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. 1987 Apr 10;15(7):2803–2821. doi: 10.1093/nar/15.7.2803

Helical repeat of DNA in solution. The V curve method.

I Goulet, Y Zivanovic, A Prunell
PMCID: PMC340700  PMID: 3562239

Abstract

The V-like dependence of the electrophoretic mobility of small DNA rings on their topological constraint, which has been documented in a recent paper [Zivanovic et al. (1986), J. Mol. Biol., 192, 645-660], has been explored as a tool to measure the helical twist of the torsionally unstressed duplex. The method was applied to single mixed sequence fragments approximately 350 to 1400 base pairs in length, providing estimates of their average helical periodicity. It was also used to compare two DNA fragments, and to evaluate the helical repeat of poly(dA.dT).poly(dA.dT) and poly(dA).poly(dT) inserts, and the helix unwindings associated with dA and dC methylations by dam and Hhal methylases, respectively. Data were found to be highly reproducible and helical repeat estimates were in good agreement with those obtained from previous techniques.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson P., Bauer W. Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry. 1978 Feb 21;17(4):594–601. doi: 10.1021/bi00597a006. [DOI] [PubMed] [Google Scholar]
  2. Buhk H. J., Messer W. The replication origin region of Escherichia coli: nucleotide sequence and functional units. Gene. 1983 Oct;24(2-3):265–279. doi: 10.1016/0378-1119(83)90087-2. [DOI] [PubMed] [Google Scholar]
  3. Cheng S. C., Herman G., Modrich P. Extent of equilibrium perturbation of the DNA helix upon enzymatic methylation of adenine residues. J Biol Chem. 1985 Jan 10;260(1):191–194. [PubMed] [Google Scholar]
  4. Crick F. H. Linking numbers and nucleosomes. Proc Natl Acad Sci U S A. 1976 Aug;73(8):2639–2643. doi: 10.1073/pnas.73.8.2639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Depew D. E., Wang J. C. Conformational fluctuations of DNA helix. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4275–4279. doi: 10.1073/pnas.72.11.4275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Engel J. D., von Hippel P. H. Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. J Biol Chem. 1978 Feb 10;253(3):927–934. [PubMed] [Google Scholar]
  7. Fuller F. B. The writhing number of a space curve. Proc Natl Acad Sci U S A. 1971 Apr;68(4):815–819. doi: 10.1073/pnas.68.4.815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Greaves D. R., Patient R. K., Lilley D. M. Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene. J Mol Biol. 1985 Oct 5;185(3):461–478. doi: 10.1016/0022-2836(85)90064-6. [DOI] [PubMed] [Google Scholar]
  9. Horowitz D. S., Wang J. C. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol. 1984 Feb 15;173(1):75–91. doi: 10.1016/0022-2836(84)90404-2. [DOI] [PubMed] [Google Scholar]
  10. Kikuchi A., Asai K. Reverse gyrase--a topoisomerase which introduces positive superhelical turns into DNA. Nature. 1984 Jun 21;309(5970):677–681. doi: 10.1038/309677a0. [DOI] [PubMed] [Google Scholar]
  11. Lilley D. M. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468–6472. doi: 10.1073/pnas.77.11.6468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Liu L. F., Wang J. C. DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell. 1978 Nov;15(3):979–984. doi: 10.1016/0092-8674(78)90281-7. [DOI] [PubMed] [Google Scholar]
