Charged polymer membrane translocation

Abstract

We study the process of charged polymer translocation, driven by an external electric potential, through a narrow pore in a membrane. We assume that the number of polymer segments, m, having passed the entrance pore mouth, is a slow variable governing the translocation process. Outside the pore the probability that there is an end segment at the entrance pore mouth, is taken as the relevant parameter. In particular we derive an expression for the free energy as a function of m, F(m). F(m) is used in the Smoluchowski equation in order to obtain the flux of polymers through the pore. In the low voltage regime we find a thresholdlike behavior and exponential dependence on voltage. Above this regime the flux depends linearly on the applied voltage. At very high voltages the process is diffusion limited and the flux saturates to a constant value. The model accounts for all features of the recent experiments by Henrickson et al. [Phys. Rev. Lett. 85, 3057 (2000)] for the flux of DNA molecules through an α-hemolysin pore as a function of applied voltage.

Colloquium: Physical approaches to DNA sequencing and detection

“…There are two fruitful approaches to this complex issue: phenomenological models and molecular dynamics. The phenomenological models provide a highly reduced description of the polymer dynamics, but they are able to elucidate the dependence of the dynamics on parameters such as the polymer length, pore dimensions, and applied field ͑Sung and Park, 1996; Lubensky and Nelson, 1999;Muthukumar, 1999Muthukumar, , 2001Chern et al, 2001;Chuang et al, 2001;Ambjörnsson et al, 2002;Kong and Muthukumar, 2002;Loebl et al, 2003;Meller, 2003;Slonkina and Kolomeisky, 2003;Luo et al, 2006;Matysiak et al, 2006;Tsai and Chen, 2007͒. On the other hand, if one wants to understand how to probe physical differences between the bases, an atomistic description of the polynucleotide dynamics is necessary.…”

Polymer capture by α-hemolysin pore upon salt concentration gradient

“…The dependence of R c on the polymer length, voltage gradient, and polymer concentration has been successfully addressed by considering the drift-diffusion and barrier penetration. [30][31][32] In general terms, for weaker voltage gradients and shorter polymers, the free energy barrier dominates capture rate and for stronger voltage gradients and longer polymers, the drift dominates. In addition, the strength of the electric field in directing the polymer in the cis compartment towards the pore entrance can be augmented by creating a gradient in the electrolyte concentration across the pore.…”

Polymer translocation through a nanopore: A two-dimensional Monte Carlo study

“…Inspired by the experiments, 7 a number of recent theories [15][16][17][18][19][20][21][22][23][24][25][26][27][28] have been developed for the dynamics of polymer translocation. Even without an external driving force, polymer translocation remains a challenging problem.…”

“…6 In addition to its biological relevance, the translocation dynamics is also a challenging topic in polymer physics. Accordingly, the polymer translocation has attracted a considerable number of experimental, [7][8][9][10][11][12][13][14] theoretical, [15][16][17][18][19][20][21][22][23][24][25][26][27][28] and numerical studies. [29][30][31][32][33][34][35][36] The translocation of a polymer through a nanopore faces a large entropic barrier due to the loss of a great number of available configurations.…”