title: Inhibition of restriction endonuclease cleavage site via triple helix formation by homopyrimidine phosphorothioate oligonucleotides.
abstract: The ability of pyrimidine rich oligonucleotide phosphorothioate to form stable triple helical structures with the sequence containing the recognition site for the class II-S restriction enzyme Ksp 632-I was examined. First, we synthesized double strand oligonucleotides corresponding to the SV40 sites and studied their interaction with homopyrimidine oligodeoxyribonucleotides including replacement of the other chain either PS group (SO-ODNs) in second nucleotide position (from 5'-terminus) and end capped with the PS group at both 3'- and 5'-ends (S2O-ODNs). The resulting perfect DNA triplexes were detected by gel-mobility shift. The phosphorothioate oligonucleotide analogues (SO-ODNs) and (S2O-ODNs) were shown to inhibit enzymatic cleavage under conditions that allow for triple helix formation. Inhibition is sequence-specific and occurs in the micromolar concentration range. Of particular interest is the Sp-phosphorothioate analogue (Sp-SO-ODNs) which inhibited endonuclease more than the other phosphorothioate oligonucleotide analogues (Rp-SO-ODNs or S2O-ODNs).
authors.affiliation: Department of Industrial Chemistry, Chiba Institute of Technology, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Tsukahara
authors.forename: S G
authors.initials: SG
authors.lastname: Kim
authors.forename: H
authors.initials: H
authors.lastname: Takaku
mesh_terms: D001483:Base Sequence; D015252:Deoxyribonucleases, Type II Site-Specific / Q000037:antagonists & inhibitors*; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000494:pharmacology*; D011743:Pyrimidines; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013873:Thionucleotides / Q000494:pharmacology*
chemical_list: D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines; D013873:Thionucleotides; C035337:CCGCGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific