Abstract
One of the recent applications of nanopores is to use them as detectors/analyzers for bio-molecules and nanopore based sequencing has been studied to quickly sequence DNA. In this paper, three categories of forces proposed in the literature to oppose the electrical driving forces in the DNA translocation process are analyzed, (1) the entropic forces of DNA uncoiling/recoiling at the pore entrance/exits, (2) the viscous drag acting on the blob like DNA outside the nanopore, and (3) the viscous drag acting on the linear DNA inside the nanopore. The magnitudes of these forces are calculated based on the parameters used in experiments and it is shown that the first two of the aforementioned categories of forces are usually small compared to the electrical driving force, while the last one is of the same order as the electrical driving force. To evaluate the viscous drag force acting on the linear DNA inside the nanopore, a hydrodynamic model based on the lubrication approximation is used to calculate the flow field and the viscous drag force acting on a DNA immobilized in a nanopore. This model is validated by good agreement with the experimental data for the tethering force used to immobilize a DNA inside the nanopore.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
H. Bayley, C.R. Martin, Resistive-pulse sensings from microbes to molecules. Chem. Rev. 100, 2575–2594 (2000)
C. Bustamante, Z. Bryant, S.B. Smith, Ten years of tension: single-molecule dna mechanics. Nature 421, 423–427 (2003)
C. Calladine, H. Drew, in Understanding DNA (Academic Press, 1992)
L. Chen, A.T. Conlisk, Electroosmotic flow and particle transport in micro/nano nozzles and diffusers. Biomedical Microdevices 10, 289–298 (2008)
L. Chen, A.T. Conlisk, Dna nanowire translocation phenomena in nanopores. Biomed. Microdevices 12(2), 235–245 (2010)
J. Dutcher, A.G. Marangoni, Soft Materials: Structural and Dynamics (CRC Press, 2004)
C. Forrey, M. Muthukumara, Langevin dynamics simulations of ds-dna translocation through synthetic nanopores. J. Chem. Phys. 127, 015102 (2007)
M.G. Fyta, S. Melchionna, E. Kaxiras, S. Succi, Multiscale coupling of molecular dynamics and hydrodynamics: application to dna translocation through a nanopore. Multiscale Model. Simul. 5(4), 1156–1173 (2006)
S. Ghosal, Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore. Phys. Rev. Lett. 98, 238104 (2007)
F.H.J. van der Heyden, D. Stein, C. Dekker, Streaming currents in a single nanofluidic channel. Phys. Rev. Lett. 95, 116104 (2005)
Y. Kantor, M. Kardar, Anomalous dynamics of forced translocation. Phys. Rev. E 69, 021806 (2004)
U.F. Keyser, B.N. Koeleman, S.V. Dorp, D. Krapf, R.M.M. Smeets, S.G. Lemay, N.H. Dekker, C. Dekker, Direct forcemeasurements on dna in a solid-state nanopore. Nat. Phys. 2, 473–477 (2006)
L.I. Klushin, A.M. Skvortsov, H.P. Hsu, K. Binder, Dragging a polymer chain into a nanotube and subsequent release. Macromolecules 18(15), 5890–5898 (2008)
J. Li, D. Stein, C. McMullan, D. Branton, M.J. Aziz, J.A. Golovchenko, Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001)
Meller, Voltage-driven dna translocations through a nanopore. Phys. Rev. Lett. 86(15), 3435–3438 (2001)
M. Muthukumar, Polymer translocation through a hole. J. Chem. Phys. 111(12), 10371–10374 (1999)
M. Muthukumar, Mechanism of dna transport through pores. Annu. Rev. Biophys. Biomol. Struct. 36, 435–450 (2007)
T. Odijk, Ten years of tension: single-molecule dna mechanics. Macromolecules 16(8), 1340–1344 (1983)
P. Prinsen, L.T. Fang, A.M. Yoffe, C.M. Knobler, W.M. Gelbart, The force acting on a polymer partially confined in a tube. J. Phys. Chem. B 113(12), 3873–3879 (2009)
R.M.M. Smeets, U.F. Keyser, D. Krapf, M.Y. Wu, N.H. Dekker, C. Dekker, Salt dependence of ion transport and dna translocation through solid-state nanopores. Nano Lett. 6(1), 89–95 (2006)
A.J. Storm, J.H. Chen, H.W. Zandbergen, C. Dekker, Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2, 537–540 (2003)
A.J. Storm, J.H. Chen, H.W. Zandbergen, C. Dekker, Translocation of double-strand dna through a silicon oxide nanopore. Phys. Rev. E 71, 051903 (2005a)
A.J. Storm, C. Storm, J. Chen, H. Zandbergen, J.F. Joanny, C. Dekker, Fast dna translocation through a solid-state nanopore. Nano. Lett. 5(7), 1193–1197 (2005b)
S. van Dorp, U.F. Keyser, N.H. Dekker, C. Dekker, S.G. Lemay, Origin of the electrophoretic force on dna in solid-state nanopores. Nat. Phys. 5, 347–351 (2009)
W. Zhu, S.J. Singer, Z. Zheng, A.T. Conlisk, Electro-osmotic flow of a model electrolyte. Phys. Rev. E 71, 041501–1–041501–12 (2005)
Acknowledgements
The authors gratefully acknowledge support of this work from National Science Foundation (NSF) Nanoscale Science and Engineering Center (NSEC), Center for Affordable Nanoengineering of Polymeric Biomedical Devices (CANPBD).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Chen, L., Conlisk, A.T. Forces affecting double-stranded DNA translocation through synthetic nanopores. Biomed Microdevices 13, 403–414 (2011). https://doi.org/10.1007/s10544-011-9509-7
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10544-011-9509-7