Quantitative super-resolution imaging with qPAINT

Nat Methods. 2016 May;13(5):439-42. doi: 10.1038/nmeth.3804. Epub 2016 Mar 28.


Counting molecules in complexes is challenging, even with super-resolution microscopy. Here, we use the programmable and specific binding of dye-labeled DNA probes to count integer numbers of targets. This method, called quantitative points accumulation in nanoscale topography (qPAINT), works independently of dye photophysics for robust counting with high precision and accuracy over a wide dynamic range. qPAINT was benchmarked on DNA nanostructures and demonstrated for cellular applications by quantifying proteins in situ and the number of single-molecule FISH probes bound to an mRNA target.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Fluorescent Dyes / chemistry
  • Humans
  • Image Enhancement / methods*
  • In Situ Hybridization, Fluorescence / methods*
  • Microscopy, Confocal / methods
  • Microscopy, Fluorescence / methods*
  • Molecular Docking Simulation
  • Sequence Analysis, DNA
  • Software


  • Fluorescent Dyes
  • DNA