Properties of triple helix formation with oligodeoxyribonucleotides containing 8-oxo-2′-deoxyadenosine and 2′-modified nucleoside derivatives Original Research Article

The ability of homopyrimidine oligonucleotides containing 8-oxo-2′-deoxyadenosine (dAOH), 2′-methoxyuridine (Um). 2′-fluorouridine (Uf), 2′-methoxycytidine (Cm), and 2′-fluorocytidine (Cf) to form stable, triple-helical structures with sequences containing the recognition site for the class II-S restriction enzyme, Ksp632-I, was studied as a function of pH. The 8-oxo-2′-deoxyadenosine substituted oligomers were shown to bind within the physiological pH range in a pH-independent fashion, without a compromise in specificity. In particular, the substitutions of three deoxycytidine residues with 8-oxo-2′-deoxyadenosine showed higher endonuclease inhibition than the substitution of either one or two deoxycytidine residues with 8-oxo-2′-deoxyadenosine. In contrast, the oligonucleotides containing 2′-modified nucleosides (Uf, Um, Uf-Cf, Um-Cm, dAOHUf, and dAOH-Um) bind in a pH-dependent manner to the target duplex.