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Nucleic Acids Research, 2001, Vol. 29, No. 11 2260-2267
© 2001 Oxford University Press

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

Serge P. Parel and Christian J. Leumann*

Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland

Triplex-forming oligodeoxynucleotide 15mers, designed to bind in the antiparallel triple-helical binding motif, containing single substitutions (Z) of the four isomeric {alpha}N7-, ßN7-, {alpha}N9- and ßN9-2-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 106 and 1.3 x 108 M–1. The following relative order in Z x X-Y base-triple stabilities was found: Z = {alpha}N7ap: T-A > A-T> C-G ~ G-C; Z = ßN7ap: A-T > C-G > G-C > T-A; Z = {alpha}N9ap: A-T = G-C > T-A > C-G; and Z = ßN9ap: G-C > A-T > C-G > T-A.

* To whom correspondence should be addressed. Tel: +41 31 631 4355; Fax: +41 31 631 3422; Email: leumann{at}ioc.unibe.ch


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