ALTERNATE STRAND RECOGNITION OF DOUBLE-HELICAL DNA BY (T,G)-CONTAINING OLIGONUCLEOTIDES IN THE PRESENCE OF A TRIPLE HELIX-SPECIFIC LIGAND

Triple helix formation requires a polypurine-polypyrimidine sequence i n the target DNA, Recent works have shown that this constraint can be circumvented by using alternate strand tripler-forming oligonucleotide s, We have previously demonstrated that (T,G)-containing tripler-formi ng oligonucleotides may adopt a parallel or an antiparallel orientatio n with respect to an oligopurine target, depending upon the sequence a nd, in particular, upon the number of 5'-GpT-3' and 5'-TpG-3' steps [S un et al, (1991) C. R, Acad. Sci, Paris Ser III, 313, 585-590], A sing le (T,G)-containing oligonucleotide can therefore interact with two ol igopurine stretches which alternate on the two strands of the target D NA, The (T,G) switch oligonucleotide contains a 5'-part targeted to on e of the oligopurine sequences in a parallel orientation followed by a 3'-part that adopts an antiparallel orientation with respect to the s econd oligopurine sequence, We show that a limitation to the stability of such a tripler may arise from the instability of the antiparallel part, composed of reverse-Hoogsteen C.GxG and T.AxT base triplets, Usi ng DNase I footprinting and ultraviolet absorption experiments, we rep ort that a benzo[e]pyridoindole derivative [(3-methoxy-7H-8-methyl-11- [(3'-amino-propyl) amino] benzo[e]pyrido [4,3b]indole (BePI)], a drug interacting more tightly with a tripler than with a duplex DNA, strong ly stabilizes triplexes with reverse-Hoogsteen C.GxG and T.AxT triplet s thus allowing a stabilization of the tripler-forming switch (T,G) ol igonucleotide on alternating oligopurine-oligopyrimidine 5'-(Pull(14)( Py)(14)-3' duplex sequences, These results lead to an extension of the range of oligonucleotide sequences for alternate strand recognition o f duplex DNA.