Selective RNA versus DNA G-quadruplex targeting by situ click chemistry

Article abstract of DOI:10.1002/anie.201206281

It all clicks into place: A potent telomere-targeting small molecule has been identified by using the copper-free 1,3-dipolar cycloaddition of a series of alkyne and azide building blocks catalyzed by a non-Watson-Crick DNA secondary structure (see picture). This method rapidly identifies, otherwise unanticipated, potent small-molecule probes to selectively target a given RNA or DNA. Copyright

Full text of DOI:10.1002/anie.201206281

Angewandte
Chemie
DOI: 10.1002/anie.201206281
Bioorganic Chemistry
Selective RNAVersus DNA G-Quadruplex Targeting by In Situ Click
Chemistry**
Marco Di Antonio, Giulia Biffi, Angelica Mariani, Eun-Ang Raiber, Raphaꢀl Rodriguez,* and
Shankar Balasubramanian*
Click chemistry has been broadly defined as chemical
reactions capable of promoting the formation of stable
covalent adducts from two distinct reactive moieties in
a mild and quantitative manner with an appreciable tolerance
to water.[1] These stringent requirements have rendered the
development of click reactions particularly challenging.[2]
More recently, the term click chemistry has referred to the
1,3-dipolar cycloaddition of alkynes and azides that is
promoted at room temperature by various copper- and
ruthenium-based catalysts.[3] This powerful reaction has
found broad applications that span from material science to
cell biology.[4] Copper-free variants involving reactive cyclo-
octyne derivatives have been widely investigated to enable its
use in cellulo, in particular for the labeling of biomolecules.[5]
Conversely, the correct orbital alignment of terminal alkynes
and azides necessary for the cycloaddition to take place is well
known to increase the negative values of DS°, thus making
the noncatalyzed reaction rather slow in a biologically
relevant environment. This feature, initially perceived as
a limitation, was exploited by Finn and Sharpless in their
concept of “in situ” click chemistry, which relies on the
specific interactions between the reactants and a given
biological target to enable the optimal orientation of the
substrates for the reaction to occur at room temperature.[6]
In situ click chemistry has led to the discovery of several
enzyme inhibitors with low nanomolar Kd values.[7] There is as
yet no report on such an approach to generate small
molecules that selectively target a defined secondary struc-
ture of a nucleic acid.
stability of the genome. This region of chromosomes is
composed of tandem repeats of guanine tracts (TTAGGG)n
that are prone to fold into polymorphic G4 structures (H-
Telo).[9] It has previously been shown that small molecules
capable of interacting with H-Telo have the ability to activate
a DNA damage response at telomeres and to trigger
senescence and apoptosis.[10] Therefore, we have explored
the ability of H-Telo to act as the reaction vessel for the 1,3-
dipolar cycloaddition to generate potent telomere-targeting
small molecules.
Two G4 binding substrates 1 and 2 (Figure 1A) containing
an alkyne substituent were used as the starting materials.
Alkynes 1 and 2 were derived from the known G4-binding
small molecule pyridostatin (PDS), but lacked a polar
function on the central pyridine core, thereby leaving room
to modulate the binding properties of the substrate through
a click reaction with a series of azides.[11] Azides 3–8, which
comprise positively and negatively charged atoms, aromatic
substrates, and a neutral sugar, were used to cover several
types of interaction modes, including p stacking as well as
electrostatic and hydrogen bonding, with the aim of max-
imizing the chances of identifying a strong DNA G4
interacting partner.
We anticipated that the presence of the DNA target in the
mixture would catalyze the formation of potent adducts
(Figure 1B).[12] In a typical experiment, alkynes 1 and 2
(25 mm), azides 3–8 (1 mm), Tris·HCl (10 mm, pH 7.4; Tris =
tris(hydroxymethyl)aminomethane), and KCl (250 mm) con-
taining buffer, with and without telomeric DNA G4 (25 mm)
were mixed together. A 40-fold excess of each individual
azide was used to alleviate any bias imposed by changes in the
concentration of the azides selected during the course of the
reaction.
