Localization of ASH1 mRNA particles in living yeast. Mol Cell 2(4):437–445
6. Buxbaum AR, Haimovich G, Singer RH
(2015) In the right place at the right time:
visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 16(2):95–109.
https://doi.org/10.1038/nrm3918
7. Babendure JR, Adams SR, Tsien RY (2003)
Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125
(48):14716–14717.
https://doi.org/10.
1021/ja037994o
8. Ouellet J (2016) RNA fluorescence with
light-up aptamers. Front Chem 4:29.
https://doi.org/10.3389/fchem.2016.
00029
9. Bouhedda F, Autour A, Ryckelynck M (2018)
Light-up RNA aptamers and their cognate
fluorogens: from their development to their
applications. Int J Mol Sci 19(1):44. https://
doi.org/10.3390/ijms19010044
10. Neubacher S, Hennig S (2019) RNA structure and cellular applications of fluorescent
light-up aptamers. Angew Chem Int Ed Engl
58(5):1266–1279.
https://doi.org/10.
1002/anie.201806482
11. Grate D, Wilson C (1999) Laser-mediated,
site-specific inactivation of RNA transcripts.
Proc Natl Acad Sci U S A 96(11):6131–6136
12. Sando S, Narita A, Aoyama Y (2007) Light-up
Hoechst-DNA aptamer pair: generation of an
aptamer-selective fluorophore from a conventional DNA-staining dye. Chembiochem 8
(15):1795–1803. https://doi.org/10.1002/
cbic.200700325
13. Sando S, Narita A, Hayami M, Aoyama Y
(2008) Transcription monitoring using fused
RNA with a dye-binding light-up aptamer as a
tag: a blue fluorescent RNA. Chem Commun
(Camb) 44(33):3858–3860. https://doi.
org/10.1039/b808449a
14. Dolgosheina EV, Jeng SC, Panchapakesan SS,
Cojocaru R, Chen PS, Wilson PD,
Hawkins N, Wiggins PA, Unrau PJ (2014)
RNA mango aptamer-fluorophore: a bright,
high-affinity complex for RNA labeling and
tracking. ACS Chem Biol 9(10):2412–2420.
https://doi.org/10.1021/cb500499x
15. Jepsen MDE, Sparvath SM, Nielsen TB,
Langvad AH, Grossi G, Gothelf KV, Andersen
ES (2018) Development of a genetically
encodable FRET system using fluorescent
RNA aptamers. Nat Commun 9(1):18.
https://doi.org/10.1038/s41467-01702435-x
16. Constantin TP, Silva GL, Robertson KL,
Hamilton TP, Fague K, Waggoner AS,
Armitage BA (2008) Synthesis of new fluorogenic cyanine dyes and incorporation into
RNA fluoromodules. Org Lett 10
(8):1561–1564. https://doi.org/10.1021/
ol702920e
17. Tan X, Constantin TP, Sloane KL, Waggoner
AS, Bruchez MP, Armitage BA (2017) Fluoromodules consisting of a promiscuous RNA
aptamer and red or blue fluorogenic cyanine
dyes: selection, characterization, and bioimaging. J Am Chem Soc 139(26):9001–9009.
https://doi.org/10.1021/jacs.7b04211
18. Paige JS, Wu KY, Jaffrey SR (2011) RNA
mimics of green fluorescent protein. Science
333(6042):642–646.
https://doi.org/10.
1126/science.1207339
19. Song W, Strack RL, Svensen N, Jaffrey SR
(2014) Plug-and-play fluorophores extend
the spectral properties of spinach. J Am
Chem Soc 136(4):1198–1201. https://doi.
org/10.1021/ja410819x
20. Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X,
Hu X, Wang H, Lei C, Nie Z, Yao S (2017)
DNA mimics of red fluorescent proteins
(RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res
45(18):10380–10392. https://doi.org/10.
1093/nar/gkx803
21. Song W, Filonov GS, Kim H, Hirsch M, Li X,
Moon JD, Jaffrey SR (2017) Imaging RNA
polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem
Biol 13(11):1187–1194. https://doi.org/
10.1038/nchembio.2477
22. Steinmetzger C, Palanisamy N, Gore KR,
Hobartner C (2019) A multicolor large
Stokes shift fluorogen-activating RNA aptamer with cationic chromophores. Chemistry
25(8):1931–1935.
https://doi.org/10.
1002/chem.201805882
23. Han KY, Leslie BJ, Fei J, Zhang J, Ha T
(2013) Understanding the photophysics of
the spinach-DFHBI RNA aptamer-fluorogen
complex to improve live-cell RNA imaging. J
Am Chem Soc 135(50):19033–19038.
https://doi.org/10.1021/ja411060p
24. You M, Jaffrey SR (2015) Structure and
mechanism of RNA mimics of green fluorescent protein. Annu Rev Biophys 44:187–206.
https://doi.org/10.1146/annurev-biophys060414-033954
25. Klymchenko AS (2017) Solvatochromic and
fluorogenic dyes as environment-sensitive
probes: design and biological applications.
