124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics

Nano Lett. 2019 Apr 10;19(4):2641-2646. doi: 10.1021/acs.nanolett.9b00508. Epub 2019 Mar 13.


Optical super-resolution techniques reach unprecedented spatial resolution down to a few nanometers. However, efficient multiplexing strategies for the simultaneous detection of hundreds of molecular species are still elusive. Here, we introduce an entirely new approach to multiplexed super-resolution microscopy by designing the blinking behavior of targets with engineered binding frequency and duration in DNA-PAINT. We assay this kinetic barcoding approach in silico and in vitro using DNA origami structures, show the applicability for multiplexed RNA and protein detection in cells, and finally experimentally demonstrate 124-plex super-resolution imaging within minutes.

Keywords: DNA nanotechnology; DNA-PAINT; Super-resolution microscopy; barcoding; multiplexing.

Publication types

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

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • Kinetics
  • Microscopy, Fluorescence / methods*
  • Nucleic Acid Conformation
  • Oligonucleotides / chemistry
  • Proteins / chemistry
  • Proteins / isolation & purification*
  • RNA / chemistry
  • RNA / isolation & purification*


  • Oligonucleotides
  • Proteins
  • RNA
  • DNA