Single-cell in situ RNA analysis with switchable fluorescent oligonucleotides

Lu Xiao, Jia Guo

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Comprehensive RNA analyses in individual cells in their native spatial contexts promise to transform our understanding of normal physiology and disease pathogenesis. Here we report a single-cell in situ RNA analysis approach using switchable fluorescent oligonucleotides (SFO). In this method, transcripts are first hybridized by pre-decoding oligonucleotides. These oligonucleotides subsequently recruit SFO to stain their corresponding RNA targets. After fluorescence imaging, all the SFO in the whole specimen are simultaneously removed by DNA strand displacement reactions. Through continuous cycles of target staining, fluorescence imaging, and SFO removal, a large number of different transcripts can be identified by unique fluorophore sequences and visualized at the optical resolution. To demonstrate the feasibility of this approach, we show that the hybridized SFO can be efficiently stripped by strand displacement reactions within 30 min. We also demonstrate that this SFO removal process maintains the integrity of the RNA targets and the pre-decoding oligonucleotides, and keeps them hybridized. Applying this approach, we show that transcripts can be restained in at least eight hybridization cycles with high analysis accuracy, which theoretically would enable the whole transcriptome to be quantified at the single molecule sensitivity in individual cells. This in situ RNA analysis technology will have wide applications in systems biology, molecular diagnosis, and targeted therapies.

Original languageEnglish (US)
Article number42
JournalFrontiers in Cell and Developmental Biology
Issue numberAPR
StatePublished - Apr 11 2018


  • Fluorescence in situ hybridization
  • Fluorescent probes
  • Genomics
  • Oligonucleotides
  • RNA expression
  • Single-cell
  • Strand displacement reactions
  • Transcriptomics

ASJC Scopus subject areas

  • Developmental Biology
  • Cell Biology


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