Abstract
A wide variety of naturally occurring duplex DNA’s are now known to possess the dual characteristics of closed circularity and superhelicity. These species of DNA may be broadly classified according to biological origin as arising from animal and bacterial viruses, animal mitochondria and extra-mitochondrial cytoplasm, protozoa, and bacteria. This latter category contains several types, including viral intracellular forms, plasmids, and episomes. A summary of the known closed circular duplex DNA’s (DNA I) is presented in Table 1.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ando, T., Kosawa, T.: Isolation of a DNA ligase from phage λC1-infected Escherichia coli. Biochim. biophys. Acta (Amst.) 204, 257 (1970).
Avers, C. J.: Heterogeneous length distribution of circular DNA filaments from yeast mitochondria. Proc. nat. Acad. Sci. (Wash.) 58, 620 (1967).
Avers, C. J., Billheimer, F. E., Hoffman, H.-P., Pauli, R. M.: Circularity of yeast mitochondrial DNA. Proc. nat. Acad. Sci. (Wash.) 61, 90 (1968).
Bauer, W., Vinograd, J.: The interaction of closed circular DNA with intercalative dyes I The superhelix density of SV40 DNA in the presence and absence of dye. J. molec. Biol. 33, 141 (1968).
Bauer, W., Vinograd, J.: A thermodynamic theory for interactiong systems at equilibrium in a buoyant density gradient: The reaction between a small molecular species and a buoyant macromolecule. Ann. N. Y. Acad. Sci. 164, Art. 1, 192 (1969).
Bauer, W., Vinograd, J.: (1) The interaction of closed circular DNA with intercalative dyes II. The free energy of superhelix formation in SV40 DNA. J. molec. Biol. 47, 419 (1970).
Bauer, W., Vinograd, J.: (2) The interaction of closed circular DNA with intercalative dyes III. Dependence of the buoyant density upon superhelix density and base composition in the presence of dye. J. molec. Biol. 54, 281 (1970).
Bazaral, M., Helinski, D. R.: (1) Circular DNA forms of colincinogenic factors E1, E2, E3 from Escherichia coli. J. molec. Biol. 36, 185 (1968).
Bazaral, M., Helinski, D. R.: (2) Characterization of multiple circular forms of colicinogenic factor Ex from Proteus mirabilis. Biochemistry 7, 3513 (1968).
Becker, A., Lyn, G., Gefter, M., Hurwitz, J.: The enzymatic repair of DNA, II Characterization of phage-induced sealase. Proc. nat. Acad. Sci. (Wash.) 58, 1996 (1967).
Billheimer, F. E., Avers, C. J.: Nuclear and mitochondrial DNA from wild type and petite yeast: Circularity, length, and buoyant density. Proc. nat. Acad. Sci. (Wash.) 64, 739 (1969).
Bloomfield, V. A.: Twisted circular DNA: sedimentation coefficients and the number of twists. Proc. nat. Acad. Sci. (Wash.) 55, 717 (1966).
Borst, P., Ruttenberg, G. J. C. M.: Renaturation of mitochondrial DNA. Biochim. biophys. Acta (Amst.) 114, 645 (1966).
Borst, P., Ruttenberg, G. J. C. M., Kroon, A. M.: (1) Mitochondrial DNA I. Preparation and properties of mitochondrial DNA from chick liver. Biochim. biophys. Acta (Amst.) 149, 140 (1967).
Borst, P., Van Brüggen, E. F. J., Ruttenberg, G. J. C. M., Kroon, A. M.: (2) Mitochondrial DNA II. Sedimentation analysis and electron microscopy of mitochondrial DNA from chick liver. Biochim. biophys. Acta (Amst.) 149, 156 (1967).
Bujard, H.: Isolation of bovine papilloma virus and characterization of its circular DNA. J. Virol. 1, 1135 (1967).
Bujard, H.: Studies on circular DNA II. Number of tertiary turns in papilloma DNA. J. molec. Biol. 33, 503 (1968).
