SEQUENCE-SELECTIVE DNA CLEAVAGE BY A TOPOISOMERASE-I POISON, NB-506

An indolocarbazole compound, NB-506, inhibits the activity of topoisom erase 1 by stabilizing the DNA-topoisomerase 1 complex (cleavable comp lex). NB-506 inhibited the religation step of topoisomerase 1 activity more potently than camptothecin or its derivative, topotecan. A cleav age assay using an end-labeled fragment of DNA revealed that the patte rn of cleavage induced by NB-506 was different from that induced by ca mptothecin. The preferred cleavage sites of NB-506 were found to be no t only T but also A or C at the 3'-terminus of the cleaved DNA (positi on -1), while the DNA cleavage sites of camptothecin always had T at p osition -1. At the 5'-terminus of the cleaved DNA (position + 1), NB-5 06 showed a preference for G, which is a feature shared in common with camptothecin. Therefore, the difference in cleavage patterns was most likely due mainly to the preferred base at position -1. Moreover, the re-ligation rate was significantly slower at NB-506-selective sites, which had C at position-1, than at camptothecin-selective sites or at sites cleaved by both NB-506 and camptothecin. Our data suggest that N B-506 is an unique topoisomerase 1 poison and that its potent inhibiti on of topoisomerase 1 is partly dependent on retardation of re-ligatio n at sites selectively induced by NB-506. (C) 1998 Wiley-Liss, Inc.