Extreme Slowdown of dsDNA and RNA:DNA Hybrids in Solid-state Nanopores for LiCl concentrations above 4 mol/L

Solid-state nanopores enable single-molecule detection and characterization through ionic-current measurements, but rapid translocation can limit the resolution of molecular features. Here, we investigated the translocation of 7.2 kb dsDNA and 3.3 kb RNA:DNA hybrids at LiCl concentrations extending to 7 mol/L. Both constructs exhibited a substantial increase of ≳ 500% in mean translocation time when increasing LiCl concentration from 2--3 M to 7 M . We also observed a decrease in translocation frequency at increasing LiCl concentration. Both observations indicate a reduction in the effective electric driving force. Further analysis indicates a substantial decrease in the relative width of secondary peaks induced by labels on the molecule. Our results show that increasing salt concentration beyond 4 mol/L is an accessible way for increasing translocation time in solid-state nanopore sensing, with possible implications for barcode sensing resolution.

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Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2026-10-30
DOI
https://doi.org/10.64898/2026.10.28.762501
Primary Topic
Nanopore and Nanochannel Transport Studies
Type
preprint

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preprint

Extreme Slowdown of dsDNA and RNA:DNA Hybrids in Solid-state Nanopores for LiCl concentrations above 4 mol/L

Ulrich F. Keyser, Simon Brauburger, Yunkai Wu
2 links
bioRxiv (Cold Spring Harbor Laboratory)
Nanopore and Nanochannel Transport Studies
preprint

Extreme Slowdown of dsDNA and RNA:DNA Hybrids in Solid-state Nanopores for LiCl concentrations above 4 mol/L

Ulrich F. Keyser, Simon Brauburger, Yunkai Wu
preprint en

Abstract

Solid-state nanopores enable single-molecule detection and characterization through ionic-current measurements, but rapid translocation can limit the resolution of molecular features. Here, we investigated the translocation of 7.2 kb dsDNA and 3.3 kb RNA:DNA hybrids at LiCl concentrations extending to 7 mol/L. Both constructs exhibited a substantial increase of ≳ 500% in mean translocation time when increasing LiCl concentration from 2--3 M to 7 M . We also observed a decrease in translocation frequency at increasing LiCl concentration. Both observations indicate a reduction in the effective electric driving force. Further analysis indicates a substantial decrease in the relative width of secondary peaks induced by labels on the molecule. Our results show that increasing salt concentration beyond 4 mol/L is an accessible way for increasing translocation time in solid-state nanopore sensing, with possible implications for barcode sensing resolution.

bioRxiv (Cold Spring Harbor Laboratory)
University of Cambridge (GB)
UK Research and Innovation, HORIZON EUROPE Framework Programme
Nanopore and Nanochannel Transport Studies
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