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. 1993 Jun 1;90(11):5307–5311. doi: 10.1073/pnas.90.11.5307

Probability of DNA knotting and the effective diameter of the DNA double helix.

V V Rybenkov 1, N R Cozzarelli 1, A V Vologodskii 1
PMCID: PMC46705  PMID: 8506378

Abstract

During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution of knot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter of the DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration.

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Selected References

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  1. BERTANI L. E. LYSOGENIC CONVERSION BY BACTERIOPHAGE P2 RESULTING IN AN INCREASED SENSITIVITY OF ESCHERICHIA COLI TO 5-FLUORODEOXYURIDINE. Biochim Biophys Acta. 1964 Aug 12;87:631–640. doi: 10.1016/0926-6550(64)90281-6. [DOI] [PubMed] [Google Scholar]
  2. Brian A. A., Frisch H. L., Lerman L. S. Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition. Biopolymers. 1981 Jun;20(6):1305–1328. doi: 10.1002/bip.1981.360200615. [DOI] [PubMed] [Google Scholar]
  3. Dröge P., Cozzarelli N. R. Topological structure of DNA knots and catenanes. Methods Enzymol. 1992;212:120–130. doi: 10.1016/0076-6879(92)12008-e. [DOI] [PubMed] [Google Scholar]
  4. Frank-Kamenetskii M. D., Lukashin A. V., Anshelevich V. V., Vologodskii A. V. Torsional and bending rigidity of the double helix from data on small DNA rings. J Biomol Struct Dyn. 1985 Feb;2(5):1005–1012. doi: 10.1080/07391102.1985.10507616. [DOI] [PubMed] [Google Scholar]
  5. Hagerman P. J. Flexibility of DNA. Annu Rev Biophys Biophys Chem. 1988;17:265–286. doi: 10.1146/annurev.bb.17.060188.001405. [DOI] [PubMed] [Google Scholar]
  6. Johnston R. F., Pickett S. C., Barker D. L. Autoradiography using storage phosphor technology. Electrophoresis. 1990 May;11(5):355–360. doi: 10.1002/elps.1150110503. [DOI] [PubMed] [Google Scholar]
  7. Klenin K. V., Vologodskii A. V., Anshelevich V. V., Dykhne A. M., Frank-Kamenetskii M. D. Computer simulation of DNA supercoiling. J Mol Biol. 1991 Feb 5;217(3):413–419. doi: 10.1016/0022-2836(91)90745-r. [DOI] [PubMed] [Google Scholar]
  8. Klenin K. V., Vologodskii A. V., Anshelevich V. V., Dykhne A. M., Frank-Kamenetskii M. D. Effect of excluded volume on topological properties of circular DNA. J Biomol Struct Dyn. 1988 Jun;5(6):1173–1185. doi: 10.1080/07391102.1988.10506462. [DOI] [PubMed] [Google Scholar]
  9. Liu L. F., Davis J. L., Calendar R. Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases. Nucleic Acids Res. 1981 Aug 25;9(16):3979–3989. doi: 10.1093/nar/9.16.3979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Liu L. F., Depew R. E., Wang J. C. Knotted single-stranded DNA rings: a novel topological isomer of circular single-stranded DNA formed by treatment with Escherichia coli omega protein. J Mol Biol. 1976 Sep 15;106(2):439–452. doi: 10.1016/0022-2836(76)90095-4. [DOI] [PubMed] [Google Scholar]
  11. Murray K., Murray N. E. Terminal nucleotide sequences of DNA from temperate coliphages. Nat New Biol. 1973 May 30;243(126):134–139. doi: 10.1038/newbio243134a0. [DOI] [PubMed] [Google Scholar]
  12. Raimondi A., Donghi R., Montaguti A., Pessina A., Dehò G. Analysis of spontaneous deletion mutants of satellite bacteriophage P4. J Virol. 1985 Apr;54(1):233–235. doi: 10.1128/jvi.54.1.233-235.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Shaw S. Y., Wang J. C. Knotting of a DNA chain during ring closure. Science. 1993 Apr 23;260(5107):533–536. doi: 10.1126/science.8475384. [DOI] [PubMed] [Google Scholar]
  14. Shishido K., Komiyama N., Ikawa S. Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants. J Mol Biol. 1987 May 5;195(1):215–218. doi: 10.1016/0022-2836(87)90338-x. [DOI] [PubMed] [Google Scholar]
  15. Stigter D. Interactions of highly charged colloidal cylinders with applications to double-stranded. Biopolymers. 1977 Jul;16(7):1435–1448. doi: 10.1002/bip.1977.360160705. [DOI] [PubMed] [Google Scholar]
  16. Sundin O., Varshavsky A. Terminal stages of SV40 DNA replication proceed via multiply intertwined catenated dimers. Cell. 1980 Aug;21(1):103–114. doi: 10.1016/0092-8674(80)90118-x. [DOI] [PubMed] [Google Scholar]
  17. Vologodskii A. V., Levene S. D., Klenin K. V., Frank-Kamenetskii M., Cozzarelli N. R. Conformational and thermodynamic properties of supercoiled DNA. J Mol Biol. 1992 Oct 20;227(4):1224–1243. doi: 10.1016/0022-2836(92)90533-p. [DOI] [PubMed] [Google Scholar]
  18. Wang J. C., Davidson N. Cyclization of phage DNAs. Cold Spring Harb Symp Quant Biol. 1968;33:409–415. doi: 10.1101/sqb.1968.033.01.047. [DOI] [PubMed] [Google Scholar]
  19. Wang J. C., Davidson N. Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA. J Mol Biol. 1966 Jan;15(1):111–123. doi: 10.1016/s0022-2836(66)80213-9. [DOI] [PubMed] [Google Scholar]
  20. Wasserman S. A., Cozzarelli N. R. Biochemical topology: applications to DNA recombination and replication. Science. 1986 May 23;232(4753):951–960. doi: 10.1126/science.3010458. [DOI] [PubMed] [Google Scholar]
  21. Wasserman S. A., Cozzarelli N. R. Supercoiled DNA-directed knotting by T4 topoisomerase. J Biol Chem. 1991 Oct 25;266(30):20567–20573. [PubMed] [Google Scholar]
  22. White J. H., Millett K. C., Cozzarelli N. R. Description of the topological entanglement of DNA catenanes and knots by a powerful method involving strand passage and recombination. J Mol Biol. 1987 Oct 5;197(3):585–603. doi: 10.1016/0022-2836(87)90566-3. [DOI] [PubMed] [Google Scholar]
  23. Yarmola E. G., Zarudnaya M. I., Lazurkin YuS Osmotic pressure of DNA solutions and effective diameter of the double helix. J Biomol Struct Dyn. 1985 Feb;2(5):981–993. doi: 10.1080/07391102.1985.10507614. [DOI] [PubMed] [Google Scholar]

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