NMR characterization of the aliphatic β/β pairing for recognition of a A•T/T•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 sequence-specific recognition in the minor groove of DNA. Because the curvature of four or five contiguous Im-Py rings does not perfectly match the canonical B-helix, beta-alanine (beta) residues have been inserted to reset the register. Complexes of three pyrrole-imidazole polyamides of sequence composition 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 site were characterized by NMR. NMR titrations and NOESY data combined with restrained molecular modeling show that each polyamide adopts an extended antiparallel 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 combination of size, flexibility, and alignment of the polyamide-paired aromatic subunits in extended, dimeric 2:1 complexes.