Supporting information
Martín-Hidalgo M. et al.
Tuning supramolecular G-quadruplexes with mono- and divalent cations
Mariana Martín-Hidalgo, Marilyn García-Arriaga, Fernando González and José M. Rivera*
Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, Puerto Rico
00931
riveralab.upr@gmail.com
Table of Contents
A. Characterization of the target compound
3
B. Metal cations studies for mAGi in acetonitrile monitored by 1H NMR
4
C. 1H-1H NOESY analysis for mAGi Hexadecamers
11
D. Mass Spectrometry
13
E. Thermal stability studies
17
F. Molecular Dynamics Simulations (MDS)
30
Table of Figures
Figure S1. 1H NMR (500 MHz, 298.15 K, CD3CN) spectra of mAGi (30 mM) with different
iodide salts. ................................................................................................................................ 5
Figure S2. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with LiI (0.5 equiv). ............ 6
Figure S3. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with KI (0.5 equiv). ............ 6
Figure S4. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NaI (0.5 equiv). .......... 7
Figure S5. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with RbI (0.5 equiv). .......... 7
Figure S6. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NH4I (0.5 equiv). ........ 8
Figure S7. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with TlI (0.5 equiv). ........... 8
Figure S8. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with SrI2 (0.125 equiv). ...... 9
Figure S9. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with BaI2 (0.125 equiv). ..... 9
Figure S10. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with PbI2 (0.125 equiv). ..10
Figure S11. NOESY (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NaI (0.5 equiv).
Highlighted in the red square are signature cross peaks showing selected interactions between
subunits in the inner and outer tetrads. .....................................................................................11
Figure S12. NOESY (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with RbI (0.5 equiv).
Highlighted in the red square are signature cross peaks showing selected interactions between
subunits in the inner and outer tetrads. .....................................................................................12
Figure S13. NOESY (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NH4I (0.5 equiv).
Highlighted in the red square are signature cross peaks showing selected interactions between
subunits in the inner and outer tetrads. .....................................................................................13
Figure S14. MS spectra of a solution of mAGi (10 mM) with LiI (0.5 equiv) in CH3CN. ............14
Figure S15. MS spectra of a solution of mAGi (10 mM) with NaI (0.5 equiv) in CH3CN. ...........14
Figure S16. MS spectra of a solution of mAGi (10 mM) with RbI (0.5 equiv) in CH3CN. ...........15
Figure S17. MS spectra of a solution of mAGi (10 mM) with NH4I (0.5 equiv) in CH3CN. .........15
Figure S18. MS spectra of a solution of mAGi (10 mM) with BaI2 (0.125 equiv) in CH3CN. ......16
Figure S19. MS spectra of a solution of mAGi (10 mM) with PbI2 (0.5 equiv) in CH3CN. ..........16
Figure S20. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM) with of
LiI (0.5 equiv). ...........................................................................................................................18
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Figure S21. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM) with of
NaI (0.5 equiv). .........................................................................................................................19
Figure S22. Melting profile (solid line) and first derivative curve (dashed line) as determined by
VT-NMR for mAGi (5 mM) with NaI (0.5 equiv) .........................................................................20
Figure S23. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM) with of
RbI (0.5 equiv). .........................................................................................................................21
Figure S24. Melting profile (solid line) as determined by VT-NMR for mAGi (5 mM) with RbI
(0.5 equiv). ................................................................................................................................22
Figure S25. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM) with of
NH4I (0.5 equiv).........................................................................................................................23
Figure S26. Melting profile (solid line) and first derivative curve (dashed line) as determined by
VT-NMR for mAGi (5 mM) with NH4I (0.5 equiv). ......................................................................24
Figure S27. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM) with of
TlI (0.5 equiv). ...........................................................................................................................25
Figure S28. Melting profile (solid line) and first derivative curve (dashed line) as determined by
VT-NMR for mAGi (5 mM) with TlI (0.5 equiv). .........................................................................26
Figure S29. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM) with of
BaI2 (0.125 equiv). ....................................................................................................................27
Figure S30. Melting profile as determined by VT-NMR for mAGi (5 mM) with BaI2 (0.125 equiv).
