Optimization of alternate-strand triple helix formation at the 5 '-TpA-3 'and 5 '-ApT-3 ' junctions

Alternate-strand triple helix formation was optimized at the two junction s teps, the 5'-TpA-3' and 5'-ApT-3' junctions, Footprint experiments, gel ret ardation assays and thermal denaturation measures on a sequence appropriate ly designed with two adjacent alternate-strand polypurine tracts points out that the addition of an adenine residue and the removal of one nucleotide should facilitate the crossing strands at the 5'-TpA-3' junction and at the 5'-ApT-3' junction, respectively. These results provide a 'switch code' fo r the construction of alternate-strand triple helix forming oligonucleotide s which open new possibilities for extending the range of applications of a ntigene strategy.