Stabilization of triple-stranded oligonucleotide complexes: Use of probes containing alternating phosphodiester and stereo-uniform cationic phosphoramidate linkages

Pyrimidine oligonucleotides containing alternating anionic and stereo-uniform cationic N-(dimethylaminopropyl)phosphoramidate linkages [e.g. d(T+T-)(7)T, d(T+T-)(2)(T+C-)(5)T and (U'+U'-)(7)dT, where U' is 2'-O-methyluridine)] are shown to bind to complementary double-stranded DNA segments in 0.1 M NaCl at pH 7 to form triple-stranded complexes with the pyrimidine.purine.pyrimidine motif. For each of the sequences investigated, one stereoisomer bound with higher affinity, and the other stereoisomer with lower affinity, than the corresponding all-phosphodiester oligonucleotide, The stereoisomer of d(T+T-)(7)T that interacted weakly with a dT.dA target in 0.1 M NaCl formed a novel dA.dA.dT triple-stranded complex with poly(dA) or d(A(15)C(4)A(15)) in 1 An NaCl; in contrast, the stereoisomer that bound strongly to the dT.dA target failed to form a dA.dA.dT triple-stranded complex.