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BY-NC-ND 3.0 license Open Access Published by De Gruyter Open Access June 17, 2012

Constrained thermal denaturation of DNA under fixed linking number

  • Amir Bar EMAIL logo , Alkan Kabakçıoğlu and David Mukamel
From the journal Open Physics

Abstract

A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation transition upon heating. However, in circular DNA chains and some experimental setups that manipulate single DNA molecules, the total number of turns (linking number) is constant at all times. The consequences of this additional topological invariant on the melting behaviour are nontrivial. Below, we investigate the melting characteristics of a homogeneous DNA where the linking number along the melting curve is preserved by supercoil formation in duplex portions. We obtain the mass fraction and the number of loops and supercoils below and above the melting temperature. We also argue that a macroscopic loop appears at T c and calculate its size as a function of temperature.

[1] R.M. Wartell, A.S. Benight, Phys. Rep. 126, 67 (1985) http://dx.doi.org/10.1016/0370-1573(85)90060-210.1016/0370-1573(85)90060-2Search in Google Scholar

[2] B. Alberts et al., Essential cell biology (Garland Science, New York, 2004) Search in Google Scholar

[3] I. Rouzina, V.A. Bloomfield, Biophys. J. 80, 882 (2001) http://dx.doi.org/10.1016/S0006-3495(01)76067-510.1016/S0006-3495(01)76067-5Search in Google Scholar

[4] S. Cocco, R. Monasson, J.F. Marko, P. Natl. Acad. Sci. USA 98, 8608 (2001) http://dx.doi.org/10.1073/pnas.15125759810.1073/pnas.151257598Search in Google Scholar PubMed PubMed Central

[5] D. Marenduzzo, A. Trovato, A. Maritan, Phys. Rev. E, 64, 031901 (2001) http://dx.doi.org/10.1103/PhysRevE.64.03190110.1103/PhysRevE.64.031901Search in Google Scholar PubMed

[6] A. Marziali, M. Akeson, Anu. Rev. Biomed Eng. 3, 195 (2001) http://dx.doi.org/10.1146/annurev.bioeng.3.1.19510.1146/annurev.bioeng.3.1.195Search in Google Scholar PubMed

[7] M.E. Fisher, J. Chem. Phys. 45, 1469 (1966) http://dx.doi.org/10.1063/1.172778710.1063/1.1727787Search in Google Scholar

[8] D. Poland, H.A. Scheraga, J. Chem. Phys. 45, 1456 (1966) http://dx.doi.org/10.1063/1.172778510.1063/1.1727785Search in Google Scholar PubMed

[9] B. Duplantier, J. Stat. Phys. 54, 581 (1989) http://dx.doi.org/10.1007/BF0101977010.1007/BF01019770Search in Google Scholar

[10] Y. Kafri, D. Mukamel, L. Peliti, Phys. Rev. Lett. 85, 4988 (2000) http://dx.doi.org/10.1103/PhysRevLett.85.498810.1103/PhysRevLett.85.4988Search in Google Scholar PubMed

[11] Z. Bryant et al., Nature 424, 338 (2003) http://dx.doi.org/10.1038/nature0181010.1038/nature01810Search in Google Scholar PubMed

[12] E.J. Rensburg, E. Orlandini, D.W. Sumners, M.C. Tesi, S.G. Whittington, J. Phys. A-Math. Gen. 26, L981, (1993) http://dx.doi.org/10.1088/0305-4470/26/19/00210.1088/0305-4470/26/19/002Search in Google Scholar

[13] J.H. White, Am. J. Math. 91, 693 (1969) http://dx.doi.org/10.2307/237334810.2307/2373348Search in Google Scholar

[14] J. Rudnick, R. Bruinsma, Phys. Rev. E. 65 030902(R) (2002) http://dx.doi.org/10.1103/PhysRevE.65.03090210.1103/PhysRevE.65.030902Search in Google Scholar PubMed

[15] T. Garel, H. Orland, E. Yeramian, arXiv:grqc/ 0407036v1 Search in Google Scholar

[16] M. Sayar, B. Avşaroğlu, A. Kabakçıoğlu, Phys. Rev. E 81, 041916 (2010) http://dx.doi.org/10.1103/PhysRevE.81.04191610.1103/PhysRevE.81.041916Search in Google Scholar PubMed

[17] A. Kabakçıoğlu, E. Orlandini, D. Mukamel, Phys Rev E. 80, 010903(R) (2009) 10.1103/PhysRevE.80.010903Search in Google Scholar PubMed

[18] A. Bar, A. Kabakçıoğlu, D. Mukamel, Phys. Rev. E 84, 041935 (2011) http://dx.doi.org/10.1103/PhysRevE.84.04193510.1103/PhysRevE.84.041935Search in Google Scholar PubMed

Published Online: 2012-6-17
Published in Print: 2012-6-1

© 2012 Versita Warsaw

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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