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Experimental study of the effect of disorder on DNA dynamics in post arrays during electrophoresis

Daniel W. Olson and Kevin D. Dorfman*

  • Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA

  • *dorfman@umn.edu
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Phys. Rev. E 86, 041909 – Published 12 October, 2012

DOI: https://doi.org/10.1103/PhysRevE.86.041909

Abstract

We used top-down fabrication techniques to create both an ordered hexagonal array and a disordered array of 1 μm diameter cylindrical posts in a silicon dioxide microchannel with the same number of posts per unit area. The electrophoretic mobility and dispersion coefficient of λ DNA in each of the arrays were obtained as a function of the electric field using ensembles of DNA molecules in a double channel device that minimizes experimental artifacts. To deepen our understanding of the transport, we also used fluorescence microscopy to examine the dynamics of single DNA molecules as they interact with the arrays at a fixed value of the electric field. Based on the results of these two types of experiments, we conclude that the electrophoretic mobility is not dependent on the array order but that band broadening in the device is greater in the disordered array.

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References (44)

  1. N. Kaji, Y. Tezuka, Y. Takamura, M. Ueda, T. Nishimoto, H. Nakanishi, Y. Horiike, and Y. Baba, Anal. Chem. 76, 15 (2004).
  2. Y. C. Chan, Y. K. Lee, and Y. Zohar, J. Micromech. Microeng. 16, 699 (2006).
  3. J. Shi, A. P. Fang, L. Malaquin, A. Pepin, D. Decanini, J. L. Viovy, and Y. Chen, Appl. Phys. Lett. 91, 153114 (2007).
  4. R. Ogawa, N. Kaji, S. Hashioka, Y. Baba, and Y. Horiike, Jpn. J. Appl. Phys. 46, 2771 (2007).
  5. J. Ou, S. J. Carpenter, and K. D. Dorfman, Biomicrofluidics 4, 013203 (2010).
  6. J. Ou, M. N. Joswiak, S. J. Carpenter, and K. D. Dorfman, J. Vac. Sci. Technol. A 29, 011025 (2011).
  7. P. S. Doyle, J. Bibette, A. Bancaud, and J. L. Viovy, Science 295, 2237 (2002).
  8. N. Minc, C. Futterer, K. D. Dorfman, A. Bancaud, C. Gosse, C. Goubault, and J. L. Viovy, Anal. Chem. 76, 3770 (2004).
  9. C. Heller, T. Duke, and J. L. Viovy, Biopolymers 34, 249 (1994).
  10. W. D. Volkmuth and R. H. Austin, Nature (London) 358, 600 (1992).
  11. N. P. Teclemariam, V. A. Beck, E. S. G. Shaqfeh, and S. J. Muller, Macromolecules 40, 3848 (2007).
  12. G. I. Nixon and G. W. Slater, Phys. Rev. E 50, 5033 (1994).
  13. N. Minc, P. Bokov, K. B. Zeldovich, C. Futterer, J.-L. Viovy, and K. D. Dorfman, Electrophoresis 26, 362 (2005).
  14. G. C. Randall, and P. S. Doyle, Macromolecules 39, 7734 (2006).
  15. P. D. Patel and E. S. G. Shaqfeh, J. Chem. Phys. 118, 2941 (2003).
  16. A. Mohan and P. S. Doyle, Phys. Rev. E 76, 040903(R) (2007).
  17. J. Ou, J. Cho, D. W. Olson, and K. D. Dorfman, Phys. Rev. E 79, 061904 (2009).
  18. D. W. Olson, J. Ou, M. Tian, and K. D. Dorfman, Electrophoresis 32, 573 (2011).
  19. D. W. Olson, S. Dutta, N. Laachi, M. Tian, and K. D. Dorfman, Electrophoresis 32, 581 (2011).
  20. S. G. Park, D. W. Olson, and K. D. Dorfman, Lab Chip 12, 1463 (2012).
  21. A. Larsson, C. Carlsson, M. Jonsson, and B. Albinsson, J. Am. Chem. Soc. 116, 8459 (1994).
  22. M. N. Joswiak, J. Ou, and K. D. Dorfman, Electrophoresis 33, 1013 (2012).
  23. O. A. Hickey, J. L. Harden, and G. W. Slater, Phys. Rev. Lett. 102, 108304 (2009).
  24. R. S. Madabhushi, Electrophoresis 19, 224 (1998).
  25. G. C. Randall and P. S. Doyle, Phys. Rev. Lett. 93, 058102 (2004).
  26. G. C. Randall and P. S. Doyle, Macromolecules 38, 2410 (2005).
  27. A. E. Nkodo, J. M. Garnier, B. Tinland, H. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, Electrophoresis 22, 2424 (2001).
  28. J. Mathé, J.-M. Di Meglio, and B. Tinland, J. Colloid Interf. Sci. 316, 831 (2007).
  29. N. C. Stellwagen, C. Gelfi, and P. G. Righetti, Biopolymers 42, 687 (1997).
  30. R. T. Kovacic, L. Comal, and A. J. Bendich, Nucleic Acids Res. 23, 3999 (1995).
  31. S. Gurrieri, K. S. Wells, I. D. Johnson, and C. Bustamante, Anal. Biochem. 249, 44 (1997).
  32. B. Akerman, and E. Tuite, Nucleic Acids Res. 24, 1080 (1996).
  33. E. Stellwagen and N. C. Stellwagen, Electrophoresis 23, 2794 (2002).
  34. D. E. Smith, T. T. Perkins, and S. Chu, Macromolecules 29, 1372 (1996).
  35. W. D. Volkmuth, T. Duke, M. C. Wu, R. H. Austin, and A. Szabo, Phys. Rev. Lett. 72, 2117 (1994).
  36. N. Minc, J.-L. Viovy, and K. D. Dorfman, Phys. Rev. Lett. 94, 198105 (2005).
  37. A. Mohan and P. S. Doyle, Macromolecules 40, 8794 (2007).
  38. K. D. Dorfman and J.-L. Viovy, Phys. Rev. E 69, 011901 (2004).
  39. J. Cho and K. D. Dorfman, J. Chromatogr. A 1217, 5522 (2010).
  40. J. Billen, P. Gzil, N. Vervoort, G. V. Baron, and G. Desmet, J. Chromatogr. A 1073, 53 (2005).
  41. M. De Pra, W. Th. Kok, J. G. E. Gardeniers, G. Desmet, S. Eeltink, J. W. van Nieuwasteele, and P. J. Schoenmakers, Anal. Chem. 78, 6519 (2006).
  42. Y. Zeng and D. J. Harrison, Anal. Chem. 79, 2289 (2007).
  43. N. Nazemifard, L. Wang, W. Ye, S. Bhattacharjee, J. H. Masliyah, and D. J. Harrison, Lab Chip 12, 146 (2012).
  44. D. S. Malkin, B. Wei, A. J. Fogiel, S. L. Staats, and M. J. Wirth, Anal. Chem. 82, 2175 (2010).

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Information

Phys. Rev. E 86, 041909– Published 12 October, 2012
  • Received 26 April 2012
Article part of CHORUS

©2012 American Physical Society

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