A photoresponsive supramolecular G-quadruplex

Article abstract of DOI:10.1021/ol400610x

Photoirradiation of a hexadecameric supramolecular G-quadruplex leads to a diastereoselective [2 + 2] cyclodimerization of half of its constituent subunits, which in turn shifts the equilibrium toward the formation of a precise heteromeric octamer.

Full text of DOI:10.1021/ol400610x

ORGANIC
LETTERS
2013
Vol. 15, No. 10
2350–2353
A Photoresponsive Supramolecular
G‑Quadruplex
ꢀ
Jose M. Rivera* and Diana Silva-Brenes
´ ´
Department of Chemistry, University of Puerto Rico, Rıo Piedras Campus, Rıo Piedras,
Puerto Rico 00931
riveralab.upr@gmail.com
Received March 6, 2013
ABSTRACT
Photoirradiation of a hexadecameric supramolecular G-quadruplex leads to a diastereoselective [2 þ 2] cyclodimerization of half of its constituent
subunits, which in turn shifts the equilibrium toward the formation of a precise heteromeric octamer.
Responsive molecules are attractive due to their poten-
tial to act as components in (supra)molecular machinery.1
Light isa particularly attractive external stimulus totrigger
a specific response due to its low cost and inherent efficiency
(i.e., speed of stimulus, lack of waste products).2,3 Up to
now, most reported examples of photoresponsive supra-
molecules are those that fluctuate between unassembled
and assembled states or between precise4 and polymeric
states (e.g., gels, fibers, micelles).5 Yet, examples of supra-
molecules in which a precise supramolecule transitions into
another remains a significant challenge.3 Here we describe
the phototransformation of a precise homomeric hexade-
camer into an equally precise heteromeric octamer.
G-quadruplexes (SGQs). SGQs are coaxially stacked
(2, 3, 4, ... n) planar hydrogen bonded guanosine tetramers
(or tetrads, T) stabilized by a wide variety of hard cations
such as potassium (Figure 1). We have, furthermore, shown
that SGQs made from 8-aryl-20-deoxyguanosine (8ArG)
derivatives could be induced to transition between two
precise supramolecular states, specifically, octamers
(2T-SGQ) and hexadecamers (4T-SGQ). In particular,
we have so far shown two independent examples of such
systems where a change in the solvent (e.g., solvoresponsive)
or a change in the cation promoter (e.g., ionoresponsive)
achieved the desired transition (Figure 1a; i/i0).6 Here we
expand this strategy to include a photoresponsive assembly
(Figure 1a; ii).
To achieve a photoresponsive SGQ, we designed an
8-chalconyl-20-deoxyguanosine derivative (1) containing
a double bond in addition to the 8-(m-carbonylphenyl)
moiety (Figure 1b). The former was to impart the desired
photoresponsiveness, while the latter was expected to
direct the reliable formation of a supramolecular hexade-
camer (116). We performed a ClaisenꢀSchmidt condensa-
tion (Figure S1), to derivatize the 8-(m-acetylphenyl)
moiety, thus ensuring the preservation of the critical
m-carbonyl group.6d,7a This leaves the hydroxyl groups on
We have recently evaluated the effects of extrinsic stimuli
on the structure and dynamics of precise supramolecular
(1) Balzani, V.; Credi, A.; Venturi, M. Molecular Devices and Machines -
A Journey into the Nano World; Wiley-VCH: Weinheim, 2003.
(2) Saha, S.; Stoddart, J. F. Chem. Soc. Rev. 2006, 36, 77–92.
(3) For selected examples of photoresponsive supramolecular systems,
see: (a) Yagai, S.; Kitamura, A. Chem. Soc. Rev. 2008, 37, 1520–1529. (b)
Bassani, D. M.; Darcos, V.; Mahony, S.; Desvergne, J.-P. J. Am. Chem.
Soc. 2000, 122, 8795–8796. (c) Rakotondradany, F.; Whitehead, M. A.;
Lebuis, A.-M.; Sleiman, H. F. Chem.;Eur. J. 2003, 9, 4771–4780. (d)
Yagai, S.; Nakajima, T.; Karatsu, T.; Saitow, K.-i.; Kitamura, A. J. Am.
