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Binding and NMR Structural Studies on Indoloquinoline–Oligonucleotide Conjugates Targeting Duplex DNA

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journal contribution
posted on 20.06.2012 by Andrea Eick, Fanny Riechert-Krause, Klaus Weisz
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.