Conformational fluctuations of a DNA electrophoretically translocating through a nanopore under the action of a motor protein

  • Harshwardhan H. Katkar
  • Murugappan MuthukumarEmail author
Regular Article
Part of the following topical collections:
  1. Polymers: From Adsorption to Translocation - Topical Issue in Memoriam Loïc Auvray (1956-2016)


Single-file single-molecule electrophoresis through a nanopore has emerged as one of the successful methods in DNA sequencing. In gaining sufficient accuracy in the readout of the sequence, it is essential to position every nucleotide of the sequence with great accuracy and precision at the interrogation point of the nanopore. A combination of a ratcheting enzyme and a threaded DNA across a protein pore under an electric field is experimentally shown to be a viable method for DNA sequencing within the single-molecule electrophoresis technique. Using coarse-grained models of the enzyme and the protein nanopore, and Langevin dynamics simulations, we have characterized the conformational fluctuations of the DNA inside the nanopore. We show that the conformational fluctuations of DNA are significant for slowly operating enzymes such as phi29 DNA polymerase. Our results imply that there is considerable uncertainty in precisely positioning a nucleotide at the interrogation point of the nanopore. The discrepancy between the results of coarse-grained simulations and the experimentally successful accurate sequencing suggests that additional features of the experiments, such as explicit treatment of electrolyte ions and hydrodynamics, must be incorporated in the simulations to accurately model experimental constructs.

Graphical abstract


Polymers: From Adsorption to Translocation - Topical Issue in Memoriam Loïc Auvray (1956-2016) 


