DNA aggregation and resolubilization in the presence of polyamines probed at the single molecule level using nanopores

Abstract

The compaction and decompaction of double-stranded DNA play a crucial role in regulating gene expression. We use solid-state nanopores to study, at the single-molecule level, the translocation of DNA chains in relation to the macroscopic phase transition induced by polyamines. To prevent nonspecific interactions between the nanopore surface and DNA, nanopores were passivated, and experiments were performed in high salt conditions. We first determine the translocation dynamics of DNA. The event frequency varies exponentially with the applied voltage and linearly with the polyelectrolyte concentration. The translocation time decreases exponentially with applied voltage. Addition of polyamine to a DNA solution leads to DNA aggregation and subsequent phase separation; a macroscopic DNA-rich and dense phase coexists with a poor-DNA (diluted) phase. We pipetted part of the diluted phase and studied chain translocation. We observe a progressively decreasing event frequency of DNA in the solution at the nanopore entry as a function of polyamine concentration, approaching zero Hertz. At this point, no DNA remained in the poor phase, and all the DNA was found in the precipitated rich phase. If we increase the polyamine concentration even further, the event frequency increases progressively until it reaches a plateau value due to the solubilization of DNA aggregates. At high salt concentrations in NaCl, we observe that the event frequency of DNA in solution remains constant as a function of polyamine concentrations. We compare DNA phase transitions using nanopore and UV bulk experiments, and we find the same charge-to-molar ratio for DNA precipitation and solubilization. We interpret these results through polyelectrolyte behavior.