Abstract
The helical structure of duplex DNA allows for the faithful duplication and transmission of genetic information from one generation to the next, at the same time maintaining the integrity of the polynucleotide chains. The complementary nature of the two antiparallel DNA strands enables each to serve as a template for the synthesis of the respective daughter DNA strands. The intertwining of these polynucleotide chains in duplex DNA further ensures the integrity of the DNA helix by physically linking the individual strands in a structure stabilized by hydrogen bonding and stacking interactions between the hydrophobic bases. However, these same features pose a number of topological constraints that affect most processes involving DNA, such as DNA replication, transcription, and nucleosome assembly (reviewed in [1–4]).
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Bjornsti, M. A. (1991) DNA topoisomerases. Curr. Opin. Struc. Biol. 1, 99–103.
Wang, J. C. (1996) DNA topoisomerases. Ann. Rev. Biochem. 65, 635–692.
Wang, J. C. and Liu, L. F. (1990) DNA Replication: Topological Aspects and the Roles of DNA Topoisomerases, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 321–340.
Froelich-Ammon, S. J. and Osheroff, N. (1995) Topoisomerase poisons: harnessing the dark side of enzyme mechanism. J. Biol. Chem. 270, 21,429–21,432.
Liu, L. F. and Wang, J. C. (1987) Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024–7027.
Gupta, M., Fujimori, A., and Pommier, Y. (1995) Eukaryotic DNA topoisomerase I. BBA 1262, 1–14.
Wang, J. C., Caron, P. R., and Kim, R. A. (1990) The role of DNA topoisomerases in recombination and genome stability: a double-edged sword? Cell 62, 403–406.
Champoux, J. (1990) Mechanistic aspects of type-I topoisomerases, Cold Spring Harbor, pp. 217–242.
Sadowski, P. D. (1995) The Flp recombinase of the 2-microns plasmid of Saccharomyces cerevisiae. Prog. Nucl. Acids Res. Mol. Biol. 51, 53–91.
Mizuuchi, K. (1997) Polynucleotidyl transfer reactions in site-specific recombination. Genes to Cells 2, 1–12.
Bergerat, A., de Massy, B., Gadelle, D., Varoutas, P.-C., Nicolas, A., and Forterre, P. (1997) An atypical topoisomerae II from archaea with implications for meiotic recombination. Nature 386, 414–417.
Wang, J. C. (1997) New break for archeal enzyme. Nature 386, 329–331.
Hanai, R., Caron, P. R., and Wang, J. C. (1996) Human TOP3—a single-copy gene encoding DNA topoisomerase III. Proc. Natl. Acad. Sci. USA 93, 3653–3657.
Wallis, J. W., Chrebet, G., Brodsky, G., Rolfe, M., and Rothstein, R. (1989) A hyper-recombination mutation in S. cerevisiae identifies a novel eukaryotic topoisomerase. Cell 58, 409–419.
Kim, R. A., Caron, P. R., and Wang, J. C. (1995) Effects of yeast DNA topoisomerase III on telomere structure. Proc. Natl. Acad. Sci. USA 92, 2667–2671.
Gangloff, S., McDonald, J. P., Bendixen, C., Arthur, L., and Rothstein, R. (1994) The Yeast Type I Topoisomerase Top3 Interacts with Sgs1, a DNA Helicase Homolog: a Potential Eukaryotic Reverse Gyrase. Mol. Cell. Biol. 14, 8391–8398.
Watt, P. M., Hickson, I. D., Borts, R. H., and Louis, E. J. (1996) SGS1, a homologue of the Bloom’s and Werner’s syndrome genes, is required for maintenance of genome stability in Saccharomyces cerevisiae. Genetics 144, 935–45.
Confalonieri, F., Elie, C., Nadal, M., Bouthier D. E., La Tour, C., Forterre, P., and Duguet, M. (1993) Reverse gyrase: A helicase-like domain and a type I topoisomerase in the same polypeptide. Proc. Natl. Acad. Sci. USA 90, 4753–4757.
Castano, I. B., Heathpagliuso, S., Sadoff, B. U., Fitzhugh, D. J., and Christman, M. F. (1996) A novel family of Trf (Dna topoisomerase L-related function) genes required for proper nuclear segregation. Nucleic Acids Research 24, 2404–2410.
Goto, T. and Wang, J. C. (1985) Cloning of yeast TOP1, the gene encoding DNA topoisomerase I, and construction of mutants defective in both DNA topoisomerase I and DNA topoisomerase II. Proc. Natl. Acad. Sci. USA 82, 7178–7182.
Lee, M. P., Brown, S. D., Chen, A., and Hsieh, T.-S. (1993) DNA topoisomerase I is essential in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 90, 6656–6660.
Morham, S. G., Kluckman, K. D., Voulomanos, N., and Smithies, O. (1996) Targeted disruption of the mouse topoisomerase I gene by camptothecin selection. Mol. Cell. Biol. 16, 6804–6809.
Corbett, A. H. and Osheroff, N. (1993) When good enzymes go bad: Conversion of Topoisomerase II to a cellular toxin by antineoplastic drugs. Chemical Research in Toxicology 6, 585–597.
Watt, P. M. and Hickson, I. D. (1994) Structure and function of type II DNA topoisomerases. Biochem. J. 303, 681–695.
Ullsperger, C. and Cozzarelli, N. R. (1996) Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Esherichia coli. J. Biol. Chem. 271, 31,549–31,555.
Roca, J. (1995) The mechanisms of DNA topoisomerases. TIBS 20, 156–160.
