title: Binding and NMR structural studies on indoloquinoline-oligonucleotide conjugates targeting duplex DNA.
abstract: An 11-phenyl-indolo[3,2-b]quinoline (PIQ) was tethered through an aminoalkyl linker to the 5'-end of four pyrimidine oligonucleotides with T/C scrambled sequences at their two 5'-terminal positions. Binding to different double-helical DNA targets formed parallel triple helices with a PIQ-mediated stabilization that strongly depends on pH and the terminal base triad at the 5'-triplex-duplex junction. The most effective stabilization was observed with a TAT triplet at the 5'-junction under low pH conditions, pointing to a protonated ligand with a high triplex binding affinity and unfavorable charge repulsions in the case of a terminal C(+)GC triplet at the junction. The latter preference of the PIQ ligand for TAT over CGC is alleviated yet still preserved at higher pH. Intercalation of PIQ at the 5'-triplex-duplex junction as suggested by the triplex melting experiments was confirmed by homonuclear and heteronuclear NMR structural studies on a specifically isotope-labeled triplex. The NMR analysis revealed two coexisting species that only differ by a 180° rotation of the indoloquinoline within the intercalation pocket. NOE-derived molecular models indicate extensive stacking interactions of the indoloquinoline moiety with the TAT base triplet and CG base pair at the junction and a phenyl substituent that is positioned in the major groove and oriented almost perpendicular to the plane of the indoloquinoline.
authors.affiliation: Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Eick
authors.forename: Fanny
authors.initials: F
authors.lastname: Riechert-Krause
authors.forename: Klaus
authors.initials: K
authors.lastname: Weisz
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D007211:Indoles / Q000737:chemistry / Q000494:pharmacology; D007364:Intercalating Agents / Q000737:chemistry* / Q000494:pharmacology; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000494:pharmacology; D011804:Quinolines / Q000737:chemistry* / Q000494:pharmacology; D013816:Thermodynamics
chemical_list: D007211:Indoles; D007364:Intercalating Agents; D009841:Oligonucleotides; D011804:Quinolines; D004247:DNA