Advertisement

Free energy of conformational isomers: The case of gapped DNA duplexes

  • Alberto Giacomo Orellana
  • Cristiano De MicheleEmail author
Regular Article
  • 24 Downloads

Abstract.

Liquid-crystalline phases in all-DNA systems have been extensively studied in the past and although nematic, cholesteric and columnar mesophases have been observed, the smectic phase remained elusive. Recently, it has been found evidence of a smectic-A ordering in an all-DNA system, where the constituent particles, which are gapped DNA duplexes, resemble chain-sticks. It has been argued that in the smectic-A phase these DNA chain-sticks should be folded as a means to suppress aggregate polydispersity and excluded volume. Nevertheless, if initial crystalline configurations are prepared in silico with gapped DNA duplexes either fully unfolded or fully folded by carrying out computer simulations one can end up with two different phases having at the same concentration and temperature the majority of gapped DNA duplexes either folded or unfolded. This result suggests that these two phases have a small free energy difference, since no transition is observed from one to the other within the simulation time span. In the present manuscript, we assess which of these two phases is thermodynamically stable through a suitable protocol based on thermodynamic integration. Our method is rather general and it can be used to discriminate stable states from metastable ones of comparable free energy.

Graphical abstract

Keywords

Soft Matter: Liquid crystals 

References

  1. 1.
    M. Nakata, G. Zanchetta, B.D. Chapman, C.D. Jones, J.O. Cross, R. Pindak, T. Bellini, N.A. Clark, Science 318, 1276 (2007)CrossRefGoogle Scholar
  2. 2.
    G. Zanchetta, Liq. Cryst. Today 18, 40 (2009)CrossRefGoogle Scholar
  3. 3.
    G. Zanchetta, F. Giavazzi, M. Nakata, M. Buscaglia, R. Cerbino, N.A. Clark, T. Bellini, Proc. Natl. Acad. Sci. U.S.A. 107, 17497 (2010)CrossRefGoogle Scholar
  4. 4.
    C. Maffeo, B. Luan, A. Aksimentiev, Nucl. Acids Res. 40, 3812 (2012)CrossRefGoogle Scholar
  5. 5.
    M. Salamonczyk, J. Zhang, G. Portale, C. Zhu, E. Kentzinger, J.T. Gleeson, A. Jakli, C. De Michele, J.K.G. Dhont, S. Sprunt et al.., Nat. Commun. 7, 13358 (2016)CrossRefGoogle Scholar
  6. 6.
    G.P. Smith, T.P. Fraccia, M. Todisco, G. Zanchetta, C. Zhu, E. Hayden, T. Bellini, N.A. Clark, Proc. Natl. Acad. Sci. U.S.A. 115, E7658 (2018)CrossRefGoogle Scholar
  7. 7.
    S.D. Leo, M. Todisco, T. Bellini, T.P. Fraccia, Liq. Cryst. 45, 2306 (2018)CrossRefGoogle Scholar
  8. 8.
    T.P. Fraccia, G.P. Smith, N.A. Clark, T. Bellini, Crystals 8, 5 (2017)CrossRefGoogle Scholar
  9. 9.
    S. Saurabh, Y. Lansac, Y.H. Jang, M.A. Glaser, N.A. Clark, P.K. Maiti, Phys. Rev. E 95, 032702 (2017)CrossRefGoogle Scholar
  10. 10.
    R. Cortini, X. Cheng, J.C. Smith, J. Phys.: Condens. Matter 29, 084002 (2017)Google Scholar
  11. 11.
    C. Robinson, Tetrahedron 13, 219 (1961)CrossRefGoogle Scholar
  12. 12.
    R.L. Rill, Proc. Natl. Acad. Sci. U.S.A. 83, 342 (1986)CrossRefGoogle Scholar
  13. 13.
    R. Brandes, D.R. Kearns, Biochemistry 25, 5890 (1986)CrossRefGoogle Scholar
  14. 14.
    D. Durand, J. Doucet, F. Livolant, J. Phys. II 2, 1769 (1992)Google Scholar
  15. 15.
    F. Livolant, A.M. Levelut, J. Doucet, J.P. Benoit, Nature 339, 724 (1989)CrossRefGoogle Scholar
  16. 16.
    T.M. Alam, G. Drobny, J. Chem. Phys. 92, 6840 (1990)CrossRefGoogle Scholar
  17. 17.
    F. Livolant, A. Leforestier, Prog. Polym. Sci. 21, 1115 (1996)CrossRefGoogle Scholar
  18. 18.
    J. Pelta, D. Durand, J. Doucet, F. Livolant, Biophys. J. 71, 48 (1996)CrossRefGoogle Scholar
  19. 19.
    K. Merchant, R.L. Rill, Biophys. J. 73, 3154 (1997)CrossRefGoogle Scholar
  20. 20.
    H.H. Strey, R. Podgornik, D.C. Rau, V.A. Parsegian, Curr. Opin. Struct. Biol. 8, 309 (1998)CrossRefGoogle Scholar
  21. 21.