Carlton, B. C., Helinski, D. R.: Heterogeneous circular DNA elements in vegetative cultures of Bacillus megaterium. Proc. nat. Acad. Sci. (Wash.) 64, 592 (1969).
Clayton, D. A., Davis, R. W., Vinograd, J.: Homology and structural relationships between the dimeric and monomeric circular forms of mitochondrial DNA from human leukemic leucocytes. J. molec. Biol. 47, 137 (1970).
Clayton, D. A., Smith, C. A., Jordan, J. M., Teplitz, M., Vinograd, J.: Occurrence of complex mitochondrial DNA in normal tissues. Nature (Lond.) 220, 976 (1968).
Clayton, D. A., Vinograd, J.: Circular dimer and catenated forms of mitochondrial DNA in human leukemic leucocytes. Nature (Lond.) 216, 652 (1967).
Cohn, G., Eisenberg, H.: Viscosity and sedimentation study of sonicated DNA-proflavine complexes. Biopolymers 8, 45 (1969).
Cozzarelli, N. R., Kelly, R. B., Kornberg, A.: A minute circular DNA from Escherichia coli 15. Proc. nat. Acad. Sci. (Wash.) 60, 992 (1968).
Crawford, L. V.: A study of shope papilloma virus DNA. J. molec. Biol. 8, 489 (1964).
Crawford, L. V.: A study of human papilloma virus DNA. J. molec. Biol. 13, 362 (1965).
Crawford, L. V., Black, P. H.: The nucleic acid of simian virus 40. Virology 24, 388 (1964).
Crawford, L. V., WARING, M. J.: Supercoiling of polyoma virus DNA measured by its interaction with ethidium bromide. J. molec. Biol. 25, 23 (1967).
Cuzin, F., Vogt, M., Drickmann, M., Berg, P.: Induction of virus multiplication in 373 cells transformed by thermosensitive mutant of polyoma virus. II. Formation of oligo- meric polyoma DNA molecules. J. molec. Biol. 47, 317 (1970).
Dawid, I. B.: Mitochondrial RNA in Xenopus laevis: Its homology to mitochondrial DNA. Fed. Proc. 28, 349 (1969).
Dawid, I. B. Wolstenholme, D. R.: Ultracentrifuge and electron microscope studies on the structure of mitochondrial DNA. J. molec. Biol. 28, 233 (1967).
Dulbecco, R., Vogt, M.: Evidence for a ring structure of polyoma virus DNA. Proc. nat. Acad. Sci. (Wash.) 50, 236 (1963).
Drummond, D. S., Simpson-Gildemeister, V. F. W., Peacocke, A. R.: Interaction of aminoacridines with DNA: Effects of ionic strength, denaturation, and structure. Bio- polymers 3, 135 (1965).
Espejo, R. T., Canelo, E. S., Sinsheimer, R. L.: DNA of bacteriophage PM 2: A closed circular double-stranded molecule. Proc. nat. Acad. Sci. (Wash.) 63, 1164 (1969).
Fan, H., Penman, S.: Mitochondrial RNA synthesis during meiosis. Science 168, 135 (1970).
Freifelder, D.: Studies on Escherichia coli sex factors IV. Molecular weights of the DNA of several F’ elements. J. molec. Biol. 35, 95 (1968).
Fuller, W., Waring, M. T.: A molecular model lor the interaction of ethidium bromide with deoxyribonucleic acid. Ber. der Bunsenges. 68, 805 (1964).
Gefter, M. L., Becher, A., Hurwitz, J.: The enzymatic repair of DNA, I. Formation of circular A DNA. Proc. nat. Acad. Sci. (Wash.) 58, 240 (1967).
Gellert, M.: Formation of covalent circles of lambda DNA by E. coli extracts. Proc. nat. Acad. Sci. (Wash.) 57, 148 (1967).
Glaubiger, D., Hearst, J. E.: The effect of superhelical structure on the secondary structure of DNA rings. Biopolymers 8, 692 (1967).