  13. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  14. McClellan J. A., Palecek E., Lilley D. M. (A-T)n tracts embedded in random sequence DNA--formation of a structure which is chemically reactive and torsionally deformable. Nucleic Acids Res. 1986 Dec 9;14(23):9291–9309. doi: 10.1093/nar/14.23.9291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Panayotatos N., Wells R. D. Cruciform structures in supercoiled DNA. Nature. 1981 Feb 5;289(5797):466–470. doi: 10.1038/289466a0. [DOI] [PubMed] [Google Scholar]
  16. Peck L. J., Nordheim A., Rich A., Wang J. C. Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc Natl Acad Sci U S A. 1982 Aug;79(15):4560–4564. doi: 10.1073/pnas.79.15.4560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Peck L. J., Wang J. C. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981 Jul 23;292(5821):375–378. doi: 10.1038/292375a0. [DOI] [PubMed] [Google Scholar]
  18. Pulleyblank D. E., Shure M., Tang D., Vinograd J., Vosberg H. P. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4280–4284. doi: 10.1073/pnas.72.11.4280. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Rhodes D., Klug A. Helical periodicity of DNA determined by enzyme digestion. Nature. 1980 Aug 7;286(5773):573–578. doi: 10.1038/286573a0. [DOI] [PubMed] [Google Scholar]
  20. Rhodes D., Klug A. Sequence-dependent helical periodicity of DNA. Nature. 1981 Jul 23;292(5821):378–380. doi: 10.1038/292378a0. [DOI] [PubMed] [Google Scholar]
  21. Shore D., Baldwin R. L. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol. 1983 Nov 15;170(4):957–981. doi: 10.1016/s0022-2836(83)80198-3. [DOI] [PubMed] [Google Scholar]
  22. Shore D., Baldwin R. L. Energetics of DNA twisting. II. Topoisomer analysis. J Mol Biol. 1983 Nov 15;170(4):983–1007. doi: 10.1016/s0022-2836(83)80199-5. [DOI] [PubMed] [Google Scholar]
  23. Singleton C. K., Klysik J., Stirdivant S. M., Wells R. D. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 1982 Sep 23;299(5881):312–316. doi: 10.1038/299312a0. [DOI] [PubMed] [Google Scholar]
  24. Smith H. O. Nucleotide sequence specificity of restriction endonucleases. Science. 1979 Aug 3;205(4405):455–462. doi: 10.1126/science.377492. [DOI] [PubMed] [Google Scholar]
  25. Strauss F., Gaillard C., Prunell A. Helical periodicity of DNA, Poly(dA) . poly(dT) and poly(dA-dT). poly(dA-dT) in solution. Eur J Biochem. 1981 Aug;118(2):215–222. doi: 10.1111/j.1432-1033.1981.tb06389.x. [DOI] [PubMed] [Google Scholar]
  26. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  27. Sutcliffe J. G. pBR322 restriction map derived from the DNA sequence: accurate DNA size markers up to 4361 nucleotide pairs long. Nucleic Acids Res. 1978 Aug;5(8):2721–2728. doi: 10.1093/nar/5.8.2721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tullius T. D., Dombroski B. A. Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science. 1985 Nov 8;230(4726):679–681. doi: 10.1126/science.2996145. [DOI] [PubMed] [Google Scholar]
  29. Wang J. C. Helical repeat of DNA in solution. Proc Natl Acad Sci U S A. 1979 Jan;76(1):200–203. doi: 10.1073/pnas.76.1.200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Zivanovic Y., Goulet I., Prunell A. Properties of supercoiled DNA in gel electrophoresis. The V-like dependence of mobility on topological constraint. DNA-matrix interactions. J Mol Biol. 1986 Dec 5;192(3):645–660. doi: 10.1016/0022-2836(86)90282-2. [DOI] [PubMed] [Google Scholar]
  31. Zmudzka B., Bollum F. J., Shugar D. Poly-5-methyldeoxycyctidylic acid and some alkylamino analogs. Biochemistry. 1969 Jul;8(7):3049–3059. doi: 10.1021/bi00835a054. [DOI] [PubMed] [Google Scholar]
  32. Zyskind J. W., Smith D. W. The bacterial origin of replication, oriC. Cell. 1986 Aug 15;46(4):489–490. doi: 10.1016/0092-8674(86)90873-1. [DOI] [PubMed] [Google Scholar]

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