RNA signal amplifier circuit with integrated fluorescence output

ACS Synth Biol. 2015 May 15;4(5):655-8. doi: 10.1021/sb500314r. Epub 2014 Nov 7.


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.

Keywords: RNA circuit; RNA engineering; Spinach aptamer; signal amplification.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Aptamers, Nucleotide / genetics
  • Base Sequence
  • Fluorescence
  • Molecular Sequence Data
  • RNA / genetics*
  • RNA, Plant / genetics*
  • Spinacia oleracea / genetics*


  • Aptamers, Nucleotide
  • RNA, Plant
  • RNA