The Genome Factor in Region-Specific DNA Damage: The NDA-Reactive Drug U-78779 Prefers Mixed A/T-G/C Seuences at the Nucleotide Level but Is Region-Specific for Long Pure AT Islands at the Genomic Level

摘要

Bizelesin is the first anticancr drug capableof damaging specific regions of the genome with clusters of its binding sites T(A/T)_4A. This study characterized the sequence-and region-specificity of a bizelesin analogue, U-78779, designed to interact with mixed A/T-G/C motifs. At the nucleotide level, U-78779 was found to prefer runs of A/Ts interspersed with 1 or 2 G/C pairs, although 25% of the identified sites corresponded to pure AT motifs similar to bizelesin sites. The in silico computational analysis shoed that the preferred mixed A/T-G/C motifs distribute uniformly at the genomic level. In contrast, the secondary, pure AT motifs (A/T)_6A were found densely clustered in the same long islands of At-rich DNA that bizelesin targets. Mapping the sites and quantitating the frequencies of U-78779 adducts in model AT island and non-AT island naked DNAs demonstrated that clusters of pure AT motifs outcompete isolated mixed A/T-G/C sites in attracting drug binding. Regional preference of U-78779 for AT island domains was verified also in DNA from drug-treated cells. Thus, while the primary sequence preference gives rise to non-region-specificity of U-78799 in the human genome. The closely corelated cytotoxic activities of U-78779 and bizelesin in several cell lines further imply that both drugs may share common cellular targets. This study underscores the significance of the genome factor in a drug's potential for region-specific DNA damage, by showing that it can take precedence over drug binding preferences at the nucleotide level.