Acc Chem Res 50(2):366–375. https://doi.
org/10.1021/acs.accounts.6b00517
96
Michael Ryckelynck
6. Buxbaum AR, Haimovich G, Singer RH
(2015) In the right place at the right time:
visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 16(2):95–109.
https://doi.org/10.1038/nrm3918
7. Babendure JR, Adams SR, Tsien RY (2003)
Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125
(48):14716–14717.
https://doi.org/10.
1021/ja037994o
8. Ouellet J (2016) RNA fluorescence with
light-up aptamers. Front Chem 4:29.
https://doi.org/10.3389/fchem.2016.
00029
9. Bouhedda F, Autour A, Ryckelynck M (2018)
Light-up RNA aptamers and their cognate
fluorogens: from their development to their
applications. Int J Mol Sci 19(1):44. https://
doi.org/10.3390/ijms19010044
10. Neubacher S, Hennig S (2019) RNA structure and cellular applications of fluorescent
light-up aptamers. Angew Chem Int Ed Engl
58(5):1266–1279.
https://doi.org/10.
1002/anie.201806482
11. Grate D, Wilson C (1999) Laser-mediated,
site-specific inactivation of RNA transcripts.
Proc Natl Acad Sci U S A 96(11):6131–6136
12. Sando S, Narita A, Aoyama Y (2007) Light-up
Hoechst-DNA aptamer pair: generation of an
aptamer-selective fluorophore from a conventional DNA-staining dye. Chembiochem 8
(15):1795–1803. https://doi.org/10.1002/
cbic.200700325
13. Sando S, Narita A, Hayami M, Aoyama Y
(2008) Transcription monitoring using fused
RNA with a dye-binding light-up aptamer as a
tag: a blue fluorescent RNA. Chem Commun
(Camb) 44(33):3858–3860. https://doi.
org/10.1039/b808449a
14. Dolgosheina EV, Jeng SC, Panchapakesan SS,
Cojocaru R, Chen PS, Wilson PD,
Hawkins N, Wiggins PA, Unrau PJ (2014)
RNA mango aptamer-fluorophore: a bright,
high-affinity complex for RNA labeling and
tracking. ACS Chem Biol 9(10):2412–2420.
https://doi.org/10.1021/cb500499x
15. Jepsen MDE, Sparvath SM, Nielsen TB,
Langvad AH, Grossi G, Gothelf KV, Andersen
ES (2018) Development of a genetically
encodable FRET system using fluorescent
RNA aptamers. Nat Commun 9(1):18.
https://doi.org/10.1038/s41467-01702435-x
16. Constantin TP, Silva GL, Robertson KL,
Hamilton TP, Fague K, Waggoner AS,
Armitage BA (2008) Synthesis of new fluorogenic cyanine dyes and incorporation into
RNA fluoromodules. Org Lett 10
(8):1561–1564. https://doi.org/10.1021/
ol702920e
17. Tan X, Constantin TP, Sloane KL, Waggoner
AS, Bruchez MP, Armitage BA (2017) Fluoromodules consisting of a promiscuous RNA
aptamer and red or blue fluorogenic cyanine
dyes: selection, characterization, and bioimaging. J Am Chem Soc 139(26):9001–9009.
https://doi.org/10.1021/jacs.7b04211
18. Paige JS, Wu KY, Jaffrey SR (2011) RNA
mimics of green fluorescent protein. Science
333(6042):642–646.
https://doi.org/10.
1126/science.1207339
19. Song W, Strack RL, Svensen N, Jaffrey SR
(2014) Plug-and-play fluorophores extend
the spectral properties of spinach. J Am
Chem Soc 136(4):1198–1201. https://doi.
org/10.1021/ja410819x
20. Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X,
Hu X, Wang H, Lei C, Nie Z, Yao S (2017)
DNA mimics of red fluorescent proteins
(RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res
45(18):10380–10392. https://doi.org/10.
1093/nar/gkx803
21. Song W, Filonov GS, Kim H, Hirsch M, Li X,
Moon JD, Jaffrey SR (2017) Imaging RNA
polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem
Biol 13(11):1187–1194. https://doi.org/
10.1038/nchembio.2477
22. Steinmetzger C, Palanisamy N, Gore KR,
Hobartner C (2019) A multicolor large
Stokes shift fluorogen-activating RNA aptamer with cationic chromophores. Chemistry
25(8):1931–1935.
https://doi.org/10.
1002/chem.201805882
23. Han KY, Leslie BJ, Fei J, Zhang J, Ha T
(2013) Understanding the photophysics of
the spinach-DFHBI RNA aptamer-fluorogen
complex to improve live-cell RNA imaging. J
Am Chem Soc 135(50):19033–19038.
https://doi.org/10.1021/ja411060p
24. You M, Jaffrey SR (2015) Structure and
mechanism of RNA mimics of green fluorescent protein. Annu Rev Biophys 44:187–206.
https://doi.org/10.1146/annurev-biophys060414-033954
25. Klymchenko AS (2017) Solvatochromic and
fluorogenic dyes as environment-sensitive
probes: design and biological applications.
Acc Chem Res 50(2):366–375. https://doi.
org/10.1021/acs.accounts.6b00517
96
Michael Ryckelynck