title: DNA topoisomerase I-mediated formation of structurally modified DNA duplexes. Effects of metal ions and topoisomerase I inhibitors.
abstract: The ability of DNA topoisomerase I to mediate the formation of structurally modified DNA duplexes was studied utilizing suicide substrates containing high-efficiency cleavage sites and acceptor oligonucleotides in which the 5'-terminal nucleotides were varied. When the substrates were nicked duplexes, the divalent cations Mg2+ and Ca2+ were found to facilitate the topoisomerase I-mediated formation of ligation products containing 3-nucleotide deletions on the scissile strand, but to suppress the formation of 1-nucleotide deletions. The presence of a complementary nucleotide at the 5'-end of the acceptor strand was not required for the ligation reaction to proceed, but duplex formation to produce duplexes containing a mismatch proceeded more slowly than formation of the fully complementary duplex. Topoisomerase I-mediated mismatch formation in the ligation reaction was inhibited more readily by camptothecin than the corresponding ligation reaction to form a fully complementary duplex; the extent of inhibition was comparable for all three mismatches studied. In comparison, the topoisomerase I inhibitors nitidine and coralyne exhibited quite different effects on the same ligation reactions.
authors.affiliation: Departments of Chemistry and Biology, University of Virginia, Charlottesville, Virginia 22901, USA.
authors.forename: X
authors.initials: X
authors.lastname: Wang
authors.forename: K A
authors.initials: KA
authors.lastname: Henningfeld
authors.forename: S M
authors.initials: SM
authors.lastname: Hecht
mesh_terms: D000818:Animals; D001483:Base Sequence; D053119:Benzophenanthridines; D001600:Berberine Alkaloids / Q000494:pharmacology; D001665:Binding Sites; D002118:Calcium / Q000494:pharmacology; D002166:Camptothecin / Q000494:pharmacology; D002413:Cations, Divalent / Q000494:pharmacology; D002417:Cattle; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004264:DNA Topoisomerases, Type I / Q000378:metabolism*; D004791:Enzyme Inhibitors / Q000494:pharmacology; D066298:In Vitro Techniques; D007700:Kinetics; D008274:Magnesium / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010617:Phenanthridines / Q000494:pharmacology; D013379:Substrate Specificity; D059004:Topoisomerase I Inhibitors; D019772:Topotecan / Q000494:pharmacology
chemical_list: D053119:Benzophenanthridines; D001600:Berberine Alkaloids; D002413:Cations, Divalent; D004791:Enzyme Inhibitors; D009838:Oligodeoxyribonucleotides; D010617:Phenanthridines; D059004:Topoisomerase I Inhibitors; C000666:coralyne; D019772:Topotecan; D004247:DNA; C013615:nitidine; D004264:DNA Topoisomerases, Type I; D008274:Magnesium; D002118:Calcium; D002166:Camptothecin