Chem. Soc. 2004, 126, 11500–11508. (e) Molard, Y.; Bassani, D. M.;
Desvergne, J.-P.; Horton, P. N.; Hursthouse, M. B.; Tucker, J. H. R.
Angew. Chem., Int. Ed. 2005, 44, 1072–1075. (f) Yagai, S.; Iwai, K.; Karatsu,
T.; Kitamura, A. Angew. Chem., Int. Ed. 2012, 51, 9679–9683.
(4) A precise supramolecule is one which not only is discrete (i.e.,
nonpolymeric) but also has a well-defined three-dimensional structure.
(5) For an example of a [2 þ 2] photodimerization of thymine-
terminated bolaamphiphile within supramolecular fibers, see: Iwaura,
R.; Shimizu, T. Angew. Chem., Int. Ed. 2006, 45, 4601–4604.
(6) (a) Martı
12485–12487. (b) Betancourt, J. E.; Rivera, J. M. J. Am. Chem. Soc.
2009, 131, 16666–16668. (c) Betancourt, J. E.; Martın-Hidalgo, M.;
Gubala, V.; Rivera, J. M. J. Am. Chem. Soc. 2009, 131, 3186–3188. (d)
Garcıa-Arriaga, M.; Hobley, G.; Rivera, J. M. J. Am. Chem. Soc. 2008,
130, 10492–10493.
´
n-Hidalgo, M.; Rivera, J. M. Chem. Commun. 2011, 47,
´
´
r
10.1021/ol400610x
Published on Web 05/03/2013
2013 American Chemical Society

the ribose available for attaching functional elements such as
hydrophilic groups,6d fluorophores,7b and dendrons.6a,7c,7d
The 1H NMR spectrum of 1, in the presence of KSCN
(0.5 equiv, in CD3CN), revealed a pair of peaks between 11
and 13 ppm corresponding to the two types of N1Hs
characteristic of a D4-symmetric 4T-SGQ or hexadecamer
(Figure 2a). The 2D NOESY spectrum also shows key
signature cross peaks in the 7ꢀ13 ppm region, correspond-
ing to the hydrogen bonded guanine moieties in the
G-quadruplex core (Figure S21). Electrospray ionization
mass spectrometry (ESI-MS) provided further evidence
for the formation of [116•3K]3þ by showing a peak at m/z
3471.8918 (Figure 2). These results show that the enhanced
steric crowding in the periphery of 1 does not interfere with
its self-assembly, underscoring the importance of the
m-carbonyl group in directing the assembly of a 4T-SGQ.
Scheme 1. Photoreaction Products Obtained by Irradiating
8-Chalconyl-20-deoxyguanosine Derivative 1 as a Monomer or
after Its Self-Assembly into Hexadecamer 116•3Kþa
a Irradiation of monomer 1 does not produce 2, as indicated by the
crossed out arrow.
Photoirradiation (30 min; 365 nm) of 1 in methanol
(unfavorable conditions for self-assembly) resulted in a
transꢀcis isomerization with a photoequilibrium of ca. 60%
Figure 1. (a) Schematic depiction of the interconversion of
various SGQs formed by 8ArG derivatives using external
stimuli. The circles with a þ sign represent a cation such as
Kþ; the 2T-SGQ, 3T-SGQ, and 4T-SGQ are highlighted
(respectively) in blue, green, and red. The dotted lines between
T2 and T3 represent potential covalent bonds between sub-
units as is the case in the present work. The dark arrows
represent achieved modes of transforming different types
of SGQs (process ii highlighted in yellow is the subject of the
current report), while the arrows in gray (ii0, iii, iii0) are
unachieved transformations. (b) Chemical and cartoon depic-
tions of a generic 8ArG tetramer (e.g., 14•Kþ; X = chalconyl
moiety and R = isobutyryl as shown in Scheme 1) indicating its
two diastereomeric sides. The head is the side shown, which has
a clockwise rotation (circular dashed arrows) around N1H to
O6 hydrogen bonds.
