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 I-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.
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