title: Topoisomerase I-mediated DNA cleavage induced by the minor groove-directed binding of bibenzimidazoles to a distal site.
abstract: Many agents (e.g. camptothecins, indolocarbazoles, indenoisoquinolines, and dibenzonaphthyridines) stimulate topoisomerase I (TOP1)-mediated DNA cleavage (a behavior termed topoisomerase I poisoning) by interacting with both the DNA and the enzyme at the site of cleavage (typically by intercalation between the -1 and +1 base-pairs). The bibenzimidazoles, which include Hoechst 33258 and 33342, are a family of DNA minor groove-directed agents that also stimulate topoisomerase I-mediated DNA cleavage. However, the molecular mechanism by which these ligands poison TOP1 is poorly understood. Toward this goal, we have used a combination of mutational, footprinting, and DNA binding affinity analyses to define the DNA binding site for Hoechst 33258 and a related derivative that results in optimal induction of TOP1-mediated DNA cleavage. We show that this DNA binding site is located downstream from the site of DNA cleavage, encompassing the base-pairs from position +4 to +8. The distal nature of this binding site relative to the site of DNA cleavage suggests that minor groove-directed agents like the bibenzimidazoles poison TOP1 via a mechanism distinct from compounds like the camptothecins, which interact at the site of cleavage.
authors.affiliation: Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854-5635, USA.
authors.forename: Qasim A
authors.initials: QA
authors.lastname: Khan
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Pilch
mesh_terms: D020029:Base Pairing / Q000187:drug effects; D001483:Base Sequence; D001562:Benzimidazoles / Q000737:chemistry / Q000494:pharmacology*; D001665:Binding Sites / Q000187:drug effects; D006690:Bisbenzimidazole / Q000737:chemistry / Q000494:pharmacology*; D002166:Camptothecin / Q000494:pharmacology; D004247:DNA / Q000737:chemistry / Q000235:genetics; D053837:DNA Cleavage; D018983:DNA Footprinting; D004264:DNA Topoisomerases, Type I / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D005453:Fluorescence; D006801:Humans; D007211:Indoles / Q000737:chemistry / Q000494:pharmacology*; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D011067:Poly dA-dT / Q000737:chemistry; D013696:Temperature
chemical_list: C513856:5-phenyl-2'-(indolo-6-yl)bibenzimidazole; D001562:Benzimidazoles; D007211:Indoles; D008024:Ligands; D011067:Poly dA-dT; D004247:DNA; D003850:Deoxyribonuclease I; D004264:DNA Topoisomerases, Type I; D006690:Bisbenzimidazole; D002166:Camptothecin