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Stacking interactions in denaturation of DNA fragments

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Abstract

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time-dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the adenine-thymine-rich portions of the fragment. The harmonic stacking coupling shifts, along the T -axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble, we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.

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References

  1. E. Schrödinger What is Life? (Cambridge University Press, 1944).

  2. R.M. Wartell, A.S. Benight, Phys. Rep. 126, 67 (1985).

    Article  ADS  Google Scholar 

  3. L.V. Yakushevich Nonlinear Physics of DNA (Wiley-VCH, Weinheim, 2004).

    Book  Google Scholar 

  4. E. Yeramian, Gene 255, 139 (2000).

    Article  Google Scholar 

  5. E. Carlon, M.L. Malki, R. Blossey, Phys. Rev. Lett. 94, 178101 (2005).

    Article  ADS  Google Scholar 

  6. D. Jost, R. Everaers, J. Phys.: Condens. Matter 21, 034108 (2009).

    Article  Google Scholar 

  7. G. Gilliland, S. Perrin, K. Blanchard, H.F. Bunn, Proc. Natl. Acad. Sci. U.S.A. 87, 2725 (1990).

    Article  ADS  Google Scholar 

  8. D. Poland, H. Scheraga, J. Chem. Phys. 45, 1456 (1966).

    Article  ADS  Google Scholar 

  9. D. Poland, H. Scheraga, J. Chem. Phys. 45, 1464 (1966).

    Article  ADS  Google Scholar 

  10. M.Y. Azbel, J. Chem. Phys. 62, 3635 (1975).

    Article  ADS  Google Scholar 

  11. M.E. Fisher, J. Chem. Phys. 45, 1469 (1966).

    Article  ADS  Google Scholar 

  12. C. Richard, A.J. Guttmann, J. Stat. Phys. 115, 925 (2004).

    Article  ADS  MATH  MathSciNet  Google Scholar 

  13. R. Blossey, E. Carlon, Phys. Rev. E 68, 061911 (2003).

    Article  ADS  Google Scholar 

  14. Y. Kafri, D. Mukamel, L. Peliti, Phys. Rev. Lett. 85, 4988 (2000).

    Article  ADS  Google Scholar 

  15. E. Carlon, E. Orlandini, A.L. Stella, Phys. Rev. Lett. 88, 198101 (2002).

    Article  ADS  Google Scholar 

  16. A. Hanke, M.G. Ochoa, R. Metzler, Phys. Rev. Lett. 100, 018106 (2008).

    Article  ADS  Google Scholar 

  17. J. Palmeri, M. Manghi, N. Destainville, Phys. Rev. E 77, 011913 (2008).

    Article  ADS  Google Scholar 

  18. M. Peyrard, A.R. Bishop, Phys. Rev. Lett. 62, 2755 (1989).

    Article  ADS  Google Scholar 

  19. T. Dauxois, M. Peyrard, A.R. Bishop, Phys. Rev. E 47, R44 (1993).

    Article  ADS  Google Scholar 

  20. N. Theodorakopoulos, T. Dauxois, M. Peyrard, Phys. Rev. Lett. 85, 6 (2000).

    Article  ADS  Google Scholar 

  21. D. Cule, T. Hwa, Phys. Rev. Lett. 79, 2375 (1997).

    Article  ADS  Google Scholar 

  22. T.S. van Erp, S. Cuesta-López, M. Peyrard, Eur. Phys. J. E 20, 421 (2006).

    Article  Google Scholar 

  23. M. Joyeux, A.M. Florescu, J. Phys.: Condens. Matter 21, 034101 (2009).

    Article  Google Scholar 

  24. J.M. Romero-Enrique, F. de los Santos, M.A. Muñoz, EPL 89, 40011 (2010).

    Article  ADS  Google Scholar 

  25. M. Guéron, M. Kochoyan, J.L. Leroy, Nature 328, 89 (1987).

    Article  ADS  Google Scholar 

  26. P. Yakovchuk, E. Protozanova, M.D. Frank-Kamenetskii, Nucleic Acids Res. 34, 564 (2006).

    Article  Google Scholar 

  27. A. Spassky, D. Angelov, J. Mol. Biol. 323, 9 (2002).

    Article  Google Scholar 

  28. C. Barbieri, S. Cocco, R. Monasson, F. Zamponi, Phys. Biol. 6, 025003 (2009).

    Article  ADS  Google Scholar 

  29. D. Marenduzzo, E. Orlandini, F. Seno, A. Trovato, Phys. Rev. E 81, 051926 (2010).

    Article  ADS  Google Scholar 

  30. S.W. Englander, N.R. Kallenbach, A.J. Heeger, J.A. Krumhansl, S. Litwin, Proc. Natl. Acad. Sci. U.S.A. 777, 7222 (1980).

    Article  ADS  Google Scholar 

  31. E.W. Prohofsky, Phys. Rev. A 38, 1538 (1988).

    Article  ADS  Google Scholar 

  32. T. Dauxois, M. Peyrard, A.R. Bishop, Phys. Rev. E 47, 684 (1993).

    Article  ADS  Google Scholar 

  33. G. Altan-Bonnet, A. Libchaber, O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003).

    Article  ADS  Google Scholar 

  34. T. Ambjörnsson, S.K. Banik, O. Krichevsky, R. Metzler, Phys. Rev. Lett. 97, 128105 (2006).

    Article  ADS  Google Scholar 

  35. H.C. Fogedby, R. Metzler, Phys. Rev. Lett. 98, 070601 (2007).

    Article  ADS  Google Scholar 

  36. R.P. Feynman, A.R. Hibbs Quantum Mechanics and Path Integrals (Mc Graw-Hill, New York, 1965).

    MATH  Google Scholar 

  37. M. Zoli, Phys. Rev. E 79, 041927 (2009).

    Article  ADS  Google Scholar 

  38. H. Kleinert Path Integrals in Quantum Mechanics, Statistics, Polymer Physics and Financial Markets (World Scientific Publishing, Singapore, 2004).

