Advertisement

Journal of Biological Physics

, Volume 42, Issue 1, pp 69–82 | Cite as

Physical origin of DNA unzipping

  • Sitichoke Amnuanpol
Original Paper

Abstract

In DNA transcription, the base pairs are unzipped in response to the enzymatic forces, separating apart two intertwined nucleotide strands. Consequently, the double-stranded DNA (dsDNA), in which two nucleotide strands wind about each other, transits structurally to the single-stranded DNA (ssDNA) in which two nucleotide strands are completely unwound and separated. The large interstrand separation is intimately related to the softening nucleotide strands. This conceptual framework is reinforced with the flow of the bending modulus toward zero under recursion relations derived from the momentum shell renormalization group. Interestingly, the stretch modulus remains the same under recursion relations. The renormalization of the bending modulus to zero has a profound implication that ssDNA has the shorter bending persistence length than does dsDNA in accordance with experiments.

Keywords

DNA unzipping Momentum shell renormalization group Linking number 

Notes

Acknowledgments

The author is indebted to N. Chaichit for his insightful discussions and to Thammasat University for the TU new research scholar, contract number 2557. He also gratefully acknowledges the anonymous reviewers for their constructive comments and invaluable suggestions.

Supplementary material

10867_2015_9393_MOESM1_ESM.pdf (96 kb)
(PDF 96.2 KB)

References

  1. 1.
    Bockelmann, U., Thomen, P., Heslot, F.: Dynamics of the DNA duplex formation studied by single molecule force measurements. Biophys. J. 87, 3388–3396 (2004)ADSCrossRefGoogle Scholar
  2. 2.
    Palmeri, J., Manghi, M., Destainville, N.: Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation. Phys. Rev. E 77, 11913–11939 (2008)ADSCrossRefGoogle Scholar
  3. 3.
    Mills, J.B., Hagerman, P.J.: Origin of the intrinsic rigidity of DNA. Nucleic Acids Res. 32, 4055–4059 (2004)CrossRefGoogle Scholar
  4. 4.
    Vologodskii, A.V., Marko, J.F.: Extension of torsionally stressed DNA by external force. Biophys. J. 73, 123–132 (1997)CrossRefGoogle Scholar
  5. 5.
    Cherstvy, A.G.: Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling. J. Biol. Phys. 37, 227–238 (2011)CrossRefGoogle Scholar
  6. 6.
    Gore, J., Bryant, Z., Nöllmann, M., Le, M.U., Cozzarelli, N.R., Bustamante, C.: DNA overwinds when stretched. Nature 442, 836–839 (2006)ADSCrossRefGoogle Scholar
  7. 7.
    Doi, M., Edwards, S.F.: The Theory of Polymer Dynamics. Oxford University Press, Oxford (2001)Google Scholar
  8. 8.
    Marko, J.F., Siggia, E.D.: Stretching DNA. Macromolecules 28, 8759–8770 (1995)ADSCrossRefGoogle Scholar
  9. 9.
    Jeon, J., Sung, W.: An effective mesoscopic model of double-stranded DNA. J. Biol. Phys. 40, 1–14 (2014)CrossRefGoogle Scholar
  10. 10.
    Lee, O., Jeon, J., Sung, W.: How dsDNA breathing enhances its flexibility and instability on short-length scales. Phys. Rev. E 81, 021906 (2010)ADSCrossRefGoogle Scholar
  11. 11.
    Alberts, B., Bray, D., Lewis, J., Ruff, M., Roberts, K., Watson, J.D.: Molecular Biology of the Cell. Garland Publishing, New York (1994)Google Scholar
  12. 12.
    Lubensky, D.K., Nelson, D.R.: Pulling pinned polymers and unzipping DNA. Phys. Rev. Lett. 85, 1572–1575 (2000)ADSCrossRefGoogle Scholar
  13. 13.
    Chaikin, P.M., Lubensky, T.C.: Principles of Condensed Matter Physics. Cambridge University Press, New York (2000)Google Scholar
  14. 14.
    The detailed calculation of the partition function Z and of the root-mean-square separation r rms(s) are presented in the online supplementary material.Google Scholar
  15. 15.
    Smith, S.B., Cui, Y., Bustamante, C.: Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795–799 (1996)ADSCrossRefGoogle Scholar
  16. 16.
    Kim, J., Jeon, J., Sung, W.: A breathing wormlike chain model on DNA denaturation and bubble: effects of stacking interactions. J. Chem. Phys. 128, 055101 (2008)ADSCrossRefGoogle Scholar
  17. 17.
    Landau, L.D., Lifshitz, E.M.: Theory of Elasticity. Pergamon, Oxford (1986)Google Scholar
  18. 18.
    Austin, R.H., Brody, J.P., Cox, E.C., Duke, T., Volkmuth, W.: Stretch genes. Phys. Today 50, 32–38 (1997)CrossRefGoogle Scholar
  19. 19.
    Gelbart, W.M., Bruinsma, R.F., Pincus, P.A., Parsegian, V.A.: DNA-inspired electrostatics. Phys. Today 53, 38–44 (2000)CrossRefGoogle Scholar
  20. 20.
    Podgornik, R., Hansen, P.L., Parsegian, V.A.: Elastic moduli renormalization in self-interacting stretchable polyelectrolytes. J. Chem. Phys. 113, 9343–9350 (2000)ADSCrossRefGoogle Scholar
  21. 21.
    Shin, J., Cherstvy, A.G., Metzler, R.: Sensing viruses by mechanical tension of DNA in responsive hydrogels. Phys. Rev. X 4, 021002 (2014)Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Physics DepartmentThammasat UniversityPathumthaniThailand

Personalised recommendations