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Related Concept Videos

Super-resolution Fluorescence Microscopy01:37

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Super-resolution fluorescence microscopy (SRFM) provides a better resolution than conventional fluorescence microscopy by reducing the point spread function (PSF). PSF is the light intensity distribution from a point that causes it to appear blurred. Due to PSF, each fluorescing point appears bigger than its actual size, and it is the PSF interference of nearby fluorophores that causes the blurred image. Various approaches to achieving higher resolution through SRFM have recently been...
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Super-resolution Imaging of the Bacterial Division Machinery
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Proximity-Based Super-Resolution Imaging Enabled by DNA Base-Stacking Interactions.

Abhinav Banerjee1, Saanya Yadav2, Vedanth Shree Vidwath1

  • 1Department of Biochemistry, Indian Institute of Science, Malleswaram, Bangalore, 560012, India.

Small (Weinheim an Der Bergstrasse, Germany)
|November 22, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces Stack-Proximity-PAINT (Stack-pPAINT), a super-resolution imaging technique. It uses DNA base-stacking to visualize proximal target pairs, enabling high-resolution cellular interactome studies.

Keywords:
DNA OrigamiDNA base‐stackingDNA‐PAINTfluorescencekinetic analysismolecular dynamicssuper‐resolution imaging

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Nanotechnology

Background:

  • Super-resolution imaging allows visualization of biomolecules at nanometer resolution.
  • Detecting proximal target pairs is crucial for understanding cellular interactions.
  • Existing methods face challenges in resolving closely located molecules.

Purpose of the Study:

  • To develop a novel super-resolution imaging technique for detecting proximal target pairs.
  • To leverage DNA base-stacking interactions for enhanced probe stability and binding.
  • To apply this technique for visualizing cellular structures and interactions at high resolution.

Main Methods:

  • Development of Stack-Proximity-PAINT (Stack-pPAINT) utilizing DNA probe hybridization and base-stacking.
  • Employing atomistic equilibrium and steered molecular dynamics (MD) simulations to study probe hybridization mechanisms.
  • Utilizing programmable DNA nanostructures for benchmarking and cellular imaging of microtubular structures.

Main Results:

  • Stack-pPAINT effectively detects target pairs in close proximity by exploiting synergistic DNA hybridization and base-stacking.
  • Molecular dynamics simulations confirmed that DNA and fluorophore stacking stabilize the imager probe.
  • Successful visualization of microtubular structures by targeting alpha- and beta-tubulin molecules was achieved.

Conclusions:

  • Stack-pPAINT offers a robust method for super-resolution imaging of proximal molecular targets.
  • The technique enhances spatial resolution and provides mechanistic insights into molecular interactions.
  • This probe technology holds significant potential for advancing cell biology research and elucidating spatial interactomes.