Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

Wong, Chiu Tai Andrew; Muthukumar, Murugappan

doi:10.1063/1.3464333

Cited by 120 publications

(173 citation statements)

References 47 publications

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“…in pH 4.5 are significantly higher than those in pH 7.5. This is consistent with our earlier result 20 and arises from attraction of the negatively charged polymer to the pore by the positive charges on the pore which are induced by lowering the pH. The more significant result is the opposite trends in the c s -dependence of R c for pH 7.5 and pH 4.5.…”

Section: A Symmetric Salt Concentrationssupporting

confidence: 81%

“…20,21 Sodium salt of poly(styrene sulfonate) (NaPSS) with weight average molecular weight of 16 kg/mol and polydispersity index of 1.13 was purchased from Scientific Polymer Products, Inc. (NY). Polydeoxythymidine (poly(dT) 80 ) was purchased from Integrated DNA Technologies, Inc. (IA).…”

Section: Methodsmentioning

confidence: 99%

“…We have used α-hemolysin pore and sodium poly(styrene sulfonate) in our study. Although the α-hemolysin pore bears heterogeneous charge distribution, 20,29,37 it is possible to determine the sign of the effective charge of α-hemolysin pore for capturing the polymer by changing salt concentration at a given pH. At high pH where the pore-polymer electrostatic interaction is repulsive, upon lowering the salt concentration both in cis and trans (leading to higher electrostatic repulsion between the polymer and pore), the capture rate should decrease.…”

Section: Introductionmentioning

confidence: 99%

“…35,36 Also, a reduction in the net negative charge of the α-hemolysin protein pore by lowering the pH is shown to dramatically increase both the capture and threading of the polymer. 20 In this paper, we investigate the combined effects of additional drift on the polymer and the pore-polymer electrostatic interaction, both arising from an imposed salt concentration gradient across the pore. We have used α-hemolysin pore and sodium poly(styrene sulfonate) in our study.…”

Section: Introductionmentioning

confidence: 99%

“…20,27 The measured translocaa) Electronic mail: muthu@polysci.umass.edu tion time, blocked current, and capture rate are intrinsically stochastic and arise from the coupled conformational fluctuations of the polymer, the pore-polymer interaction, and the electrohydrodynamic flow fields in these systems. In order to fully understand the relative contributions of these factors, it is necessary to investigate the phenomenon under simpler conditions.…”

Section: Introductionmentioning

confidence: 99%

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Polymer capture by α-hemolysin pore upon salt concentration gradient

Jeon

Muthukumar

2014

The Journal of Chemical Physics

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We have measured the rate of capture of single molecules of sodium poly(styrene sulfonate) by α-hemolysin protein pore by varying applied voltage, pH, and the salt concentration asymmetry across the pore. We show that electrostatic interaction between the polyelectrolyte and the protein pore significantly affects the polymer capture rate in addition to the enhancement of drift arising from electrolyte concentration gradient. At higher pH values where the electrostatic interaction between the polymer and the α-hemolysin pore is repulsive, an antagonistic coupling with the drift induced by salt concentration gradient emerges. This antagonistic coupling results in a nonmonotonic dependence of the polymer capture rate on the salt concentration in the donor compartment. The coupling between the pore-polymer interaction and drift can be weakened by increasing the strength of the electric field that drives the polymer translocation. In contrast, at lower pH values where the polymer-pore interaction is attractive, a synergy with the additional drift from salt concentration asymmetry arises and the capture rate depends monotonically on the donor salt concentration. For higher pH, we identify two regimes for the enhancement of capture rate by salt concentration gradient: (a) driftdominated regime, where the capture rate is roughly quadratic in the ratio of salt concentration in the receiver compartment to that in the donor compartment, and (b) antagonistic coupling regime at higher values of this ratio with a linear relation for the polymer capture rate. © 2014 AIP Publishing LLC. [http://dx

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Section: A Symmetric Salt Concentrationssupporting

confidence: 81%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Polymer capture by α-hemolysin pore upon salt concentration gradient

Jeon

Muthukumar

2014

The Journal of Chemical Physics

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Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse‐Grained Molecular Dynamics Simulations Study

2022

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We study the influence of polymer pore interactions and focus on the role played by the concentration gradient of salt in the translocation of polyelectrolytes (PE) through nanopores explicitly using coarse-grained Langevin dynamics simulations. The mean translocation time is calculated by varying the applied voltage, the pH, and the salt concentration gradient. Changing the pH can alter the electrostatic interaction between the protein pore and the polyelectrolyte chain. The polymer pore interaction is weakened by the increase in the strength of the externally applied electric field that drives translocation. Additionally, the screening effect of the salt can reduce the strong charge-charge repulsion between the PE beads which can make translocation faster. The simulation results show there can be antagonistic or synergistic coupling between the salt concentration-induced screening effect and the drift force originating from the salt concentration gradient thereby affecting the translocation time. Our simulation results are explained qualitatively with free energy calculations.

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Translocation of single‐stranded DNA through the α‐hemolysin protein nanopore in acidic solutions

et al. 2011

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The effect of acidic pH on the translocation of single-stranded DNA through the α-hemolysin pore is investigated. Two significantly different types of events, i.e., deep blockades and shallow blockades, are observed at low pH. The residence times of the shallow blockades are not significantly different from those of the DNA translocation events obtained at or near physiological pH, while the deep blockades have much larger residence times and blockage amplitudes. With a decrease in the pH of the electrolyte solution, the percentage of the deep blockades in the total events increases. Furthermore, the mean residence time of these long-lived events is dependent on the length of DNA, and also varies with the nucleotide base, suggesting that they are appropriate for use in DNA analysis. In addition to be used as an effective approach to affect DNA translocation in the nanopore, manipulation of the pH of the electrolyte solution provides a potential means to greatly enhance the sensitivity of nanopore stochastic sensing.

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Polymer translocation through α-hemolysin pore with tunable polymer-pore electrostatic interaction

Cited by 120 publications

References 47 publications

Polymer capture by α-hemolysin pore upon salt concentration gradient

Polymer capture by α-hemolysin pore upon salt concentration gradient

Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse‐Grained Molecular Dynamics Simulations Study

Translocation of single‐stranded DNA through the α‐hemolysin protein nanopore in acidic solutions

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