Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

Nat Methods. 2014 Mar;11(3):313-8. doi: 10.1038/nmeth.2835. Epub 2014 Feb 2.


Super-resolution fluorescence microscopy is a powerful tool for biological research, but obtaining multiplexed images for a large number of distinct target species remains challenging. Here we use the transient binding of short fluorescently labeled oligonucleotides (DNA-PAINT, a variation of point accumulation for imaging in nanoscale topography) for simple and easy-to-implement multiplexed super-resolution imaging that achieves sub-10-nm spatial resolution in vitro on synthetic DNA structures. We also report a multiplexing approach (Exchange-PAINT) that allows sequential imaging of multiple targets using only a single dye and a single laser source. We experimentally demonstrate ten-color super-resolution imaging in vitro on synthetic DNA structures as well as four-color two-dimensional (2D) imaging and three-color 3D imaging of proteins in fixed cells.

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

  • Color
  • Cytological Techniques / methods*
  • DNA / chemistry
  • Imaging, Three-Dimensional*
  • Microscopy, Fluorescence / trends*


  • DNA