Nanoscale imaging of RNA with expansion microscopy

Nat Methods. 2016 Aug;13(8):679-84. doi: 10.1038/nmeth.3899. Epub 2016 Jul 4.

Abstract

The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be covalently attached to a swellable polyelectrolyte gel synthesized throughout a biological specimen. Then, postexpansion, fluorescent in situ hybridization (FISH) imaging of RNA can be performed with high yield and specificity as well as single-molecule precision in both cultured cells and intact brain tissue. Expansion FISH (ExFISH) separates RNAs and supports amplification of single-molecule signals (i.e., via hybridization chain reaction) as well as multiplexed RNA FISH readout. ExFISH thus enables super-resolution imaging of RNA structure and location with diffraction-limited microscopes in thick specimens, such as intact brain tissue and other tissues of importance to biology and medicine.

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

  • Acrylamides / chemistry*
  • Animals
  • Brain / cytology
  • Brain / metabolism*
  • Cells, Cultured
  • HeLa Cells
  • Humans
  • Image Processing, Computer-Assisted / methods
  • In Situ Hybridization, Fluorescence / methods*
  • Mice
  • Microscopy, Fluorescence / methods*
  • Nanotechnology / methods*
  • Oligonucleotide Probes / chemistry
  • Optical Imaging / methods*
  • RNA / analysis*
  • RNA / chemistry
  • RNA / metabolism

Substances

  • Acrylamides
  • Oligonucleotide Probes
  • RNA