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Related Experiment Video

Updated: Jul 13, 2025

Author Spotlight: Single-Molecule Surface-Enhanced Raman Scattering Measurements Enabled by Plasmonic DNA Origami Nanoantennas
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DNA Origami-Based Single-Molecule Force Spectroscopy and Applications.

Kevin Kramm1, Tim Schröder2, Andrés Manuel Vera2

  • 1University of Regensburg, Department of Microbiology and Archaea Centre, Regensburg, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|October 12, 2023
PubMed
Summary
This summary is machine-generated.

We developed a novel DNA origami force clamp (FC) to precisely measure single-molecule protein-DNA interactions. This freely diffusing nanodevice overcomes thermal noise, enabling detailed studies of force-dependent binding events.

Keywords:
BiophysicsDNA nanotechnologyDNA origamiDNA-protein interactionFluorescence spectroscopyForce spectroscopyMechanobiologySingle-molecule FRET

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Area of Science:

  • Biophysics
  • Nanotechnology
  • Molecular Biology

Background:

  • Single-molecule force spectroscopy reveals mechanical stimuli's role in biochemical signaling.
  • Existing methods like AFM and tweezers are limited by thermal noise.
  • A freely diffusing nanodevice is needed to overcome these limitations.

Purpose of the Study:

  • Introduce a DNA origami force clamp (FC) for piconewton force generation.
  • Provide a protocol for designing and generating a custom FC.
  • Enable sensitive detection of protein binding via FRET.

Main Methods:

  • Utilized molecular cloning for DNA scaffold modification, production, and purification.
  • Generated fluorescently labeled DNA via enzymatic ligation for FRET detection.
  • Employed thermal annealing and agarose gel electrophoresis for FC assembly and purification.

Main Results:

  • Successfully designed and generated a DNA origami FC.
  • Demonstrated FRET-based detection of protein binding to DNA under tension.
  • Quantified force-dependent DNA-protein interactions using single-molecule FRET.

Conclusions:

  • The DNA origami FC overcomes thermal noise limitations of traditional methods.
  • This approach allows parallelized, single-molecule analysis of thousands of molecules.
  • Enables precise quantification of force-dependent DNA-protein interactions.