Skip to main content
SpringerLink
Log in

Elastic and Electrostatic Model for DNA in Rotation–Extension Experiments

  • Conference paper
  • First Online:
IUTAM Symposium on Cellular, Molecular and Tissue Mechanics

Part of the book series: IUTAM Bookseries ((IUTAMBOOK,volume 16))

  • 751 Accesses

Abstract

We present a self-contained theory for the mechanical response of DNA in extension–rotation single molecule experiments. The theory is based on the elasticity of the double-helix and the electrostatic repulsion between two DNA duplex. The configuration of the molecule at large imposed rotation is assumed to comprise two phases, linear and superhelical DNA. Thermal fluctuations are accounted for in the linear phase and electrostatic repulsion is treated in the superhelical phase. This analytical model enables the computation of the supercoiling radius and angle of DNA during experiments. The torsional stress in the molecule and the slope of the linear region of the experimental curve are also predicted and compared successfully with experimental data.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

References

  1. Bednar J, Furrer P, Stasiak A, Dubochet J, Egelman EH, Bates AD (1994) 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 235(3):825–847

    CAS  Google Scholar 

  2. Bustamante C, Macosko JC, Wuite GJL (2000) Grabbing the cat by the tail: Manipulating molecules one by one. Nat Rev Mol Cell Biol 1(2):130–136

    Article  CAS  Google Scholar 

  3. Charvin G, Allemand JF, Strick T, Bensimon D, Croquette V (2004) Twisting DNA: Single molecule studies. Contemp Phys 45(5):383–403

    Article  CAS  Google Scholar 

  4. Clauvelin N, Audoly B, Neukirch S (2008) Mechanical response of plectonemic DNA: An analytical solution. Macromolecules 41(12):4479–4483

    Article  CAS  Google Scholar 

  5. Coleman BD, Swigon D (2004) Theory of self-contact in Kirchhoff rods with applications to supercoiling of knotted and unknotted DNA plasmids. Philos Trans Roy Soc A Math Phys Eng Sci 362(1820):1281–1299

    Article  Google Scholar 

  6. Deufel C, Forth S, Simmons CR, Dejgosha S, Wang MD (2007) Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection. Nat Meth 4(3):223–225

    Article  CAS  Google Scholar 

  7. Goyal S, Perkins NC, Lee CL (2005) Nonlinear dynamics and loop formation in Kirchhoff rods with implications to the mechanics of DNA and cables. J Computat Phys 209(1):371–389

    Article  CAS  Google Scholar 

  8. Goyal S, Perkins NC, Lee CL (2008) Non-linear dynamic intertwining of rods with self-contact. Int J Non-Linear Mech 43(1):65–73

    Article  Google Scholar 

  9. Klenin KV, Vologodskii AV, Anshelevich VV, Dykhne AM, Frank-Kamenetskii MD (1991) Computer simulation of DNA supercoiling. J Mol Biol 217(3):413–419

    Article  CAS  Google Scholar 

  10. Marko JF (2007) Torque and dynamics of linking number relaxation in stretched supercoiled DNA. Phys Rev E (Statistical, Nonlinear, and Soft Matter Physics) 76(2):021,926

    Google Scholar 

  11. Marko JF, Siggia ED (1995) Stretching DNA. Macromolecules 28(26):8759–8770

    Article  CAS  Google Scholar 

  12. Moroz JD, Nelson P (1997) Torsional directed walks, entropic elasticity, and DNA twist stiffness. Proc Natl Acad Sci USA 94:14, 418

    Google Scholar 

  13. Neukirch S (2004) Extracting DNA twist rigidity from experimental supercoiling data. Phys Rev Lett 93(19):198, 107

    Google Scholar 

  14. Purohit PK (2008) Plectoneme formation in twisted fluctuating rods. J Mech Phys Solid 56(5):1715–1729

    Article  CAS  Google Scholar 

  15. Ray J, Manning GS (1994) An attractive force between two rodlike polyions mediated by the sharing of condensed counterions. Langmuir 10(7):2450–2461

    Article  CAS  Google Scholar 

  16. Stigter D (1995) Evaluation of the counterion condensation theory of polyelectrolytes. Biophys J 69(2):380–388

    Article  CAS  Google Scholar 

  17. Strick TR, Allemand JF, Bensimon D, Bensimon A, Croquette V (1996) The elasticity of a single supercoiled DNA molecule. Science 271(5257):1835–1837

    Article  CAS  Google Scholar 

  18. Ubbink J, Odijk T (1999) Electrostatic-undulatory theory of plectonemically supercoiled DNA. Biophys J 76(5):2502–2519

    Article  CAS  Google Scholar 

  19. Wang MD, Yin H, Landick R, Gelles J, Block SM (1997) Stretching DNA with optical tweezers. Biophys J 72(3):1335–1346

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CNRS and UPMC Univ Paris 06, UMR 7190, IJLRDA, 4, Place Jussieu, Paris, F-75005, France

    S. Neukirch, N. Clauvelin & B. Audoly

Authors
  1. S. Neukirch
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. Clauvelin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. B. Audoly
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. Neukirch .

Editor information

Editors and Affiliations

  1. Dept. Mechanical Engineering, University of Michigan, Ann Arbor, 48109-2121, U.S.A.

    Krishna Garikipati

  2. Dept. Mechanical Engineering, University of Michigan, Ann Arbor, 48109-2121, U.S.A.

    Ellen M. Arruda

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media B.V.

About this paper

Cite this paper

Neukirch, S., Clauvelin, N., Audoly, B. (2010). Elastic and Electrostatic Model for DNA in Rotation–Extension Experiments. In: Garikipati, K., Arruda, E. (eds) IUTAM Symposium on Cellular, Molecular and Tissue Mechanics. IUTAM Bookseries, vol 16. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3348-2_10

Download citation

Publish with us

Policies and ethics

Search

Navigation