SpringerProtocols: Abstract: 1. Assaying DNA Topoisomerase I Relaxation Activity

1. Assaying DNA Topoisomerase I Relaxation Activity

By: Lance Stewart, James J. Champoux

Abstract

Full Text

Download PDF (173K)

Type I topoisomerases catalyze topological changes in duplex DNA by reversibly nicking one strand, whereas type II enzymes catalyze the transient breakage of both strands simultaneously. The type I enzymes alter the linking number of covalently closed circular DNA in steps of one, presumably by allowing an unbroken segment of one strand of the DNA to move through the transient single-strand break in the other strand. The type II enzymes alter the linking number in steps of two by allowing an unbroken segment of duplex DNA to pass through the transient double-strand break.

Book Title: DNA Topoisomerase Protocols : Volume II: Enzymology and Drugs

Series: Methods in Molecular Biology | Volume: 95 | Pub. Date: Oct-20-2000 | Page Range: 1-11 | DOI: 10.1385/1-59259-057-8:1

Subject: Genetics/Genomics

References

Download References

1.	Roca J. (1995) The mechanisms of DNA topoisomerases. Trends Biochem. Sci. 20, 156–160.

2.	Champoux J. J. (1990) Mechanistic aspects of type-I topoisomerases, in DNA Topology and Its Biological Effects (Cozzarelli N. R. and Wang J. C., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, p. 217–242.

3.	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.

4.	Zhang H. L., Malpure S., and DiGate R. J. (1995) Escherichia coli DNA topoisomerase III is a site-specific DNA binding protein that binds asymmetrically to its cleavage site. J. Biol. Chem. 270, 23,700–23,705.

5.	Srivenugopal K. S., Lockshon D., and Morris D. R. (1984) Escherichia coli DNA topoisomerase III: purification and characterization of a new type I enzyme. Biochemistry 23, 1899–1906.

6.	Kovalsky O. I., Kozyavkin S. A., and Slesarev A. I. (1990) Archaebacterial reverse gyrase cleavage-site specificity is similar to that of eubacterial DNA topoisomerases I. Nucleic Acids Res. 18, 2801–2805.

7.	Confalonieri F., Elie C., Nadal M., de 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. Published erratum appears in Proc. Natl. Acad. Sci. USA 8, 3478.

8.	Jaxel C., Nadal M., Mirambeau G., Forterre P., Takahashi M., and Duguet M. (1989) Reverse gyrase binding to DNA alters the double helix structure and produces single-strand cleavage in the absence of ATP. EMBO J. 8, 3135–3139.

9.	Slesarev A. I., Zaitzev D. A., Kopylov V. M., Stetter K. O., and Kozyavkin S. A. (1991) DNA topoisomerase III from extremely thermophilic archaebacteria. ATP-independent type I topoisomerase from Desulfurococcus amylolyticus drives extensive unwinding of closed circular DNA at high temperature. J. Biol. Chem. 266, 12,321–12,328.

10.	Kim R. A. and Wang J. C. (1992) Identification of the yeast TOP3 gene product as a single strand-specific DNA topoisomerase. J. Biol. Chem. 267, 17,178–17,185.

11.	Wigley D. B. (1995) Structure and mechanism of DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct. 24, 185–208.

12.	Liu L. F. (1990) Anticancer drugs that convert DNA topoisomerases into DNA damaging agents, in DNA Topology and Its Biological Effects (Cozzarelli N. R. and Wang J. C., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor,NY, pp. 371–389.

13.	Wang J. C. (1971) Interaction between DNA and an Escherichia coli protein ω. J. Mol. Biol. 55, 523–533.

14.	Champoux J. J., and Dulbecco R. (1972) An activity from mammalian cells that untwists superhelical DNA—a possible swivel for DNA replication (polyomaethidium bromide-mouse-embryo cells-dye binding assay). Proc. Natl. Acad. Sci. USA 69, 143–146.

15.	McConaughy B. L., Young L. S., and Champoux J. J. (1981) The effect of salt on the binding of the eucaryotic DNA nicking-closing enzyme to DNA and chromatin. Biochim. Biophys. Acta 655, 1–8.

16.	Morgan A. R. and Pulleyblank D. E. (1974) Native and denatured DNA, crosslinked and plaindromic DNA and circular covalently-closed DNA anlaysed by a sensitive fluorometric procedure. Biochem. Biophys. Res. Commun. 61, 396–403.

17.	Keller W. (1975) Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc. Natl. Acad. Sci. USA 72, 4876–4880.

18.	Stewart L. Ireton G. C., Parker L. H., Madden K. R., and Champoux J. J. (1996) Biochemical and biophysical analyses of recombinant forms of human topoisomerase I. J. Biol. Chem. 271, 7593–7601.

19.	Wang J. C. and Becherer K. (1983) Cloning of the gene topA encoding for DNA topoisomerase I and the physical mapping of the cysB-topA-trp region of Escherichia coli. Nucleic Acids Res. 11, 1773–1790.

20.	Shure M., Pulleyblank D. E., and Vinograd J. (1977) The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity. Nucleic Acids Res. 4, 1183–1205.

21.	Liu L. F. and Miller K. G. (1981) Eukaryotic DNA topoisomerases: two forms of type I DNA topoisomerases from HeLa cell nuclei. Proc. Natl. Acad. Sci. USA 78, 3487–3491.

22.	Depew D. E. and Wang J. C. (1975) Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA 72, 4275–4279.

23.	Pulleyblank D. E., Shure M., Tang D., Vinograd J., and Vosberg H. P. (1975) Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc. Natl. Acad. Sci. USA 72, 4280–4284.

24.	Wang J. C. (1969) Degree of superhelicity of covalently closed cyclic DNA’s from Escherichia coli. J. Mol. Biol. 43, 263–272.

25.	Madden K. R., Stewart L., and Champoux J. J. (1995) Preferential binding of human topoisomerase I to superhelical DNA. EMBO J. 14, 5399–5409.

26.	Zechiedrich E. L. and Osheroff N. (1990) Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. EMBO J. 9, 4555–4562.

27.	Roca J., Berger J. M., and Wang J. C. (1993) On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices. J. Biol. Chem. 268, 14,250–14,255.

Comments (Loading...)

Post comment/View all comments