Journal of Mechanical Science and Technology

, Volume 33, Issue 11, pp 5311–5319 | Cite as

Effect of non-uniform fields on DNA entering nano-channel

  • Minsub HanEmail author
  • Byoung Choul Kim


The translocation of deoxyribonucleic-acid (DNA) segments into a nanoscale channel from a bulk solution has significance to genome-related fields such as gene sequencing and genetic profiling. However, its dynamic characteristics are poorly understood because of complexities involving the size and character of the confining spaces, polymeric evolution, and driving sources. The DNA translocation was studied by mesoscale simulation using a worm-like-chain model of DNA and the dissipative particle dynamics method. Three driving sources — electric field, suction flow, and constant body force were individually applied to a λ-DNA entering a nanoscale cylindrical channel. Each source altered the translocation actions, mainly due to marked differences in conformational transformation processes. The suction flow uniquely induced strong extension of the DNA chain before channel entry. Consequently, the flow was more effective at overcoming the free-energy barrier with narrower confinements. Other driving sources permitted the DNA chain to enter in a more globular form, which was effective for larger entrances. Combining different sources is the most versatile means of controlling the trans-location of genetic materials in highly confined spaces.


Crack Gene sequencing Molecular dynamics simulation Nanochannel 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



This work was supported by the Incheon National University Research Grant in 2015.


