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

Abstract

Alternate-strand triple helix formation was optimized at the two junction steps, the 5'-TpA-3' and 5'-ApT-3' junctions. Footprint experiments, gel retardation assays and thermal denaturation measures on a sequence appropriately 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' for the construction of alternate-strand triple helix forming oligonucleotides which open new possibilities for extending the range of applications of antigene strategy.