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s41467-018-06942-3
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crystal structure of the malachite green aptamer. J Mol Biol 301(1):117–128. https://
doi.org/10.1006/jmbi.2000.3951
49. Huang H, Suslov NB, Li NS, Shelke SA,
Evans ME, Koldobskaya Y, Rice PA, Piccirilli
JA (2014) A G-quadruplex-containing RNA
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50. Warner KD, Chen MC, Song W, Strack RL,
Thorn A, Jaffrey SR, Ferre-D’Amare AR
(2014) Structural basis for activity of highly
efficient RNA mimics of green fluorescent
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nsmb.2865
51. Fernandez-Millan P, Autour A, Ennifar E,
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iSpinach aptamer in complex with DFHBI.
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MWL, Panchapakesan SSS, Jeng SCY, Unrau
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AR (2017) Structural principles of fluorescent
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tips.2017.06.007
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Cojocaru R, Knutson JR, Ryckelynck M,
Unrau PJ, Ferre-D’Amare A (2018) Crystal
structures of the Mango-II RNA aptamer
reveal heterogeneous fluorophore binding
and guide engineering of variants with
improved selectivity and brightness. Biochemistry. https://doi.org/10.1021/acs.bio
chem.8b00399
55. Trachman RJ 3rd, Autour A, Jeng SCY,
Abdolahzadeh A, Andreoni A, Cojocaru R,
Garipov R, Dolgosheina EV, Knutson JR,
Ryckelynck M, Unrau PJ, Ferre-D’Amare
AR (2019) Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nat Chem Biol 15(5):472–479. https://
doi.org/10.1038/s41589-019-0267-9
56. Trachman RJ 3rd, Stagno JR, Conrad C,
Jones CP, Fischer P, Meents A, Wang YX,
Ferre-D’Amare AR (2019) Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta
Crystallogr F Struct Biol Commun 75
(Pt 8):547–551. https://doi.org/10.1107/
S2053230X19010136
57. Guo JU, Bartel DP (2016) RNA
G-quadruplexes are globally unfolded in
eukaryotic cells and depleted in bacteria. Science 353(6306). https://doi.org/10.1126/
science.aaf5371
58. Strack RL, Disney MD, Jaffrey SR (2013) A
superfolding Spinach2 reveals the dynamic
nature of trinucleotide repeat-containing
RNA. Nat Methods 10(12):1219–1224.
https://doi.org/10.1038/nmeth.2701
59. Ageely EA, Kartje ZJ, Rohilla KJ, Barkau CL,
Gagnon KT (2016) Quadruplex-flanking
stem structures modulate the stability and
metal ion preferences of RNA mimics of
GFP. ACS Chem Biol 11(9):2398–2406.
https://doi.org/10.1021/acschembio.
6b00047
60. Filonov GS, Song W, Jaffrey SR (2019) Spectral tuning by a single nucleotide controls the
fluorescence properties of a fluorogenic aptamer.
Biochemistry
58(12):1560–1564.
https://doi.org/10.1021/acs.biochem.
9b00048
61. Furuhata Y, Kobayashi M, Maruyama R,
Sato Y, Makino K, Michiue T, Yui H,
Nishizawa S, Yoshimoto K (2019) Programmable RNA detection with a fluorescent RNA
aptamer using optimized three-way junction
formation. RNA 25(5):590–599. https://
doi.org/10.1261/rna.069062.118
62. Warner KD, Sjekloca L, Song W, Filonov GS,
Jaffrey SR, Ferre-D’Amare AR (2017) A
homodimer interface without base pairs in
an RNA mimic of red fluorescent protein.
Nat Chem Biol 13(11):1195–1201. https://
doi.org/10.1038/nchembio.2475
63. Guet D, Burns LT, Maji S, Boulanger J,
Hersen P, Wente SR, Salamero J, Dargemont
C (2015) Combining Spinach-tagged RNA
and gene localization to image gene expression in live yeast. Nat Commun 6:8882.
https://doi.org/10.1038/ncomms9882
64. Zinskie JA, Roig M, Janetopoulos C, Myers
KA, Bruist MF (2018) Live-cell imaging of
small nucleolar RNA tagged with the broccoli
98
Michael Ryckelynck
ymeth.2019.04.021
47. Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP,
Waggoner AS, Bruchez MP, Armitage BA,
Piccirilli JA (2018) Structural basis for activation of fluorogenic dyes by an RNA aptamer
lacking a G-quadruplex motif. Nat Commun
9(1):4542.
https://doi.org/10.1038/
s41467-018-06942-3
48. Baugh C, Grate D, Wilson C (2000) 2.8 A
crystal structure of the malachite green aptamer. J Mol Biol 301(1):117–128. https://
doi.org/10.1006/jmbi.2000.3951
49. Huang H, Suslov NB, Li NS, Shelke SA,
Evans ME, Koldobskaya Y, Rice PA, Piccirilli
JA (2014) A G-quadruplex-containing RNA
activates fluorescence in a GFP-like fluorophore. Nat Chem Biol 10(8):686–691.
