title: Triplex-forming oligonucleotides trigger conformation changes of a target hairpin sequence.
abstract: We used a DNA duplex formed between the 5' end of a 69mer (69T) and an 11mer (OL7) as a substrate for BamHI. The former oligonucleotide folds into a hairpin structure, the stem of which contains a stretch of pyrimidines in one strand and consequently a stretch of purines in the other strand. The oligomer 69T was used as a target for complementary oligodeoxypyrimidines made of 10 nt (OL1), 16 nt (OL5) or 26 nt (OL2) which can engage the same 10 pyrimidine-purine-pyrimidine triplets with the 69T hairpin stem. Although the binding site of OL7 did not overlap that of OL1, OL2 or OL5, the BamHI activity on 69T-OL7 complexes was drastically modified in the presence of these triplex-forming oligomers: OL1 abolished the cleavage by BamHI whereas OL5 and OL2 strongly increased it. Using footprinting assays and point-mutated oligonucleotides we demonstrated that these variations were due to different conformations of the 69T-OL7 complex induced by the binding of oligomers OL1, OL2 or OL5. Therefore, oligonucleotides can act as structural switchers, offering one additional mode for modulating gene expression.
authors.affiliation: Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia.
authors.forename: E
authors.initials: E
authors.lastname: Brossalina
authors.forename: E
authors.initials: E
authors.lastname: Demchenko
authors.forename: Y
authors.initials: Y
authors.lastname: Demchenko
authors.forename: V
authors.initials: V
authors.lastname: Vlassov
authors.forename: J J
authors.initials: JJ
authors.lastname: Toulmé
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D018983:DNA Footprinting; D015245:Deoxyribonuclease BamHI / Q000378:metabolism; D007891:Leishmania / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism; D016376:Oligonucleotides, Antisense / Q000737:chemistry* / Q000378:metabolism; D017354:Point Mutation; D015203:Reproducibility of Results
chemical_list: D009838:Oligodeoxyribonucleotides; D016376:Oligonucleotides, Antisense; C051802:triplex DNA; D004247:DNA; D015245:Deoxyribonuclease BamHI