title: RNA signal amplifier circuit with integrated fluorescence output.
abstract: 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.
authors.affiliation: †Department of Biomedical Engineering, University of California, Davis 451 Health Sciences Drive, Davis, California 95616, United States.
authors.forename: Farhima
authors.initials: F
authors.lastname: Akter
authors.affiliation: †Department of Biomedical Engineering, University of California, Davis 451 Health Sciences Drive, Davis, California 95616, United States.|‡Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Yokobayashi
mesh_terms: D052157:Aptamers, Nucleotide / Q000235:genetics; D001483:Base Sequence; D005453:Fluorescence; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D018724:Spinacia oleracea / Q000235:genetics*
chemical_list: D052157:Aptamers, Nucleotide; D018749:RNA, Plant; D012313:RNA
keywords: RNA circuit; RNA engineering; Spinach aptamer; signal amplification