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Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study

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A Publisher's Erratum to this article was published on 01 January 2021

Abstract.

The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K+ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32mV/Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05-0.4)mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K+ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30mV/Å the double helix undergoes a phase transition from a double-stranded to a single-strand state.

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References

  1. G.S. Manning, Q. Rev. Biophys. 11, 179 (1978)

    Article  Google Scholar 

  2. M.D. Frank-Kamenetskii, V.V. Anshelevich, A.V. Lukashin, Sov. Phys. Usp. 30, 317 (1987)

    Article  ADS  Google Scholar 

  3. S. W, Principles of Nucleic Acid Structure (Springer-Verlag, 1984)

  4. C.K. Materese, A. Savelyev, G.A. Papoian, J. Am. Chem. Soc. 131, 15005 (2009)

    Article  Google Scholar 

  5. N. Korolev, A. Allahverdi, A.P. Lyubartsev, L. Nordenskiöld, Soft Matter 8, 9322 (2012)

    Article  ADS  Google Scholar 

  6. R.M. Fuoss, A. Katchalsky, S. Lifson, Proc. Natl. Acad. Sci. U.S.A. 37, 579 (1951)

    Article  ADS  Google Scholar 

  7. A. Deshkovski, S. Obukhov, M. Rubinstein, Phys. Rev. Lett. 86, 2341 (2001)

    Article  ADS  Google Scholar 

  8. R. Das, T.T. Mills, L.W. Kwok, G.S. Maskel, I.S. Millett, S. Doniach, K.D. Finkelstein, D. Herschlag, L. Pollack, Phys. Rev. Lett. 90, 188103 (2003)

    Article  ADS  Google Scholar 

  9. K. Andresen, R. Das, H.Y. Park, H. Smith, L.W. Kwok, J.S. Lamb, E.J. Kirkland, D. Herschlag, K.D. Finkelstein, L. Pollack, Phys. Rev. Lett. 93, 248103 (2004)

    Article  ADS  Google Scholar 

  10. X. Qiu, K. Andresen, J.S. Lamb, L.W. Kwok, L. Pollack, Phys. Rev. Lett. 101, 228101 (2008)

    Article  ADS  Google Scholar 

  11. G. Corongiu, E. Clementi, Biopolymers 20, 2427 (1981)

    Article  Google Scholar 

  12. U.C. Singh, S.J. Weiner, P. Kollman, Proc. Natl. Acad. Sci. U.S.A. 82, 755 (1985)

    Article  ADS  Google Scholar 

  13. G.L. Seibel, U.C. Singh, P.A. Kollman, Proc. Natl. Acad. Sci. U.S.A. 82, 6537 (1985)

    Article  ADS  Google Scholar 

  14. E. Clementi, G. Corongiu, J. Detrich, H. Kahnmohammadbaigi, S. Chin, L. Domingo, A. Laaksonen, N. Nguyen, Physica B+C 131, 74 (1985)

    Article  ADS  Google Scholar 

  15. W.F. Gunsteren, H.J.C. Berendsen, R.G. Geurtsen, H.R.J. Zwinderman, Ann. N. Y. Acad. Sci. 482, 287 (1986)

    Article  ADS  Google Scholar 

  16. M. Nilges, G.M. Clore, A.M. Gronenborn, A.T. Brunger, M. Karplus, L. Nilsson, Biochemistry 26, 3718 (1987)

    Article  Google Scholar 

  17. A. Laaksonen, L.G. Nilsson, B. Jönsson, O. Teleman, Chem. Phys. 129, 175 (1989)

    Article  Google Scholar 

  18. T.E.I. Cheatham, J.L. Miller, T. Fox, T.A. Darden, P.A. Kollman, J. Am. Chem. Soc. 117, 4193 (1995)

    Article  Google Scholar 

  19. F. Mocci, A. Laaksonen, Soft Matter 8, 9268 (2012)

    Article  ADS  Google Scholar 

  20. C. Maffeo, J. Yoo, J. Comer, D.B. Wells, B. Luan, A. Aksimentiev, J. Phys.: Condens. Matter 26, 413101 (2014)

    Google Scholar 

  21. M.A. Young, B. Jayaram, D.L. Beveridge, J. Am. Chem. Soc. 119, 59 (1997)

    Article  Google Scholar 

  22. A.D. MacKerell, J. Phys. Chem. B 101, 646 (1997)

    Article  Google Scholar 

  23. A.P. Lyubartsev, A. Laaksonen, J. Biomol. Struct. Dyn. 16, 579 (1998)

    Article  Google Scholar 

  24. K.J. McConnell, D. Beveridge, J. Mol. Biol. 304, 803 (2000)

    Article  Google Scholar 

  25. V. Bartenev, E. Golovamov, K. Kapitonova, M. Mokulskii, L. Volkova, I. Skuratovskii, J. Mol. Biol. 169, 217 (1983)

    Article  Google Scholar 

  26. P. Varnai, Nucl. Acids Res. 32, 4269 (2004)

    Article  Google Scholar 

  27. S.Y. Ponomarev, K.M. Thayer, D.L. Beveridge, Proc. Natl. Acad. Sci. U.S.A. 101, 14771 (2004)

    Article  ADS  Google Scholar 

  28. M. Rueda, E. Cubero, C.A. Laughton, M. Orozco, Biophys. J. 87, 800 (2004)

    Article  Google Scholar 

  29. F. Mocci, G. Saba, Biopolymers 68, 471 (2003)

    Article  Google Scholar 

  30. J. Yoo, A. Aksimentiev, J. Phys. Chem. Lett. 3, 45 (2012)

    Article  Google Scholar 

  31. R. Lavery, J.H. Maddocks, M. Pasi, K. Zakrzewska, Nucl. Acids Res. 42, 8138 (2014)

    Article  Google Scholar 

  32. M. Pasi, J.H. Maddocks, R. Lavery, Nucl. Acids Res. 43, 2412 (2015)

    Article  Google Scholar 

  33. P.D. Dans, L. Danilāne, I. Ivani, T. Dršata, F. Lankaš, A. Hospital, J. Walther, R.I. Pujagut, F. Battistini, J.L. Gelpí, R. Lavery, M. Orozco, Nucl. Acids Res. 44, 4052 (2016)