.................................................................................................................................................28
Figure S31. Variable temperature 1H NMR (500 MHz, 298.2 K in CD3CN) spectra for mAGi (5
mM) with of PbI2 (0.5 equiv). .....................................................................................................29
Figure S32. Melting profile (solid line) and first derivative curve (dashed line) as determined by
VT-NMR for mAGi (5 mM) with PbI2 (0.5 equiv). .......................................................................30
Figure S33. Supramolecular structures of mAGi16 with: a) Na+; b) Rb+; c) Li+; d) NH4+; e) Cs+. 33
Figure S34. Histogram plots of the distribution of the root mean square displacements of mAGi
hexadecamer. a) K+; b) Na+; c) Rb+; d) Li+; e) NH4+; f) Cs+. The color code and labels are the
same as in the main text. ..........................................................................................................34
Figure S35. a) Trajectory of the dynamics of mAGi8 with Li+(yellow) using the structure with K+
(orange) as a reference; b) distribution of the corresponding RMSD values from a. ..................34
Figure S36. Supramolecular structure for mAGi8•Li+ ................................................................35
Figure S37. Histogram plots of the distribution of the root mean square displacements of mAGi8
a) K+ (orange) and b) Li+ (yellow). The color code and labels are the same as in the main text. 35
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A. Characterization of the target compound
NMR spectra were recorded on Bruker DRX-500 or AV-500 spectrometer, equipped with
either a 5 mm BBO or a TXI probe and with nominal frequencies of 500.13 MHz for
proton and 125.77 MHz for carbon respectively. All NMR experiments were performed at
298.15 K unless otherwise stated. All the assemblies were characterized with 1H NMR
and 2D NMR techniques such as COSY and NOESY.
The synthesis and characterization for mAGi was reported in Gubala, V.; Betancourt, J.
E.; Rivera, J. M. Org. Lett. 2004, 6, 4735-4738.
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B. 1H NMR studies for the SGQs formed by mAGi as a function of
different cations in acetonitrile
Different monovalent and divalent cations were used to promote the cation-templated
self-assembly of mAGi. The addition of 0.5 equiv of LiI, NaI, KI, RbI, CsI, TlI, PbI2 and
0.125 equiv of SrI2, BaI2cations into 30 mM solutions of the analoguesin CD3CN yield the
formation of different SGQs, fidelities from moderate to high were observed (Table S1).1
Table S1. Type and relative amounts (fidelity) of SGQs formed by mAGi (30 mM) determined
by 1H NMR (0.5 equiv of LiI, NaI, KI, RbI, CsI, TlI, PbI 2 and 0.125 equiv of SrI2 and BaI2, at
298.15 K) in CD3CN.
Monomer Cation
mAGi
Li+
Na+
K+
Rb+
NH4+
Cs+
Tl+
Sr2+
Ba2+
Pb2+
Assembly (%)
OD4
H
US
95
5
95
5
90
10
67
33
86
14
100
58
42
100
90
10
77
23
Note: O = Octamer; H = Hexadecamer; US = Unidentified Species
All measurements have an estimated 5% error
1. Fidelity refers to the percentage of the desired supramolecule when there are two or more potential
outcomes. For more information see: Todd, E. M.; Quinn, J. R.; Park, T.; Zimmerman, S. C., Fidelity in the
supramolecular assembly of triply and quadruply hydrogen-bonded complexes. I. J. Chem. 2005, 45, 381389.
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Figure S1. 1H NMR (500 MHz, 298.15 K, CD3CN) spectra of mAGi (30 mM) with different
iodide salts.
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Figure S2. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with LiI (0.5 equiv).
Figure S3. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with KI (0.5 equiv).
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Figure S4. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NaI (0.5 equiv).
Figure S5. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with RbI (0.5 equiv).
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Figure S6. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NH4I (0.5 equiv).
Figure S7. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with TlI (0.5 equiv).
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Figure S8. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with SrI2 (0.125 equiv).
Figure S9. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with BaI2 (0.125 equiv).
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Figure S10. 1H NMR (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with PbI2 (0.125 equiv).
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C. 1H-1H NOESY analysis for mAGi Hexadecamers
A phase-sensitive 2D-NOESY pulse sequences with gradients (noesygpph) and
a mixing time of 500 ms were used. NMR cuts of the characteristics NOE’s
observed between the interphases of the outer and inner tetrads of the
hexadecamers form by mAGi (30mM) with NaI, KI and RbI (1/2 equiv with
respect to the monomer) in CD3CN at 298.15 K are shown.
Figure S11. NOESY (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NaI (0.5 equiv).
Highlighted in the red square are signature cross peaks showing selected interactions
between subunits in the inner and outer tetrads.
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Figure S12. NOESY (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with RbI (0.5 equiv).
Highlighted in the red square are signature cross peaks showing selected interactions
between subunits in the inner and outer tetrads.
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Figure S13. NOESY (500 MHz, 298.2 K, CD3CN) of mAGi (30 mM) with NH4I (0.5
equiv). Highlighted in the red square are signature cross peaks showing selected
interactions between subunits in the inner and outer tetrads.
