EXTENSION OF THE RANGE OF DNA-SEQUENCES AVAILABLE FOR TRIPLE-HELIX FORMATION - STABILIZATION OF MISMATCHED TRIPLEXES BY ACRIDINE-CONTAININGOLIGONUCLEOTIDES

Triple helix formation usually requires an oligopyrimidine oligopurine sequence in the target DNA. A triple helix is destabilized when the o ligopyrimidine oligopurine target contains one (or two) purine pyrimid ine base pair inversion(s). Such an imperfect target sequence can be r ecognized by a third strand oligonucleotide containing an internally i ncorporated acridine intercalator facing the inverted purine pyrimidin e base pair(s). The loss of tripler stability due to the mismatch is p artially overcome. The stability of triplexes formed at perfect and im perfect target sequences was investigated by UV thermal denaturation e xperiments. The stabilization provided by an internally incorporated a cridine third strand oligonucleotide depends on the sequences flanking the inverted base pair. For triplexes containing a single mismatch th e highest stabilization is observed for an acridine or a propanediol t ethered to an acridine on its 3'-side facing an inverted A.T base pair and for a cytosine with an acridine incorporated to its 3'-side or a guanine with an acridine at its 5'-side facing an inverted G.C base pa ir. Fluorescence studies provided evidence that the acridine was inter calated into the tripler. The target sequences containing a double bas e pair inversion which form very unstable triplexes can still be recog nized by oligonucleotides provided they contain an appropriately incor porated acridine facing the double mismatch sites. Selectivity for an A.T base pair inversion was observed with an oligonucleotide containin g an acridine incorporated at the mismatched site when this site is fl anked by two T.AT base triplets. These results show that the range of DNA base sequences available for tripler formation can be extended by using oligonucleotide intercalator conjugates.