Triple-helix formation in the antiparallel binding motif of oligodeoxynucleotides containing N(9)- and N(7)-2-aminopurine deoxynucleosides

Triplex-forming oligodeoxynucleotide 15mers, designed to bind in the antiparallel triple-helical binding motif, containing single substitutions (Z) of the four isomeric αN(7)-, βN(7)-, αN(9)- and βN(9)-2-aminopurine (ap)-deoxyribonucleosides were prepared. Their association with double-stranded DNA targets containing all four natural base pairs (X-Y) opposite the aminopurine residues was determined by quantitative DNase I footprint titration in the absence of monovalent metal cations. The corresponding association constants were found to be in a rather narrow range between 1.0 × 10(6) and 1.3 × 10(8) M(–1). The following relative order in Z × X-Y base-triple stabilities was found: Z = αN(7)ap: T-A > A-T> C-G ∼ G-C; Z = βN(7)ap: A-T > C-G > G-C > T-A; Z = αN(9)ap: A-T = G-C > T-A > C-G; and Z = βN(9)ap: G-C > A-T > C-G > T-A.