Pyrimidine morpholino oligonucleotides form a stable triple helix in the absence of magnesium ions

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 m odified at either the backbone or base level are routinely used. Morpholino oligonucleotides appeared recently as a promising modification for antisen se 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 oligonueleotide. At a neutral pH and in the presence of a high magnesium ion concentration (10 mM), the p hosphoramidate oligomer forms the most stable triple helix, whereas in the absence of magnesium ion but at a physiological monovalent cation concentra tion (0.14 M) only morpholino oligonucleotides form a stable triplex. To ou r knowledge, this is the first report of a stable triple helix in the pyrim idine motif formed by a noncharged oligonucleotide third strand (the morpho lino oligonucleotide) and a DNA duplex. We show here that the structure for med with the morpholino oligomer is a bona fide triple helix and it is dest abilized by high concentrations of potassium ions or divalent cations(Mg2+) . (C) 2000 Academic Press.