To ensure that products of the click reaction were the
result of specific interactions between the reactants and the
structured DNA G4, we independently performed a reaction
either in the presence of a double-stranded DNA (ds-DNA)
control (25 mm) or with the telomeric oligonucleotides pre-
annealed in a lithium-containing buffer, which is known to
prevent G4 formation.[13] Each solution was stirred at room
temperature for six days, before trifluoroacetic acid (TFA)
was added to denature the DNA (20% aq). The mixture was
monitored by LC-MS to simultaneously identify the nature
and quantify the respective amounts of each product from
a reaction that could, in principle, contain up to 24 cyclo-
adducts, including 1,4- and 1,5-regioisomers (Figure 1C). The
mass spectrometer was programmed to independently detect
the mass of each possible adduct and alkyne substrate by
using a single ion monitoring protocol, thus enabling the
Herein, we demonstrate the value of in situ click chemis-
try approaches to identify potent and selective small mole-
cules that bind G-quadruplexes (G4). We have selected the
human telomeric DNA as a suitable target because of its
relevance to cancer biology.[8] Telomeres play a crucial
cellular function by protecting chromosomes from shortening
after several rounds of replication, thereby sustaining the
[*] Dr. M. Di Antonio, A. Mariani, Dr. E.-A. Raiber, Dr. R. Rodriguez,
Prof. S. Balasubramanian
University of Cambridge, Department of Chemistry
Lensfield Road, Cambridge, CB2 1EW (UK)
E-mail: rr324@cam.ac.uk
sb10031@cam.ac.uk
G. Biffi, Prof. S. Balasubramanian
Cambridge Research Institute, Cancer Research UK
Li Ka Shing Centre, Cambridge, CB2 0RE (UK)
[**] We thank the BBSRC and Cancer Research UK for funding.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201206281.
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considering
previously
reported
data
recorded for the potent G4 ligand PDS and
other amine-containing G4-binding small
molecules.[16] Additionally, no adduct could
be detected when azide 4 was removed from
the reaction mixture. This finding indicates
that specific interactions occur between 1, 4,
and the DNA catalyst, while the other azides,
once bound to H-Telo, may be held remote
from the alkyne substrates in a way that does
not favor the cycloaddition under these con-
ditions. Overall, these results show that 1 is
a better ligand than 2 and that adduct 10
exhibits enhanced interacting capabilities
compared to the other possible adducts and
starting materials.
The clear effect of H-Telo on the 1,3-
dipolar cycloaddition prompted us to inves-
tigate whether the presence of copper could
compensate for the poor kinetics, whilst
preserving a good selectivity. Thus, a similar
reaction containing all the building blocks and
an excess of a copper catalyst was performed.
Figure 1. A) Molecular structure of alkyne and azide building blocks; B) adducts gener-
ated by treating 1 and 2 with 3–8; C) in situ synthesis of triazoles catalyzed by H-Telo.
analysis of the complex reaction mixture with high resolution.
Interestingly, we observed the formation of the single 1,4-
adduct 10, which results from the cycloaddition of 1 and 4 in
the presence of H-Telo (Figure 2), whereas no adduct could
be detected when reactions were either conducted in the
absence of DNA or in the presence of ds-DNA.[14] In addition,
no adduct was observed when the telomeric oligonucleotide
was pre-annealed in lithium-containing buffer prior to its use,
thus demonstrating that the G4 structure is required for the
1,3-dipolar cycloaddition to occur under the mild reaction
conditions used. These data suggest that the dynamic and
reversible assembly of alkynes and azides with the G4 catalyst
is a fast process that allows the system to select the most
potent building blocks prior to slowly reacting with one
another to generate the adduct, a procedure evocative of
dynamic combinatorial processes.[15] It is noteworthy that the
neutral sugar-containing azide was selected at the expense of
positively charged azides, a rather counterintuitive outcome
Figure 3A depicts a stochastic distribution of the reaction
products that reflects the initial concentration and intrinsic
Figure 3. Chromatogram tuned on the 14 mass channels of alkynes
1 and 2 and adducts 9–20 obtained from the reaction carried out in
the presence of A) a Cu catalyst and B) a Cu/H-Telo catalyst. C) Histo-
gram showing the relative abundance of each product obtained in
copper- (control), Cu/H-Telo-, and Cu/ds-DNA-catalyzed reactions.
Data were plotted as the surface area measured under each individual
chromatogram signal.
Figure 2. Chromatogram tuned on 14 mass channels of alkynes 1 and
2 and adducts 9–20 obtained from the reaction carried out in the
presence of H-Telo.
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reactivity of each individual starting material. Under these
reaction conditions, incubation at room temperature for 3 h
was sufficient for the reaction to reach completion. In
a separate experiment where a substoichiometric amount of
H-Telo (0.05 molequiv) was added to the mixture containing
the copper catalyst, we observed that the distribution of
products was biased towards sugar-containing adducts 10 and
16 at the expense of the others identified in the presence of
only copper (Figure 3B). This indicates that, to some extent,
the DNA G4 overrides the lack of specificity imposed by the
kinetically favored copper-catalyzed reaction.