Gray, H. B.: The sedimentation coefficient of polyoma virus DNA. Biopolymers 5, 1009 (1967).
Gray, H. B., Bloomfield, V. A., Hearst, J. E.: Sedimentation coefficients of linear and cyclic wormlike coils with excluded-volume effects. J. chem. Phys. 46, 1493 (1967).
Gray, H. B., Upholt, W. D., Vinograd, J.: A buoyant method for the determination of superhelix density in closed circular DNA. Manuscript in preparation (1971).
Hearst, J. E., Stockmayer, W. H.: Sedimentation constants of broken chains and wormlike coils. J. chem. Phys. 37, 1425 (1962).
Herskovits, T. T.: Nonaqueous solutions of DNA: Factors determining the stability of the helical configuration insolution. Arch. Biochem. 97, 474 (1962).
Hickson, F. T., Roth, T. F., Helinski, D. R.: Circular DNA forms of a bacterial sex factor. Proc. nat. Acad. Sci. (Wash.) 58, 1731 (1967).
Hollenberg, C. P., Borst, P., Thuring, R. W. J., Van Brüggen, E. F. J.: Size, structure and genetic complexity of yeast mitochondrial DNA. Biochim. biophys. Acta (Amst.) 186, 417 (1969).
Hotta, Y., Bassel, A.: Molecular size and circularity of DNA in cells of mammals and higher plants. Proc. nat. Acad. Sci. (Wash.) 53, 356 (1965).
Hudson, B., Clayton, D. A., Vinograd, J.: Complex mitochondrial DNA. Cold Spr. Harb. Symp. quant. Biol. 33, 435 (1968).
Hudson, B., Upholt, W. B., Devinny, J., Vinograd, J.: The use of an ethidium analogue in the dye-buoyant density procedure for the isolation of closed circular DNA: The variation of the superhelix density of mitochondrial DNA. Proc. nat. Acad. Sci. (Wash.) 62, 813 (1969).
Hudson, B., Vinograd, J.: Catenated circular DNA molecules in HeLa cell mitochondria. Nature (Lond.) 216, 647 (1967).
Jansz, H. S., Zandberg, J., Van De Pol, J. H., Van Brüggen, E. F. J.: Circular DNA from Shigellaparadysenteriae. Europ. J. Biochem. 9, 156 (1969).
Jordan, J. M., Van Der Eb, A., Vinograd, J.: Complex mitochondiral DNA in cultured cells in an experimentally induced tumor. Manuscript in preparation (1970).
Kirkwood, J. G.: The general theory of irreversible processes in solutions of macro-molecules. J. Polymer Sci. 12, 1 (1954).
Knight, E., Jr.: Mitochondria-associated RNA of the HeLa cell. Effect of ethidium bromide on the synthesis of ribosomal and 4S RNA. Biochemistry 8, 5089 (1969).
Kroon, A. M., Borst, P., Van Brüggen, E. F. J., Ruttenberg, G. J. C. M.: Mitochondrial DNA from sheep heart. Proc. nat. Acad. Sci. (Wash.) 56, 1836 (1966).
Kurata, M.: Hydrodynamic properties of dilute solutions of ring polymers, II. Twisted ring polymers. Bull. Inst. Chem. Res. Kyoto Univ. 44, 150 (1966).
Langridge, R., Seeds, W. E., Wilson, H. R., Hooper, C. W., Wilkins, M. H. F., Hamilton, L. D.: Molecular structure of DNA. J. biophys. biochem. Cytol. 3, 767 (1957).
Lee, C. S., Davidson, N.: Covalently closed minicircular DNA in Micrococcus lysodeikticus. Biochem. biophys. Res. Commun. 32, 757 (1968).
Lee, C. S., Davidson, N.: Physicochemical studies on the minicircular DNA in Escherichia coli 15. Biochim. biophys. Acta (Amst.) 204, 285 (1970).