Berger, J. M., Gamblin, S. J., Harrison, S. C., and Wang, J. C. (1996) Structure and mechanism of DNA topoisomerase II. Nature 379, 225–232.
Osheroff, N. (1986) Eukaryotic topoisomerase II. Characterization of enzyme turnover. J. Biol. Chem. 261, 9944–9950.
Jensen, S., Redwood, C. S., Jenkins, J. R., Andersen, A. H., and Hickson, I. D. (1996) Human DNA topoisomerases II alpha and II beta can functionally substitute for yeast TOP2 in chromosome segregation and recombination. Mol. Gen. Genet. 252, 79–86.
Keeney, S., Giroux, C. N., and Kleckner, N. (1997) Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88, 375–384.
Chen, A. and Liu, L. F. (1994) DNA topoisomerases: essential enzymes and lethal targets. Ann. Rev. Pharmacol. Toxicol. 34, 191–218.
Bjornsti, M.-A., Knab, A. M., and Benedetti, P. (1994) Yeast Saccharomyces cerevisiae as a model system to study the cytotoxic activity of the antitumor drug camptothecin. Cancer Chemother. Pharmacol. 34, S1–S5.
Lenfant, F., Mann, R. K., Thomsen, B., Ling, X., and Grunstein, M. (1996) All four core histone N-termini contain sequences required for hte repression of basal transcription in yeast. EMBO J. 15, 3974–3985.
Schnetz, K. and Wang, J. C. (1996) Silencing of the Escherichia coli bgl promoter: effects of template supercoiling and cell extracts on promoter activity in vitro. Nuc. Acids. Res. 24, 2422–2428.
Caserta, M. and di Mauro, E. (1996) The active role of DNA as a chromatin organizer. Bioessays 18, 685–693.
van Holde, K. and Zlatanova, J. (1994) Unusual DNA structures, chromatin and transcription. Bioessays 16, 59–68.
Cress, W. D. and Nevins, J. R. (1996) A role for a bent DNA structure in E2F-mediated transcription activation. Mol. Cell. Biol. 16, 2119–2127.
Tse-Dinh, Y. C. and Wang, J. C. (1986) Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I. J. Mol. Biol. 191, 321–331.
DiGate, R. J. and Marians, K. J. (1989) Molecular cloning and DNA sequence of Escherichia coli topB, the gene encoding DNA topoisomerase III. J. Biol. Chem. 264, 17,924–17,930.
Thrash, C., Bankier, A. T., Barrell, B. G., and Sternglanz, R. (1985) Cloning, characterization and sequence of the yeast DNA topoisomerase I gene. Proc. Natl. Acad. Sci. USA 82, 4374–4378.
D’Arpa, P., Machlin, P. S., Ratrie, H., Rothfield, N. F., Cleveland, D. W., and Earnshaw, W. C. (1988) cDNA cloning of human DNA topoisomerase I: catalytic activity of 67.7-kDa carboxyl-terminal fragment. Proc. Natl. Acad. Sci. USA 85, 2543–2547.
Slesarev, A. I., Stetter, K. O., Lake, J. A., Gellert, M., Krah, R., and Kozyavkin, S. A. (1993) DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote. Nature 364, 735–737.
Shuman, S. and Moss, B. (1987) Identification of a vaccina virus gene encoding a type I DNA topoisomerase. Pro. Natl. Acad. Sci. USA 84, 7478–7482.
Adachi, T., Mizuuchi, M., Robinson, E. A., Appella, E., O’Dea, M. H., Gellert, M., and Mizuuchi, K. (1987) DNA sequence of the E. coli gyrA gene: application of a new sequencing strategy. Nuc. Acids Res. 15, 771–784.
Swanberg, S. L. and Wang, J. C. (1987) Cloning and sequencing of the Escherichia coli gyrA gene coding for the A subunit of DNA gyrase. J. Mol. Biol. 197, 729–736.
Kato, J., Nishimura, Y., Iamura, R., Niki, H., Hiraga, S., and Suzuki, H. (1990) New topoisomerase essential for chomosome segregation in E. coli. Cell 63, 393–404.
Jenkins, J. R., Ayton, P., Jones, T., Davies, S. L., Simmons, D. L., Harris, A. L., Sheer, D., and Hickson, I. (1992) Isolation of cDNA clones encoding the beta isozyme of human DNA topoisomerase II and localisation of the gene to chromosome 3p24. Nucl. Acids Res. 20, 5587–5592.
Giaever, G. N., Lynn, R. M., Goto, T., and Wang, J. C. (1986) The complete nucleotide sequence of the structural gene TOP2 of yeast DNA topoisomerase II. J. Biol. Chem. 261, 12448–12454.
Tsai-Pflugfelder, M., Liu, L. F., Liu, A. A., Tewey, K. M., Whang-Peng, J., Knutsen, T., Huebner, K., Croce, C. M., and Wang, J. C. (1988) Cloning and sequencing of cDNA encoding human DNA topoisomerase II and localization of the gene to chromosome region 17q21–22. Proc. Natl. Acad. Sci. USA 85, 7177–7181.
Huang, W. M., Ao, S. Z., Casjens, S., Orlandi, R., Zeikus, R., Weiss, R., Winge, D., and Fang, M. (1988) A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60. Science 239, 1005–1012.
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Bjornsti, MA., Osheroff, N. (1999). Introduction to DNA Topoisomerases. In: Bjornsti, MA., Osheroff, N. (eds) DNA Topoisomerase Protocols. Methods in Molecular Biology, vol 94. Humana, Totowa, NJ. https://doi.org/10.1385/1-59259-259-7:1
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DOI: https://doi.org/10.1385/1-59259-259-7:1
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