    MATH  Google Scholar 

  39. M. Zoli, Phys. Rev. E 81, 051910 (2010).

    Article  ADS  Google Scholar 

  40. S. Srivastava, N. Singh, J. Chem. Phys. 134, 115102 (2011).

    Article  ADS  Google Scholar 

  41. Y.L. Zhang, W.M. Zheng, J.X. Liu, Y.Z. Chen, Phys. Rev. E 56, 7100 (1997).

    Article  ADS  Google Scholar 

  42. Z. Rapti, A. Smerzi, K.O. Rasmussen, A.R. Bishop, C.H. Choi, A. Usheva, Phys. Rev. E 73, 051902 (2006).

    Article  ADS  Google Scholar 

  43. F. de los Santos, O. Al Hammal, M.A. Muñoz, Phys. Rev. E 77, 032901 (2008).

    Article  ADS  Google Scholar 

  44. M. Peyrard, S. Cuesta-López, G. James, Nonlinearity 6, 21 (2008).

    Google Scholar 

  45. M. Joyeux, S. Buyukdagli, Phys. Rev. E 72, 051902 (2005).

    Article  ADS  Google Scholar 

  46. S. Ares, N.K. Voulgarakis, K.O. Rasmussen, A.R. Bishop, Phys. Rev. Lett. 94, 035504 (2005).

    Article  ADS  Google Scholar 

  47. R.D. Blake, S.G. Delcourt, Nucleic Acids Res. 26, 3323 (1998).

    Article  Google Scholar 

  48. S. Buyukdagli, M. Joyeux, Phys. Rev. E 77, 031903 (2008).

    Article  ADS  Google Scholar 

  49. Y. Kim, K.V. Devi-Prasad, E.W. Prohofsky, Phys. Rev. B 32, 5185 (1985).

    Article  ADS  Google Scholar 

  50. A. Campa, A. Giansanti, Phys. Rev. E 58, 3585 (1998).

    Article  ADS  Google Scholar 

  51. A. Hanke, R. Metzler, J. Phys. A: Math. Gen. 36, L473 (2003).

    Article  ADS  MATH  MathSciNet  Google Scholar 

  52. M. Peyrard, S. Cuesta-López, G. James, J. Biol. Phys. 35, 73 (2009).

    Article  Google Scholar 

  53. M. Zoli, Adv. Condens. Matter Phys. 2010, 815917 (2010).

    Google Scholar 

  54. G.D. Mahan Many Particle Physics (Plenum Press, New York, 1981).

    Google Scholar 

  55. L.D. Landau, E.M. Lifshitz Quantum Mechanics (Butterworth-Heinemann, Oxford, 1977).

    Google Scholar 

  56. Y. Zeng, A. Montrichok, G. Zocchi, Phys. Rev. Lett. 91, 148101 (2003).

    Article  ADS  Google Scholar 

  57. M. Zoli, Phys. Rev. B 70, 184301 (2004).

    Article  ADS  Google Scholar 

  58. M. Zoli, Phys. Rev. B 71, 184308 (2005).

    Article  ADS  Google Scholar 

  59. M. Zoli, Phys. Rev. B 71, 205111 (2005).

    Article  ADS  Google Scholar 

  60. T.V. Chalikian, J. Völker, G.E. Plum, K.J. Breslauer, Proc. Natl. Acad. Sci. U.S.A. 96, 7853 (1999).

    Article  ADS  Google Scholar 

  61. Y. Zeng, A. Montrichok, G. Zocchi, J. Mol. Biol. 339, 67 (2004).

    Article  Google Scholar 

  62. A. Krueger, E. Protozanova, M.D. Frank-Kamenetskii, Biophys. J. 90, 3091 (2006).

    Article  Google Scholar 

  63. S. Buyukdagli, M. Sanrey, M. Joyeux, Chem. Phys. Lett. 419, 434 (2006).

    Article  ADS  Google Scholar 

  64. N. Theodorakopoulos, Phys. Rev. E 82, 021905 (2010).

    Article  ADS  Google Scholar 

  65. S. Buyukdagli, M. Joyeux, Phys. Rev. E 76, 021917 (2007).

    Article  ADS  Google Scholar 

  66. A. Wildes, N. Theodorakopoulos, J. Valle-Orero, S. Cuesta-López, J. Garden, M. Peyrard, Phys. Rev. Lett. 106, 048101 (2011).

    Article  ADS  Google Scholar 

  67. I.S. Gradshteyn, I.M. Ryzhik Tables of Integrals, Series and Products (Academic Press, New York, 1965).

    Google Scholar 

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  1. School of Science and Technology - CNISM, Università di Camerino, I-62032, Camerino, Italy

    M. Zoli

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Zoli, M. Stacking interactions in denaturation of DNA fragments. Eur. Phys. J. E 34, 68 (2011). https://doi.org/10.1140/epje/i2011-11068-9

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