Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs

Pyrrole-imidazole polyamides with three-ring subunits linked by beta-alanine have a high sequence-specific recognition and binding affinity for the minor groove of DNA with 9-13 base pairs (bp). The DNA-binding affinities of polyamides with the general sequence ImPyPy-X-PyPyPy-Dp, where X = Py, G, beta, or gamma, for the 9 bp site 5'-TGTTAAACA-3' and the 13 bp sites 5'-AAAAAGACAAAAA-3' and 5'-ATATAGACATATA-3' sequences are examined. The binding affinities are determined using the results of quantitative DNase I footprint titrations.