Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn2+ ions

We present evidence of formation of an intramolecular parallel triple helix with T.A.T and G.G.C base triplets (where represents the hydrogen bonding interaction between the third strand and the duplex while represents the Wa tson-Crick interactions which stabilize the duplex). The third GT strand, c ontaining seven GpT/TpG steps, targets the polypurine sequence 5'-AGG-AGG-G AG-GAG-3'. The triple helix is obtained by the folding back twice of a 36me r, formed by three dodecamers tethered by hydroxyalkyl linkers (-L-), Due t o the design of the oligonucleotide, the third strand orientation is parall el with respect to the polypurine strand. Triple helical formation has been studied in concentration conditions in which native gel electrophoresis ex periments showed the absence of intermolecular structures. Circular dichroi sm (CD) and UV spectroscopy have been used to evidence the tripler structur e. A CD spectrum characteristic of triple helical formation as well as biph asic UV and CD melting curves have been obtained in high ionic strength NaC l solutions in the presence of Zn2+ ions, Specific interactions with Zn2+ i ons in low water activity conditions are necessary to stabilize the paralle l tripler.