Triplex-forming oligonucleotides with unexpected affinity for a nontargeted GA repeat sequence

We examined the affinity and the specificity of tripler formation for different purine ODNs directed against two portions of a purine sequence derived from the mouse fli-1 gene. As expected, the ODNs antiparallel to the purine strand of their target can form tripler DNA. One parallel ODN showed binding to its target sequence, We explain this unusual binding by an interaction of the ODN with a GA repetition present in the sequence, We further examined the interaction of this ODN with a target composed of 14 GA repetitions, Unexpectedly, one ODN shows higher affinity for a partially complementary GA target relative to its completely complementary target. For another ODN, the binding to the GA target is weaker and might involve skipping of bases in a way that resembles alternate strand tripler formation.