Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1998 Apr;74(4):2016–2028. doi: 10.1016/S0006-3495(98)77908-1

Behavior of supercoiled DNA.

T R Strick 1, J F Allemand 1, D Bensimon 1, V Croquette 1
PMCID: PMC1299542  PMID: 9545060

Abstract

We study DNA supercoiling in a quantitative fashion by micromanipulating single linear DNA molecules with a magnetic field gradient. By anchoring one end of the DNA to multiple sites on a magnetic bead and the other end to multiple sites on a glass surface, we were able to exert torsional control on the DNA. A rotating magnetic field was used to induce rotation of the magnetic bead, and reversibly over- and underwind the molecule. The magnetic field was also used to increase or decrease the stretching force exerted by the magnetic bead on the DNA. The molecule's degree of supercoiling could therefore be quantitatively controlled and monitored, and tethered-particle motion analysis allowed us to measure the stretching force acting on the DNA. Experimental results indicate that this is a very powerful technique for measuring forces at the picoscale. We studied the effect of stretching forces ranging from 0.01 pN to 100 pN on supercoiled DNA (-0.1 < sigma < 0.2) in a variety of ionic conditions. Other effects, such as stretching-relaxing hysteresis and the braiding of two DNA molecules, are discussed.

Full Text

The Full Text of this article is available as a PDF (194.5 KB).

