title: Methods to characterize the effect of DNA-modifying compounds on nucleosomal DNA.
abstract: Eukaryotic DNA forms a complex with an equal mass of proteins to form chromatin. To fully understand the action of DNA-reactive antitumor antibiotics in the cell, their effect must be studied in a chromatin context. In particular, it is of interest to investigate how the distortion of DNA, in the context of a nucleosome, affects the action of drugs with either monoalkylation or crosslinking activity, and how modified DNA is assembled into chromatin. Here, we present experimental approaches that allow one to compare the effect of such drugs on free DNA and nucleosomes. We find significant differences that likely arise from the different geometry of nucleosomal DNA compared to free DNA and also find that drug-mediated DNA crosslinking affects nucleosome assembly.
authors.affiliation: Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
authors.forename: Vidya
authors.initials: V
authors.lastname: Subramanian
authors.forename: Robert M
authors.initials: RM
authors.lastname: Williams
authors.forename: Dale L
authors.initials: DL
authors.lastname: Boger
authors.forename: Karolin
authors.initials: K
authors.lastname: Luger
mesh_terms: D000478:Alkylation / Q000187:drug effects; D000818:Animals; D000903:Antibiotics, Antineoplastic / Q000494:pharmacology*; D003432:Cross-Linking Reagents / Q000494:pharmacology*; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004249:DNA Damage; D004587:Electrophoresis, Agar Gel; D006801:Humans; D007211:Indoles / Q000494:pharmacology; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000187:drug effects* / Q000378:metabolism*
chemical_list: D000903:Antibiotics, Antineoplastic; D003432:Cross-Linking Reagents; D007211:Indoles; D009707:Nucleosomes; D004247:DNA; D008836:Micrococcal Nuclease