Abstract
Supercoiling, knotting, and catenation are three common higher-order structures involving coiling of the axis of double-stranded DNA. These forms appear as a result of a number of important biological activities, including topoisomerase action, DNA replication, and genetic recombination (1-3). All of these species have mobilities in agarose gels that are distinct from those of normal open circular and linear DNA molecules of the same size. The electrophoretic properties of linking number topoisomers are dealt with elsewhere in this volume; this chapter focuses on the separation and characterization of mixtures of knotted or catenated forms.
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References
Sundin, O. and Varshavsky, A. (1981) Arrest of segregation leads to accumulation of highly intertwined catenated dimers: dissection of the final stages of SV40 DNA replication. Cell 25, 659–669.
Bliska, J. B. and Cozzarelli, N. R. (1987) Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J. Mol. Biol. 194, 205–218.
Ullsperger, C. J., Vologodskii, A. V., and Cozzarelli, N. R. (1995) Unlinking of DNA by topoisomerases during DNA replication, in Nucleic Acids and Molecular Biology, vol. 9 (Eckstein, F. and Lilley, D. M. J., eds.), Springer-Verlag, Heidelberg, Germany, pp. 115–142.
Benjamin, H. W. and Cozzarelli, N. R. (1986) DNA-directed synapsis in recombination: slithering and random collision of sites, in Proceedings of the Robert A. Welch Foundation Conferences on Chemical Research, vol. XXIX, Genetic Chemistry: The Molecular Basis of Heredity, Robert A. Welch Foundation, Houston, TX, pp. 107–126.
Wasserman, S. A. and Cozzarelli, N. R. (1986) Biochemical topology: application to DNA recombination and replication. Science 232, 951–960.
Adams, C. C. (1994) The Knot Book. An Elementary Introduction to the Mathematical Theory of Knots. W. H. Freeman, New York, NY, p. 33.
Shapiro, T. A. and Englund, P. T. (1995) The structure and replication of kinetoplast DNA. Annu. Rev. Microbiol. 49, 117–143.
Adams, D. E., Shekhtman, E. L., Zechiedrich, E. L., Schmid, M. B., and Cozzarelli, N. R. (1992) The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell 71, 277–288.
Spengler, S. J., Stasiak, A., and Cozzarelli, N. R. (1985) The stereostructure of knots and catenanes produced by phage μ integrative recombination: implications for mechanism and DNA structure. Cell 42, 325–334.
Beatty, L. G., Babineau-Clary, D., Hogrefe, C., and Sadowski, P. D. (1986) FLP site-specific recombinase of yeast 2-μm plasmid. Topological features of the reaction. J. Mol. Biol. 188, 529–544.
Landy, A. (1989) Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58, 913–949.
Better, M., Lu, C., Williams, R. C., and Echols, H. (1982) Site-specific DNA condensation and pairing mediated by the int protein of bacteriophage λ. Proc. Natl. Acad. Sci. USA 79, 5837–5841.
Richet, E., Abcarian, P., and Nash, H. A. (1988) Synapsis of attachment sites during lambda integrative recombination involves capture of a naked DNA by a protein-DNA complex. Cell 52, 9–17.
Crisona, N. J., Kanaar, R., Gonzales, T. N., Zechiedrich, E. L., Klippel, A., and Cozzarelli, N. R. (1994) Processive recombination by wild-type Gin and an enhancer-independent mutant. Insight into the mechanisms of recombination and strand exchange. J. Mol. Biol. 243, 437–457.
Krasnow, M. A., Stasiak, A., Spengler, S. J., Dean, F., Koller, T., and Cozzarelli, N. R. (1983) Determination of the absolute handedness of knots and catenanes of DNA. Nature 304, 559–560.
Lee, E. C., Gumport, R. I., and Gardner, J. F. (1990) Genetic analysis of bacte-riophage λ integrase interactions with arm-type attachment site sequences. J. Bacteriol. 172, 1529–1538.
Nash, H. A. (1983) Purification and properties of the bacteriophage lambda Int protein. Methods Enzymol. 100, 210–216.
Nash, H. A., Robertson, C. A., Flamm, E., Weisberg, R. A., and Miller, H. I. (1987) Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits. J. Bacteriol. 169, 4124–4127.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1. Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 1.21–1.53.
Barzilai, R. (1973) SV40 DNA: quantitative conversion of closed circular to open circular form by an ethidium bromide-restricted endonuclease. J. Mol. Biol. 74, 739–742.
Rybenkov, V. V., Cozzarelli, N. R., and Vologodskii, A. V. (1993) Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA 90, 5307–5311.
Wasserman, S. A. and Cozzarelli, N. R. (1991) Supercoiled DNA-directed knotting by T4 topoisomerase. J. Biol. Chem. 266, 20,567–20,573.
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Levene, S.D., Tsen, H. (1999). Analysis of DNA Knots and Catenanes by Agarose-Gel Electrophoresis. In: Bjornsti, MA., Osheroff, N. (eds) DNA Topoisomerase Protocols. Methods in Molecular Biology, vol 94. Humana, Totowa, NJ. https://doi.org/10.1385/1-59259-259-7:75
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DOI: https://doi.org/10.1385/1-59259-259-7:75
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