Sit, Roll Over, Play Dead: Investigating the Effects of pH on the Translocation of Double-Strand DNA through Solid-State Nanopores

Abstract

Nanopore translocation experiments have revealed many interesting single molecule characteristics, including molecular size and local structure. In this work, we investigate the effects of pH on Lambda (Δ) DNA translocations through solid-state nanopores. We measure dwell time and conductance blockage of unfolded Δ DNA while varying the pH systematically over a range from 3 to 10. Our measurements indicate that electrophoresis (EP), electroosmosis (EM), and diffusion (DF) all play important roles during the transport process. We find that Δ DNA mean dwell times increase as the electrolyte pH approaches the DNA isoelectric point and translocation direction changes polarity at low pH. The relative contributions of EP, EM and DF change at different rates with pH to produce the observed net effects. Our results emphasize the importance of DNA and nanopore zeta potential considerations when analyzing single molecule translocation dynamics and offer a possible route towards reduced translocation speed while retaining high signal-to-noise ratio.