Isostructural self-assembly of 2′-deoxyguanosine derivatives in aqueous and organic media

Article abstract of DOI:10.1021/ja8039019

We report the self-assembly of a hydrophilic 8-(m-acetylphenyl)-2′-deoxyguanosine (mAG) derivative into a discrete and thermally stable hexadecameric supramolecule in aqueous media. We demonstrate that this hexadecamer is isostructural to the one formed by a related lipophilic derivative in organic media. This mAG moiety represents a rare example of a small-molecule recognition motif that is capable of assembling isostructurally and with high fidelity in both organic and aqueous media. Copyright

Full text of DOI:10.1021/ja8039019

Published on Web 07/22/2008
Isostructural Self-Assembly of 2′-Deoxyguanosine Derivatives in Aqueous
and Organic Media
Marilyn Garc´ıa-Arriaga, Gerard Hobley, and Jose´ M. Rivera*
Department of Chemistry, UniVersity of Puerto Rico, R´ıo Piedras Campus, R´ıo Piedras, Puerto Rico 00931
Received May 23, 2008; E-mail: jmrivortz@mac.com
Water plays a central role in how weak noncovalent interactions
dictate the outcome of vital processes such as protein folding as
well as the formation of protein-protein and protein-nucleic acid
complexes.1 Recently, there has been an increased interest in the
construction of synthetic self-assembled supramolecular nanostruc-
tures in water due to their potential use in biomedical applications.2
Even though the field of supramolecular chemistry has made great
strides in the construction of complex self-assembled structures in
organic media, similar advances in aqueous environments have
lagged behind.3 Nonetheless, progress in this area has been achieved
primarily in the construction of stacked and micellar assemblies of
indefinite sizes.4 The synthesis of discrete and well-defined
structures in water has been mostly limited to systems that use
coordinative covalent bonds for their formation, in particular, in
the construction of capsular supramolecules.5 In contrast, examples
of discrete supramolecular assemblies made exclusively with
noncovalent interactions have remained somewhat elusive.5c
Recently, Schrader and co-workers6 reported an elegant system
based on aminopyrazole peptides that self-assembled into discrete
Figure 1. (a) Chemical structure of the mAG tetrad. (b) Cartoon
representation for the formation of a hexadecamer formed by mAGx
hexameric nanorosettes in water. Unfortunately, the prevalence of
Shrader’s hexamer, even at 275 K, was just 40% at 45 mM and
15% at 23 mM in peptide monomers. This example underscores
the challenges of developing self-assembling small molecules from
scratch. Herein we report the self-assembly of a hydrophilic 8-(m-
acetylphenyl)-2′-deoxyguanosine (mAG) derivative into a discrete
and thermally stable hexadecameric supramolecule in aqueous
media. Furthermore, we demonstrate that this hexadecamer is
isostructural to the one formed by a related lipophilic mAG
derivative in organic media.
derivatives in aqueous or organic media. A hexadecamer is composed of
two sets of tetrads that occur in distinct chemical environments.
We have previously demonstrated7 that the self-assembly of
lipophilic 8-phenyl-2′-deoxyguanosine derivatives into G-quadru-
plexes8 (GQs) could be modulated by replacement of the H8 in
the guanine base with a functionalized phenyl group (Figure 1).
The position of the functional group in the phenyl ring enables the
modulation of the molecularity and thermal stability of the resulting
supramolecules. In particular, the mAG scaffold forms hexadecam-
ers in organic media very reliably, regardless of the group attached
to the sugar. We recently reported taking advantage of this strategy
to construct hexadecameric self-assembled dendrimers.7b
Figure 2. 1H NMR and partial 2D NOESY spectra showing signature cross-
peak patterns of (a) mAGcat (10 mM) in H2O-D2O (9:1) with KCl; (b)
mAGi (50 mM) in CD3CN saturated in KI (o ) outer, i ) inner). (See
Figure S24 for more details.)
1H NMR experiments with mAGcat in H2O-D2O (9:1, with
water suppression) reveal many of the signatures of a quadruplex
assembly in a solution containing KCl (1 M).10 The presence of
two peaks between 11 and 13 ppm is characteristic of the N1H
protons, which are in slow exchange with the solvent (Figure 2).
A comparison with the spectrum of mAGi in CD3CN reveals
striking similarities between the two species in key areas of their
spectra. In contrast, control experiments with the parent compound
dGcat show no evidence of self-assembly even at higher concentra-
tions (Figure S18).11 These findings underscore the importance of
the 8-phenyl group in the self-assembly, which enhances the
noncovalent interactions such as hydrophobic contacts, stacking,
and H bonds.
In this study, we aimed at elucidating if the mAG scaffold could
also self-assemble in water, and if it did, what would it form. We
hypothesized that, because the GQs were held together by a
combination of noncovalent interactions,9 the self-assembly in water
was possible as long as we could synthesize soluble derivatives.
We achieved this by making the dimethylamino derivatives
mAGcat and the control compound dGcat (which has no 8-phenyl
substitution) using a synthetic methodology similar to that previ-
ously described by our group (Scheme S1).7 At neutral pH, the
positively charged ammonium groups render both derivatives
soluble in water.
The CD spectra of both mAGcat and mAGi exhibit very similar
signatures with a negative band near 330 nm and a positive band
9
10492 J. AM. CHEM. SOC. 2008, 130, 10492–10493
10.1021/ja8039019 CCC: $40.75
2008 American Chemical Society

