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
- Nanopore-based Manipulation and Separation of Single-stranded DNA Molecules through Tuning pH Values
- Chinese Journal of Polymer Science 2026年44卷第7期页码：2361-2369
- Affiliations：
  
  School of Physics, Zhejiang University of Technology, Hangzhou 310023, China
- Author bio：
  
  sunlizhen@zjut.edu.cn
- Funds：
  
  This work was financially supported by the Zhejiang Provincial Natural Science Foundation of China under (No. LZ24A040003).;The authors declare no interest conflict.Electronic supplementary information (ESI), which includes calculations of pH-dependent charges on the nanopore surface (Section S1 in ESI), detailed descriptions of the coarse-grained model-matched potential (Section S2 in ESI), derivations of the parameters in the coarse-grained model (Section S3 in ESI), calculations of the total electric field (Section S4 in ESI), and correlations between waiting times and chain conformations (Section S5 in ESI), PDB identifications of the selected ssDNA structures (Table S1 in ESI), parameters included in the simulation system (Table S2 in ESI), simulation data for this article (Tables S3‒S6 in ESI), is available free of charge in the online version of this article at http://doi.org/10.1007/s10118-026-3640-7.The data that support the findings of this study are available from the corresponding author upon reasonable request.
- DOI：10.1007/s10118-026-3640-7
  中图分类号：
- 收稿：2026-01-30，
  
  修回：2026-02-21，
  
  录用：2026-03-01，
  
  网络首发：2026-04-07，
  
  纸质出版：2026-07-05
- 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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