Determining the Effective DNA Charge Density from Nanopore Translocation Dynamics.

Abstract

Knowledge of the effective charge density (λ) of polymers is crucial for quantifying the electrophoretic force in nanopore translocation. Here, we derive a phenomenological scaling relationship for DNA translocation dwell times that incorporates hydrodynamic drag and electrokinetic effects, allowing the direct determination of λ. We validate this relationship through DNA translocation experiments across nanopipettes under systematically varied conditions, including pore diameter, applied voltage, salt concentration, and alkali cation type (LiCl, NaCl, and KCl). λ values decrease with increasing cation size, indicating that Li⁺ is the most effective at charge screening. These findings are corroborated by independent mechanical unzipping experiments of a DNA hairpin with optical tweezers, in which Li⁺ yields the highest unzipping force. Our approach provides a general framework for estimating the effective charge density of biopolymers─such as peptides and proteins─from dwell-time measurements, where electro-osmotic and electrophoretic forces compete in translocation dynamics.