Antiparallel side-by-side heterodimer for sequence-specific recognition in the minor groove of DNA by a distamycin/1-methylimidazole-2-carboxamide-netropsin pair

The two peptides distamycin A(D) and 1-methylimidazole-2-carboxamide-netropsin (2-ImN) simultaneously bind the five-base-pair sequence 5'-TGTTA-3'. Footprinting experiments indicate that both molecules are necessary for binding to this sequence while affinity cleaving data define the orientations with which each peptide binds to this sequence. The footprinting and affinity cleaving data are consistent with a model wherein the two peptides bind as a side-by-side antiparallel heterodimer in the minor groove of double-helical DNA.