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Updated: Jan 1, 2026

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Flossing DNA in a Dual Nanopore Device.

Xu Liu1, Philip Zimny1, Yuning Zhang2

  • 1Ontera Inc., Santa Cruz, CA, 95060, USA.

Small (Weinheim an Der Bergstrasse, Germany)
|December 21, 2019
PubMed
Summary
This summary is machine-generated.

Active control using dual solid-state nanopores, termed "flossing," significantly reduces molecular noise in single-molecule DNA mapping. This technique improves DNA linearization and enables precise mapping of molecular motifs for genomic applications.

Keywords:
DNA sensingactive controlgenome mappingnanoporessingle molecules

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Area of Science:

  • Biophysics
  • Nanotechnology
  • Genomics

Background:

  • Solid-state nanopores offer single-molecule analysis, overcoming ensemble averaging limitations.
  • Mapping molecular motifs on DNA using nanopores and barcoding is promising but hindered by noise.
  • Existing methods struggle with molecular noise and DNA linearization for accurate mapping.

Purpose of the Study:

  • To introduce an active control technique called "flossing" using a dual nanopore device.
  • To suppress molecular noise and enhance DNA linearization for precise single-molecule mapping.
  • To demonstrate the utility of flossing for genome mapping and structural variation analysis.

Main Methods:

  • Utilized a dual nanopore device for active control and trapping of protein-tagged DNA molecules.
  • Performed hundreds of bidirectional electrical scans of DNA molecules within seconds.
  • Employed protein motifs on λ-DNA as detectable features for triggering bidirectional control.

Main Results:

  • Flossing suppressed molecular noise by averaging multiscan data, yielding accurate inter-tag distance estimates.
  • Achieved >98% trans-pore DNA linearization by the second scan, a significant improvement over single-pore passage (35%).
  • Demonstrated comparable inter-tag distance estimates to known values for protein motifs on λ-DNA.

Conclusions:

  • The dual-pore flossing technique effectively reduces noise and enhances DNA linearization for single-molecule mapping.
  • This method shows potential for applications in genome mapping, structural variation analysis, and epigenetic locus mapping.
  • Flossing, combined with barcoding, advances the capabilities of nanopore-based molecular analysis.