Isohelicity and Strand Selectivity in the Minor Groove Binding of Chiral (1R,2R)- and (1S,2S)-Bis(netropsin)-1,2-cyclopropanedicarboxamide Ligands to Duplex DNA

The sequence-selective DNA binding within the minor groove of four base pairs long AT rich segments for the naturally occurring oligopyrrolecarboxamides, netropsin and distamycin, have been characterized by NMR and X-ray techniques which provide valuable information on the factors for specific molecular recognition and binding efficiency. A special interest in developing longer dimeric bis-netropsin and bis-distamycin compounds arises from their potential applications as gene control agents targeted against larger DNA segments in a sequence specific manner. Herein we describe the use of fixed C sub(2)-symmetric dimeric arrangements of netropsin segments, in opposing orientations and joined through optically pure cyclopropane-1,2-dicarboxamide templates, to "extend the code" for isohelical and chiral recognition of eight AT base pairs long minor groove in a right-handed B-DNA fragment. The structural analysis of the diastereomeric complex formed between d(CGAAAATTTTCG) sub(2) and (-)-(1R,2R)-bis(netropsin) -1,2-cyclopropanedicarboxamide (BNC), and of that between the same DNA fragment and the enantiomeric (+)-(1S,2S)-BNC ligand, was performed by one- and two-dimensional NMR methods. These results indicate a perfectly matching isohelical and strand specific binding for (1R,2R)-BNC where each of the two netropsin subunits is oriented against a 5'-TTTT site. The cyclopropane linker and the N-methylpyrrole rings follow the natural right-handed twist of the base pairs along the minor groove of the 5'-AAAATTTT segment, and the complex is stabilized by single linear hydrogen bonds with the thymidine O2 atoms, instead of the three-center bifurcated bonds proposed for the binding of netropsin to alternating AT segments. The relative orientation of the cyclopropane group (with its methylene projected away from the DNA) for the (1S,2S)-BNC enantiomer is the same as observed for (1R,2R)-BNC which forces each netropsin subunit to be aligned differently in a less favorable arrangement (against 5'-AAAA sites). Binding in this case therefore induces a further twist of the planar amide groups and two N-methylpyrrole ring systems in each of the netropsin subunits. The twisting is detected by NOE interactions and, in contrast with the situation for (1R,2R)-BNC, is attributed to the adjustments that are required by the inherent affinity for hydrogen-bonding by the amide NHs of (1S,2S)-BNC to the continguous arrangement of thymidine O2 atoms on the complementary strand.