Effect of strand orientation on the interaction of berenil with DNA triple helices

Abstract.

Using circular dichroism spectroscopy the ability of berenil, a minor groove binding drug, to induce triple helix formation was investigated with two oligonucleotides designed to form two intramolecular triplexes containing T*A:T and G*G:C triplets, which differ only by the orientation of their third strand: 5′-d(G₄A₄G₄-[T₄]-C₄T₄C₄-[T₄]-G₄T₄G₄), and 5′-d(G₄T₄G₄-[T₄]-G₄A₄G₄-[T₄]-C₄T₄C₄), where [T₄] represents a stretch of four thymine residues. We demonstrate that when added to the duplex form of these oligonucleotides, berenil induces triplex structure formation only if the orientation of third strand is antiparallel to the purine strand.