1
cis-1 as confirmed by UVꢀvis spectroscopy and H NMR
(Scheme 1; Figures S7ꢀS10).8,9 In contrast, photoirradiation
of 116 (20 min, in CD3CN) lead to the disappearance of all
the signature peaks with the concomitant broadening of
the remaining visible signals (Figures 3 and S18). Initially it
seemed as if the formation of cis-1 had induced the
disassembly of 116,10 but a day later it became clear that
1
this was not the case because the H NMR spectrum
revealed the emergence of a species with sharp signals,
(8) Irradiation for up to 60 min leads to no significant changes relative to
shorter irradiation times. cis-1 decays slowly back to 1 (Figure S10).
(9) Spada reported that the cisꢀtrans isomerization of an 8-styryl-20-
deoxyguanosine derivative leads to the reversible assemblyꢀdisassembly of
the corresponding octameric supramolecule. Lena, S.; Neviani, P.; Masiero,
S.; Pieraccini, S.; Spada, G. P. Angew. Chem., Int. Ed. 2010, 49, 3657–3660.
(10) An experiment using a 1:1 mixture of 1:cis-1 (Figure S17)
indicates that even at these proportions cis-1 does not disrupt hexade-
camer formation.
(7) (a) Gubala, V.; Betancourt, J. E.; Rivera, J. M. Org. Lett. 2004, 6,
4735–4738. (b) Rivera, J. M.; Martın-Hidalgo, M.; Rivera-Rıos, J. C.
´ ´
Org. Biomol. Chem. 2012, 10, 7562–7565. (c) Rivera, L. R.; Betancourt,
J. E.; Rivera, J. M. Langmuir 2011, 27, 1409–1414. (d) Betancourt, J. E.;
Rivera, J. M. Org. Lett. 2008, 10, 2287–2290.
Org. Lett., Vol. 15, No. 10, 2013
2351

which became dominant after several more days. An
interesting feature of this new species was the triple set of
signals, which offered the first hint of an assembly with
three tetrads or a 3T-SGQ (Figures 2b, 3). The question
remained, however, as to what type of 3T-SGQ was it.
The peak pattern of the NMR of the new species
(Figures 2b and S19),11 and the observed mass of m/z
2613.6326 (Figures 2 and S20), led us to hypothesize that
the isomerization toward cis-1 induced the formation of a
dodecamer. This possibility was quickly dismissed due to
1
the near absence of cis-1 in the H NMR in DMSO-d6
(a solvent that disrupts the assembly), in addition to the
observed 1:1 ratio of 1 with a new species (2) that showed
a double set of signals (Scheme 1, Figure 3b). Further
HPLC-MS analysis of 2 demonstrated it to have twice the
mass of 1 (Figures S6, S14) supporting its assignment as a
covalent dimer (Scheme 1). Further NMR experiments
with2 confirmed the presence of a cyclobutyl moiety, likely
formed via a [2 þ 2] photocycloaddition between the
double bonds in the chalconyl moiety.
The reason why irradiation of 116 enables a [2 þ 2]
cycloaddition reaction is the increased proximity of four
pairs of chalconyl double bonds in the supramolecule
(Figure 3a).12,13 The formation of a single diastereomer
of 2 and the negligible formation of cis-1 are indicative of
the kinetic stability, well-defined spatial orientation of the
double bonds, and the relatively crowded environment
within 116. Molecular modeling studies suggest the stereo-
chemistry around the cyclobutyl moiety in 2 is the so-called
δ-truxinate14 due to the relative orientation of the olefins
prior to the dimerization (Figure S26). Minimization of the
dimer by itself, followed by its superposition over the
structure of 1424, shows minimal deviations in the overall
geometry of the subunits (Figure S26). Those small devia-
tions, however, are likely responsible for the reluctance of
2 to form a homomeric octamer due to its reduced flex-
ibility relative to 1. The association of two different tetrads
(14 þ 24) provides enough flexibility to accommodate the
increased rigidity of the subunits of 2.
