The DNA-sequence specificity of daunomycin was investigated by DNase I footprinting and an E. coli RNA polymerase transcription-inhibition assay. The 5'-CA sequence was identified as being the highest affinity binding site, although other modest affinity (5'-GC, CG, CT, TC, AC) and poor affinity sites (5'-AA, AT, TA) were also observed. The preference of daunomycin for 5'-CA nucleotide sequence suggests that its biological activity may arise from association with the 5'-CA-containing sequences thought to be associated with genetic regulatory elements in eukaryotes.
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Skorobogaty et al. (1988) studied this question.
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