Indeed, these data demonstrate that while copper controls
the reaction kinetics, the selectivity is still imposed by the
DNA template, thus suggesting a cooperative behavior of the
H-Telo and copper catalysts in a manner that is reminiscent of
DNAzymes.[17]
eral trend in which adducts derived from 1 generally exhibit
slightly better stabilizing properties than the analogues
derived from 2. Furthermore, we observed that the stabiliza-
tion properties of each adduct followed the general trend of
neutral (sugar) > positively charged (amines) > negatively
charged (carboxylic acids), with DTm values ranging from
30 K for sugars to 20 K for amines and 6 K for carboxylic
acids. Finally, adducts were generally more potent than the
starting materials 1 and 2, with the exception of negatively
charged adducts, which were even weaker stabilizers. This
general trend is in strong agreement with the DNA-guided
synthesis profiles observed in the copper-catalyzed reaction,
thus supporting a model whereby the DNA G4 catalyzes the
formation of the most potent interacting small molecules (i.e
sugar and amino analogues).
Shelterin is a six-protein complex that binds to telomeric
DNA to protect telomeres from the DNA damage response
machinery and to prevent chromosomes from shortening.[21]
This complex is transiently dissociated from DNA during the
dynamic processes of replication and transcription, hence
enabling small molecules to interact with the DNA and to
compete out shelterin components. Therefore, we investi-
gated the ability of diverse adducts to target telomeric DNA
by measuring the amount of the shelterin component
telomeric repeat-binding factor 1 (TRF1) at telomeres by
using fluorescence microscopy. Human MRC5-SV40 fibro-
blasts were incubated with various analogues at 2 mm for 24 h
and the TRF1 protein was visualized and quantified by using
an anti-TRF1 antibody. Remarkably, the number of TRF1
foci per cell strongly decreased in a dose-dependent manner
upon treatment with 10 compared to untreated cells, with an
IC50 value of (1.3 Æ 0.3) mm, whereas a negligible effect was
observed for the negatively charged control 20 and precursors
1 and 2 (Figure 4). This result is in strong agreement with the
copper-free in situ synthesis of the ligand, where only the
selected molecule 10 is able to compete out the shelterin
component from telomeres. Consistent with this, negligible
TRF1 displacement was observed for other adducts such as 9
or carboxypyridostatin (13) under the same conditions (see
the Supporting Information), thus validating the in situ
approach for the discovery of structure-selective small
molecules. It is noteworthy that the parent molecule PDS
induced the highest increase in the melting temperature of H-
Telo (Table 1), but did not induce significant phenotypic
changes at telomeres under similar conditions. Overall, these
results demonstrate that in situ click chemistry is an accurate
and unbiased method to generate and evaluate biologically
active small molecules in a single step and can be more
powerful than preexisting methods based on rational design.
This concept may be exemplified by the observation that PDS
was predicted to be the most potent hit for this particular
target according to FRET melting experiments, with
a DTm value of 35 K compared to 30 K for 10, while in situ
click selection generated the slightly weaker stabilizer 10 that
is a more potent TRF1 competitor in cellular experiments.
Finally, we sought to explore whether our method would
enable the identification of small molecules with the ability to
selectively interact with RNA G4 structures but not their
DNA counterparts. To this end, the telomeric repeat-con-
Furthermore, this result suggests that 10 does not poison
the DNA catalyst, despite a higher shift in the melting
temperature of H-Telo induced by 10 compared to 1,
according to fluorescence resonance energy transfer
(FRET) melting experiments, thereby showing that 10 is
a better stabilizer than 1 (see Table 1).[18,19]
Table 1: FRET melting values for H-Telo and ds-DNA in K.
Compound (1 mm)
DTm (H-Telo)
DTm (ds-DNA)
1
2
9
16.0Æ0.1
12.8Æ0.2
21.1Æ0.2
30.0Æ0.1
18.8Æ0.6
22.5Æ0.7
11.2Æ0.1
6.3Æ0.4
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.1Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
0.0Æ0.1
10
11
12
13
14
15
16
17
18
19
20
PDS
19.1Æ0.3
28.2Æ1.1
17.2Æ0.3
20.1Æ0.2
9.1Æ0.5
5.9Æ0.3
35.4Æ1.2
The favorable turnover observed may be the result of the
well-known folding/unfolding dynamic properties of G4
nucleic acids.[13,20] In contrast, the production of negatively
charged adducts, which are known to be weaker binders
because of electrostatic repulsions, was poor compared to
those of other adducts, and significantly lower than their
respective amounts obtained from experiments conducted in
the absence of H-Telo. In line with the data obtained from
copper-free experiments, the presence of ds-DNA in copper-
catalyzed reactions had negligible effect on the product
distribution, as shown in Figure 3C (see also the Supporting
Information). To provide a rationale underlying the catalytic
effect of H-Telo we analyzed the stabilization properties of
each individual starting material and adduct by FRET melting
experiments. Table 1 displays the increase in the melting
temperatures of H-Telo (DTm) in the presence of each
compound, measured independently. These data show a gen-
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Figure 4. A) Fluorescent microscopy images of untreated MRC5-SV40
cells or treated with 2 mm compound for 24 h. Cells were stained with
4,6-diamidino-2-phenylindole (DAPI) and anti-TRF1 antibody; scale
bar: 20 mm, zoom images are 25X magnified. B) Dose-response read-
out based on the number of TRF1 foci per cell upon treatment with 10
for 24 h. C) Number of TRF1 foci per cell upon treatment with various
adducts and PDS (2 mm, 24 h).
