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DNA translocation through pH-dependent soft nanopores

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Abstract

Controlling the translocation velocity of DNA is the main challenge in the process of sequencing by means of nanopores. One of the main methods to overcome this challenge is covering the inner walls of the nanopore with a layer of polyelectrolytes, i.e., using soft nanopores. In this paper the translocation of DNA through soft nanopores, whose inner polyelectrolyte layer (PEL) charge is pH-dependent, is theoretically studied. We considered the polyelectrolyte to be made up of either acidic or basic functional groups. It was observed that the electroosmotic flow (EOF) induced by the PEL charge is in the opposite/same direction of DNA electrophoresis (EPH) when the PEL is made up of acidic/basic groups. It was found that, not only the DNA charge and consequently the EPH, but also the EOF are influenced by the electrolyte acidity. The synergy between the changes in the retardation, EOF and EPH, determines how the intensity and direction of DNA translocation alter with pH. In fact, for both cases, at mild values of pH (as long as \(\mathrm{E}\mathrm{O}\mathrm{F}<\mathrm{E}\mathrm{P}\mathrm{H}\) for the case that PEL is of acidic nature), the more the pH, the less the translocation velocity. However, for PELs of acidic nature, higher values of pH increase the intensity of the EOF so much that DNA may experience a change in the translocation direction. Ultimately, conducting the process at a particular range of pH values, and at higher pH values, in the cases of using PELs of acidic nature, and basic nature, respectively, was recommended.

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Abbreviations

a :

Radius cylindrical rod assumed to be model of DNA (m)

b :

Distance from center of nanopore to electrolyte/ PE brush interface (m)

c i :

Concentration of the ionic species (mol m−3)

D i :

Diffusivity of the ionic species (m2 s−1)

e :

Elementary charge (C)

E 0 :

Axial electric field (V m−1)

F m :

Manning factor (1)

F e :

Electric force acting per unit length of DNA segment (N)

F v :

Viscous force acting per unit length of DNA segment (N)

K a :

Ionization constant of acidic groups (mol m−3)

K b :

Ionization constant of basic groups (mol m−3)

K B :

Boltzmann constant (J K−1)

L :

Channel and DNA length (m)

N A :

Avogadro constant (mol−1)

N i :

The flux of the ionic species (mol m−2 s−1)

n i :

Number density of the ionic species (m−3)

n 0 :

Bulk number density (m−3)

R :

Nanochannel radius (m)

T :

Temperature (K)

u :

Electrokinetic velocity (m s−1)

u e :

Electrophoretic velocity of DNA (m s−1)

z i :

Valance of the ionic species (1)

γ :

PEL brush hydrodynamic friction coefficient (Pa s m−2)

γ a :

Maximum surface site density of the acidic group (m−3)

γ b :

Maximum surface site density of the basic group (m−3)

γ DNA :

Maximum site number of the phosphate groups in the DNA backbone (m−1)

ε :

Electrolyte permittivity (F m−1)

ζp :

Zeta potential (V)

λ bare :

Bare line charge density of DNA (C m−1)

λ D :

Debye length (m)

λ DNA :

Effective line charge density of DNA (C m−1)

\(\lambda _{s}^{{ - 1}}\) :

Softness parameter (m)

μ :

Electrolyte viscosity (Pa s)

ρ :

Fluid density (kg m−3)

ρ p :

Volume charge density of the PEL charges (C m−3)

ψ :

Electric potential (V)

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Acknowledgements

The research council at Iran University of Science and Technology (IUST) is highly appreciated for its financial support during the course of this research.

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Authors and Affiliations

  1. Research Lab for Advanced Separation Processes, Department of Chemical Engineering, Iran University of Science and Technology, 16846-13114, Narmak, Tehran, Iran

    Alireza Yousefi, Ardalan Ganjizade & Seyed Nezameddin Ashrafizadeh

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  1. Alireza Yousefi
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  2. Ardalan Ganjizade
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  3. Seyed Nezameddin Ashrafizadeh
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Correspondence to Seyed Nezameddin Ashrafizadeh.

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Yousefi, A., Ganjizade, A. & Ashrafizadeh, S.N. DNA translocation through pH-dependent soft nanopores. Eur Biophys J 50, 905–914 (2021). https://doi.org/10.1007/s00249-021-01552-2

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  • DOI: https://doi.org/10.1007/s00249-021-01552-2

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