title: Rational design of a triple helix-specific intercalating ligand.
abstract: DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. Molecular modeling and thermal denaturation experiments suggest that benzo[f]pyrido[3, 4-b]quinoxaline derivatives intercalate into triple helices by stacking preferentially with the Hoogsteen-paired bases. Based on this model, it was predicted that a benzo[f]quino[3,4-b]quinoxaline derivative, which possesses an additional aromatic ring, could engage additional stacking interactions with the pyrimidine strand of the Watson-Crick double helix upon binding of this pentacyclic ligand to a triplex structure. This compound was synthesized. Thermal denaturation experiments and inhibition of restriction enzyme cleavage show that this new compound can indeed stabilize triple helices with great efficiency and specificity and/or induce triple helix formation under physiological conditions.
authors.affiliation: Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, Institut National de la Santé et de la Recherche Médicale U 201, Centre National de la Recherche Scientifique, Unité de Recherche Associ-ee 481, Paris, France.
authors.forename: C
authors.initials: C
authors.lastname: Escudé
authors.forename: C H
authors.initials: CH
authors.lastname: Nguyen
authors.forename: S
authors.initials: S
authors.lastname: Kukreti
authors.forename: Y
authors.initials: Y
authors.lastname: Janin
authors.forename: J S
authors.initials: JS
authors.lastname: Sun
authors.forename: E
authors.initials: E
authors.lastname: Bisagni
authors.forename: T
authors.initials: T
authors.lastname: Garestier
authors.forename: C
authors.initials: C
authors.lastname: Hélène
mesh_terms: D000818:Animals; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D005786:Gene Expression Regulation; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011810:Quinoxalines / Q000737:chemistry*
chemical_list: D008024:Ligands; D011810:Quinoxalines; C032931:benzoquinoxaline; D004247:DNA