required to obtain maximal fluorescence emission. Mango-II shares
the same overall structure except that five adenines are contributed
by the G-quadruplex propellers and allow to better constrain and
accommodate the fluorogen [54] without significantly modifying
a TO1-Biotin/Mango
G-quartet
TO1-Biot.
A25
A20
U15
A25
A20
U15
d OTB-SO3/DIR2s
Base triple
OTB-SO3
OTB-SO3
A40
G39
G39
b TO1-Biotin/Mango-II
G-quartet
TO1-Biot.
A28
A23
A22
A17
A28
A23
A22
A12
A17
A15
c TO1-Biotin/Mango-III
G-quartet
TO1-Biot.
A10
U12
U17
A10
U12
U17
f DFHBI/Spinach
G-quartet
DFHBI
DFHBI
Base triple
G31
A69
g DFHO/Corn
G-quartet
Monomer 1
G-quartet
Monomer 2
DFHO
a11
A24
A14
A11
a14
a11
A24
a14
A14
A11
G-quartet
Monomer 1
G-quartet
Monomer 2
e Malachite Green/MGA
Base quadruple
Mal. Green
C28-G8
C28
G8
A30
A9
U25
U25
Fig. 4 Structural organization of the main fluorogen-binding sites. (a) Binding of TO1-Biotin to Mango aptamer.
Based on model PDB 5V3F [52]. (b) Binding of TO1-Biotin to Mango-II aptamer. Based on model PDB 6C63
[54]. (c) Binding of TO1-Biotin to Mango-III aptamer. Based on model PDB 6E8S [55]. (d) Binding of OTB-SO3
to DIR2s aptamer. Based on model PDB 6DB8 [47]. (e) Binding of malachite green to MGA aptamer. Based on
model PDB 1F1T [48]. (f) Binding of DFHBI to Spinach aptamer. Based on model PDB 4TS2 [50]. (g) Binding of
DFHO to Corn aptamer. Based on model PDB 5BJO [62]. Nucleotides contributed by Monomer1 (upper case
nucleotides) or distinguished from those contributed by Monomer2 (lower case nucleotides). In every model,
only the elements in direct contact with the fluorogen are represented. For G-quadruplex-containing RNAs,
only the proximal quartet is shown. For each fluorogen/aptamer pair a side (left picture) and top (right picture)
view of the complex is represented. Elements are colored as follows: fluorogen-binding platform (G-quartet,
base quadruple, or base triple) in dark gray, surrounding and capping residues in yellow, and fluorogen colored
according to their emission wavelength (i.e., OTB-SO3 in blue, TO1-Biotin and DFHBI in green, DFHO in
orange, and malachite green in red)
84
Michael Ryckelynck
the same overall structure except that five adenines are contributed
by the G-quadruplex propellers and allow to better constrain and
accommodate the fluorogen [54] without significantly modifying
a TO1-Biotin/Mango
G-quartet
TO1-Biot.
A25
A20
U15
A25
A20
U15
d OTB-SO3/DIR2s
Base triple
OTB-SO3
OTB-SO3
A40
G39
G39
b TO1-Biotin/Mango-II
G-quartet
TO1-Biot.
A28
A23
A22
A17
A28
A23
A22
A12
A17
A15
c TO1-Biotin/Mango-III
G-quartet
TO1-Biot.
A10
U12
U17
A10
U12
U17
f DFHBI/Spinach
G-quartet
DFHBI
DFHBI
Base triple
G31
A69
g DFHO/Corn
G-quartet
Monomer 1
G-quartet
Monomer 2
DFHO
a11
A24
A14
A11
a14
a11
A24
a14
A14
A11
G-quartet
Monomer 1
G-quartet
Monomer 2
e Malachite Green/MGA
Base quadruple
Mal. Green
C28-G8
C28
G8
A30
A9
U25
U25
Fig. 4 Structural organization of the main fluorogen-binding sites. (a) Binding of TO1-Biotin to Mango aptamer.
Based on model PDB 5V3F [52]. (b) Binding of TO1-Biotin to Mango-II aptamer. Based on model PDB 6C63
[54]. (c) Binding of TO1-Biotin to Mango-III aptamer. Based on model PDB 6E8S [55]. (d) Binding of OTB-SO3
to DIR2s aptamer. Based on model PDB 6DB8 [47]. (e) Binding of malachite green to MGA aptamer. Based on
model PDB 1F1T [48]. (f) Binding of DFHBI to Spinach aptamer. Based on model PDB 4TS2 [50]. (g) Binding of
DFHO to Corn aptamer. Based on model PDB 5BJO [62]. Nucleotides contributed by Monomer1 (upper case
nucleotides) or distinguished from those contributed by Monomer2 (lower case nucleotides). In every model,
only the elements in direct contact with the fluorogen are represented. For G-quadruplex-containing RNAs,
only the proximal quartet is shown. For each fluorogen/aptamer pair a side (left picture) and top (right picture)
view of the complex is represented. Elements are colored as follows: fluorogen-binding platform (G-quartet,
base quadruple, or base triple) in dark gray, surrounding and capping residues in yellow, and fluorogen colored
according to their emission wavelength (i.e., OTB-SO3 in blue, TO1-Biotin and DFHBI in green, DFHO in
orange, and malachite green in red)
84
Michael Ryckelynck