DNA sequence selectivity of topoisomerases and topoisomerase poisons

Capranico, Giovanni; Binaschi, Monica

doi:10.1016/s0167-4781(98)00135-3

Cited by 117 publications

(97 citation statements)

References 65 publications

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“…3 and Table I). This result agrees well with previous analyses (18,29). Preference on the opposite strand showed a complementary (although slightly weaker) preference for G at position ϩ5.…”

Section: Different Base Preferences Of Amsacrine-and Mitoxantronestabsupporting

confidence: 93%

“…For human top2␣, a preference for A at the ϩ1 position was observed, along with a complementary T ϩ4 preference as previously reported (18,29). A statistically significant preference at the Ϫ1 position was not observed.…”

Section: Discussionsupporting

confidence: 82%

“…From these results, it has been proposed that drugs bind at the enzyme-DNA interface and form a ternary complex with top2 and the DNA. This model has been referred to as the drug stacking model (8,18) or position poison model (19,20).…”

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confidence: 99%

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Molecular Analysis of Yeast and Human Type II Topoisomerases

Strumberg

Nitiss²,

Dong³

et al. 1999

Journal of Biological Chemistry

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The DNA sequence selectivity of topoisomerase II (top2)-DNA cleavage complexes was examined for the human (top2␣), yeast, and Escherichia coli (i.e. gyrase) enzymes in the absence or presence of anticancer or antibacterial drugs. Species-specific differences were observed for calcium-promoted DNA cleavage. Similarities and differences in DNA cleavage patterns and nucleic acid sequence preferences were also observed between the human, yeast, and E. coli top2 enzymes in the presence of the non-intercalators fluoroquinolone CP-115,953, etoposide, and azatoxin and the intercalators amsacrine and mitoxantrone. Additional base preferences were generally observed for the yeast when compared with the human top2␣ enzyme. Preferences in the immediate flanks of the top2-mediated DNA cleavage sites are, however, consistent with the drug stacking model for both enzymes. We also analyzed and compared homologous mutations in yeast and human top2, i.e. Ser 740 3 Trp and Ser 763 3 Trp, respectively. Both mutations decreased the reversibility of the etoposide-stabilized cleavage sites and produced consistent base sequence preference changes. These data demonstrate similarities and differences between human and yeast top2 enzymes. They also indicate that the structure of the enzyme/DNA interface plays a key role in determining the specificity of top2 poisons and cleavage sites for both the intercalating and non-intercalating drugs.DNA topoisomerases are enzymes that catalyze changes in the topology of DNA via a mechanism involving the transient breakage and rejoining of phosphodiester bonds in the DNA backbone (1, 2). Studies in both prokaryotic and eukaryotic cells have demonstrated the importance of topoisomerases in transcription, DNA replication, and chromosome segregation. The type II topoisomerases (top2) 1 make transient DNA double-strand breaks and change the linking number of DNA in steps of two. They play key roles in DNA metabolism and chromosome structure and are essential in eukaryotic cells (2, 3). In order to maintain the integrity of the cleaved DNA during this process, the top2 enzymes form a proteinaceous bridge that spans the DNA break. This bridge is anchored by covalent phosphotyrosyl bonds established between each of the active site tyrosine residues of the homodimeric enzyme and the 5Ј-

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Section: Different Base Preferences Of Amsacrine-and Mitoxantronestabsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 82%

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Molecular Analysis of Yeast and Human Type II Topoisomerases

Strumberg

Nitiss²,

Dong³

et al. 1999

Journal of Biological Chemistry

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“…Stacking of topoisomerase poisons with the DNA base pairs immediately flanking the topoisomerase cleavage site was initially hypothesized as the mechanism of poisoning of topoisomerase II by several inhibitors of this enzyme (34)(35)(36)(37)(38). The base-stacking hypothesis has been extended to top1 poisons (camptothecins) (6,39).…”