  1. [1]
    G. Church, The race for the 1000 genome, Science, 311 (2006) 1544–1546.Google Scholar
  2. [2]
    J. A. Schloss, How to get genomes at one ten-thousandth the cost, Nature Biotechnology, 26 (2008) 1113.Google Scholar
  3. [3]
    K. D. Dorfman, S. B. King, D. W. Olson, J. D. Thomas and D. R. Tree, Beyond gel electrophoresis: Microfluidi. separations, fluorescence burs. analysis, and DNA stretching, Chemical Reviews, 113 (2012) 2584–2667.Google Scholar
  4. [4]
    X. Hu, P. E. Boukany, O. L. Hemminger and L. J. Lee, The use of microfluidics in rheology, Macromolecular Materials and Engineering, 296 (2011) 308–320.Google Scholar
  5. [5]
    D. J. Mai, C. Brockman and C. M. Schroeder, Microfluidic systems for single DNA dynamics, Soft Matter, 8 (2012) 10560–10572.Google Scholar
  6. [6]
    W. Reisner, J. N. Pedersen and R. H. Austin, DNA confinement in nanochannels: Physics and biological applications, Reports on Progress in Physics, 75 (2012) 106601.Google Scholar
  7. [7]
    S. B. Smith, Y. Cui and C. Bustamante, Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules, Science, 271 (1996) 795–799.Google Scholar
  8. [8]
    E. T. Lam et al., Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly, Nature Biotechnology, 30 (2012) 771.Google Scholar
  9. [9]
    T. Ohshiro, K. Matsubara, M. Tsutsui, M. Furuhashi, M. Taniguchi and T. Kawai, Single-molecule electrical random resequencing of DNA and RNA, Scientific Reports, 2 (2012) 501.Google Scholar
  10. [10]
    Y. Wang, D. R. Tree and K. D. Dorfman, Simulation of DNA extension in nanochannels, Macromolecules, 44 (2011) 6594–6604.Google Scholar
  11. [11]
    T. Matsuoka, B. C. Kim, J. Huang, N. J. Douville, M. Thouless and S. Takayama, Nanoscale squeezing in elastomeric nanochannels for single chromatin linearization, Nano Letters, 12 (2012) 6480–6484.Google Scholar
  12. [12]
    P. Espanol and P. Warren, Statistical mechanics of dissipative particle dynamics, EPL (Europhysics Letters), 30 (1995) 191.Google Scholar
  13. [13]
    R. D. Groot and P. B. Warren, Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation, The Journal of Chemical Physics, 107 (1997) 4423–4435.Google Scholar
  14. [14]
    M. Han, B. C. Kim, T. Matsuoka, M. Thouless and S. Takayama, Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels, Biomicrofluidics, 10 (2016) 064108.Google Scholar
  15. [15]
    A. Malevanets and R. Kapral, Mesoscopic model for solvent dynamics, The Journal of Chemical Physics, 110 (1999) 8605–8613.Google Scholar
  16. [16]
    S. Chen and G. D. Doolen, Lattice Boltzmann method for fluid flows, Annual Review of Fluid Mechanics, 30 (1998) 329–364.MathSciNetzbMATHGoogle Scholar
  17. [17]
    Z. Li, J. Kang, J. H. Park and Y. K. Suh, Numerical simulation of the droplet formation in a crossjunction microchannel using the lattice Boltzmann method, Journal of Mechanical Science and Technology, 21 (2007) 162–173.Google Scholar
  18. [18]
    J. Han and H. G. Craighead, Separation of long DNA molecules in a microfabricated entropic trap array, Science, 288 (2000) 1026–1029.Google Scholar
  19. [19]
    J. Han, S. Turner and H. G. Craighead, Entropic trapping and escape of long DNA molecules at submicron size constriction, Physical Review Letters, 83 (1999) 1688.Google Scholar
  20. [20]
    D. Duong-Hong, J. Han, J. S. Wang, N. G. Hadjiconstantinou, Y. Z. Chen and G. R. Liu, Realistic simulations of xombined DNA electrophoretic flow and EOF in nanofluidic devices, Electrophoresis, 29 (2008) 4880–4886.Google Scholar
  21. [21]
    E. Moeendarbary, T. Ng, H. Pan and K. Lam, Migration of DNA molecules through entropic trap arrays: A dissipative particle dynamics study, Microfluidics and Nanofluidics, 8 (2010) 243–254.Google Scholar
  22. [22]
    J. Zhou, Y. Wang, L. D. Menard, S. Panyukov, M. Rubinstein and J. M. Ramsey, Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels, Nature Communications, 8 (2017) 807.Google Scholar
  23. [23]
    D. Huh, K. Mills, X. Zhu, M. A. Burns, M. Thouless and S. Takayama, Tuneable elastomeric nanochannels for nanofluidic manipulation, Nature Materials, 6 (2007) 424.Google Scholar
  24. [24]
    A. R. Abate and D. A. Weitz, Syringevacuum microfluidics: A portable technique to create monodisperse emulsions, Biomicrofluidics, 5 (2011) 014107.Google Scholar
  25. [25]
    B. C. Kim, P. Weerappuli, M. Thouless and S. Takayama, Fracture fabrication of a multi-scale channel device that efficiently captures and linearizes DNA from dilute solutions, Lab on a Chip, 15 (2015) 1329–1334.Google Scholar
  26. [26]
    B. C. Kim, C. Moraes, J. Huang, T. Matsuoka, M. Thouless and S. Takayama, Fracture-based fabrication of normall. closed, adjustable, and fully reversible microscale fluidic channels, Small, 10 (2014) 4020–4029.Google Scholar
  27. [27]
    P. J. Flory, Principles of Polymer Chemistry, Cornell University Press (1953).Google Scholar
  28. [28]
    D. Schaefer, J. Joanny and P. Pincus, Dynamics of semiflexible polymers in solution, Macromolecules, 13 (1980) 1280–1289.Google Scholar
  29. [29]
    P.-G. De Gennes and P.-G. Gennes, Scaling Concepts in Polymer Physics, Cornell University Press (1979).zbMATHGoogle Scholar
  30. [30]
    S. Jun, D. Thirumalai and B.-Y. Ha, Compression and stretching of a self-avoiding chain in cylindrical nanopores, Physical Review Letters, 101 (2008) 138101.Google Scholar
  31. [31]
    T. Odijk, Scaling theory of DNA confined in nanochannels and nanoslits, Physical Review E, 77 (2008) 060901.Google Scholar
  32. [32]
    A. V. Dobrynin and M. Rubinstein, Theory of polyelectrolytes in solutions and at surfaces, Progress in Polymer Science, 30 (2005) 1049–1118.Google Scholar
  33. [33]
    R. Probestein, Physicochemical Hydrodynamics, John Wiley & Sons (2003).Google Scholar
  34. [34]
    D. Long, J.-L. Viovy and A. Ajdari, Simultaneous action of electric fields and nonelectric forces on a polyelectrolyte: Motion and deformation, Physical Review Letters, 76 (1996) 3858.Google Scholar
  35. [34a]
    O. A. Hickey, C. Holm and J. Smiatek, Lattice-Boltzmann simulations of the electrophoretic stretching of polyelectrolytes: The importance of hydrodynamic interactions, The Journal of Chemical Physics, 140 (2014) 164904.Google Scholar
  36. [35a]
    P. T. Underhill and P. S. Doyle, On the coarsegraining of polymers into bead-spring chains, Journal of Nonnewtonian Fluid Mechanics, 122 (2004) 3–31.zbMATHGoogle Scholar
  37. [36]
    W. Jiang, J. Huang, Y. Wang and M. Laradji, Hydrodynamic interaction in polymer solutions simulated with dissipative particle dynamics, The Journal of Chemical Physics, 126 (2007) 044901.Google Scholar
  38. [37]
    X. Fan, N. Phan-Thien, S. Chen, X. Wu and T. Yon. Ng, Simulating flow of DNA suspension using dissipative particle dynamics, Physics of Fluids, 18 (2006) 063102.zbMATHGoogle Scholar
  39. [38]
    M. Han, Applying boundary condition in dissipative particle dynamics using mirror-image particles, Journal of Mechanical Science and Technology, 30 (2016) 5125–5133.Google Scholar
  40. [39]
    S. Willemsen, H. Hoefsloot and P. Iedema, No-slip boundary condition in dissipative particle dynamics, International Journal of Modern Physics C, 11 (2000) 881–890.Google Scholar
  41. [40]
    A. E. Nkodo et al., Diffusion coefficient of DNA molecules during free solution electrophoresis, Electrophoresis, 22 (2001) 2424–2432.Google Scholar

Copyright information

© KSME & Springer 2019

Authors and Affiliations

  1. 1.Department of Mechanical EngineeringIncheon National UniversityIncheonKorea
  2. 2.Division of Nano-BioengineeringIncheon National UniversityIncheonKorea

Personalised recommendations