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

Cheng-Kai Zhou; Sheng-Wen Miao; Li-Zhen Sun

doi:10.1007/s10118-026-3640-7

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

RESEARCH ARTICLE | Updated：2026-07-01

- Nanopore-based Manipulation and Separation of Single-stranded DNA Molecules through Tuning pH Values
- Chinese Journal of Polymer Science Vol. 44, Issue 7, Pages: 2361-2369(2026)
- Affiliations：
  
  School of Physics, Zhejiang University of Technology, Hangzhou 310023, China
- Author bio：
  
  sunlizhen@zjut.edu.cn
- Funds：
- DOI：10.1007/s10118-026-3640-7
  CLC：
- Received：30 January 2026，
  
  Revised：2026-02-21，
  
  Accepted：01 March 2026，
  
  Online First：07 April 2026，
  
  Published：05 July 2026
- Accepted：
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Zhou, C. K.; Miao, S. W.; Sun, L. Z. Nanopore-based manipulation and separation of single-stranded DNA molecules through tuning pH values. Chinese J. Polym. Sci. 2026, 44, 2361–2369

Cheng-Kai Zhou, Sheng-Wen Miao, Li-Zhen Sun. Nanopore-based Manipulation and Separation of Single-stranded DNA Molecules through Tuning pH Values[J]. Chinese Journal of Polymer Science, 2026, 44(7): 2361-2369.
Zhou, C. K.; Miao, S. W.; Sun, L. Z. Nanopore-based manipulation and separation of single-stranded DNA molecules through tuning pH values. Chinese J. Polym. Sci. 2026, 44, 2361–2369 DOI： 10.1007/s10118-026-3640-7.

Cheng-Kai Zhou, Sheng-Wen Miao, Li-Zhen Sun. Nanopore-based Manipulation and Separation of Single-stranded DNA Molecules through Tuning pH Values[J]. Chinese Journal of Polymer Science, 2026, 44(7): 2361-2369. DOI： 10.1007/s10118-026-3640-7.

摘要

The distinct pH sensitivities of adenine and thymine bases under acidic conditions result in non-overlapped translocation time distributions for the single-stranded DNA (ssDNA) chains polyadenine (poly(dA)) and polythymine (poly(dT)) at low pH values in their individual translocation and facilitate the separation of the chains during competitive translocation through a nanopore.

Abstract

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.

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references

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