title: Properties of triple helix formation with oligodeoxyribonucleotides containing 8-oxo-2'-deoxyadenosine and 2'-modified nucleoside derivatives.
abstract: 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, dAOH-Uf, and dAOH-Um) bind in a pH-dependent manner to the target duplex.
authors.affiliation: Department of Industrial Chemistry, Chiba Institute of Technology, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Ishibashi
authors.forename: H
authors.initials: H
authors.lastname: Yamakawa
authors.forename: Q
authors.initials: Q
authors.lastname: Wang
authors.forename: S
authors.initials: S
authors.lastname: Tsukahara
authors.forename: K
authors.initials: K
authors.lastname: Takai
authors.forename: T
authors.initials: T
authors.lastname: Maruyama
authors.forename: H
authors.initials: H
authors.lastname: Takaku
mesh_terms: D001665:Binding Sites; D003562:Cytidine / Q000031:analogs & derivatives / Q000737:chemistry; D004279:DNA, Viral / Q000187:drug effects / Q000378:metabolism*; D003839:Deoxyadenosines / Q000737:chemistry*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000187:drug effects / Q000378:metabolism*; D004586:Electrophoresis / Q000379:methods; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D009705:Nucleosides / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D011487:Protein Conformation; D013539:Simian virus 40 / Q000235:genetics; D013696:Temperature; D014529:Uridine / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D004279:DNA, Viral; D003839:Deoxyadenosines; D009692:Nucleic Acid Heteroduplexes; D009705:Nucleosides; D009838:Oligodeoxyribonucleotides; D003562:Cytidine; C078251:2'-deoxy-7,8-dihydro-8-oxoadenosine; C057073:endodeoxyribonuclease Ksp632I; D015252:Deoxyribonucleases, Type II Site-Specific; D014529:Uridine