Polymer capture by electro-osmotic flow of oppositely charged nanopores

Abstract

The authors have addressed theoretically the hydrodynamic effect on the translocation of DNA through nanopores. They consider the cases of nanopore surface charge being opposite to the charge of the translocating polymer. The authors show that, because of the high electric field across the nanopore in DNA translocation experiments, electro-osmotic flow is able to create an absorbing region comparable to the size of the polymer around the nanopore. Within this capturing region, the velocity gradient of the fluid flow is high enough for the polymer to undergo coil-stretch transition. The stretched conformation reduces the entropic barrier of translocation. The diffusion limited translocation rate is found to be proportional to the applied voltage. In the authors' theory, many experimental variables (electric field, surface potential, pore radius, dielectric constant, temperature, and salt concentration) appear through a single universal parameter. They have made quantitative predictions on the size of the adsorption region near the pore for the polymer and on the rate of translocation.

Electro-osmotic flow through a nanopore

“…When the free translocation of the polymer is hindered by tethering it to a colloid held in an optical trap, the tethering force has been shown to be determined by the electroosmotic flow within the pore (Ghosal 2007b;Keyser et al 2006;Laohakunakorn et al 2013a). Furthermore, it has been argued that the flow outside and in the vicinity of the nanopore controls the capture rate of polymers into the pore (Wong & Muthukumar 2007), though the experimental evidence for this appears tentative at present.…”

Theory of capture rate in polymer translocation

“…1, a cylindrical coordinate system must be used as in Ref. 25 and the local concentration of the polymer depends on the radial distance from the pore. While the mathematical details are simpler in the one-dimensional description here, the physics is unaltered for the present problem.…”

“…1͑b͒ is based on the previous calculations. 16,[21][22][23][24][25] The free energy landscape sketched in Fig. 1 can be richer due to the chemical decorations of the pore and the pore geometry.…”

Stiff filamentous virus translocations through solid-state nanopores

“…According to the conventional theoretical picture, the electrokinetic driving force 10,12,13 and stochastic thermal forces 8,9,15 are balanced by the total viscous drag on the translocating polymer. The translocation is also retarded by electro-osmotic fluid flow through the nanopore 11,31 .…”

“…It senses when a single biopolymer threads it by registering a change in its ionic conductance 1,2 . The possibility of applying nanopores to the analysis of nucleic acids, in particular DNA sequencing, has generated interest 3 , and motivated fundamental studies of the physics of nanopore translocations [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . The uses of solid-state nanopores have recently expanded to include detecting single proteins 18 , mapping structural features along RecA-bound DNA-protein complexes 19 and detecting spherical and icosahedral virus strains [20][21][22] .…”