Section: Discussionmentioning

confidence: 99%

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

Pommier

Laco

Kohlhagen

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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DNA topoisomerase I (top1) is the target of potent anticancer agents, including camptothecins and DNA intercalators, which reversibly stabilize (trap) top1 catalytic intermediates (cleavage complexes). The aim of the present study was to define the structural relationship between the site(s) of covalently bound intercalating agents, whose solution conformations in DNA are known, and the site(s) of top1 cleavage. Two diastereomeric pairs of oligonucleotide 22-mers, derived from a sequence used to determine the crystal structure of top1-DNA complexes, were synthesized. One pair contained either a trans-opened 10R-or 10S-benzo[a]pyrene 7,8-diol 9,10-epoxide adduct at the N 6 -amino group of a central 2 -deoxyadenosine residue in the scissile strand, and the other pair contained the same two adducts in the nonscissile strand. These adducts were derived from the (؉)-(7R,8S,9S,10R)-and (؊)-(7S,8R,9R,10S)-7,8-diol 9,10-epoxides in which the benzylic 7-hydroxyl group and the epoxide oxygen are trans. On the basis of analogy with known solution conformations of duplex oligonucleotides containing these adducts, we conclude that top1 cleavage complexes are trapped when the hydrocarbon adduct is intercalated between the base pairs flanking a preexisting top1 cleavage site, or between the base pairs immediately downstream (3 relative to the scissile strand) from this site. We propose a model with the ؉1 base rotated out of the duplex, and in which the intercalated adduct prevents religation of the corresponding nucleotide at the 5 end of the cleaved DNA. These results suggest mechanisms whereby intercalating agents interfere with the normal function of human top1. D NA topoisomerase I (top1) is an essential enzyme in higher eukaryotes (1, 2). It can relax DNA supercoiling and relieve torsional strain during DNA processing, including replication, transcription, and repair. It can also perform intermolecular religation leading to DNA recombinations (3, 4). The catalytic intermediate of top1 is a cleavage complex in which a tyrosine (Tyr-723 for human top1) in the enzyme attacks a DNA phosphodiester and forms a covalent bond to the phosphorus at the 3Ј side of the cleavage site while a 5Ј-hydroxyl is generated at the other side (1, 2). The reaction occurs with short duplex oligodeoxynucleotides (5, 6), as evidenced by recent crystal structures of top1-DNA complexes (7,8).top1 is the cellular target of several anticancer drugs, including the camptothecins, which have recently been approved by the Food and Drug Administration for the treatment of colon and ovarian carcinomas. The anticancer activity of these drugs results from the trapping of top1 cleavage complexes such that the enzyme is reversibly inactivated as it cleaves DNA (9-11). These agents are often referred to as ''top1 poisons.'' They represent an exemplary case of pharmacological interference whereby the drug stabilizes the interactions of two macromolecules (i.e., top1 and DNA) by formation of a ternary complex. Because of the clinical efficacy of camptothecins, no...

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“…The substrate contained a single, well characterized cleavage site for topoisomerase II that was derived from pBR322 plasmid DNA (14,42,43). The cleavage site did not fit the "consensus sequence" for etoposide (C at the Ϫ1 position relative to the point of scission) (44,45), but rather contained a Ϫ1 G on both the top and bottom strands. However, equilibrium levels of scission on each individual strand increased nearly 30-fold at 500 M drug (Fig.…”

Section: Treatment Of Human Topoisomerase Ii␣ With Etoposide Stimulatmentioning

confidence: 99%

A Two-drug Model for Etoposide Action against Human Topoisomerase IIα

Bromberg¹,

Burgin²,

Osheroff

2003

Journal of Biological Chemistry

129

140

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The widely used anticancer drug etoposide kills cells by increasing levels of topoisomerase II-mediated DNA breaks. While it is known that the drug acts by inhibiting the ability of topoisomerase II to ligate cleaved DNA molecules, the precise mechanism by which it accomplishes this action is not well understood. Because there are two scissile bonds per enzyme-mediated doublestranded DNA break, it has been assumed that there are two sites for etoposide in every cleavage complex. However, it is not known whether the action of etoposide at only one scissile bond is sufficient to stabilize a doublestranded DNA break or whether both drug sites need to be occupied. An oligonucleotide system was utilized to address this important issue. Results of DNA cleavage and ligation assays support a two-drug model for the action of etoposide against human topoisomerase II␣. This model postulates that drug interactions at both scissile bonds are required in order to increase enzymemediated double-stranded DNA breaks. Etoposide actions at either of the two scissile bonds appear to be independent of one another, with each individual drug molecule stabilizing a strand-specific nick rather than a double-stranded DNA break. This finding suggests (at least in the presence of drug) that there is little or no communication between the two promoter active sites of topoisomerase II. The two-drug model has implications for cancer chemotherapy, the cellular processing of etoposide-stabilized enzyme-DNA cleavage complexes, and the catalytic mechanism of eukaryotic topoisomerase II.

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DNA sequence selectivity of topoisomerases and topoisomerase poisons

Cited by 117 publications

References 65 publications

Molecular Analysis of Yeast and Human Type II Topoisomerases

Molecular Analysis of Yeast and Human Type II Topoisomerases

Position-specific trapping of topoisomerase I–DNA cleavage complexes by intercalated benzo[ a ]- pyrene diol epoxide adducts at the 6-amino group of adenine

A Two-drug Model for Etoposide Action against Human Topoisomerase IIα

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