title: Conjugation of a 3-(1H-phenanthro[9,10-d]imidazol-2-yl)-1H-indole intercalator to a triplex oligonucleotide and to a three-way junction.
abstract: A new intercalating nucleic acid monomer M comprising a 4-(1-indole)-butane-1,2-diol moiety was synthesized via a classical alkylation reaction of indole-3-carboxaldehyde followed by a condensation reaction with phenanthrene-9,10-dione in the presence of ammonium acetate to form a phenanthroimidazole moiety linked to the indole ring. Insertion of the new intercalator as a bulge into a Triplex Forming Oligonucleotide resulted in good thermal stability of the corresponding Hoogsteen-type triplexes. Molecular modeling supports the possible intercalating ability of M. Hybridisation properties of DNA/DNA and RNA/DNA three-way junctions (TWJ) with M in the branching point were also evaluated by their thermal stability at pH 7. DNA/DNA TWJ showed increase in thermal stability compared to wild type oligonucleotides whereas this was not the case for RNA/DNA TWJ.
authors.affiliation: Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
authors.forename: Maha I
authors.initials: MI
authors.lastname: Fatthalla
authors.forename: Yehya M
authors.initials: YM
authors.lastname: Elkholy
authors.forename: Nermeen S
authors.initials: NS
authors.lastname: Abbas
authors.forename: Adel H
authors.initials: AH
authors.lastname: Mandour
authors.forename: Per T
authors.initials: PT
authors.lastname: Jørgensen
authors.forename: Niels
authors.initials: N
authors.lastname: Bomholt
authors.forename: Erik B
authors.initials: EB
authors.lastname: Pedersen
mesh_terms: D004247:DNA / Q000737:chemistry; D007093:Imidazoles / Q000737:chemistry*; D007211:Indoles / Q000737:chemistry*; D007364:Intercalating Agents / Q000138:chemical synthesis / Q000737:chemistry*; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry*; D014466:Ultraviolet Rays
chemical_list: D007093:Imidazoles; D007211:Indoles; D007364:Intercalating Agents; D009841:Oligonucleotides; C029899:imidazole; D004247:DNA