C O M M U N I C A T I O N S
related compounds to construct self-assembled nanostructures in
aqueous media for biomedical applications.2
Acknowledgment. We thank Prof. Gian Piero Spada (Universita´
di Bologna) and Prof. Beatriz Zayas (UMET, PR) for assistance
with CD and MS studies, respectively. We also thank Ivonne
Andu´jar and Jose´ E. Betancourt for their helpful technical assistance.
G.H. thanks NIH-SCoRE (2506GM08102), and M.G-A. thanks
NIH-RISE (2R25GM61151), NSF-EPSCoR (EPS0223152), PRL-
SAMP-HRD-0114586, and SLOAN for graduate fellowships.
Supporting Information Available: Detailed experimental protocols
and spectroscopic data. This material is available free of charge via
the Internet at http://pubs.acs.org.
Figure 3. Comparison of the relative sizes for the hexadecamers of
mAGcat (blue, r′H) and mAGi (red, r′′H) highlighting the hydrodynamic
radii. Only the top tetrads are highlighted for clarity. The purple sphere
represents a potassium cation.14
References
(1) Ball, P. Chem. ReV. 2008, 108, 74–108.
near 290 nm (Figure S14). Despite their different environments,
the close correlation of their CD spectra is a strong indication they
share a similar structure at the core.12
(2) For examples of self-assembled nanostructures used for biomedical
applications, see: (a) Dankers, P. Y. W.; Meijer, E. W. Bull. Chem. Soc.
Jpn. 2007, 80, 2047–2073. (b) Jun, H.; Paramonov, S. E.; Hartgerink, J. D.
Soft Matter 2006, 177–181.
(3) Oshovsky, G. V.; Reinhoudt, D. N.; Verboom, W. Angew. Chem., Int. Ed.
2007, 46, 2366–2393.
The hexadecamers of both mAGcat and mAGi display parallel
signature cross-peak patterns in their 2D NOESY spectra in
H2O-D2O (9:1) and CD3CN, respectively (Figure 2). These
experiments offer further evidence to support that mAGcat and
mAGi form supramolecules of the same molecularity (hexa-
decamers). Furthermore, parallel to the CD results, the NOESY
spectra indicate that the stereochemical arrangement of the mAG
moieties within the core of the quadruplex is nearly identical (i.e.,
isostructural).
(4) (a) Fenniri, H.; Deng, B.-L.; Ribbe, A. E.; Hallenga, K.; Jacob, J.;
Thiyagarajan, P. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6487–6492. (b)
Fenniri, H.; Mathivanan, P.; Vidale, K. L.; Sherman, D. M.; Hallenga, K.;
Wood, K. V.; Stowell, J. G. J. Am. Chem. Soc. 2001, 123, 3854–3855. (c)
Hartgerink, J. D.; Beniash, E.; Stupp, S. I. Science 2001, 294, 1684–1688.
(d) Hartgerink, J. D.; Beniash, E.; Stupp, S. I. Proc. Natl. Acad. Sci. U.S.A.
2002, 99, 5133–5138. (e) Ryu, J. H.; Hong, D. J.; Lee, M. Chem. Commun.
2008, 1043–1054. (f) Kato, T.; Mizoshita, N.; Kishimoto, K. Angew. Chem.,
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(5) For representative examples of capsular assemblies made with coordinative
covalent bonds, see: (a) Fujita, M.; Tominaga, M.; Hori, A.; Therrien, B.
Acc. Chem. Res. 2005, 38, 369–378. (b) Fiedler, D.; Leung, D. H.; Bergman,
R. G.; Raymond, K. N. Acc. Chem. Res. 2005, 38, 349–358. For an example
of a hydrophobically driven self-assembled capsule, see: (c) Gibb, C. L. D.;
Gibb, B. C. J. Am. Chem. Soc. 2004, 126, 11408–11409.
(6) Rzepecki, P.; Hochdorffer, K.; Schaller, T.; Zienau, J.; Harms, K.;
Ochsenfeld, C.; Xie, X.; Schrader, T. J. Am. Chem. Soc. 2008, 130, 586–
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4738. (b) Betancourt, J. E.; Rivera, J. M. Org. Lett. 2008, 10, 2287–2290.
(c) Hobley, G.; Gubala, V.; Rivera-Sa´nchez, M. C.; Rivera, J. M. Synlett
2008, 1510–1514.
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(9) Rehm, T.; Schmuck, C. Chem. Commun. 2008, 801–813.