    Article  Google Scholar 

  34. A. Atzori, S. Liggi, A. Laaksonen, M. Porcu, A.P. Lyubartsev, G. Saba, F. Mocci, Canad. J. Chem. 94, 1181 (2016)

    Article  Google Scholar 

  35. H. Grassi, M.A. Rix-Montel, H. Kranck, D. Vasilescu, Biopolymers 14, 2525 (1975)

    Article  Google Scholar 

  36. H. Kranck, C. Hesse-Bezot, M.A. Rix-Montel, H. Grassi, D. Vasilescu, Biopolymers 15, 599 (1976)

    Article  Google Scholar 

  37. I.A. Kuznetsov, N.V. Apolonnik, Biopolymers 20, 2083 (1981)

    Article  Google Scholar 

  38. S.I.S. Kuznetsov I. A., Apolonnik N. V., Biopolym. Cell 3, 72 (1987)

    Article  Google Scholar 

  39. T. Vuletić, S.D. Babić, D. Grgičin, D. Aumiler, J. Rädler, F. Livolant, S. Tomić, Phys. Rev. E 83, 041803 (2011)

    Article  ADS  Google Scholar 

  40. O. Liubysh, O. Alekseev, S.Y. Tkachov, S. Perepelytsya, Ukr. J. Phys. 59, 479 (2014)

    Article  Google Scholar 

  41. N.A. Ismailov, Electro Chemistry of Solutions (Chemistry, 1976)

  42. S.M. Perepelytsya, S.N. Volkov, Eur. Phys. J. E 24, 261 (2007)

    Article  Google Scholar 

  43. S.M. Perepelytsya, S.N. Volkov, Eur. Phys. J. E 31, 201 (2010)

    Article  Google Scholar 

  44. S.W. Kowalczyk, D.B. Wells, A. Aksimentiev, C. Dekker, Nano Lett. 12, 1038 (2012)

    Article  ADS  Google Scholar 

  45. J. Comer, A. Aksimentiev, J. Phys. Chem. C 116, 3376 (2012)

    Article  Google Scholar 

  46. M. Belkin, A. Aksimentiev, ACS Appl. Mater. Interfaces 8, 12599 (2016)

    Article  Google Scholar 

  47. Y.s. Yu, X. Lu, H.m. Ding, Y.q. Ma, Phys. Chem. Chem. Phys. 20, 9063 (2018)

    Article  Google Scholar 

  48. R.M. Zadegan, M.L. Norton, Int. J. Mol. Sci. 13, 7149 (2012)

    Article  Google Scholar 

  49. C.Y. Li, E.A. Hemmig, J. Kong, J. Yoo, S. Hernández-Ainsa, U.F. Keyser, A. Aksimentiev, ACS Nano 9, 1420 (2015)

    Article  Google Scholar 

  50. H.R. Drew, R.M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R.E. Dickerson, Proc. Natl. Acad. Sci. U.S.A. 78, 2179 (1981)

    Article  ADS  Google Scholar 

  51. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem. 26, 1781 (2005)

    Article  Google Scholar 

  52. A.D. MacKerell, N.K. Banavali, J. Comput. Chem. 21, 105 (2000)

    Article  Google Scholar 

  53. N. Foloppe, A.D. MacKerell jr., J. Comput. Chem. 21, 86 (2000)

    Article  Google Scholar 

  54. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 14, 33 (1996)

    Article  Google Scholar 

  55. X.J. Lu, W.K. Olson, Nucl. Acids Res. 31, 5108 (2003)

    Article  Google Scholar 

  56. R. Kumar, H. Grubmüller, Bioinformatics 31, 2583 (2015)

    Article  Google Scholar 

  57. J.P. Ryckaert, G. Ciccotti, H.J. Berendsen, J. Comput. Phys. 23, 327 (1977)

    Article  ADS  Google Scholar 

  58. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, J. Chem. Phys. 79, 926 (1983)

    Article  ADS  Google Scholar 

  59. D. Beglov, B. Roux, J. Chem. Phys. 100, 9050 (1994)

    Article  ADS  Google Scholar 

  60. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 98, 10089 (1993)

    Article  ADS  Google Scholar 

  61. S. Perepelytsya, Ukr. J. Phys. 65, 500 (2020)

    Article  Google Scholar 

  62. Y. Wu, W. Koch, K. Pratt, J. Res. Natl. Inst. Stand. Technol. 96, 191 (1991)

    Article  Google Scholar 

  63. M.R. Singleton, M.S. Dillingham, D.B. Wigley, Annu. Rev. Biochem. 76, 23 (2007)

    Article  Google Scholar 

  64. A. Vologodskii, M.D. Frank-Kamenetskii, Phys. Life Rev. 25, 1 (2018)

    Article  ADS  Google Scholar 

  65. U. Bockelmann, P. Thomen, F. Heslot, Biophys. J. 87, 3388 (2004)

    Article  ADS  Google Scholar 

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Zdorevskyi, O.O., Perepelytsya, S.M. Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study. Eur. Phys. J. E 43, 77 (2020). https://doi.org/10.1140/epje/i2020-12000-0

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