NMR characterization of the aliphatic beta/beta pairing for recognition ofa A center dot T/T center dot A base pairs in the minor groove of DNA

Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be combined in antiparallel side-by-side dimeric complexes for s equence-specific recognition in the minor groove of DNA. Because the curvat ure of four or five contiguous Im-Py rings does not perfectly match the can onical B-helix, beta-alanine (beta) residues have been inserted to reset th e register. Complexes of three pyrrole-imidazole polyamides of sequence com position ImPyPy-X-PyPyPy-Dp, where X = Py, beta, or glycine (G), bound to a 13 base pair DMA duplex containing a 9 base pair 5'-TGTATATCA-3' match sit e were characterized by NMR. NMR titrations and NOESY data combined with re strained molecular modeling show that each polyamide adopts an extended ant iparallel dimeric conformation with the ligands fully overlapped: around a central Py/Py, G/G, or beta/beta pair. Conformational exchange is seen near the linker for the G-linked complex, but not with the beta or Py linkers. In addition to providing the first direct structural evidence for formation sf the aliphatic beta/beta pairing in the minor groove, models support the idea that the beta linker of ImPyPy-beta-PyPyPy-Dp provides an optimal com bination of size, flexibility, and alignment of the polyamide-paired aromat ic subunits in extended, dimeric 2:1 complexes.