Design of peptides that bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif

The designed peptides pyridine-2-carboxamide-netropsin (2-PyN) and 1-methylimidazole-2-carboxamide-netropsin (2-ImN) are crescent-shaped synthetic analogs of the natural products netropsin (N) and distamycin A (D). Footprinting experiments indicate that the peptides 2-PyN and 2-ImN bind specifically the 5 base pair sequence 5'-TGTCA-3'. Affinity cleaving data suggest that the complexes, 2-ImN.5'-TGTCA-3' and 2-PyN.5'-TGTCA-3', are composed of two equivalent orientations which disfavor a 1:1 model. The footprinting and affinity cleaving data are in accord with a 2:1 complex where a novel side-by-side antiparallel dimer binds in the minor groove of double-helical DNA.