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Current issue   Ukr. J. Phys. 2015, Vol. 60, N 5, p.433-442
https://doi.org/10.15407/ujpe60.05.0433   Paper

Liubysh O.O.1, Vlasiuk A.V.2, Perepelytsya S.M.3

1 Taras Shevchenko National University of Kyiv
(64, Volodymyrs’ka Str., Kyiv 01033, Ukraine; e-mail: lubish.olya@gmail.com)
2 The Biotechnology Center of the Technische Universität Dresden
(47/49, Tatzberg Str., Dresden 01307, Germany; e-mail: anastasiia.vlasiuk@yandex.ua)
3 Bogolyubov Institute for Theoretical Physics, Nat. Acad. of Sci. of Ukraine
(14b, Metrolohichna Str., Kyiv 03680, Ukraine; e-mail: perepelytsya@bitp.kiev.ua)

Structurization Of Counterions Around DNA Double Helix: A Molecular Dynamics Study

Section: Soft matter
Language: English

Abstract: The structurization of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in a water solution with alkali metal counterions Na+, K+, and Cs+ has been simulated. The systems have been considered in the regimes without excess salt and with different added salts (0.5 M of NaCl, KCl, or CsCl). The results have shown that the Na+ counterions interact with the phosphate groups directly from outside of the double helix and via water molecules at the top edge of the DNA minor groove. The potassium ions are mostly localized in the grooves of the double helix, and the cesium ions penetrate deeply inside the minor groove, being bonded directly to atoms of the nucleic bases. Due to the electrostatic repulsion, the chlorine ions tend to be localized at large distances from the DNA polyanion, but some Cl- anions have been detected near atomic groups of the double helix, by forming electrically neutral pairs with counterions already condensed on DNA. The DNA sites, where counterions are incorporated, are characterized by local changes in the double helix structure. The lifetime of Na+ and K+ in the complex with DNA atomic groups is less than 0.5 ns, while it can reach several nanoseconds in the case of cesium ions. On this time scale, the Cs+ counterions form a structured system of charges in the DNA minor groove that can be considered as ionic lattice.

Key words: DNA, macromolecule, structure counterions, molecular dynamics.


