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DNA translocation through pH-dependent soft nanopores.

Alireza Yousefi1, Ardalan Ganjizade1, Seyed Nezameddin Ashrafizadeh2

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

European Biophysics Journal : EBJ
|June 13, 2021
PubMed
Summary

Controlling DNA translocation through soft nanopores is key for sequencing. Polyelectrolyte layer charge, influenced by pH, alters DNA movement by modifying electroosmotic flow and electrophoresis.

Keywords:
DNA translocationElectrophoresisNanoporespH-regulated polyelectrolytes

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Area of Science:

  • Nanotechnology
  • Biophysics
  • Molecular Biology

Background:

  • Controlling DNA translocation velocity through nanopores is crucial for DNA sequencing.
  • Soft nanopores, with polyelectrolyte layers (PELs), offer a method to regulate this translocation.
  • The pH-dependent charge of the PEL significantly impacts DNA movement.

Purpose of the Study:

  • To theoretically investigate DNA translocation through soft nanopores with pH-dependent PEL charge.
  • To analyze the influence of PEL composition (acidic or basic groups) on DNA translocation dynamics.
  • To understand the interplay between electroosmotic flow (EOF), electrophoresis (EPH), and DNA charge in response to pH variations.

Main Methods:

  • Theoretical study of DNA translocation dynamics.
  • Modeling of soft nanopores with pH-responsive polyelectrolyte layers.
  • Analysis of electroosmotic flow (EOF) and electrophoresis (EPH) under varying pH conditions.

Main Results:

  • The direction of EOF relative to EPH depends on whether the PEL consists of acidic or basic groups.
  • Both DNA charge (EPH) and EOF are affected by electrolyte acidity (pH).
  • Increasing pH generally decreases translocation velocity, but high pH can reverse DNA translocation direction for acidic PELs due to strong EOF.

Conclusions:

  • The synergy between retardation, EOF, and EPH dictates DNA translocation velocity and direction.
  • Optimal pH ranges exist for controlling DNA translocation, with higher pH values being beneficial for acidic PELs and basic PELs, respectively.
  • This research provides insights for optimizing nanopore DNA sequencing technologies.