Figure 2. Phototriggered transformation of 116 into 1424 as a
function of time. (a) Partial 1H NMR (500 MHz, CD3CN,
0.5 equiv KSCN, 298 K) showing the region corresponding to
the N1H peaks. (b) Cartoon depiction of the corresponding
SGQs [116•3K]3þ and [1424•3K]3þ; the measured and calculated
isotope patterns obtained from ESI-MS are included above and
below (respectively) the corresponding cartoon depictions.
After irradiation, many of the potential supramolecular
states, including, for example, the heteromeric dodecamer
1824 or the homomeric octamer 28, are not favored.15 This
islikely acombination ofthe detrimental strainimposed by
the cyclobutyl moiety combined with the putative entropic
advantage of a heteromeric assembly over a homomeric
one. More specifically, isolated dimer 2 (with 0.5 equiv of
KSCN in CD3CN) self-assembles with very poor fidelity
leading to a complex mixture of assemblies (Figure S24),
yet, adding 1 equiv of 1 leads to the relatively slow
formation of 1424 (Figure S25). The many transient peaks
observed right after the irradiation of 116 (Figure 2;
Figures S18, S19), and up until the new equilibrium is
established, points to a rough energy landscape (thus, the
relatively long equilibration process) containing multiple
metastable assemblies (i.e., kinetic traps) where 1424 re-
presents a significantly deeper well to shift the equilibrium
with high fidelity.16 The proportion of subunits (1:1) is
precisely determined by not only the information encoded
ꢀ
´
(11) (a) Rivera-Sanchez, M. d. C.; Andujar-de-Sanctis, I.; Garcıa-
Arriaga, M.; Gubala, V.; Hobley, G.; Rivera, J. M. J. Am. Chem. Soc.
2009, 131, 10403–10405. (b) Gonzalez-Rodriguez, D.; van Dongen,
J. L. J.; Lutz, M.; Spek, A. L.; Schenning, A. P. H. J.; Meijer, E. W.
Nat. Chem. 2009, 1, 151–155.
(12) The [2 þ 2] cycloaddition in solution is not usually the favoured
dissipative process after photoexcitation (heat dissipation, transꢀcis
isomerization, and emission being usually favoured). And while still
relatively rare, relative to examples [2 þ 2] cycloaddition reactions
can occur in crystalline environments: (a) Bhogala, B.; Captain, B.;
Parthasarathy, A.; Ramamurthy, V. J. Am. Chem. Soc. 2010, 132,
ꢀ
13434–13442. (b) MacGillivray, L. R.; Papaefstathiou, G. S.; Friscic,
T.; Hamilton, T. D.; Bucar, D.-K.; Chu, Q.; Varshney, D. B.; Georgiev,
I. G. Acc. Chem. Res. 2008, 41, 280–291. (c) Yang, S.-Y.; Naumov,
P. e.; Fukuzumi, S. J. Am. Chem. Soc. 2009, 131, 7247–7249.
(13) (a) Ushakov, E. N.; Vedernikov, A. I.; Alfimov, M. V.; Gromov,
€
S. P. Photochem. Photobiol. Sci. 2011, 10, 15–18. (b) Svoboda, J.; Konig,
B. Chem. Rev. 2006, 106, 5413–5430. (c) Mizoguchi, J.-i.; Kawanami, Y.;
Wada, T.; Kodama, K.; Anzai, K.; Yanagi, T.; Inoue, Y. Org. Lett. 2006,
8, 6051–6054. (d) Iwaura, R.; Shimizu, T. Angew. Chem., Int. Ed. 2006,
45, 4601–4604.
(14) Although the double bonds in 1 could be positioned in a relative
geometry that would lead to the R-truxilate, analysis of the resulting
mixed octamer of 1424 made with it revealed many detrimental interac-
tions that would prevent its formation. McClenaghan, N. D.; Bassani,
D. M. Int. J. Photoenergy 2004, 6, 185–192.
(15) The peak at m/z = 3471 could correspond to [116•3K]3þ or
[1824•3K]3þ (Figure S20), which leaves open the possibility that the latter
(a mixed dodecamer) could form at least in the gas phase as well as in
small amounts in solution.