  1. 1.
    X. Chen, I. Rungger, C.D. Pemmaraju, U. Schwingenschloegl, S. Sanvito, Phys. Rev. B 85, 115436 (2012)ADSCrossRefGoogle Scholar
  2. 2.
    D. Stoddart, A.J. Heron, E. Mikhailova, G. Maglia, H. Bayley, Proc. Natl. Acad. Sci. U.S.A. 106, 7702 (2009)ADSCrossRefGoogle Scholar
  3. 3.
    R.F. Purnell, K.K. Mehta, J.J. Schmidt, Nano Lett. 8, 3029 (2008)ADSCrossRefGoogle Scholar
  4. 4.
    J. Kasianowicz, E. Brandin, D. Branton, D. Deamer, Proc. Natl. Acad. Sci. U.S.A. 93, 13770 (1996)ADSCrossRefGoogle Scholar
  5. 5.
    S. Carson, M. Wanunu, Proc. SPIE 26, 074004 (2015)Google Scholar
  6. 6.
    L. Payet, M. Martinho, C. Merstorf, M. Pastoriza-Gallego, J. Pelta, V. Viasnoff, L. Auvray, M. Muthukumar, J. Mathé, Biophys. J. 109, 1600 (2015)ADSCrossRefGoogle Scholar
  7. 7.
    G. Gibrat, M. Pastoriza-Gallego, B. Thiebot, M.F. Breton, L. Auvray, J. Pelta, J. Phys. Chem. B 112, 14687 (2008)CrossRefGoogle Scholar
  8. 8.
    M. Muthukumar, J. Chem. Phys. 118, 5174 (2003)ADSCrossRefGoogle Scholar
  9. 9.
    K. Luo, T. Ala-Nissila, S.C. Ying, A. Bhattacharya, J. Chem. Phys. 126, 145101 (2007)ADSCrossRefGoogle Scholar
  10. 10.
    B. Luan, G. Stolovitzky, G. Martyna, Nanoscale 4, 1068 (2012)ADSCrossRefGoogle Scholar
  11. 11.
    K. Ding, Q. Yan, N. Wang, F. Wu, Z. Wu, Eur. Phys. J. Appl. Phys. 58, 31201 (2012)ADSCrossRefGoogle Scholar
  12. 12.
    C.J. Rasmussen, A. Vishnyakov, A.V. Neimark, J. Chem. Phys. 137, 144903 (2012)ADSCrossRefGoogle Scholar
  13. 13.
    J.A. Cohen, A. Chaudhuri, R. Golestanian, Phys. Rev. X 2, 021002 (2012)Google Scholar
  14. 14.
    H.H. Katkar, M. Muthukumar, J. Chem. Phys. 140, 135102 (2014)ADSCrossRefGoogle Scholar
  15. 15.
    G. Maglia, M.R. Restrepo, E. Mikhailova, H. Bayley, Proc. Natl. Acad. Sci. U.S.A. 105, 19720 (2008)ADSCrossRefGoogle Scholar
  16. 16.
    I. Jou, M. Muthukumar, Biophys. J. 113, 1664 (2017)ADSCrossRefGoogle Scholar
  17. 17.
    B.N. Anderson, M. Muthukumar, A. Meller, ACS Nano 7, 1408 (2013)CrossRefGoogle Scholar
  18. 18.
    M.G. Gauthier, G.W. Slater, J. Chem. Phys. 128, 175103 (2008)ADSCrossRefGoogle Scholar
  19. 19.
    S. Banerjee, J. Wilson, J. Shim, M. Shankla, E.A. Corbin, A. Aksimentiev, R. Bashir, Adv. Funct. Mater. 25, 936 (2014)CrossRefGoogle Scholar
  20. 20.
    M. Wanunu, J. Sutin, B. McNally, A. Chow, A. Meller, Biophys. J. 95, 4716 (2008)ADSCrossRefGoogle Scholar
  21. 21.
    D.K. Lubensky, D.R. Nelson, Biophys. J. 77, 1824 (1999)ADSCrossRefGoogle Scholar
  22. 22.
    G. Oukhaled, L. Bacri, J. Math, J. Pelta, L. Auvray, EPL 82, 48003 (2008)ADSCrossRefGoogle Scholar
  23. 23.
    S.W. Kowalczyk, D.B. Wells, A. Aksimentiev, C. Dekker, Nano Lett. 12, 1038 (2012)ADSCrossRefGoogle Scholar
  24. 24.
    S.W. Kowalczyk, C. Dekker, Nano Lett. 12, 4159 (2012)ADSCrossRefGoogle Scholar
  25. 25.
    M. Wanunu, W. Morrison, Y. Rabin, A.Y. Grosberg, A. Meller, Nat. Nanotechnol. 5, 160 (2010)ADSCrossRefGoogle Scholar
  26. 26.
    B.J. Jeon, M. Muthukumar, J. Chem. Phys. 140, 015101 (2014)ADSCrossRefGoogle Scholar
  27. 27.
    B.J. Jeon, M. Muthukumar, Macromolecules 49, 9132 (2016)ADSCrossRefGoogle Scholar
  28. 28.
    J. Ivica, P.T.F. Williamson, M.R.R. de Planque, Anal. Chem. 89, 8822 (2017)CrossRefGoogle Scholar
  29. 29.
    I.C. Nova, I.M. Derrington, J.M. Craig, M.T. Noakes, B.I. Tickman, K. Doering, H. Higinbotham, A.H. Laszlo, J.H. Gundlach, PLOS ONE 12, e0181599 (2017)CrossRefGoogle Scholar
  30. 30.
    J. Sha, H. Shi, Y. Zhang, C. Chen, L. Liu, Y. Chen, ACS Sens. 2, 506 (2017)CrossRefGoogle Scholar
  31. 31.
    C.T.A. Wong, M. Muthukumar, J. Chem. Phys. 133, 045101 (2010)ADSCrossRefGoogle Scholar
  32. 32.
    A. Meller, L. Nivon, E. Brandin, J. Golovchenko, D. Branton, Proc. Natl. Acad. Sci. U.S.A. 97, 1079 (2000)ADSCrossRefGoogle Scholar
  33. 33.
    D. Fologea, J. Uplinger, B. Thomas, D.S. McNabb, J. Li, Nano Lett. 5, 1734 (2005)ADSCrossRefGoogle Scholar
  34. 34.
    H.W. de Haan, G.W. Slater, J. Chem. Phys. 136, 204902 (2012)ADSCrossRefGoogle Scholar
