RNA Signal Amplifier Circuit with Integrated Fluorescence Output

Farhima Akter, Yohei Yokobayashi

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


(Figure Presented). We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.

Original languageEnglish (US)
Pages (from-to)655-658
Number of pages4
JournalACS Synthetic Biology
Issue number5
StatePublished - May 15 2015


  • RNA circuit
  • RNA engineering
  • signal amplification
  • Spinach aptamer

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Biomedical Engineering

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