition of Mn2+ ions has been studied by UV and FTIR spectroscopies. We have characterized the sugar conformations of this triplex. All strands are found to contain S type sugars (C2'endo, B family form). Progressive addition of propidium iodide induces a complete reorientation of the sugar geometry to a N type conformation (C3'endo, A family form). This sugar repuckering is consistent with a conformational transition from a collapsed to an extended DNA triple helical structure.