U-pin polyamide motif for recognition of the DNA minor groove

DNA-binding hairpin pyrrole-imidazole polyamides with gamma-aminobutyric acid as a turn-forming residue tolerate A . T or T . A base pairs under the turn. U-pins-polyamides with a different turn-have been synthesized and their DNA binding properties were studied. The two turn-forming residues are connected via the ring nitrogens using variable length aliphatic linkers ((CH2)(n), n = 3 - 6). Through optimization of the linker length and the substituents at the 2-position of the pyrrole residue on the U-turn, polyamides with G - C/C - G tolerant turns could be found, which bind to DNA in a predictable manner.