  1. G.S. Manning, Q. Rev. Biophys. 11, 179 (1978). CrossRef
  2. W. Saenger, Principles of Nucleic Acid Structure (Springer, New York, 1984). CrossRef
  3. M.D. Frank-Kamenetskii, V.V. Anshelevich, and A.V. Lukashin, Sov. Phys. Usp. 151, 595 (1987). CrossRef
  4. Yu.P. Blagoi, V.L. Galkin, V.L. Gladchenko, S.V. Kornilova, V.A. Sorokin, and A.G. Shkorbatov, The Complexes of Nucleic Acids and Metals in the Solutions (Naukova Dumka, Kiev, 1991).
  5. V.Ya. Maleev, M.A. Semenov, M.A. Gassan, and V.A. Kashpur, Biofizika 38, 768 (1993).
  6. Y. Levin, Rep. Prog. Phys. 65, 1577 (2002). CrossRef
  7. A.A. Kornyshev, D.J. Lee, S. Leikin, and A. Wynveen, Rev. Mod. Phys. 79, 943 (2007). CrossRef
  8. V.B. Teif and K. Bohinc, Progr. Biophys. Mol. Biol. 105, 208 (2011). CrossRef
  9. A. Estevez-Torres and D. Baigl, Soft Matter 7, 6746 (2011). CrossRef
  10. M.L. Ainalem and T. Nylander, Soft Matter 7, 4577 (2011). CrossRef
  11. S.M. Perepelytsya, G.M. Glibitskiy, and S.N. Volkov, Biopolymers 99, 508 (2013). CrossRef
  12. C.C. Sines, L. McFail-Isom, S.B. Howerton, D. VanDerveer, and L.D. Williams, J. Am. Chem. Soc. 122, 11048 (2000). CrossRef
  13. K.K. Woods, L. McFeil-Isom, C.C Sines, S.B. Howerton, R.K. Stephens, and L.D. Williams, J. Am. Chem. Soc. 122, 1546 (2000). CrossRef
  14. V. Tereshko, C.J. Wilds, G. Minasov, T.P. Prakash, M.A. Maier, A. Howard, Z. Wawrzak, M. Manoharan, and M. Egli, Nucl. Acids Res. 29, 1208 (2001). CrossRef
  15. R. Das, T.T. Mills, L.W. Kwok, G.S. Maskel, I.S. Millett, S. Doniach, K.D. Finkelstein, D. Herschlag, and L. Pollack, Phys. Rev. Lett. 90, 188103 (2003). CrossRef
  16. K. Andersen, R. Das, H.Y. Park, H. Smith, L.W. Kwok, J.S. Lamb, E.J. Kirkland, D. Herschlag, K.D. Finkelstein, and L. Pollack, Phys. Rev. Lett. 93, 248103 (2004). CrossRef
  17. K. Andresen, X. Qiu, S.A. Pabit, J.S. Lamb, H.Y. Park, L.W. Kwok, and L. Pollack, Biophys. 95, 287 (2008).
  18. X. Qiu, K. Andersen, J.S. Lamb, L.W. Kwok, and L. Pollack, Phys. Rev. Lett. 101, 228101 (2008). CrossRef
  19. F. Mocci and A. Laaksonen, Soft Matter, 8, 9268 (2012). CrossRef
  20. A. Perez, F.J. Luque, and M. Orozco, Acc. of Chem. Res.45, 196 (2012). CrossRef
  21. R. Lavery, J.H. Maddocks, M. Pasi, and K Zakrzewska, Nucleic Acids Res. 42, 8138 (2014). CrossRef
  22. M. Pasi, J.H. Maddocks, and R. Lavery, Nucleic Acids Res. 43, 2412 (2015). CrossRef
  23. M.A. Young, B. Jayaram, and D.L. Beveridge, J. Am. Chem. Soc. 119, 59 (1997). CrossRef
  24. M.A. Young, G. Ravishanker, and D.L. Beveridge, Biophys. J. 73, 2313 (1997). CrossRef
  25. L. McFail-Isom, C.C. Sines, and L.D. Williams, Cur. Opin. Sruct. Biol. 9, 298 (1999). CrossRef
  26. K.J.McConnel and D.L.Beveridge, J. Mol. Biol. 304, 803 (2000). CrossRef
  27. A.P. Lyubartsev and A. Laaksonen, J. Biomol. Struct. Dynam. 16, 579 (1998). CrossRef
  28. A. Savelyev and G. Papoian, J. Am. Chem. Soc. 128, 14506 (2003). CrossRef
  29. P. Varnai and K. Zakrzewska, Nucleic Acids Res. 32, 4269 (2004). CrossRef
  30. S.Y. Ponomarev, K.M. Thayer, and D.L. Beveridge, Proc. Nat. Acad. Sci. USA 101, 14771 (2004). CrossRef
  31. Y. Cheng, N. Korolev, and L. Nordenskiold, Nucleic Acids Res. 34, 686 (2006). CrossRef
  32. A. Perez, F.J. Luque, M. Orozco, J. Am. Chem. Soc. 129, 14739 (2007). CrossRef
  33. W. Li, L. Nordenskiold, and Y. Mu, J. Phys. Chem. B 115, 14713 (2011). CrossRef
  34. X. Shen, B. Gu, S.A. Che, and F.S. Zhang, J. Chem. Phys. 135, 034509 (2011). CrossRef
  35. X. Shen, N.A. Atamas, and F.S. Zhang, Phys. Rev. E 85, 051813 (2012).
  36. Y.K. Lee, J. Lee, J.Y. Choi, and C. Seok, Bull. Korean Chem. Soc. 33, 3719 (2012). CrossRef
  37. Yu Yang Xin and Fujimoto Shintaro, Sci. Chin. Chem. 56, 1735 (2013). CrossRef
  38. F. Pan, C. Roland, and C. Sagui, Nucleic Acids Res. 42, 13981 (2014). CrossRef
  39. S.M. Perepelytsya and S.N. Volkov, Ukr. J. Phys. 49, 1074 (2004).
  40. S.M. Perepelytsya and S.N. Volkov, Eur. Phys. J. E 24, 261 (2007). CrossRef
  41. S.M. Perepelytsya and S.N. Volkov, Eur. Phys. J. E 31, 201 (2010). CrossRef
  42. S.M. Perepelytsya and S.N. Volkov, J. Mol. Liq. 5, 1182 (2011).
  43. S.M. Perepelytsya and S.N. Volkov, Ukr. J. Phys. 58, No. 2, 554 (2013). CrossRef
  44. L.A. Bulavin, S.N. Volkov, S.Yu. Kutovy, and S.M. Perepelytsya, Dopov. Nats. Akad. Ukr., No. 11, 69–73 (2007); arXiv:0805.0696.
  45. O.O. Liubysh, O.M. Alekseev, S.Yu. Tkachov, and S.M. Perepelytsya, Ukr. J. Phys. 59, 479 (2014). CrossRef
  46. H.R. Drew, R.M. Wing, T. Takano, C. Broka, S. Takana, K. Itakura, and R.E. Dickerson, Proc. Natl. Acad. Sci. USA 78, 2179 (1981). CrossRef
  47. J.C. Phillips et al. J. Comp. Chem. 26, 1781 (2005). CrossRef
  48. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus, J. Comp. Chem. 4(2), 187 (1983). CrossRef
  49. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen, J. Comp. Phys. 32, 327 (1977). CrossRef
  50. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993). CrossRef
  51. W. Humphrey, A Dalke, and K. Schulten, J. Molec. Graphics 14(1), 33 (1996). CrossRef
  52. R. Lavery, M. Moakher, J.H. Maddocks, D. Petkeviciute, and K. Zakrzewska, Nucleic Acids Res. 37, 5917 (2009). CrossRef
  53. V.I. Ivanov, L.E. Minchenkova, A.K. Schyolkina, and A.I. Poletayev, Biopolymers 12, 89 (1973). CrossRef
  54. N.A. Izmailov, Electrochemistry of Solutions (Khimiya, Moscow, 1976) (in Russian).
  55. P. Auffiner, T.E. Cheatham III, and A.C. Vaiana. J. Chem. Theor. Comput., 3, 1851 (2007). CrossRef