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acssynbio.7b00059
85. Bhadra S, Ellington AD (2014) Design and
application
of
cotranscriptional
non-enzymatic RNA circuits and signal transducers. Nucleic Acids Res 42(7):e58. https://
doi.org/10.1093/nar/gku074
86. Akter F, Yokobayashi Y (2015) RNA signal
amplifier circuit with integrated fluorescence
output. ACS Synth Biol 4(5):655–658.
https://doi.org/10.1021/sb500314r
87. Tang X, Deng R, Sun Y, Ren X, Zhou M, Li J
(2018) Amplified tandem spinach-based aptamer transcription enables low background
miRNA
detection.
Anal
Chem
90
(16):10001–10008.
https://doi.org/10.
1021/acs.analchem.8b02471
88. Ying ZM, Tu B, Liu L, Tang H, Tang LJ,
Jiang JH (2018) Spinach-based fluorescent
light-up biosensors for multiplexed and
label-free detection of microRNAs. Chem
Commun
(Camb)
54(24):3010–3013.
https://doi.org/10.1039/c8cc00123e
89. Zhou M, Teng X, Li Y, Deng R, Li J (2019)
Cascade transcription amplification of RNA
aptamer for ultrasensitive microRNA detection. Anal Chem 91(8):5295–5302. https://
doi.org/10.1021/acs.analchem.9b00124
90. Hofer K, Langejurgen LV, Jaschke A (2013)
Universal aptamer-based real-time monitoring of enzymatic RNA synthesis. J Am Chem
Soc 135(37):13692–13694. https://doi.
org/10.1021/ja407142f
91. Pothoulakis G, Ceroni F, Reeve B, Ellis T
(2013) The Spinach RNA aptamer as a characterization tool for synthetic biology. ACS
Synth
Biol.
https://doi.org/10.1021/
sb400089c
92. Chizzolini F, Forlin M, Cecchi D, Mansy SS
(2014) Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter
strength. ACS Synth Biol 3(6):363–371.
https://doi.org/10.1021/sb4000977
93. Chizzolini F, Forlin M, Yeh Martin N,
Berloffa G, Cecchi D, Mansy SS (2017) Cellfree translation is more variable than transcription. ACS Synth Biol 6(4):638–647.
https://doi.org/10.1021/acssynbio.
6b00250
94. Auslander S, Fuchs D, Hurlemann S,
Auslander D, Fussenegger M (2016) Engineering a ribozyme cleavage-induced split
fluorescent aptamer complementation assay.
Nucleic Acids Res 44(10):e94. https://doi.
org/10.1093/nar/gkw117
95. Poudyal RR, Benslimane M, Lokugamage
MP, Callaway MK, Staller S, Burke DH
(2017) Selective inactivation of functional
RNAs by ribozyme-catalyzed covalent modification. ACS Synth Biol 6(3):528–534.
https://doi.org/10.1021/acssynbio.
6b00222
96. Bhadra S, Ellington AD (2014) A Spinach
molecular beacon triggered by strand displacement. RNA 20(8):1183–1194. https://
doi.org/10.1261/rna.045047.114
97. Goldsworthy V, LaForce G, Abels S, Khisamutdinov EF (2018) Fluorogenic RNA aptamers: a nano-platform for fabrication of
simple and combinatorial logic gates. Nanomaterials (Basel) 8(12). https://doi.org/10.
3390/nano8120984
98. Shu D, Shu Y, Haque F, Abdelmawla S, Guo
P (2011) Thermodynamically stable RNA
three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat Nanotechnol 6(10):658–667.
https://doi.org/10.1038/nnano.2011.105
99. Shu D, Khisamutdinov EF, Zhang L, Guo P
(2014) Programmable folding of fusion RNA
in vivo and in vitro driven by pRNA 3WJ
motif of Phi29 DNA packaging motor.
Nucleic Acids Res 42(2):e10. https://doi.
org/10.1093/nar/gkt885
100. Afonin KA, Bindewald E, Yaghoubian AJ,
Voss N, Jacovetty E, Shapiro BA, Jaeger L
(2010) In vitro assembly of cubic
RNA-based scaffolds designed in silico. Nat
Nanotechnol 5(9):676–682. https://doi.
org/10.1038/nnano.2010.160
101. Afonin KA, Viard M, Martins AN, Lockett SJ,
Maciag AE, Freed EO, Heldman E, Jaeger L,
Blumenthal R, Shapiro BA (2013) Activation
of different split functionalities on
re-association of RNA-DNA hybrids. Nat
Nanotechnol 8(4):296–304. https://doi.
org/10.1038/nnano.2013.44
102. Chopra A, Sagredo S, Grossi G, Andersen ES,
Simmel FC (2019) Out-of-plane aptamer
functionalization of RNA three-helix tiles.
