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Determining the Effective DNA Charge Density from Nanopore Translocation Dynamics.

Alejandro Colchero1, Isabel Pastor1,2, Felix Ritort1,2,3

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Summary

Determining the effective charge density (λ) of polymers is key for understanding nanopore translocation. This study introduces a method using DNA translocation dwell times to directly measure λ, finding Li+ most effective for charge screening.

Keywords:
DNAcharge densitydwell timesnanoporeoptical tweezerstranslocation

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Area of Science:

  • Polymer physics
  • Nanopore science
  • Biophysics

Background:

  • Effective charge density (λ) is critical for quantifying electrophoretic forces during polymer translocation through nanopores.
  • Existing methods for determining λ are limited, hindering accurate modeling of translocation dynamics.

Purpose of the Study:

  • To derive and validate a phenomenological scaling relationship for direct determination of polymer effective charge density (λ) from translocation dwell times.
  • To investigate the influence of salt concentration and cation type on λ during DNA translocation.

Main Methods:

  • Derivation of a scaling relationship incorporating hydrodynamic drag and electrokinetic effects for DNA translocation dwell times.
  • Experimental validation using DNA translocation through nanopipettes under varied conditions (pore diameter, voltage, salt concentration, cation type).
  • Independent corroboration using mechanical DNA hairpin unzipping with optical tweezers.

Main Results:

  • The derived scaling relationship successfully allows direct determination of effective charge density (λ).
  • DNA translocation dwell times and λ are influenced by pore diameter, applied voltage, and salt concentration.
  • Effective charge density (λ) decreases with increasing cation size, with Li+ exhibiting the strongest charge screening effect.
  • Mechanical unzipping experiments confirm Li+ as the most effective cation for charge screening.

Conclusions:

  • The developed approach provides a general framework for estimating the effective charge density of biopolymers from translocation dwell-time measurements.
  • Understanding cation-specific charge screening is crucial for controlling and predicting polymer translocation dynamics in nanopores.
  • This method offers a pathway to study electrokinetic and electrophoretic forces in biopolymer translocation, applicable to peptides and proteins.