https://doi.org/10.1038/nchembio.1561
50. Warner KD, Chen MC, Song W, Strack RL,
Thorn A, Jaffrey SR, Ferre-D’Amare AR
(2014) Structural basis for activity of highly
efficient RNA mimics of green fluorescent
protein. Nat Struct Mol Biol 21
(8):658–663.
https://doi.org/10.1038/
nsmb.2865
51. Fernandez-Millan P, Autour A, Ennifar E,
Westhof E, Ryckelynck M (2017) Crystal
structure and fluorescence properties of the
iSpinach aptamer in complex with DFHBI.
RNA 23(12):1788–1795. https://doi.org/
10.1261/rna.063008.117
52. Trachman RJ 3rd, Demeshkina NA, Lau
MWL, Panchapakesan SSS, Jeng SCY, Unrau
PJ, Ferre-D’Amare AR (2017) Structural
basis for high-affinity fluorophore binding
and activation by RNA Mango. Nat Chem
Biol 13(7):807–813. https://doi.org/10.
1038/nchembio.2392
53. Trachman RJ 3rd, Truong L, Ferre-D’Amare
AR (2017) Structural principles of fluorescent
RNA aptamers. Trends Pharmacol Sci 38
(10):928–939. https://doi.org/10.1016/j.
tips.2017.06.007
54. Trachman R, Abdolahzadeh A, Andreoni A,
Cojocaru R, Knutson JR, Ryckelynck M,
Unrau PJ, Ferre-D’Amare A (2018) Crystal
structures of the Mango-II RNA aptamer
reveal heterogeneous fluorophore binding
and guide engineering of variants with
improved selectivity and brightness. Biochemistry. https://doi.org/10.1021/acs.bio
chem.8b00399
55. Trachman RJ 3rd, Autour A, Jeng SCY,
Abdolahzadeh A, Andreoni A, Cojocaru R,
Garipov R, Dolgosheina EV, Knutson JR,
Ryckelynck M, Unrau PJ, Ferre-D’Amare
AR (2019) Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nat Chem Biol 15(5):472–479. https://
doi.org/10.1038/s41589-019-0267-9
56. Trachman RJ 3rd, Stagno JR, Conrad C,
Jones CP, Fischer P, Meents A, Wang YX,
Ferre-D’Amare AR (2019) Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta
Crystallogr F Struct Biol Commun 75
(Pt 8):547–551. https://doi.org/10.1107/
S2053230X19010136
57. Guo JU, Bartel DP (2016) RNA
G-quadruplexes are globally unfolded in
eukaryotic cells and depleted in bacteria. Science 353(6306). https://doi.org/10.1126/
science.aaf5371
58. Strack RL, Disney MD, Jaffrey SR (2013) A
superfolding Spinach2 reveals the dynamic
nature of trinucleotide repeat-containing
RNA. Nat Methods 10(12):1219–1224.
https://doi.org/10.1038/nmeth.2701
59. Ageely EA, Kartje ZJ, Rohilla KJ, Barkau CL,
Gagnon KT (2016) Quadruplex-flanking
stem structures modulate the stability and
metal ion preferences of RNA mimics of
GFP. ACS Chem Biol 11(9):2398–2406.
https://doi.org/10.1021/acschembio.
6b00047
60. Filonov GS, Song W, Jaffrey SR (2019) Spectral tuning by a single nucleotide controls the
fluorescence properties of a fluorogenic aptamer.
Biochemistry
58(12):1560–1564.
https://doi.org/10.1021/acs.biochem.
9b00048
61. Furuhata Y, Kobayashi M, Maruyama R,
Sato Y, Makino K, Michiue T, Yui H,
Nishizawa S, Yoshimoto K (2019) Programmable RNA detection with a fluorescent RNA
aptamer using optimized three-way junction
formation. RNA 25(5):590–599. https://
doi.org/10.1261/rna.069062.118
62. Warner KD, Sjekloca L, Song W, Filonov GS,
Jaffrey SR, Ferre-D’Amare AR (2017) A
homodimer interface without base pairs in
an RNA mimic of red fluorescent protein.
Nat Chem Biol 13(11):1195–1201. https://
doi.org/10.1038/nchembio.2475
63. Guet D, Burns LT, Maji S, Boulanger J,
Hersen P, Wente SR, Salamero J, Dargemont
C (2015) Combining Spinach-tagged RNA
and gene localization to image gene expression in live yeast. Nat Commun 6:8882.
https://doi.org/10.1038/ncomms9882
64. Zinskie JA, Roig M, Janetopoulos C, Myers
KA, Bruist MF (2018) Live-cell imaging of
small nucleolar RNA tagged with the broccoli
98
Michael Ryckelynck