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Triplex-forming oligodeoxynucleotide 15mers, designed to bind in the antiparallel triple-helical binding motif, containing single substitutions (Z) of the four isomeric alphaN(7)-, betaN(7)-, alphaN(9)- and betaN(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 x 10(6) and 1.3 x 10(8) M(-1). The following relative order in Z x X-Y base-triple stabilities was found: Z = alphaN(7)ap: T-A &gt; A-T&gt; C-G approximately G-C; Z = betaN(7)ap: A-T &gt; C-G &gt; G-C &gt; T-A; Z = alphaN(9)ap: A-T = G-C &gt; T-A &gt; C-G; and Z = betaN(9)ap: G-C &gt; A-T &gt; C-G &gt; T-A.

Triple-helix formation in the antiparallel binding motif of oligodeoxynucleotides containing N9- and N7-2-aminopurine deoxynucleosides