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<p>The unique regulatory effect of pH on electrostatic interactions offers a powerful approach for manipulating and separating single-stranded DNA (ssDNA) molecules. In this study, we employ Langevin dynamics simulations to investigate the translocation dynamics of two ssDNAs, poly(dA) and poly(dT), through a silicon nitride nanopore under acidic conditions. The key distinction between the two chains is their different pH-dependent protonation. At low pH, the highly protonated adenine bases experience repulsive interactions from the similarly protonated nanopore surface and the retarding force from the external voltage, whereas neutral thymine bases do not. Consequently, compared to poly(dT), poly(dA) exhibits a lower capture probability and slower translocation speed under strongly acidic conditions. However, the difference in the translocation behaviors between the two chains gradually diminishes as the pH increases. Based on their distinct pH-dependent behaviors, poly(dA) and poly(dT) of identical length can be successfully separated through the translocation strategy at low pH, even when they are initially mixed on the same side of the nanopore.</p>

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Nanopore-based Manipulation and Separation of Single-stranded DNA Molecules through Tuning pH Values

  • 期刊论文

  • 发表日期：

    2026年4月7日

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  • Cheng-Kai Zhou,
  • Sheng-Wen Miao,
  • Li-Zhen Sun

摘要

The unique regulatory effect of pH on electrostatic interactions offers a powerful approach for manipulating and separating single-stranded DNA (ssDNA) molecules. In this study, we employ Langevin dynamics simulations to investigate the translocation dynamics of two ssDNAs, poly(dA) and poly(dT), through a silicon nitride nanopore under acidic conditions. The key distinction between the two chains is their different pH-dependent protonation. At low pH, the highly protonated adenine bases experience repulsive interactions from the similarly protonated nanopore surface and the retarding force from the external voltage, whereas neutral thymine bases do not. Consequently, compared to poly(dT), poly(dA) exhibits a lower capture probability and slower translocation speed under strongly acidic conditions. However, the difference in the translocation behaviors between the two chains gradually diminishes as the pH increases. Based on their distinct pH-dependent behaviors, poly(dA) and poly(dT) of identical length can be successfully separated through the translocation strategy at low pH, even when they are initially mixed on the same side of the nanopore.