Selected References

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

  1. Allemand J. F., Bensimon D., Jullien L., Bensimon A., Croquette V. pH-dependent specific binding and combing of DNA. Biophys J. 1997 Oct;73(4):2064–2070. doi: 10.1016/S0006-3495(97)78236-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beattie K. L., Wiegand R. C., Radding C. M. Uptake of homologous single-stranded fragments by superhelical DNA. II. Characterization of the reaction. J Mol Biol. 1977 Nov;116(4):783–803. doi: 10.1016/0022-2836(77)90271-6. [DOI] [PubMed] [Google Scholar]
  3. Bednar J., Furrer P., Stasiak A., Dubochet J., Egelman E. H., Bates A. D. The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. J Mol Biol. 1994 Jan 21;235(3):825–847. doi: 10.1006/jmbi.1994.1042. [DOI] [PubMed] [Google Scholar]
  4. Benham C. J. Energetics of the strand separation transition in superhelical DNA. J Mol Biol. 1992 Jun 5;225(3):835–847. doi: 10.1016/0022-2836(92)90404-8. [DOI] [PubMed] [Google Scholar]
  5. Bensimon A., Simon A., Chiffaudel A., Croquette V., Heslot F., Bensimon D. Alignment and sensitive detection of DNA by a moving interface. Science. 1994 Sep 30;265(5181):2096–2098. doi: 10.1126/science.7522347. [DOI] [PubMed] [Google Scholar]
  6. Boles T. C., White J. H., Cozzarelli N. R. Structure of plectonemically supercoiled DNA. J Mol Biol. 1990 Jun 20;213(4):931–951. doi: 10.1016/S0022-2836(05)80272-4. [DOI] [PubMed] [Google Scholar]
  7. Bustamante C., Marko J. F., Siggia E. D., Smith S. Entropic elasticity of lambda-phage DNA. Science. 1994 Sep 9;265(5178):1599–1600. doi: 10.1126/science.8079175. [DOI] [PubMed] [Google Scholar]
  8. Cluzel P., Lebrun A., Heller C., Lavery R., Viovy J. L., Chatenay D., Caron F. DNA: an extensible molecule. Science. 1996 Feb 9;271(5250):792–794. doi: 10.1126/science.271.5250.792. [DOI] [PubMed] [Google Scholar]
  9. Dunaway M., Ostrander E. A. Local domains of supercoiling activate a eukaryotic promoter in vivo. Nature. 1993 Feb 25;361(6414):746–748. doi: 10.1038/361746a0. [DOI] [PubMed] [Google Scholar]
  10. Gelles J., Schnapp B. J., Sheetz M. P. Tracking kinesin-driven movements with nanometre-scale precision. Nature. 1988 Feb 4;331(6155):450–453. doi: 10.1038/331450a0. [DOI] [PubMed] [Google Scholar]
  11. Jannink G., Duplantier B., Sikorav J. L. Forces on chromosomal DNA during anaphase. Biophys J. 1996 Jul;71(1):451–465. doi: 10.1016/S0006-3495(96)79247-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Klenin K. V., Frank-Kamenetskii M. D., Langowski J. Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. Biophys J. 1995 Jan;68(1):81–88. doi: 10.1016/S0006-3495(95)80161-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kowalski D., Natale D. A., Eddy M. J. Stable DNA unwinding, not "breathing," accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9464–9468. doi: 10.1073/pnas.85.24.9464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Marko J. F., Siggia E. D. Fluctuations and supercoiling of DNA. Science. 1994 Jul 22;265(5171):506–508. doi: 10.1126/science.8036491. [DOI] [PubMed] [Google Scholar]
  15. Marko JF, Siggia ED. Statistical mechanics of supercoiled DNA. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995 Sep;52(3):2912–2938. doi: 10.1103/physreve.52.2912. [DOI] [PubMed] [Google Scholar]
  16. Palecek E. Local supercoil-stabilized DNA structures. Crit Rev Biochem Mol Biol. 1991;26(2):151–226. doi: 10.3109/10409239109081126. [DOI] [PubMed] [Google Scholar]
  17. Patterton H. G., von Holt C. Negative supercoiling and nucleosome cores. I. The effect of negative supercoiling on the efficiency of nucleosome core formation in vitro. J Mol Biol. 1993 Feb 5;229(3):623–636. doi: 10.1006/jmbi.1993.1068. [DOI] [PubMed] [Google Scholar]
  18. Pauling L., Corey R. B. A Proposed Structure For The Nucleic Acids. Proc Natl Acad Sci U S A. 1953 Feb;39(2):84–97. doi: 10.1073/pnas.39.2.84. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Schlick T., Olson W. K. Supercoiled DNA energetics and dynamics by computer simulation. J Mol Biol. 1992 Feb 20;223(4):1089–1119. doi: 10.1016/0022-2836(92)90263-j. [DOI] [PubMed] [Google Scholar]
  20. Smith S. B., Cui Y., Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 1996 Feb 9;271(5250):795–799. doi: 10.1126/science.271.5250.795. [DOI] [PubMed] [Google Scholar]
  21. Smith S. B., Finzi L., Bustamante C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 1992 Nov 13;258(5085):1122–1126. doi: 10.1126/science.1439819. [DOI] [PubMed] [Google Scholar]
  22. Strick T. R., Allemand J. F., Bensimon D., Bensimon A., Croquette V. The elasticity of a single supercoiled DNA molecule. Science. 1996 Mar 29;271(5257):1835–1837. doi: 10.1126/science.271.5257.1835. [DOI] [PubMed] [Google Scholar]
  23. Timsit Y., Moras D. Self-fitting and self-modifying properties of the B-DNA molecule. J Mol Biol. 1995 Sep 1;251(5):629–647. doi: 10.1006/jmbi.1995.0461. [DOI] [PubMed] [Google Scholar]
  24. Vinograd J., Lebowitz J., Radloff R., Watson R., Laipis P. The twisted circular form of polyoma viral DNA. Proc Natl Acad Sci U S A. 1965 May;53(5):1104–1111. doi: 10.1073/pnas.53.5.1104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. 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]
  26. Wang J. C. DNA topoisomerases. Annu Rev Biochem. 1996;65:635–692. doi: 10.1146/annurev.bi.65.070196.003223. [DOI] [PubMed] [Google Scholar]
  27. Wang Z., Dröge P. Long-range effects in a supercoiled DNA domain generated by transcription in vitro. J Mol Biol. 1997 Aug 29;271(4):499–510. doi: 10.1006/jmbi.1997.1197. [DOI] [PubMed] [Google Scholar]
  28. Wu H. Y., Shyy S. H., Wang J. C., Liu L. F. Transcription generates positively and negatively supercoiled domains in the template. Cell. 1988 May 6;53(3):433–440. doi: 10.1016/0092-8674(88)90163-8. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES