Super-Resolution Spatial Proximity Detection with Proximity-PAINT

Angew Chem Int Ed Engl. 2021 Jan 11;60(2):716-720. doi: 10.1002/anie.202009031. Epub 2020 Nov 9.


Visualizing the functional interactions of biomolecules such as proteins and nucleic acids is key to understanding cellular life on the molecular scale. Spatial proximity is often used as a proxy for the direct interaction of biomolecules. However, current techniques to visualize spatial proximity are either limited by spatial resolution, dynamic range, or lack of single-molecule sensitivity. Here, we introduce Proximity-PAINT (pPAINT), a variation of the super-resolution microscopy technique DNA-PAINT. pPAINT uses a split-docking-site configuration to detect spatial proximity with high sensitivity, low false-positive rates, and tunable detection distances. We benchmark and optimize pPAINT using designer DNA nanostructures and demonstrate its cellular applicability by visualizing the spatial proximity of alpha- and beta-tubulin in microtubules using super-resolution detection.

Keywords: DNA-PAINT; Protein-Protein interactions; Proximity detection; Single Molecule Imaging; Super-resolution microscopy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibodies / immunology
  • DNA / chemistry
  • DNA / metabolism
  • Fluorescence Resonance Energy Transfer
  • Microscopy, Fluorescence / methods*
  • Microtubules / chemistry
  • Nanostructures / chemistry
  • Nucleic Acid Hybridization
  • Tubulin / analysis*
  • Tubulin / immunology


  • Antibodies
  • Tubulin
  • DNA