Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1993 Nov;12(11):4407–4412. doi: 10.1002/j.1460-2075.1993.tb06125.x

DNA curvature influences the internal motions of supercoiled DNA.

W Kremer 1, K Klenin 1, S Diekmann 1, J Langowski 1
PMCID: PMC413738  PMID: 8223450

Abstract

We present evidence that short curved DNA segments can act as mediators for the ordering of large domains in superhelical DNA. Using a non-invasive solution method (dynamic light scattering), we investigated the effect of permanently curved inserts on the solution structure and on the internal motions of superhelical plasmid DNA. We find that the dynamics of superhelical DNA are strongly influenced by sequence- or protein-induced bending: in superhelical plasmids containing curved inserts the amplitude of the internal motion is lower than that of non-curved controls. Furthermore, the relative arrangement of curved sequences in the plasmids can influence the overall shape of the superhelical DNA. On linearized forms of the plasmids, these effects are not observed.

Full text

PDF
4407

Selected References

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

  1. Bolshoy A., McNamara P., Harrington R. E., Trifonov E. N. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2312–2316. doi: 10.1073/pnas.88.6.2312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bracco L., Kotlarz D., Kolb A., Diekmann S., Buc H. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 1989 Dec 20;8(13):4289–4296. doi: 10.1002/j.1460-2075.1989.tb08615.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Diekmann S. Sequence specificity of curved DNA. FEBS Lett. 1986 Jan 20;195(1-2):53–56. doi: 10.1016/0014-5793(86)80128-4. [DOI] [PubMed] [Google Scholar]
  4. Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res. 1987 Jan 12;15(1):247–265. doi: 10.1093/nar/15.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Giladi H., Koby S., Gottesman M. E., Oppenheim A. B. Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage lambda pL promoter. J Mol Biol. 1992 Apr 20;224(4):937–948. doi: 10.1016/0022-2836(92)90461-r. [DOI] [PubMed] [Google Scholar]
  6. Goodman S. D., Nash H. A. Functional replacement of a protein-induced bend in a DNA recombination site. Nature. 1989 Sep 21;341(6239):251–254. doi: 10.1038/341251a0. [DOI] [PubMed] [Google Scholar]
  7. Heichman K. A., Johnson R. C. The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer. Science. 1990 Aug 3;249(4968):511–517. doi: 10.1126/science.2166334. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Kanaar R., Klippel A., Shekhtman E., Dungan J. M., Kahmann R., Cozzarelli N. R. Processive recombination by the phage Mu Gin system: implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell. 1990 Jul 27;62(2):353–366. doi: 10.1016/0092-8674(90)90372-l. [DOI] [PubMed] [Google Scholar]
  10. Kapp U., Langowski J. Preparation of DNA topoisomers by RP-18 high-performance liquid chromatography. Anal Biochem. 1992 Nov 1;206(2):293–299. doi: 10.1016/0003-2697(92)90369-i. [DOI] [PubMed] [Google Scholar]
  11. Keller W. Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4876–4880. doi: 10.1073/pnas.72.12.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Langowski J., Giesen U. Configurational and dynamic properties of different length superhelical DNAs measured by dynamic light scattering. Biophys Chem. 1989 Sep 15;34(1):9–18. doi: 10.1016/0301-4622(89)80036-5. [DOI] [PubMed] [Google Scholar]
  14. Langowski J., Giesen U., Lehmann C. Dynamics of superhelical DNA studied by photon correlation spectroscopy. Biophys Chem. 1986 Dec 15;25(2):191–200. doi: 10.1016/0301-4622(86)87010-7. [DOI] [PubMed] [Google Scholar]
  15. Langowski J., Kremer W., Kapp U. Dynamic light scattering for study of solution conformation and dynamics of superhelical DNA. Methods Enzymol. 1992;211:430–448. doi: 10.1016/0076-6879(92)11023-c. [DOI] [PubMed] [Google Scholar]
  16. Langowski J. Salt effects on internal motions of superhelical and linear pUC8 DNA. Dynamic light scattering studies. Biophys Chem. 1987 Sep;27(3):263–271. doi: 10.1016/0301-4622(87)80066-2. [DOI] [PubMed] [Google Scholar]
  17. Laundon C. H., Griffith J. D. Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell. 1988 Feb 26;52(4):545–549. doi: 10.1016/0092-8674(88)90467-9. [DOI] [PubMed] [Google Scholar]
  18. Lazarus L. R., Travers A. A. The Escherichia coli FIS protein is not required for the activation of tyrT transcription on entry into exponential growth. EMBO J. 1993 Jun;12(6):2483–2494. doi: 10.1002/j.1460-2075.1993.tb05903.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Muzard G., Théveny B., Révet B. Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models. EMBO J. 1990 Apr;9(4):1289–1298. doi: 10.1002/j.1460-2075.1990.tb08238.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nash H. A. Bending and supercoiling of DNA at the attachment site of bacteriophage lambda. Trends Biochem Sci. 1990 Jun;15(6):222–227. doi: 10.1016/0968-0004(90)90034-9. [DOI] [PubMed] [Google Scholar]
  22. Pagel J. M., Winkelman J. W., Adams C. W., Hatfield G. W. DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli. J Mol Biol. 1992 Apr 20;224(4):919–935. doi: 10.1016/0022-2836(92)90460-2. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Shure M., Vinograd J. The number of superhelical turns in native virion SV40 DNA and minicol DNA determined by the band counting method. Cell. 1976 Jun;8(2):215–226. doi: 10.1016/0092-8674(76)90005-2. [DOI] [PubMed] [Google Scholar]
  25. Singleton C. K., Wells R. D. The facile generation of covalently closed, circular DNAs with defined negative superhelical densities. Anal Biochem. 1982 May 15;122(2):253–257. doi: 10.1016/0003-2697(82)90277-9. [DOI] [PubMed] [Google Scholar]
  26. Stellwagen N. C. Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels. Biochemistry. 1983 Dec 20;22(26):6186–6193. doi: 10.1021/bi00295a023. [DOI] [PubMed] [Google Scholar]
  27. Thomas J. C., Allison S. A., Appellof C. J., Schurr J. M. Torison dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral phi 29 DNA. Biophys Chem. 1980 Oct;12(2):177–188. doi: 10.1016/0301-4622(80)80050-0. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Wang J. C. DNA topoisomerases. Sci Am. 1982 Jul;247(1):94-7, 100-9. doi: 10.1038/scientificamerican0782-94. [DOI] [PubMed] [Google Scholar]
  30. ten Heggeler-Bordier B., Wahli W., Adrian M., Stasiak A., Dubochet J. The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template. EMBO J. 1992 Feb;11(2):667–672. doi: 10.1002/j.1460-2075.1992.tb05098.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES