pH-mediated regulation of polymer transport through SiN pores

Buyukdagli, Sahin; Ala-Nissilä, Tapio

doi:10.1209/0295-5075/123/38003

Cited by 9 publications

(10 citation statements)

References 27 publications

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“…Moreover, we assume that the membrane carries a negative charge with surface density −σ m < 0, which is uniformly distributed on the membrane and constant during the translocation process. The negative membrane charge is a consequence of a low degree of protonation occurring in the typical high pH conditions of translocation experiments [41].…”

Section: Modelmentioning

confidence: 99%

“…This requires taking into account both the presence of counterions in the solution and the dielectric properties of the membrane through which the polyelectrolyte is translocating. Recently there has been an intense effort to model polyeletrolyte translocation including the details of the pore electrohydrodynamics and/or electrostatic polymer-membrane interactions, however, with the price of neglecting conformational polymer fluctuations [5,39,41]. This simplified modeling has allowed to characterize the electrohydrodynamic mechanism of experimentally observed DNA mobility reversal by charge inversion [42] and pressure-voltage traps [43], and also enabled to identify strategies for faster polymer capture and slower translocation required for accurate biosequencing.…”

Section: Introductionmentioning

confidence: 99%

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Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

Sarabadani

Buyukdagli

Ala-Nissilä

2020

J. Phys.: Condens. Matter

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We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation theory with electrostatics for a negatively charged biopolymer pulled through a nanopore embedded in a similarly charged anionic membrane. We show that in the realistic case of a single-stranded DNA molecule, dilute salt conditions characterized by weak charge screening, and a negatively charged membrane, the translocation dynamics is unexpectedly accelerated despite the presence of large repulsive electrostatic interactions between the polymer coil on the cis side and the charged membrane. This is due to the rapid release of the electrostatic potential energy of the coil during translocation, leading to an effectively attractive force that assists end-driven translocation. The speedup results in non-monotonic polymer length and membrane charge dependence of the exponent α characterizing the translocation time τ ∝ N α 0 of the polymer with length N 0. In the regime of long polymers N 0 500, the translocation exponent exceeds its upper limit α = 2 previously observed for the same system without electrostatic interactions.

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Section: Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

Sarabadani

Buyukdagli

Ala-Nissilä

2020

J. Phys.: Condens. Matter

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“…Moreover, we assume that the translocated membrane carries a positive charge with surface charge density σ m > 0. The positive membrane charge is a consequence of a high degree of protonation occurring in low pH conditions (or high bulk H + concentration) for amphoteric substrates such as silicon-based membranes [42].…”

Section: Modelmentioning

confidence: 99%

“…This requires taking into account both the presence of counterions in the solution and the dielectric properties of the membrane through which the polyelectrolyte is translocating. Recently there has been an intense effort to model polyeletrolyte translocation including the details of the pore electrohydrodynamics and/or electrostatic polymer-membrane interactions, however, with the price of neglecting conformational polymer fluctuations [5,[39][40][41][42][43]. This simplified modeling has allowed to characterize the electrohydrodynamic mechanism of experimentally observed DNA mobility reversal by charge inversion [45] and pressure-voltage traps [46], and also enabled to identify strategies for faster polymer capture and slower translocation required for accurate biosequencing.…”

Section: Introductionmentioning

confidence: 99%

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

Sarabadani,

Buyukdagli,

Ala-Nissila

2019

Preprint

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We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation (IFTP) theory with electrostatics for an anionic biopolymer pulled through a nanopore embedded in a cationic membrane. We show that for the realistic case of an anionic polyelectrolyte such as a single-stranded DNA, the translocation dynamics at low salt where screening is weak and at finite positive membrane charge, is governed by the attractive electrostatic interactions between the polymer coil on the cis side and the charged membrane. These interactions result in a non-monotonic polymer length and membrane charge dependence of the exponent α characterizing the translocation time τ ∝ N α 0 of the polymer with length N0. Due to the same electrostatic polymer-membrane coupling, in the regime of long polymers N0 500, the translocation exponent exceeds its upper limit α = 2 previously observed for the same system without electrostatic interactions.

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“…However, the control of these flows requires the adjustment of the nanopore surface charge via the acidity of the buffer solution, which equally modifies the polymer surface charge subjected to protonation [43]. The resulting complexity of the pH-dependent translocation rates [44] indicates the necessity to tune the translocation speed without activating the surface chemistry of the polymer. In this article, we show that via the adequate choice of the electrolyte composition, the dielectric properties of CNT-coated membranes allow to generate EO flows whose magnitude and direction can be controlled without affecting the polymer surface charge.…”

Section: Introductionmentioning

confidence: 99%

Dielectric manipulation of polymer translocation dynamics in engineered membrane nanopores

Buyukdagli

2021

Preprint

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The alteration of the dielectric membrane properties by carbon nanotube (CNT) coating opens the way to novel molecular transport strategies for biosensing purposes. In this article, we predict a macromolecular transport mechanism enabling the dielectric manipulation of the polymer translocation dynamics in surface-coated pores confining mixed electrolytes. In the giant permittivity regime of CNT-coated membranes governed by attractive polarization forces, multivalent ions adsorbed by the membrane nanopore trigger a monovalent ion separation and set an electroosmotic (EO) flow. The drag force exerted by this flow is sufficiently strong to suppress and invert the electrophoretic (EP) velocity of anionic polymers, and also to generate the mobility of neutral polymers whose speed and direction can be solely adjusted by the charge and concentration of the added multivalent ions. These features identify the dielectrically generated transport mechanism as an efficient mean to drive overall neutral or weakly charged analytes that cannot be controlled by an external voltage. We also reveal that in anionic polymer translocation, multivalent cation addition into the monovalent salt solution amplifies the electric current signal by several factors. The signal amplification is caused by the electrostatic many-body interactions replacing the monovalent polymer counterions by the multivalent cations of higher electric mobility. The strength of this elektrokinetic charge discrimination points out the potential of multivalent ions as current amplifiers capable of providing boosted resolution in nanopore-based biosensing techniques.

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pH-mediated regulation of polymer transport through SiN pores

Cited by 9 publications

References 27 publications

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics

Dielectric manipulation of polymer translocation dynamics in engineered membrane nanopores

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