Lee, C. S., Davidson, N., Scalleti, J. V.: Covalently closed circular DNA from Micrococcus lysodeikticus cells infected with phage Nl. Biochem. biophys. Res. Commun. 32, 752 (1968).
Lepecq, J. B.: Etude spectrofluorimetrique des modalités d’interaction du bromhydrate d’éthidium avec les acides nucléiques. Thèses, Faculté des Sciences de l’Université de Paris 1965.
Lepecq, J. B., Paoletti, C.: A fluorescent complex between ethidium bromide and nucleic acids. J. molec. Biol. 27, 87 (1967).
Lerman, L. S.: Structural considerations in the interaction of DNA and acridines. J. molec. Biol. 3, 18 (1961).
Lerman, L. S.: The structure of the DNA-acidine complex. Proc. nat. Acad. Sci. (Wash.) 49, 94 (1963).
Lerman, L. S.; Amino group reactivity in DNA-aminoacridine complexes. J. molec. Biol. 10, 367 (1964).
Li, H. J., Crothers, D. M.: (1) Studies of the optical properties of the proflavine-DNA complex. Biopolymers 8, 217 (1969).
Li, H. J., Crothers, D. M.: (2) Relaxation studies of the proflavine-DNA complex: The kinetics of an intercalation reaction. J. molec. Biol. 39, 461 (1969).
Luzzanti, V., Masson, F., Lerman, L. S.: Interaction of DNA and proflavine: A small-angle AT-ray scattering study. J. molec. Biol. 3, 634 (1961).
Mackinlay, A. G., Kaiser, A. D.: DNA replication in head mutants of bacteriophage X. J. molec. Biol. 39, 679 (1969).
Nass, M. M. K.: The circularity of mitochondrial DNA. Proc. nat. Acad. Sci. (Wash.) 56, 1215 (1966).
Nass, M. M. K.: (1) Mitochondrial DNA II. Structure and physiochemical properties of isolated DNA. J. molec. Biol. 42, 529 (1960).
Nass, M. M. K.: (2) Reversible generation of circular dimer and higher multiple forms of mitochondrial DNA. Nature (Lond.) 223, 1124 (1969).
Neville, D. M., Davies, D. R.: The interaction of acridine dyes with DNA: An A-ray diffraction and optical investigation. J. molec. Biol. 17, 57 (1966).
Olivera, B. M., Lehman, I. R.: (1) Linkage of polynucleotides through phosphodiester bonds by an enzyme from Escherichia coli. Proc. nat. Acad. Sci. (Wash.) 57, 1426 (1967).
Olivera, B. M., Lehman, I. R.: (2) Diphosphopyridine nucleotide: A cofactor for the polynucleotide — joining enzyme from Escherichia coli. Proc. nat. Acad. Sci. (Wash.) 57, 1700 (1967).
Peacocke, A. R., Skerrett, J. N. H.: The interaction of aminoacridines with nucleic acids. Trans. Faraday Soc. 52, 261 (1956).
Piko, L., Blair, D. G., Tyler, A., Vinograd, J.: Cytoplasmic DNA in the unfertilized sea urchin egg: Physical properties of circular mitochondrial DNA and the occurrence of catenated forms. Proc. nat. Acad. Sci. (Wash.) 59, 838 (1968).
Piko, L., Tyler, A., Vinograd, J.: Amount, location, priming capacity, circularity and other properties of cytoplasmic DNA in sea urchin eggs. Biol. Bull. 132, 68 (1967).
Radloff, R., Bauer, W., Vinograd, J.: A dye-buoyant density method for the detection and isolation of closed circular duplex DNA: The closed circular DNA in HeLa cells. Proc. nat. Acad. Sci. (Wash.) 57, 1514 (1967).
Rhoades, M., Thomas, C. A., Jr.: The 22P bacteriophage DNA molecule II. Circular intracellular forms. J. molec. Biol. 37, 41 (1968).
