Skip to main content
Log in

DNA triplex folding: Moderate versus high salt conditions

  • Regular Article
  • Published:
The European Physical Journal E Aims and scope Submit manuscript

Abstract.

Some specific sequences in duplex DNA can give rise to local formation of a triple helical DNA called triplex together with a separate strand. Recent single-molecule FRET experiments, performed on DNA strands designed to fold into a triplex, allow us to measure the folding and unfolding time distributions under neutral p H conditions. The average times of both processes are of the order of 1s. The folding time is moderately sensitive to salt concentration. The average unfolding time is found to be nearly constant. Interestingly, the distributions of the unfolding time revealed heterogeneous kinetics at moderate salt concentration (∼ 10 mM), but not at high salt (∼ 100 mM). We relate this salt dependence to different folding paths and folded states, which are governed by the (salt-dependent) stiffness of the third single-stranded donor sequence. Finally we comment on the formation of intramolecular triplex named H-DNA in a torsionally constrained duplex under physiological salt conditions, which mimics the in vivo situation of triplex folding.

Graphical abstract

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. G. Felsenfeld, D.R. Davies, A. Rich, J. Am. Chem. Soc. 79, 2023 (1957)

    Article  Google Scholar 

  2. M. Duca, P. Vekhoff, K. Oussedik, L. Halby, Nucleic Acids Res. 36, 5123 (2008)

    Article  Google Scholar 

  3. K. Hoogsteen, Acta Crystallogr. 16, 907 (1963)

    Article  Google Scholar 

  4. M.D. Frank-Kamenetskii, S.M. Mirkin, Annu. Rev. Biochem. 64, 65 (1995)

    Article  Google Scholar 

  5. I.-B. Lee, S.-C. Hong, N.-K. Lee, A. Johner, Biophys. J. 103, 2492 (2012)

    Article  ADS  Google Scholar 

  6. I. Cisse, H. Kim, T. Ha, Nat. Struct. Mol. Biol 19, 623 (2012)

    Article  Google Scholar 

  7. A. Kovacs, J.C. Kandala, K.T. Weber, R.V. Guntaka, J. Biol. Chem. 271, 1805 (1996)

    Article  Google Scholar 

  8. E. Grabczyk, K. Usdin, Nucleic Acids Res. 28, 2815 (2000)

    Article  Google Scholar 

  9. B.P. Belotserkovskii, E.D. Silva, S. Tornaletti, G. Wang, K.M. Vasquez, P.C. Hanawalt, J. Biol. Chem. 282, 32433 (2007)

    Article  Google Scholar 

  10. G. Bar-Nahum, V. Epshtein, A.E. Ruckenstein, R. Rafikov, A. Mustaev, E. Nudler, Cell 120, 183 (2005)

    Article  Google Scholar 

  11. M.N. Dessinges, B. Maier, Y. Zhang, M. Peliti, D. Bensimon, V. Croquette, Phys. Rev. Lett. 89, 248102 (2002)

    Article  ADS  Google Scholar 

  12. T. Odijk, J. Polymer Sci. 15, 477 (1997)

    Google Scholar 

  13. R. Everaers, A. Milchev, V. Yamakov, Eur. Phys. J. E 8, 3 (2002)

    Article  Google Scholar 

  14. B. O'Shaughnessy, D. Vavylonis, Eur. Phys. J. E 11, 213 (2003)

    Article  Google Scholar 

  15. J. Thopson, G. van der Heijden, S. Neukirch, Proc. R. Soc. London, Ser. A 458, 959 (2002)

    Article  ADS  Google Scholar 

  16. J.-F. Joanny, J. Phys. (Paris) 49, 1981 (1988)

    Article  Google Scholar 

  17. B. Duplantier, Phys. Rev. Lett. 62, 2340 (1989)

    MathSciNet  ADS  Google Scholar 

  18. G.R. Pack, L. Wong, G. Lamm, Int. J. Quantum Chem. 70, 1177 (1998)

    Article  Google Scholar 

  19. E. Grabczyk, M. Mancuso, C. Sammarco, Nucleic Acids Res. 35, 5351 (2007)

    Article  Google Scholar 

  20. N.-K. Lee, S.-C. Hong, A. Johner, Eur. Phys. J. E 24, 229 (2007)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, NK., Johner, A., Lee, IB. et al. DNA triplex folding: Moderate versus high salt conditions. Eur. Phys. J. E 36, 57 (2013). https://doi.org/10.1140/epje/i2013-13057-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1140/epje/i2013-13057-4

Keywords

Navigation