Determining the Effective DNA Charge Density from Nanopore Translocation Dynamics.

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.