Skip to main content

Superhelical DNA Studied by Solution Scattering and Computer Models

  • Chapter
Structural Biology and Functional Genomics

Part of the book series: NATO Science Series ((ASHT,volume 71))

  • 296 Accesses

Abstract

We present here recent results on the structure of superhelical DNA and its changes with salt concentration between 0.01 and 1.5 M NaCI. Scattering curves of two different superhelical DNAs were determined by static light scattering. The measured radii of gyration do not change significantly with salt concentration. Small-angle neutron scattering, together with calculations from a Monte-Carlo model, allows to determine the superhelix diameter. Measured and simulated scattering curves agreed almost quantitatively. Experimentally we find that the diameter decreases from (16.0±0.9) nm at 10 mM to (9.0±0.7) nm at 100 mM NaCI. The superhelix diameter from the simulated conformations decreased from (18.0±1.5) nm at 10 mM to (9.4±1.5) nm at 100 mM NaCI. At higher salt concentrations up to 1.5 M NaC1, the diameter stays constant at 9 nm

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adrian, M., B. ten Heggeler-Bordier, W. Wahli, A. Z. Stasiak, A. Stasiak, and J. Dubochet. 1990. Direct visualization of supercoiled DNA molecules in solution. The EMBO Journal 9:4551–4554.

    PubMed  CAS  Google Scholar 

  2. Bednar, J., P. Furrer, A. Stasiak, J. Dubochet, E. H. Egelman, and A. D. Bates. 1994. The twist, writhe and overall shape of superhelical DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. Journal of Molecular Biology 235:825–847.

    Article  PubMed  CAS  Google Scholar 

  3. Boles, T. C., J. H. White, and N. R. Cozzarelli. 1990. Structure of plectonemically supercoiled DNA. J. Mol. Biol 213:931–951.

    Article  PubMed  CAS  Google Scholar 

  4. Cantor, C. R., and P. R. Schimmel. 1980. Biophysical Chemistry. Part II: Techniques for the Study of Biological Structure and Function. Freeman, New York.

    Google Scholar 

  5. Chirico, G., and J. Langowski. 1996. Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys J 71:955–971.

    Article  PubMed  CAS  Google Scholar 

  6. Gebe, J. A., J. J. Delrow, P. J. Heath, B. S. Fujimoto, D. W. Stewart, and J. M. Schurr. 1996. Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments. J Mol Biol 262:105–128.

    Article  PubMed  CAS  Google Scholar 

  7. Hammermann, M., N. Brun, K. V. Klenin, R. May, K. Tóth, and J. Langowski. 1998. Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations. Biophysical J. 75:in press.

    Google Scholar 

  8. Hammermann, M., C. Steinmaier, H. Merlitz, U. Kapp, W. Waldeck, G. Chirico, and J. Langowski. 1997. Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics. Biophys J 73:2674–2687.

    Article  PubMed  CAS  Google Scholar 

  9. Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys J 74:780–788.

    Article  PubMed  CAS  Google Scholar 

  10. Klenin, K. V., M. D. Frank-Kamenetskii, and J. Langowski. 1995. Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. Biophys J 68:81–88.

    Article  PubMed  CAS  Google Scholar 

  11. Rippe, K., N. Mucke, and J. Langowski. 1997. Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution. Nucleic Acids Res 25:1736–1744.

    Article  PubMed  CAS  Google Scholar 

  12. Rybenkov, V. V., A. V. Vologodskii, and N. R. Cozzarelli. 1997a. The effect of ionic conditions on the conformations of supercoiled DNA.I. Sedimentation analysis. J Mol Biol 267:299–311.

    Article  CAS  Google Scholar 

  13. Rybenkov, V. V., A. V. Vologodskii, and N. R. Cozzarelli. 1997b. The effect of ionic conditions on the conformations of supercoiled DNA. 2. Equilibrium catenation. J Mol Biol 267:312–323.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1999 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Langowski, J., Hammermann, M., Klenin, K., Tóth, K. (1999). Superhelical DNA Studied by Solution Scattering and Computer Models. In: Bradbury, E.M., Pongor, S. (eds) Structural Biology and Functional Genomics. NATO Science Series, vol 71. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4631-9_4

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-4631-9_4

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-0-7923-5782-7

  • Online ISBN: 978-94-011-4631-9

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics