title: The genome factor in region-specific DNA damage: the DNA-reactive drug U-78779 prefers mixed A/T-G/C sequences at the nucleotide level but is region-specific for long pure AT islands at the genomic level.
abstract: Bizelesin is the first anticancer drug capable of damaging specific regions of the genome with clusters of its binding sites T(A/T)(4)A. 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 showed that the preferred mixed A/T-G/C motifs distribute uniformly at the genomic level. In contrast, the secondary, pure AT motifs (A/T)(6)A 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-specific scattered lesions, the clustering of the minor pure AT binding motifs seems to determine region-specificity of U-78779 in the human genome. The closely correlated 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.
authors.affiliation: Cancer Therapy and Research Center, 14960 Omicron Drive, San Antonio, Texas 78245, USA.
authors.forename: Maryanne C S
authors.initials: MC
authors.lastname: Herzig
authors.forename: Karl A
authors.initials: KA
authors.lastname: Rodriguez
authors.forename: Alex V
authors.initials: AV
authors.lastname: Trevino
authors.forename: Jaroslaw
authors.initials: J
authors.lastname: Dziegielewski
authors.forename: Brenda
authors.initials: B
authors.lastname: Arnett
authors.forename: Laurence
authors.initials: L
authors.lastname: Hurley
authors.forename: Jan M
authors.initials: JM
authors.lastname: Woynarowski
mesh_terms: D000227:Adenine Nucleotides / Q000302:isolation & purification / Q000378:metabolism; D018906:Antineoplastic Agents, Alkylating / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D001665:Binding Sites / Q000187:drug effects / Q000235:genetics; D002467:Cell Nucleus / Q000737:chemistry / Q000187:drug effects / Q000378:metabolism; D003432:Cross-Linking Reagents / Q000737:chemistry / Q000378:metabolism; D003597:Cytosine Nucleotides / Q000378:metabolism; D018736:DNA Adducts / Q000737:chemistry / Q000378:metabolism; D004249:DNA Damage; D004273:DNA, Neoplasm / Q000737:chemistry* / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry / Q000378:metabolism; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D018900:Dinucleotide Repeats / Q000187:drug effects*; D000080890:Duocarmycins; D015894:Genome, Human; D006150:Guanine Nucleotides / Q000378:metabolism; D006801:Humans; D007211:Indoles / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D007424:Intracellular Fluid / Q000737:chemistry / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013539:Simian virus 40 / Q000187:drug effects / Q000235:genetics; D013942:Thymine Nucleotides / Q000302:isolation & purification / Q000378:metabolism; D014407:Tumor Cells, Cultured; D014508:Urea / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity
chemical_list: D000227:Adenine Nucleotides; D018906:Antineoplastic Agents, Alkylating; D003432:Cross-Linking Reagents; D003597:Cytosine Nucleotides; D018736:DNA Adducts; D004273:DNA, Neoplasm; D004278:DNA, Superhelical; D004279:DNA, Viral; D000080890:Duocarmycins; D006150:Guanine Nucleotides; D007211:Indoles; D013942:Thymine Nucleotides; D014508:Urea; C072257:bizelesin