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

Tripler-forming oligodeoxynucleotide 15mers, designed to bind in the antipa rallel triple-helical binding motif, containing single substitutions (Z) of the four isomeric alphaN(7)-, betaN(7)-, alphaN(9)- and betaN(9)-2-amino-p urine (ap)-deoxyribonucleosides were prepared. Their association with doubl e-stranded DNA targets containing all four natural base pairs (X-Y) opposit e the aminopurine residues was determined by quantitative DNase I footprint titration in the absence of monovalent metal cations, The corresponding as sociation constants were found to be in a rather narrow range between 1.0 x 10(6) and 1.3 x 10(8) M-1. The following relative order in Z x X-Y base-tr iple stabilities was found: Z = alphaN(7)ap: T-A > A-T > C-G similar to G-C ; Z = betaN(7)ap: A-T > C-G > G-C > T-A; Z = alphaN(9)ap: A-T = G-C > T-A > C-G; and Z = betaN(9)ap: G-C > A-T > C-G > T-A.