RNA Signal Amplifier Circuit with Integrated Fluorescence Output

Farhima Akter, Yohei Yokobayashi

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

(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
Volume4
Issue number5
DOIs
StatePublished - May 15 2015

Fingerprint

Spinacia oleracea
RNA
Fluorescence
Networks (circuits)
Nucleotide Aptamers
Amplification
Chemical activation
Ligands
Catalysts
Molecules

Keywords

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

ASJC Scopus subject areas

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

Cite this

RNA Signal Amplifier Circuit with Integrated Fluorescence Output. / Akter, Farhima; Yokobayashi, Yohei.

In: ACS Synthetic Biology, Vol. 4, No. 5, 15.05.2015, p. 655-658.

Research output: Contribution to journalArticle

Akter, Farhima ; Yokobayashi, Yohei. / RNA Signal Amplifier Circuit with Integrated Fluorescence Output. In: ACS Synthetic Biology. 2015 ; Vol. 4, No. 5. pp. 655-658.
@article{3721fe0ee0524c1cb18c39782b15fe68,
title = "RNA Signal Amplifier Circuit with Integrated Fluorescence Output",
abstract = "(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.",
keywords = "RNA circuit, RNA engineering, signal amplification, Spinach aptamer",
author = "Farhima Akter and Yohei Yokobayashi",
year = "2015",
month = "5",
day = "15",
doi = "10.1021/sb500314r",
language = "English (US)",
volume = "4",
pages = "655--658",
journal = "ACS Synthetic Biology",
issn = "2161-5063",
publisher = "American Chemical Society",
number = "5",

}

TY - JOUR

T1 - RNA Signal Amplifier Circuit with Integrated Fluorescence Output

AU - Akter, Farhima

AU - Yokobayashi, Yohei

PY - 2015/5/15

Y1 - 2015/5/15

N2 - (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.

AB - (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.

KW - RNA circuit

KW - RNA engineering

KW - signal amplification

KW - Spinach aptamer

UR - http://www.scopus.com/inward/record.url?scp=84929627568&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84929627568&partnerID=8YFLogxK

U2 - 10.1021/sb500314r

DO - 10.1021/sb500314r

M3 - Article

C2 - 25354355

AN - SCOPUS:84929627568

VL - 4

SP - 655

EP - 658

JO - ACS Synthetic Biology

JF - ACS Synthetic Biology

SN - 2161-5063

IS - 5

ER -