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Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection.

Tilman Schlotter1, Tom Kloter1, Julian Hengsteler1

  • 1Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland.

ACS Nano
|February 14, 2024
PubMed
Summary

Researchers developed a new nanopore sensing method using DNA aptamers to detect specific amino acids in peptides. This advance brings single-molecule proteomics closer by enabling precise identification of phenylalanine in single-molecule analysis.

Keywords:
DNAfluid force microscopyforce-controlled interface nanoporeoptical waveguide lightmode spectroscopyphenylalaninesingle-molecule sensing

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Area of Science:

  • Biotechnology
  • Nanotechnology
  • Analytical Chemistry

Background:

  • Single-molecule proteomics using nanopore technology shows promise but faces challenges.
  • Achieving single amino acid resolution requires precise control of nanopore size and translocation speed.

Purpose of the Study:

  • To develop a nanopore sensing method with single amino acid resolution.
  • To integrate dynamically tunable nanopores with amino acid-specific DNA aptamers.

Main Methods:

  • Interface nanopores with dynamically tunable sizes were created.
  • Amino acid-specific DNA aptamers (phenylalanine aptamer) were integrated into the nanopores.
  • Optical waveguide lightmode spectroscopy was used to differentiate specific and nonspecific binding.
  • Ionic current signals were analyzed at varying applied voltages.

Main Results:

  • Phenylalanine aptamers recognized specific phenylalanine-containing peptides by binding to the benzyl/phenyl and carbonyl groups.
  • Aptamer-modified nanopores successfully differentiated phenylalanine peptides from control peptides (tyrosine, tryptophan).
  • Lowering voltage prolonged aptamer-target interactions, revealing discrete ionic current levels with repetitive motifs.

Conclusions:

  • The developed method demonstrates the potential for single amino acid recognition in nanopore sensing.
  • This technique represents a significant step towards achieving single-molecule proteomics.
  • Dynamically tunable aptamer-modified nanopores offer a pathway for precise peptide analysis.