Double helix topoisomerases

Substances known as intercalators, such as rifamycin and actinomycin D (bottom) are deposited in the DNA double helix and thereby interfere with replication and transcription (B). As DNA is the same in all cells, intercalating antibiotics are also toxic for eukaryotes, however. They are therefore only used as cytostatic agents (see p. 402). Synthetic inhibitors of DNA topoisomerase II (see p. 240), known as gyrase inhibitors (center), restrict replication and thus bacterial reproduction. 

As the two strands of the double helix are separated, positive supercoils are produced in the region of DNA ahead of the replication fork. These interfere with further unwinding of the double helix. DNA topoisomerases Types I and II remove supercoils. Human topoiso-merase II is targeted by anticancer agents, such as etoposide, and DNA gyrase (a Type II topoisomerase found in E. coli that can introduce negative supercoils) is targeted by the antimicrobial quinolones. 

Other drugs classified as plant alkaloids include etoposide, irinotecan, teniposide, and topotecan (see Table 36 1). These drugs inhibit specific enzymes known as topoisomerase enzymes, which are necessary for DNA replication.11 Inhibition of these enzymes causes a break in both strands of the DNA double helix, which leads to DNA destruction and cell death. Etoposide and teniposide inhibit the topoisomerase I form of this enzyme, and irinotecan and topotecan inhibit the topoisomerase II form of this enzyme. These drugs are therefore used to limit cell division and cancer growth in various types of neoplastic disease (see Table 36-4). 

Because only one strand can serve as a template for synthesis in the 5 to 3 direction (the template goes in the 3 to 5 direction, because the double helix is antiparallel), only one strand, the leading strand, can be elongated continuously. Ahead of the replication fork, DNA gyrase (topoisomerase II) helps unwind the DNA double helix and keep the double strands from tangling during replication. 

DNA can also be a target for alkaloids planar and lipophilic alkaloids, such as berberine and sanguinarine (Figure 1.6) are intercalating compounds that assemble between the stacks of paired nucleotides in the DNA double helix [2,3,18,23]. DNA intercalation can disturb replication, DNA repair, and DNA topoisomerases. Frameshift mutations are one of the adverse consequences of intercalating compounds. Some alkaloids, such as pyrrolizidine alkaloids, aristolochic acids, cycasin, and furoquinoline alkaloids, are known to form covalent adducts with DNA bases. Mutations and tumor formation can be the result of such interactions. DNA alkylation occurs in some alkaloids only after activation by liver enzymes, such as cytochrome p450 oxidases (pyrrolizidine alkaloids, aristolochic acids) [17,18,24]. 

Supercoiling is catalyzed by type II topoisomerases. These elegant molecular machines couple the binding and hydrolysis of ATP to the directed passage of one DNA double helix through another that has been temporarily cleaved. These enzymes have several mechanistic features in common with the type I topoisomerases. 

J.C. Wang. 1998. Moving one DNA double helix through another by a type 11 DNA topoisomerase The story of a simple molecular machine Q. Rev. Biophys. 31 107-144. (PubMed)... 

As described in section 4.1 the DNA double helix must unwind to allow access of the polymerase enzymes to produce two new strands of DNA. This is facilitated by topoisomerase I (DNA gyrase) which is the target of the fluoroquinolones. Some agents interfere with the unwinding of the chromosome by physical obstruction. These include the acridine dyes, of which the topical antiseptic proflavine is the most familiar, and the antimalarial acridine mepacrine. They prevent strand separation by... 

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