    R. Podgornik, H.H. Strey, V.A. Parsegian, Curr. Opin. Colloid Interface Sci. 3, 534 (1998)CrossRefGoogle Scholar
  22. 22.
    F. Tombolato, A. Ferrarini, J. Chem. Phys. 122, 054908 (2005)CrossRefGoogle Scholar
  23. 23.
    T.E. Strzelecka, M.W. Davidson, R.L. Rill, Nature 331, 457 (1988)CrossRefGoogle Scholar
  24. 24.
    F. Livolant, Y. Bouligand, J. Phys. (Paris) 47, 1813 (1986)CrossRefGoogle Scholar
  25. 25.
    C. De Michele, T. Bellini, F. Sciortino, Macromolecules 45, 1090 (2012)CrossRefGoogle Scholar
  26. 26.
    C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)CrossRefGoogle Scholar
  27. 27.
    C. De Michele, G. Zanchetta, T. Bellini, E. Frezza, A. Ferrarini, ACS Macro Lett. 5, 208 (2016)CrossRefGoogle Scholar
  28. 28.
    K.T. Nguyen, A. Battisti, D. Ancora, F. Sciortino, C. De Michele, Soft Matter 11, 2934 (2015)CrossRefGoogle Scholar
  29. 29.
    M. Schoen, A.J. Haslam, G. Jackson, Langmuir 33, 11345 (2017)CrossRefGoogle Scholar
  30. 30.
    P. Bolhuis, D. Frenkel, J. Chem. Phys. 106, 666 (1997)CrossRefGoogle Scholar
  31. 31.
    A. Haji-Akbari, M. Engel, S.C. Glotzer, J. Chem. Phys. 135, 194101 (2011)CrossRefGoogle Scholar
  32. 32.
    G. Navascués, E. Velasco, Phys. Rev. E 95, 032140 (2017)MathSciNetCrossRefGoogle Scholar
  33. 33.
    B. Cheng, M. Ceriotti, Phys. Rev. B 97, 054102 (2018)CrossRefGoogle Scholar
  34. 34.
    M. Radu, P. Pfleiderer, T. Schilling, J. Chem. Phys. 131, 164513 (2009)CrossRefGoogle Scholar
  35. 35.
    M. Müller, K.C. Daoulas, J. Chem. Phys. 128, 024903 (2008)CrossRefGoogle Scholar
  36. 36.
    C. Greco, Y. Jiang, J.Z.Y. Chen, K. Kremer, K.C. Daoulas, J. Chem. Phys. 145, 184901 (2016)CrossRefGoogle Scholar
  37. 37.
    K.T. Nguyen, F. Sciortino, C. De Michele, Langmuir 30, 4814 (2014)CrossRefGoogle Scholar
  38. 38.
    C. Vega, E. Sanz, J.L.F. Abascal, E.G. Noya, J. Phys.: Condens. Matter 20, 153101 (2008)Google Scholar
  39. 39.
    P.A. O’Brien, M.P. Allen, D.L. Cheung, M. Dennison, A. Masters, Phys. Rev. E 78, 051705 (2008)CrossRefGoogle Scholar
  40. 40.
    L.V. Woodcock, Nature 385, 141 (1997)CrossRefGoogle Scholar
  41. 41.
    P.G. Bolhuis, D. Frenkel, S.C. Mau, D.A. Huse, Nature 388, 235 (1997)CrossRefGoogle Scholar
  42. 42.
    K. Kendall, C. Stainton, F. van Swol, L.V. Woodcock, Int. J. Thermophys. 23, 175 (2002)CrossRefGoogle Scholar
  43. 43.
    E.G. Noya, N.G. Almarza, Mol. Phys. 113, 1061 (2015)CrossRefGoogle Scholar
  44. 44.
    I.P. Dolbnya, A.V. Petukhov, D.G.A.L. Aarts, G.J. Vroege, H.N.W. Lekkerkerker, Europhys. Lett. 72, 962 (2005)CrossRefGoogle Scholar
  45. 45.
    R. Zandi, P. van der Schoot, D. Reguera, W. Kegel, H. Reiss, Biophys. J. 90, 1939 (2006)CrossRefGoogle Scholar
  46. 46.
    C.A. Koh, A.K. Sum, E.D. Sloan, J. Appl. Phys. 106, 061101 (2009)CrossRefGoogle Scholar
  47. 47.
    D.K. Staykova, W.F. Kuhs, A.N. Salamatin, T. Hansen, J. Phys. Chem. B 107, 10299 (2003)CrossRefGoogle Scholar
  48. 48.
    U. Ranieri, M.M. Koza, W.F. Kuhs, S. Klotz, A. Falenty, P. Gillet, L.E. Bove, Nat. Commun. 8, 1076 (2017)CrossRefGoogle Scholar
  49. 49.
    S. Schaack, U. Ranieri, P. Depondt, R. Gaal, W.F. Kuhs, A. Falenty, P. Gillet, F. Finocchi, L.E. Bove, J. Phys. Chem. C 122, 11159 (2018)CrossRefGoogle Scholar
  50. 50.
    L. Bove, U. Ranieri, Philos. Trans. R. Soc. A 377, 20180262 (2019)CrossRefGoogle Scholar
  51. 51.
    E. Sloan, C. Koh, Clathrate Hydrates of Natural Gases, 3rd edition (CRC Press, Boca Raton, Florida, 2008)Google Scholar
  52. 52.
    L.C. Jacobson, V. Molinero, J. Am. Chem. Soc. 133, 6458 (2011)CrossRefGoogle Scholar

Copyright information

© EDP Sciences, Società Italiana di Fisica and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Alberto Giacomo Orellana
    • 1
  • Cristiano De Michele
    • 2
    Email author
  1. 1.SISSAScuola Internazionale Superiore Studi AvanzatiTriesteItaly
  2. 2.Dipartimento di Fisica“Sapienza” Università di RomaRomaItaly

Personalised recommendations