Fluorescent Probes for Live-Cell RNA Detection

Annu Rev Biomed Eng. 2009;11:25-47. doi: 10.1146/annurev-bioeng-061008-124920.


Commonly used techniques for analyzing gene expression, such as polymerase chain reaction (PCR), microarrays, and in situ hybridization, have proven invaluable in understanding RNA processing and regulation. However, these techniques rely on the use of lysed and/or fixed cells and are therefore limited in their ability to provide important spatial-temporal information. This has led to the development of numerous techniques for imaging RNA in living cells, some of which have already provided important insight into the dynamic role RNA plays in dictating cell behavior. Here we review the fluorescent probes that have allowed for RNA imaging in living cells and discuss their utility and limitations. Common challenges faced by fluorescent probes, such as probe design, delivery, and target accessibility, are also discussed. It is expected that continued advancements in live cell imaging of RNA will open new and exciting opportunities in a wide range of biological and medical applications.

Publication types

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

MeSH terms

  • 3' Untranslated Regions
  • Cell Membrane / metabolism
  • Electroporation
  • Fluorescence Resonance Energy Transfer
  • Fluorescent Dyes / analysis*
  • Fluorescent Dyes / chemistry
  • Gene Expression Profiling / instrumentation
  • Green Fluorescent Proteins / chemistry
  • Humans
  • In Situ Hybridization
  • Microscopy, Fluorescence / instrumentation
  • Microscopy, Fluorescence / methods*
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • RNA / metabolism
  • RNA, Messenger / metabolism


  • 3' Untranslated Regions
  • Fluorescent Dyes
  • RNA, Messenger
  • Green Fluorescent Proteins
  • RNA