Figure 5. A) Chromatogram tuned on the 14 mass channels of alkynes
1 and 2 and adducts 9–20 obtained from the reaction carried out in
the presence of Cu/TERRA catalysts. B) Histogram showing the
relative abundance of 13 obtained from Cu- (control), Cu/H-Telo-, Cu-
TERRA-, and Cu/ds-DNA-catalyzed reactions. C) Histogram showing
the shift in the melting temperature of doubly labeled TERRA in the
presence of 13 or PDS (2 mm) and increasing amounts of unlabeled
H-Telo competitor.
taining RNA (TERRA), known to form a stable G4 structure
in vitro, was used as a catalyst.[22] Analysis of the reaction
mixture conducted in the presence of Cu/TERRA catalysts
revealed significant differences in the respective abundance
of the products compared to the reaction conducted in the
presence of the Cu/H-Telo catalysts (Figure 5A; see also the
Supporting Information).
Strikingly, the negatively charged adduct 13 was the most
prevalent product of the reaction conducted in the presence
of Cu/TERRA, whereas its abundance was decreased in the
presence of H-Telo (Figures 3 and 5A,B). In contrast, the
abundance of the other negatively charged adduct 14
containing an aromatic moiety was lower in the reaction
conducted in the presence of Cu/TERRA compared to that in
the copper-catalyzed reaction. This finding indicates that very
selective interactions are involved between the RNA catalyst
and substrates 1 and 7. It also challenges the idea that
selective nucleic acid targeting is restricted to neutral and
positively charged small molecules.[23] This difference in
chemical reactivity may be the result of hydrogen bonding
of the carboxylate moiety of 7 and the 2’-OH group of the
RNA substrate, which is absent in the corresponding DNA
template. This notion is further supported by the fact that the
RNA G4 unit present in the 5’-UTR of NRAS exhibited
a similar catalytic effect as TERRA, with isolation of 13 as the
major product of the reaction.[24] FRET melting experiments
confirmed that 13 is a better TERRA stabilizer than the
alkyne precursor 1 and product 14, with DTm values of (20.7 Æ
0.1) K, (15.1 Æ 0.2) K, and (6.4 Æ 0.2) K at 1 mm compound,
respectively, whereas PDS was the most potent stabilizer with
a DTm value of (22.2 Æ 0.1) K (see the Supporting Informa-
tion). In competition experiments where TERRA was doubly
labeled (l-TERRA) and an excess of the unlabeled H-Telo
target competitor was added, we observed that the ability of
13 to stabilize TERRA was not affected by the presence of up
to 100 molequiv DNA competitor, whereas the ability of PDS
to stabilize TERRA decreased by (19.5 Æ 0.4) K upon titra-
tion with the H-Telo target (Figure 5C). This result demon-
strates that while PDS is a good generic RNA and DNA G4-
interacting small molecule, the negatively charged adduct 13
is a selective RNA G4-interacting compound.[25]
We previously reported the existence of other G4
structures in the coding region of human genes and showed
that PDS was a potent generic G4-interacting small molecule,
somewhat lacking the ability to trigger a strong response at
telomeres after a short treatment period.[26] The cellular
phenotype induced by PDS, that is the induction of DNA
damage at specific human genomic site containing G4
clusters, may to some extent be linked to RNA G4 structures,
in particular with respect to RNA splicing during tran-
scription and telomere maintenance. For example, it has been
proposed that TERRA acts as a negative regulator of
telomerase by competing with the DNA substrate.[27] The
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J. A. Pfeilsticker, K. B. Sharpless, J. R. Heath, J. Am. Chem. Soc.
unique ability of carboxypyridostatin to selectively stabilize
the TERRA G4 structure but not H-Telo provides the means
to elucidate the existence, and decipher the biological
function, of RNA selectively from DNA G4 structures in
human cells. This study demonstrates that unbiased
approaches based on in situ click chemistry are suitable to
enhance the ability of small molecules to interact with a given
nucleic acid structure. Such a strategy paves the way towards
structure-selective nucleic acid targeting, which is notoriously
difficult to achieve.
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Received: August 5, 2012
Published online: October 4, 2012
Keywords: click chemistry · DNA · G-quadruplexes · RNA ·
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(19.2 Æ 0.2) K at 1 mm (see the Supporting Information). This is
in line with the fact that H-Telo does not catalyze the formation
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