Nanomaterials (Basel) 9(4). https://doi.
org/10.3390/nano9040507
103. Afonin KA, Danilov EO, Novikova IV, Leontis NB (2008) TokenRNA: a new type of
sequence-specific, label-free fluorescent biosensor for folded RNA molecules. Chembiochem 9(12):1902–1905. https://doi.org/
10.1002/cbic.200800183
104. O’Hara JM, Marashi D, Morton S, Jaeger L,
Grabow WW (2019) Optimization of the
split-Spinach aptamer for monitoring
100
Michael Ryckelynck
acssynbio.7b00059
85. Bhadra S, Ellington AD (2014) Design and
application
of
cotranscriptional
non-enzymatic RNA circuits and signal transducers. Nucleic Acids Res 42(7):e58. https://
doi.org/10.1093/nar/gku074
86. Akter F, Yokobayashi Y (2015) RNA signal
amplifier circuit with integrated fluorescence
output. ACS Synth Biol 4(5):655–658.
https://doi.org/10.1021/sb500314r
87. Tang X, Deng R, Sun Y, Ren X, Zhou M, Li J
(2018) Amplified tandem spinach-based aptamer transcription enables low background
miRNA
detection.
Anal
Chem
90
(16):10001–10008.
https://doi.org/10.
1021/acs.analchem.8b02471
88. Ying ZM, Tu B, Liu L, Tang H, Tang LJ,
Jiang JH (2018) Spinach-based fluorescent
light-up biosensors for multiplexed and
label-free detection of microRNAs. Chem
Commun
(Camb)
54(24):3010–3013.
https://doi.org/10.1039/c8cc00123e
89. Zhou M, Teng X, Li Y, Deng R, Li J (2019)
Cascade transcription amplification of RNA
aptamer for ultrasensitive microRNA detection. Anal Chem 91(8):5295–5302. https://
doi.org/10.1021/acs.analchem.9b00124
90. Hofer K, Langejurgen LV, Jaschke A (2013)
Universal aptamer-based real-time monitoring of enzymatic RNA synthesis. J Am Chem
Soc 135(37):13692–13694. https://doi.
org/10.1021/ja407142f
91. Pothoulakis G, Ceroni F, Reeve B, Ellis T
(2013) The Spinach RNA aptamer as a characterization tool for synthetic biology. ACS
Synth
Biol.
https://doi.org/10.1021/
sb400089c
92. Chizzolini F, Forlin M, Cecchi D, Mansy SS
(2014) Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter
strength. ACS Synth Biol 3(6):363–371.
https://doi.org/10.1021/sb4000977
93. Chizzolini F, Forlin M, Yeh Martin N,
Berloffa G, Cecchi D, Mansy SS (2017) Cellfree translation is more variable than transcription. ACS Synth Biol 6(4):638–647.
https://doi.org/10.1021/acssynbio.
6b00250
94. Auslander S, Fuchs D, Hurlemann S,
Auslander D, Fussenegger M (2016) Engineering a ribozyme cleavage-induced split
fluorescent aptamer complementation assay.
Nucleic Acids Res 44(10):e94. https://doi.
org/10.1093/nar/gkw117
95. Poudyal RR, Benslimane M, Lokugamage
MP, Callaway MK, Staller S, Burke DH
(2017) Selective inactivation of functional
RNAs by ribozyme-catalyzed covalent modification. ACS Synth Biol 6(3):528–534.
https://doi.org/10.1021/acssynbio.
6b00222
96. Bhadra S, Ellington AD (2014) A Spinach
molecular beacon triggered by strand displacement. RNA 20(8):1183–1194. https://
doi.org/10.1261/rna.045047.114
97. Goldsworthy V, LaForce G, Abels S, Khisamutdinov EF (2018) Fluorogenic RNA aptamers: a nano-platform for fabrication of
simple and combinatorial logic gates. Nanomaterials (Basel) 8(12). https://doi.org/10.
3390/nano8120984
98. Shu D, Shu Y, Haque F, Abdelmawla S, Guo
P (2011) Thermodynamically stable RNA
three-way junction for constructing multifunctional nanoparticles for delivery of therapeutics. Nat Nanotechnol 6(10):658–667.
https://doi.org/10.1038/nnano.2011.105
99. Shu D, Khisamutdinov EF, Zhang L, Guo P
(2014) Programmable folding of fusion RNA
in vivo and in vitro driven by pRNA 3WJ
motif of Phi29 DNA packaging motor.
Nucleic Acids Res 42(2):e10. https://doi.
org/10.1093/nar/gkt885
100. Afonin KA, Bindewald E, Yaghoubian AJ,
Voss N, Jacovetty E, Shapiro BA, Jaeger L
(2010) In vitro assembly of cubic
RNA-based scaffolds designed in silico. Nat
Nanotechnol 5(9):676–682. https://doi.
org/10.1038/nnano.2010.160
101. Afonin KA, Viard M, Martins AN, Lockett SJ,
Maciag AE, Freed EO, Heldman E, Jaeger L,
Blumenthal R, Shapiro BA (2013) Activation
of different split functionalities on
re-association of RNA-DNA hybrids. Nat
Nanotechnol 8(4):296–304. https://doi.
org/10.1038/nnano.2013.44
102. Chopra A, Sagredo S, Grossi G, Andersen ES,
Simmel FC (2019) Out-of-plane aptamer
functionalization of RNA three-helix tiles.
Nanomaterials (Basel) 9(4). https://doi.
org/10.3390/nano9040507
103. Afonin KA, Danilov EO, Novikova IV, Leontis NB (2008) TokenRNA: a new type of
sequence-specific, label-free fluorescent biosensor for folded RNA molecules. Chembiochem 9(12):1902–1905. https://doi.org/
10.1002/cbic.200800183
104. O’Hara JM, Marashi D, Morton S, Jaeger L,
Grabow WW (2019) Optimization of the
split-Spinach aptamer for monitoring
100
Michael Ryckelynck