(16) Furlan, R. L. E.; Otto, S.; Sanders, J. K. M. Proc. Natl. Acad.
Sci. U.S.A. 2002, 99, 4801–4804.
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Org. Lett., Vol. 15, No. 10, 2013

In summary, the phenomenon described here goes as
follows: (1) irradiation of monomer 1 leads to isomerization
to cis-1; (2) irradiation of 116 leads to a [2 þ 2] photocy-
cloaddition of two subunits of 1 to form a covalent dimer 2;
(3) the dimer still preserves some of the information for
assembling, but it cannot self-assemble by itself into a
well-defined discrete supramolecule. Instead, it self-
sorts with subunits of 1 to form a heteromeric octamer
1424; (4) formation of 2 does not abolish all assemblies
because, although a homomeric assembly of dimer 2 is
not viable, in combination with 1 the resulting system
can fulfill a larger number of noncovalent interactions
(e.g., hydrogen bonds, πꢀπ interactions), which would
otherwise go unmet. The resulting heteromeric SGQ is
structurally anisotropic along the assembly’s main (C4)
axis (i.e., a Janus type supramolecule). The 4T-SGQ 116
is, to the best of our knowledge, the first example of a
precise photoresponsive supramolecular assembly able to
shift to an alternative precise supramolecule (1424). The
synthesis of related derivatives containing functional ele-
ments (e.g., fluorophores, dendrons) will provide a platform
for the development of molecularly precise multifunctional
supramolecules for a wide variety of applications.
Acknowledgment. This research was financially supported
by the NIH-SCoRE (Grant No. 5SC1GM093994). D.S.B.
thanks the NIH-MBRS-RISE Program (2R25GM061151)
and the Alfred P. Sloan Foundation for fellowships.
Dedicated to the memory of Professor Gian Piero Spada
Figure 3. Molecular models of (a) 116 and (b) 1424 showing the
spatial proximity of the reactive double bonds and the resulting
cyclobutyl moiety, respectively (both highlighted in yellow). Ad-
jacent double bonds from T1 are highlighted in green, and due to
their large separation the dimerization occurs exclusively between
ꢁ
(Universita di Bologna) a pioneer in the field of supramo-
lecular G-quadruplexes.
1
T2/T3 or T1/T4. (c) H NMR (500 MHz, DMSO-d6, 298 K) of
1424 sample. DMSO-d6 effectively disrupts the assembly, allowing
characterization of both 1(magenta) and 2 (orange) as monomers.
Peaks marked with asterisks correspond to cis-1 (∼4%).
Supporting Information Available. Experimental details,
characterization, and spectral data. This material is available
free of charge via the Internet at http://pubs.acs.org.
in the constituent subunits in 1424 but also the spatial
distribution of such subunits, where tetramers 14 and 24
self-sort17 at opposite sides of the supramolecule. The
resulting symmetry can only result from a mixed assembly
with a Janus type configuration (Figure 3b).18
(18) In principle, an assembly having twice as many tetrads (i.e., six)
may show similar NMR and MS spectra. This possibility was discarded
on the basis of the evidence provided in previous studies by our group
where we have shown that 8ArG derivatives cannot form assemblies
with more than four tetrads. This is because the enhanced repulsive
interactions (steric, electronic) for stacking five or more tetrads are not
sufficiently compensated by attractive noncovalent interactions. For
relevant information see refs 6c, 6d, 7, and 11a.
ꢀ
€
(17) (a) Safont-Sempere, M. M.; Fernandez, G.; Wurthner, F. Chem.
Rev. 2011, 111, 5784–5814. (b) Wu, A.; Isaacs, L. J. Am. Chem. Soc.
2003, 125, 4831–4835.
The authors declare no competing financial interest.
Org. Lett., Vol. 15, No. 10, 2013
2353