  35. 35.
    L. Brun, M. Pastoriza-Gallego, G. Oukhaled, J. Math, L. Bacri, L. Auvray, J. Pelta, Phys. Rev. Lett. 100, 158302 (2008)ADSCrossRefGoogle Scholar
  36. 36.
    R.J. Murphy, M. Muthukumar, J. Chem. Phys. 126, 051101 (2007)ADSCrossRefGoogle Scholar
  37. 37.
    A. Meller, L. Nivon, D. Branton, Phys. Rev. Lett. 86, 3435 (2001)ADSCrossRefGoogle Scholar
  38. 38.
    T. Auger, J. Mathé, V. Viasnoff, G. Charron, J.M. Di Meglio, L. Auvray, F. Montel, Phys. Rev. Lett. 113, 028302 (2014)ADSCrossRefGoogle Scholar
  39. 39.
    B. Lu, D.P. Hoogerheide, Q. Zhao, D. Yu, Phys. Rev. E 86, 011921 (2012)ADSCrossRefGoogle Scholar
  40. 40.
    C.T.A. Wong, M. Muthukumar, J. Chem. Phys. 126, 164903 (2007)ADSCrossRefGoogle Scholar
  41. 41.
    P. Rowghanian, A.Y. Grosberg, Phys. Rev. E 87, 042723 (2013)ADSCrossRefGoogle Scholar
  42. 42.
    M.M. Hatlo, D. Panja, R. van Roij, Phys. Rev. Lett. 107, 068101 (2011)ADSCrossRefGoogle Scholar
  43. 43.
    J.W.F. Robertson, C.G. Rodrigues, V.M. Stanford, K.A. Rubinson, O.V. Krasilnikov, J.J. Kasianowicz, Proc. Natl. Acad. Sci. U.S.A. 104, 8207 (2007)ADSCrossRefGoogle Scholar
  44. 44.
    J.E. Reiner, J.J. Kasianowicz, B.J. Nablo, J.W.F. Robertson, Proc. Natl. Acad. Sci. U.S.A. 107, 12080 (2010)ADSCrossRefGoogle Scholar
  45. 45.
    S. Kumar, C. Tao, M. Chien, B. Hellner, A. Balijepalli, J.W.F. Robertson, Z. Li, J.J. Russo, J.E. Reiner, J.J. Kasianowicz et al., Sci. Rep. 2, 684 (2012)ADSCrossRefGoogle Scholar
  46. 46.
    C.W. Fuller, S. Kumar, M. Porel, M. Chien, A. Bibillo, P.B. Stranges, M. Dorwart, C. Tao, Z. Li, W. Guo et al., Proc. Natl. Acad. Sci. U.S.A. 113, 5233 (2016)ADSCrossRefGoogle Scholar
  47. 47.
    A.J. Berman, S. Kamtekar, J.L. Goodman, J.M. Lázaro, M. de Vega, L. Blanco, M. Salas, T.A. Steitz, EMBO J. 26, 3494 (2007)CrossRefGoogle Scholar
  48. 48.
    B. Ibarra, Y.R. Chemla, S. Plyasunov, S.B. Smith, J.M. Lázaro, M. Salas, C. Bustamante, EMBO J. 28, 2794 (2009)CrossRefGoogle Scholar
  49. 49.
    G.M. Cherf, K.R. Lieberman, H. Rashid, C.E. Lam, K. Karplus, M. Akeson, Nat. Biotechnol. 30, 344 (2012)CrossRefGoogle Scholar
  50. 50.
    E.A. Manrao, I.M. Derrington, A.H. Laszlo, K.W. Langford, M.K. Hopper, N. Gillgren, M. Pavlenok, M. Niederweis, J.H. Gundlach, Nat. Biotechnol. 30, 349 (2012)CrossRefGoogle Scholar
  51. 51.
    K.R. Lieberman, G.M. Cherf, M.J. Doody, F. Olasagasti, Y. Kolodji, M. Akeson, J. Am. Chem. Soc. 132, 17961 (2010)CrossRefGoogle Scholar
  52. 52.
    K.R. Lieberman, J.M. Dahl, A.H. Mai, M. Akeson, H. Wang, J. Am. Chem. Soc. 134, 18816 (2012)CrossRefGoogle Scholar
  53. 53.
    J.M. Dahl, A.H. Mai, G.M. Cherf, N.N. Jetha, D.R. Garalde, A. Marziali, M. Akeson, H. Wang, K.R. Lieberman, J. Biol. Chem. 287, 13407 (2012)CrossRefGoogle Scholar
  54. 54.
    K.R. Lieberman, J.M. Dahl, A.H. Mai, A. Cox, M. Akeson, H. Wang, J. Am. Chem. Soc. 135, 9149 (2013)CrossRefGoogle Scholar
  55. 55.
    B.S. Glick, Cell 80, 11 (1995)CrossRefGoogle Scholar
  56. 56.
    T.C. Elston, Biophys. J. 82, 1239 (2002)ADSCrossRefGoogle Scholar
  57. 57.
    M. Faller, M. Niederweis, G.E. Schulz, Science 303, 1189 (2004)ADSCrossRefGoogle Scholar
  58. 58.
    M. Muthukumar, C.Y. Kong, Proc. Natl. Acad. Sci. U.S.A. 103, 5273 (2006)ADSCrossRefGoogle Scholar
  59. 59.
    E.L. Cussler, Diffusion: Mass Transfer in Fluid Systems (Cambridge University Press, 2000)Google Scholar
  60. 60.
    M. Muthukumar, Polymer Translocation (Boca Raton: Taylor & Francis, 2011)Google Scholar
  61. 61.
    S. Plimpton, J. Comput. Phys. 117, 1 (1995) ADSCrossRefGoogle Scholar
  62. 62.
    A.H. Laszlo, I.M. Derrrington, J.H. Gundlach, Methods Enzymol. 582, 387 (2017)CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Harshwardhan H. Katkar
    • 1
    • 2
  • Murugappan Muthukumar
    • 2
    Email author
  1. 1.Department of ChemistryThe University of ChicagoChicagoUSA
  2. 2.Department of Polymer Science and EngineeringUniversity of MassachusettsAmherstUSA

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