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Related Experiment Video

Updated: May 23, 2026

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Visualizing poloidal orientation in DNA minicircles.

Tony Lemos1, Harold D Kim1

  • 1School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430, USA.

Biophysical Journal
|May 22, 2026
PubMed
Summary
This summary is machine-generated.

Researchers experimentally confirmed DNA minicircles adopt specific orientations. Using atomic force microscopy, they visualized preferred poloidal orientations in double-stranded DNA (dsDNA) minicircles, validating theoretical predictions.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • DNA minicircles are formed by ligating short double-stranded DNA (dsDNA) molecules.
  • Theoretical models predict sequence-dependent, nonuniform bending energetics cause DNA minicircles to adopt a specific inside-out orientation, termed poloidal orientation.
  • Experimental evidence for this poloidal orientation has been limited.

Purpose of the Study:

  • To experimentally visualize and confirm the predicted poloidal orientation of DNA minicircles.
  • To investigate sequence-specific differences in DNA minicircle orientation.
  • To provide empirical support for theoretical predictions regarding DNA minicircle structure.

Main Methods:

  • Development of a single-molecule approach utilizing atomic force microscopy (AFM).
  • Construction of DNA minicircles with a single biotin label at varying positions along the dsDNA.
  • Imaging the location of biotin-bound NeutrAvidin relative to the DNA minicircle to infer orientation.

Main Results:

  • Observed distinct shifts in NeutrAvidin positions (inside/outside minicircle) for different DNA sequences, indicating varied poloidal orientations.
  • AFM results were consistent with coarse-grained simulations, which showed narrowly distributed poloidal orientations with sequence-specific mean orientations.
  • Provided the first experimental confirmation of preferred poloidal orientations in DNA minicircles.

Conclusions:

  • DNA minicircles exhibit experimentally verified preferred poloidal orientations, influenced by their specific DNA sequences.
  • This study bridges the gap between theoretical predictions and experimental observation of DNA minicircle dynamics.
  • Findings offer valuable insights into the intrinsic structural dynamics and conformational preferences of circular DNA molecules.