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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
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Sequence-Dependent Single-Molecule DNA Sensing Using Covalent Organic Framework Nanopores.

Linru Guo1, Xiao-Lei Xing1,2, Qiaobo Liao1

  • 1State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.

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Summary

Researchers developed a novel covalent organic framework (COF) nanopore for enzyme-free single-molecule DNA sequencing. This solid-state nanopore shows promise for distinguishing DNA bases and sequences, advancing nanopore sequencing technology.

Keywords:
COF nanoporesmononucleotidenanopipettesequencingsimulationsingle-molecule DNA

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Area of Science:

  • Nanotechnology
  • Molecular Biology
  • Materials Science

Background:

  • Enzyme-free single-molecule sequencing using nanopore technology offers broad applications but faces challenges with solid-state nanopores.
  • Accurate single-molecule DNA sequencing requires precise control over nanopore size and conformity, which conventional solid-state nanopores struggle to achieve.
  • Biological nanopores are suitable for enzyme-free sequencing, but solid-state alternatives are sought for greater control and scalability.

Purpose of the Study:

  • To fabricate and characterize a novel solid-state nanopore device for enzyme-free single-molecule DNA sequencing.
  • To assess the capability of the developed nanopore to distinguish DNA bases and identify sequence-specific patterns.
  • To investigate the factors influencing DNA molecule translocation and signal detection within the nanopore.

Main Methods:

  • Fabrication of nanopore devices using ultrathin two-dimensional (2D) covalent organic framework (COF) nanosheets on quartz nanopipette tips.
  • Characterization of COF nanopore size (≈ 1.1 nm) and atomic-scale structural consistency.
  • Conducting electrical measurements to detect current blockades from individual DNA molecules and performing finite element simulations.

Main Results:

  • The COF nanopore device demonstrated the ability to roughly distinguish between the four DNA bases (dAMP, dCMP, dGMP, dTMP).
  • Distinct sequence-specific resistive current patterns were observed for 150-nucleotide model DNA molecules, with significant percentages of unique blockade events.
  • Finite element simulations confirmed that DNA current blockade patterns are dependent on the nanopore's relative position within the nanopipette.

Conclusions:

  • Covalent organic framework (COF) nanosheets enable the fabrication of solid-state nanopores with precise dimensions suitable for single-molecule DNA analysis.
  • The developed COF nanopore device shows potential for enzyme-free single-molecule DNA sequencing by detecting sequence-dependent electrical signals.
  • This study represents a significant advancement towards achieving accurate single-molecule DNA sequencing using solid-state nanopore technology.