D. Mass Spectrometry
High resolution electrospray ionization mass spectrometry (ESI MS) was
recorded on a Q-Tof Ultima Global mass spectrometer (Micromass) equipped
with a Z-spray source. Electrospray ionization was achieved in the positive mode
by 3 kV on the needle. 10 mM solutions of monomer in acetonitrile with 0.5 equiv
(0.125 equiv for Ba2+) or of the corresponding metal cation, at room temperature,
were directly and continuously infused at a flow rate of 5 µL/min with a syringe
pump. The source block temperature was maintained at 60 °C and the
desolvation gas was heated to 80 °C. Argon was used as the collision gas and
the cone voltage was set to 35 V. The mass spectrometer was operated in the
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mass range 0-4000 amu.
Figure S14. MS spectra of a solution of mAGi (10 mM) with LiI (0.5 equiv) in CH3CN.
Figure S15. MS spectra of a solution of mAGi (10 mM) with NaI (0.5 equiv) in CH3CN.
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Figure S16. MS spectra of a solution of mAGi (10 mM) with RbI (0.5 equiv) in CH3CN.
Figure S17. MS spectra of a solution of mAGi (10 mM) with NH4I (0.5 equiv) in CH3CN.
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Figure S18. MS spectra of a solution of mAGi (10 mM) with BaI2 (0.125 equiv) in
CH3CN.
Figure S19. MS spectra of a solution of mAGi (10 mM) with PbI2 (0.5 equiv) in CH3CN.
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E. Thermal stability studies
Variable temperature experiments were performed at 5 mM of mAGi. At this
particular concentration there is enough monomer and self-assembled species to
enable the construction of a melting profile (with the exception of Lithium
sample). Integration of the area under the H1’ peaks and the first derivative
calculations allows a good approximation of the melting temperature for the
assemblies. The fraction () of assembly (fidelity) = XSA/XT , is reported as the
ratio between the total self-assembled species (XSA) and the total concentration
of mAGi (XT), see figures for more information.
Table S2. Melting temperatures (Tm) for various SGQs (O: octamer; H: hexadecamer)
formed by mAGi (5 mM) as promoted by various cations.
Cation
LiI
NaI
KI
RbI
NH4I
TlI
SrI2
BaI2
PbI2
Molecularity
O
H
H
H
H
O
O
O
O
Tm
ND*
309
329
ND*
310
304
 333
 333
313
* ND: Not determined; under the conditions of the experiments the Tm values for
these samples could not be determined. All the Tm values are within an estimated
5% error.
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Figure S20. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM)
with of LiI (0.5 equiv).
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Figure S21. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM)
with of NaI (0.5 equiv).
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Figure S22. Melting profile (solid line) and first derivative curve (dashed line) as
determined by VT-NMR for mAGi (5 mM) with NaI (0.5 equiv)
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Figure S23. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM)
with of RbI (0.5 equiv).
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Figure S24. Melting profile (solid line) as determined by VT-NMR for mAGi (5 mM) with
RbI (0.5 equiv).
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Figure S25. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM)
with of NH4I (0.5 equiv).
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Figure S26. Melting profile (solid line) and first derivative curve (dashed line) as
determined by VT-NMR for mAGi (5 mM) with NH4I (0.5 equiv).
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Figure S27. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM)
with of TlI (0.5 equiv).
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Figure S28. Melting profile (solid line) and first derivative curve (dashed line) as
determined by VT-NMR for mAGi (5 mM) with TlI (0.5 equiv).
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Figure S29. Variable temperature 1H NMR (500 MHz, CD3CN) spectra for mAGi (5 mM)
with of BaI2 (0.125 equiv).
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Figure S30. Melting profile as determined by VT-NMR for mAGi (5 mM) with BaI2 (0.125
equiv).
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Figure S31. Variable temperature 1H NMR (500 MHz, 298.2 K in CD3CN) spectra for
mAGi (5 mM) with of PbI2 (0.5 equiv).
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Figure S32. Melting profile (solid line) and first derivative curve (dashed line) as
determined by VT-NMR for mAGi (5 mM) with PbI2 (0.5 equiv).
F. Molecular Dynamics Simulations (MDS)
Initially, the structures of all the monomers were built using Maestro 8.0.315.
