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Abstract
We have prepared novel DNA footprinting substrates that contain all 64 symmetrical
hexanucleotide sequences. These were contained in two restriction fragments that were
cloned into the pUC19 polylinker site; each fragment was also obtained in both orientations.
These fragments were used to assess the sequence binding preferences of the synthetic
quinoxaline antibiotic TANDEM. We found that, although the ligand binds to most TpA
steps, the affinity is affected by the flanking sequences. The best binding sites
contain the tetranucleotide sequence ATAT, although YATATR is a better site than RATATY.
TTAA always is a poor binding site, especially TTTAAA. The binding to GTAC is strongly
dependent on the flanking bases, with good binding to GGTACC but none at all to CGTACG.