Suguira, M., Okamoto, T., Takanimi, M.: Starting nucleotide sequences of RNA synthesized on the replicative form DNA of coliphage fd. J. molec. Biol. 43, 299 (1969).
Suyama, Y., Muira, K.: Size and variations of mitochondrial DNA. Proc. nat. Acad. Sci. (Wash.) 60, 235 (1968).
Upholt, W. D., Gray, H. B., Vinograd, J.: The sedimentation velocity properties of closed circular SV40 DNA as a function of superhelix density and ionic strength. Manuscript in preparation (1971).
Vinograd, J., Bruner, R., Kent, R., Weigle, J.: Band-centrifugation of macromolecules and viruses in self-generating density gradients. Proc. nat. Acad. Sci. (Wash.) 49, 902 (1963).
Vinograd, J., Lebowitz, J.: Physical and topological properties of circular DNA. J. gen. Physiol. 49, 103 (1966).
Vinograd, J., Lebowitz, J., Radloff, R., Watson, R., Laipis, P.: The twisted circular form of polyoma viral DNA. Proc. nat. Acad. Sci. (Wash.) 53, 1104 (1965).
Vinograd, J., Lebowitz, J., Watson, R.: Early and late helix-coil transitions in closed circular DNA: The number of superhelical turns in polyoma DNA. J. molec. Biol. 33, 173 (1968).
Wang, J. C.: (1) Variation of the average rotation angle of the DNA helix and the super- helical turns of covalently closed cyclic X DNA. J. molec. Biol. 43, 25 (1969).
Wang, J. C.: (2) Degree of superhelicity of covalently closed cyclic DNA’s from Escherichia coli. J. molec. Biol. 43, 263 (1969).
Wang, J. C., Baumgarten, D., Olivera, B. M.: On the origin of tertiary turns in covalently closed double-stranded cyclic DNA. Proc. nat. Acad. Sci. (Wash.) 58, 1852 (1967).
Waring, M. J.: Complex formation with DNA and inhibition of Escherichia coli RNA polymerase by ethidium bromide. Biochim. biophys. Acta (Amst.) 87, 358 (1964).
Weil, R., Vinograd, J.: The cyclic helix and cyclic coil forms of polyoma viral DNA. Proc. nat. Acad. Sci. (Wash.) 50, 730 (1963).
Weiss, B., Richardson, C. C.: Enzymatic breakage and joining of DNA, I. Repair of single-strand breaks in DNA by an enzyme from E. coli infected with T4 bacteriophage. Proc. nat. Acad. Sci. (Wash.) 57, 1021 (1967).
Wolstenholme, D. R., Dawid, I. B.: Circular mitochondrial DNA from Xenopus laevis and Rana pipiens. Chromosoma (Berl.) 20, 445 (1967).
Zimmerman, S. B., Little, J. W., Oshinsky, C. K., Gellert, M.: Enzymatic joining of DNA strands: A novel reaction of diphosphopyridine nucleotide. Proc. nat. Acad. Sci. (Wash.) 57, 1841 (1967).
Zyber, E., Penman, S.: Mitochondrial-associated 4S RNA synthesis inhibition by ethidium bromide. J. molec. Biol. 46, 201 (1969).
Zyber, E., Vesco, C., Penman, S.: Selective inhibition of the synthesis of mitochondria-associated RNA by ethidium bromide. J. molec. Biol. 44, 195 (1969).
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1971 Springer-Verlag Berlin · Heidelberg
About this chapter
Cite this chapter
Bauer, W., Vinograd, J. (1971). The Use of Intercalative Dyes in the Study of Closed Circular DNA. In: Hahn, F.E. (eds) Proceedings of the Research Symposium on Complexes of Biologically Active Substances with Nucleic Acids and Their Modes of Action. Progress in Molecular and Subcellular Biology, vol 2. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-65141-0_17
Download citation
DOI: https://doi.org/10.1007/978-3-642-65141-0_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-65143-4
Online ISBN: 978-3-642-65141-0
eBook Packages: Springer Book Archive