title: Pyrimidine morpholino oligonucleotides form a stable triple helix in the absence of magnesium ions.
abstract: Oligonucleotides can be used as sequence-specific DNA ligands by forming a local triple helix. In order to form more stable triple-helical structures or prevent their degradation in cells, oligonucleotide analogues that are modified at either the backbone or base level are routinely used. Morpholino oligonucleotides appeared recently as a promising modification for antisense applications. We report here a study that indicates the possibility of a triple helix formation with a morpholino pyrimidine TFO and its comparison with a phosphodiester and a phosphoramidate oligonucleotide. At a neutral pH and in the presence of a high magnesium ion concentration (10 mM), the phosphoramidate oligomer forms the most stable triple helix, whereas in the absence of magnesium ion but at a physiological monovalent cation concentration (0.14 M) only morpholino oligonucleotides form a stable triplex. To our knowledge, this is the first report of a stable triple helix in the pyrimidine motif formed by a noncharged oligonucleotide third strand (the morpholino oligonucleotide) and a DNA duplex. We show here that the structure formed with the morpholino oligomer is a bona fide triple helix and it is destabilized by high concentrations of potassium ions or divalent cations (Mg(2+)).
authors.affiliation: Laboratoire de Biophysique, Muséum National d'Histoire Naturelle INSERM U201, CNRS UMR8646, 43, rue Cuvier, Paris, 75005, France.
authors.forename: L
authors.initials: L
authors.lastname: Lacroix
authors.forename: P B
authors.initials: PB
authors.lastname: Arimondo
authors.forename: M
authors.initials: M
authors.lastname: Takasugi
authors.forename: C
authors.initials: C
authors.lastname: Hélène
authors.forename: J L
authors.initials: JL
authors.lastname: Mergny
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D017931:DNA Primers; D004586:Electrophoresis / Q000379:methods; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism*; D009025:Morpholines / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics; D013873:Thionucleotides / Q000737:chemistry
chemical_list: D017931:DNA Primers; D009025:Morpholines; D011742:Pyrimidine Nucleotides; D013873:Thionucleotides; C051802:triplex DNA; D004247:DNA; D008274:Magnesium