These monomers were used to construct various SGQs that were manually
assembled into supramolecular structures. The coordinates for these initial
configurations were in accordance with the structural information obtained from
the 2D NOESY spectrum of the various supramolecular GQs studied in our
laboratory. Energy minimizations were performed to these SGQS using the
MacroModel suite of programs employing the AMBER 94 force field.2
From these optimized structures two different configurations of the monomer (the
structure of the monomer in the inner and outer tetramers) were used to derive
electrostatic charges using the standard procedure for the AMBER force field, as
2. MacroModel Version 9.5, Maestro 8.0.315; Schrödinger, LLC: New York, NY, 2007.
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implemented in RED III.3 Briefly, the procedure followed various steps: (i) each
monomer was optimized using the HF/6-31G* method, from Gaussian 03
package; (ii) frequency calculations were performed to verify the identity of each
stationary point as a minimum; (iii) the minimized structure was used to obtain
the charges of each atom using the ESP software. In this calculation the charges
corresponding to the sugar and the guanine moiety were fixed according to the
force field. When the AMBER force field parameters were not available for
particular atoms, the GAFF force field parameters were used.
One, two and three cations were placed between G-tetrads using Maestro.4
Xleap was used to import the pdb and add the corresponding counterion (Cl-),
using the addions2 command, to neutralize the system. A 10 Å truncated
octahedron, with a minimum distance of 10 Å from the molecular surface to the
boundaries surface, using CH3CN as solvent, was added to solvate the structure
giving a total system of approximate 4704 atoms in the case of the mAGi16. The
molecular dynamics simulations were carried out using the AMBER 10 suite of
programs with the AMBER-99SB, as modified by Sponer.5 The atoms in the
simulation were given a 12 Å cut-off and the particle mesh Ewald method was
implemented to treat the long range electrostatics and to reduce the negative
effects of the introduction of the cut-off. The temperature and pressure were fixed
300 K and 1 atm, respectively. SANDER was used to carry out the minimizations
and the molecular dynamics runs. The total simulation time was 10 ns. VMD was
3. (a) Cornell, W. D.; Cieplak, P.; Baily, C. I.; Gould, I. R.; K. M. Merz, J.; Ferguson, D. C.; Fox,
T.; Caldwell, J. W.; Kollman., P. A., A second generation force field for the simulation of proteins,
nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179–5197. (b) Dupradeau,
F. Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.;
Cieplak, P., The R.E.D. tools: Advances in RESP and ESP charge derivation and force field
library building. Phys. Chem. Chem. Phys. 2010, 12, 7821-7839. (c) Cieplak, P.; Cornell, W. D.;
Bayly, C.; Kollman, P. A., Application of tne multimolecule and multiconformational RESP
methodology to biopolymers - charge derivation for DNA, RNA, and proteins J. Comput. Chem.
1995, 16 (11), 1357-1377.
4. Maestro Version 9.5, Maestro 8.0.315; Schrödinger, LLC: New York, NY, 2007.
5. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; T.E. Cheatham, I.; DeBolt, S.;
Ferguson, D.; Seibel, G.; Kollman, P., AMBER, a package of computer programs for applying
molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to
simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 1995, 91,
1-41.
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used for graphical representations of the generated trajectories.6 As in previous
studies, the variation of RMSD as a function of time was used as an indication of
the stability of the system. Specifically, increments in RMSD values imply a
deviation from the initial structure, which in this study was based on 2D NOESY
experiments. As the deviation increases, the system diverges more from the
experimental structure, and hence becomes less stable.
For the statistical analysis (histogram plots) of the distribution of the root mean
square deviations for all the structures were generated. Using a maximum
number of counts of 4500 for all the structures, with bin sizes of 70. These plots
are in agreement with the one shown in the text by means of a probability density
representation.
6. Humphrey, W.; Dalke, A.; Schulten, K., VMD: visual molecular dynamics. J. Mol. Graph. 1996,
14 (1), 33-38.
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b.
d.
e.
Figure S33. Supramolecular structures of mAGi16 with: a) Na+; b) Rb+; c) Li+; d) NH4+; e)
Cs+.
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Figure S34. Histogram plots of the distribution of the root mean square displacements of
various hexadecamers mAGi16•3X+ for X = a) K+; b) Na+; c) Rb+; d) Li+; e) NH4+; f) Cs+.
The color code and labels are the same as in the main text.
a.
b.
8
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(arb. units)
7
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Figure S35. a) Trajectory of the dynamics of mAGi8 with Li+(yellow) using the structure
with K+ (orange) as a reference; b) distribution of the corresponding RMSD values from
a.
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a.
Figure S36. Supramolecular structure for mAGi8•Li+
b.
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Figure S37. Histogram plots of the distribution of the root mean square displacements of
mAGi8 a) K+ (orange) and b) Li+ (yellow). The color code and labels are the same as in
the main text.
S35