Preferred binding sites for [N-MeCYs(3), N-MeCys(7)]TANDEM determined using a universal footprinting substrate

We have prepared a novel footprinting substrate which contains all 136 tetranucleotide sequences and have used this to determine the preferred binding sites for the synthetic quinoxaline antibiotic [N-MeCys(3),N-MeCys(7)]TANDEM. We find that, although the ligand binds to all TpA steps, it binds best to the tetranucleotide sequence ATAT and shows only weak interaction with TTAA and GTAC. The best binding sites contain the sequences ATAX and XTAT.