(10) Although the studies reported here were performed using 1 M KCl, titration
experiments of mAGcat with KCl show the presence of 31% hexadecamer
even with 0.6 mM KCl (Figure S17).
(11) Studies with 5′-GMP have also shown that it self-assembles with low fidelity
in aqueous KCl solutions but only at very high concentrations (0.15-1.0
M), giving a mixture of columnar aggregates of indefinite length (stacks
of <24-87 tetrads): (a) Fisk, C. L.; Becker, E. D.; Miles, H. T.; Pinnavaia,
T. J. J. Am. Chem. Soc. 1982, 104, 3307–3314. (b) Bouhoutsos-Brown,
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(12) From the CD results, it can be inferred that the helical twist between the
planar tetrads is very similar for the hexadecamers of mAGcat and mAGi
due to the relative stereochemical arrangements of the subunits. For further
information, see: Paramasivan, S.; Rujan, I.; Bolton, P. H. Methods 2007,
43, 324–331.
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(14) Minimizations were performed using: AMBER* (MacroModel), Version
9.5, Maestro 8.0.315; Schro¨dinger, LLC: New York, 2007, representing
water as a continuum solvent.
(15) These thermodynamic parameters are similar to those determined from the
calorimetric measurements obtained for DNA aptamers capable of forming
G-quadruplexes. See: (a) Olsen, C. M.; Gmeiner, W. H.; Marky, L. A. J.
Phys. Chem. B 2006, 110, 6962–6969. (b) Mergny, J. L.; De Cian, A.;
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In order to get a sense of the size of the (mAGcat)16•3KCl, we
performed 1H DOSY NMR experiments to determine its molecular
translational coefficient (D). We found that D ) (0.776 ( 0.020)
× 10-10 m2 s-1 at 298 K, which corresponds to a hydrodynamic
radius (r′H) of 25.5 Å.13 This value is in close agreement with 24.8
Å, which was obtained from a molecular model of the mAGcat
hexadecamer (Figures S25 and S26).14 In contrast, (mAGi)16•3KI
has a D ) (6.430 ( 0.114) × 10-10 m2 s-1 at 298 K in CD3CN,
which corresponds to a smaller r′′H of 10.0 Å. The differences in
sizes are due to the shorter isopropyl side chains in mAGi and the
fact that the side chains in mAGcat are more extended due to the
repulsion between the cationic ammonium groups (Figure 3).
Analysis of the melting curve of mAGcat, obtained by variable
temperature (VT) NMR, reveals a Tm of 60.7 °C, which is once
again remarkably close to the value obtained for mAGi in CD3CN
of 56.4 °C (Figure S27).7 A detailed thermodynamic profile using
differential scanning calorimetry (DSC) shows a monophasic
transition at 55.1 °C with a favorable ∆G (293 K) value, -2.1 kcal/
mol (∆H ) -33.7 kcal/mol, T∆S -31.6 kcal/mol) for the formation
of the quadruplex and results from the compensation of a favorable
enthalpy with an unfavorable entropy contribution (assembly of
16 subunits and 3 cations).15 Compared to dGcat, mAGcat has a
larger surface area and greater hydrophobicity, both of which have
been shown to stabilize supramolecular structures in water due to
enhanced van der Waals and π-stacking.16 The mAGcat tetrads
can also form up to four additional H bonds due to the expanded
Hoogsteen edge (Figure 1a).7,17
In conclusion, the mAG moiety represents a remarkable example
of a small-molecule recognition motif that is capable of assembling
isostructurally in organic or aqueous media with high fidelity and
stability. We expect that this and related derivatives will offer
important insights into the rules that govern the self-assembly of
small molecules in aqueous media. We are currently using this and
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