Enantioselective Diels-Alder reactions using a G-triplex DNA-based catalyst

Article abstract of DOI:10.1016/j.catcom.2015.09.012

In this study, it was found that the G-triplex DNA could be used as an enantioselective catalyst without further addition of ligands in Diels-Alder reactions when coordinated with copper ions, for the first time. The efficiency and selectivity of the cata

Full text of DOI:10.1016/j.catcom.2015.09.012

Catalysis Communications 74 (2016) 16–18
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Catalysis Communications
journal homepage: www.elsevier.com/locate/catcom
Short communication
Enantioselective Diels–Alder reactions using a G-triplex
DNA-based catalyst
Xiaowei Xu a,b, ,1, Wuxiang Mao a,1, Feng Lin a, Jianlin Hu a, Zhiyong He a, Xiaocheng Weng a,
⁎
Chun-Jiang Wang a, Xiang Zhou a,
⁎
a
College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Hubei, Wuhan 430072, People's Republic of China
State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, Jiangsu 210009, People's Republic of China
b
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 10 August 2015
Received in revised form 15 September 2015
Accepted 18 September 2015
Available online 21 September 2015
In this study, it was found that the G-triplex DNA could be used as an enantioselective catalyst without further
addition of ligands in Diels–Alder reactions when coordinated with copper ions, for the first time. The efficiency
and selectivity of the catalyst were investigated. The kinetic measurements were made using ultraviolet (UV)
light. The stability of the catalyst in aqueous buffer was confirmed by circular dichroism (CD) and nuclear magnetic
resonance (NMR) spectra.
© 2015 Published by Elsevier B.V.
Keywords:
Diels–Alder
G-triplex
DNA
Asymmetric catalysis
Enantioselectivity
1. Introduction
which brings the reactants into, or very close to, the G-quadruplex
host [7].
Since the double-stranded DNA (dsDNA) has been recognized as a
catalytic species and used in various key asymmetric reactions [1],
DNA-based asymmetric catalysis has attracted the attention of many
chemists. Recently, the concept was extended to G-quadruplex DNA
sequences. Unlike dsDNA, the G-quadruplex, exhibiting polymorphous
strand orientation and various loop sizes [2], constructs a semi-enclosed
structure [3], providing a rigid and finite space for chiral transformation,
which induced appreciable levels of enantioselectivity in Diels–Alder
(D–A) reactions [4], confirming that the G-quadruplex structure could
also act as a suitable chiral template [5].
Earlier research works reported that a DNA-based catalyst comprises
a nonchiral ligand by the supramolecular and covalent anchoring strat-
egies, which can chelate a transition metal ion. Therefore, the catalyzed
reaction takes place in, or very close to, the DNA helix to allow the trans-
fer of chirality of the DNA to the reaction [1c]. In the G-quadruplex, the
G-tetrad is a square planar alignment of four guanines connected by
cyclic Hoogsteen hydrogen bonds [6] and plays a very important role
in recognizing planar aromatic ligands through π–π stacking [4] mainly,
Compared with the G-quadruplex DNA, the G-triplex, intensely
studied recently [8], seems to be more attractive because of its contro-
versial but noncanonical structure and biological functions [9]. This
structure was first characterized as an intermediate formation of
the G-quadruplex, but a stable conformation [6b]. Similarly to the
G-quadruplex, the G-triplex is stabilized by Hoogsteen-like hydrogen
bonds [10]. Because of the G-quadruplex's role and function in the
enantioselective D–A reaction, we hypothesized that the G-triplex
structure would also exert asymmetric induction in D–A reactions to
some extent if similar structural and electrical requirements are met.
Furthermore, the G-triplex has not yet found significant application in
the development of asymmetric catalysis. Our discovery of asymmetric
induction of Cu2+/G-triplex DNA complex may allow the G-triplex
motif to be used for the construction of novel and comparatively inex-
pensive chiral catalysts.
2. Experimental
2.1. Materials and methods
⁎
Corresponding authors at: College of Chemistry and Molecular Sciences, Key
Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Hubei,
Wuhan 430072, People's Republic of China; State Key Laboratory of Natural Medicines,
Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University,
Nanjing, Jiangsu 210009, People's Republic of China.
DNA oligodeoxynucleotides 5′-GGTTGGTGTGG-3′ (ODN-1) were
purchased from Invitrogen, whose strand concentrations were deter-
mined by measuring the absorbance at 260 nm using the extinction co-
efficient values. All the other solvents and reactants were purchased
from Shanghai Chemical Reagent Co., Ltd. of Chinese Medicine Group.
E-mail addresses: 1020152484@cpu.edu.cn (X. Xu), xzhou@whu.edu.cn (X. Zhou).
1
These authors contributed equally to the study.
http://dx.doi.org/10.1016/j.catcom.2015.09.012
1566-7367/© 2015 Published by Elsevier B.V.

X. Xu et al. / Catalysis Communications 74 (2016) 16–18
17
Table 1
Diels–Alder reaction catalyzed by G-triplex based catalyst. All data are the average of two experiments.
Entry
Catalyst
Conversion [%]a
endo/exoa
ee [%]b
1
2
3
4
None
9
66
13
99
85:15
90:10
90:10
91:9
0
0
−14
−51
Cu2+
ODN-1
ODN-1 + Cu2+
a
Determined for the crude product by HPLC analysis on a chiral stationary phase; results are reproducible within 5%.
Determined for the endo isomer by HPLC analysis on a chiral stationary phase; results are reproducible within 5%.
b
2.2. General procedure
This observation supported our hypothesis that ODN-1 possesses
asymmetric induction in the D–A reaction. In order to further improve
the enantioselectivity and conversion of the reaction, Cu(NO3)2 was in-
troduced into the system.
An aqueous solution of ODN-1 (5′-GGTTGGTGTGG-3′, 25-μM final
concentration) was added to a 3-(N-morpholino) propanesulfonic
acid (MOPS) buffer (2 mL, 20 mM, pH = 7.0) containing KCl (70 mM)
and KH2PO4 (10 mM). After stirring for 30 min below 5 °C, a solution
of Cu(NO3)2 (25-μM final concentration) was added. Then, aza-
chalcone 1 in CH3CN (20 μL of a 0.1-M solution) was added. The reaction
was initiated by the addition of freshly distilled cyclopentadiene 2
(15 μL), and the mixture was stirred for 24 h at 4 °C, and then extracted
with diethyl ether (3 × 6 mL). After drying the extracted mixture with
anhydrous Na2SO4 and removing the solvent, the crude products were
directly analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy,
and then through high-performance liquid chromatography (HPLC) on a
chiral stationary phase. The conversions of the crude product were deter-
mined by HPLC (only for 3a).
Interestingly, under these reaction conditions, the ODN-1–Cu2+
complex increased the yield with full conversion (Table 1, entries 4 and
2) together with enhanced endo/exo ratio (90:10 to 93:7). The
enantioselectivity (51% ee) of the product 3a (endo) was also significantly
improved. These results demonstrated that the ODN-1–Cu2+ complex
could be used as an efficient catalyst for asymmetric D–A reaction.
In order to confirm that ODN-1 forms a G-triplex and further co-
ordinates with Cu2+ under these reaction conditions, we analyzed
the circular dichroism (CD) spectrum of ODN-1 in aqueous buffer.
Limongelli reported that the G-triplex is stable in a buffer containing
70-mM KCl, 10-mM KH2PO4, and 0.2-mM ethylenediaminetetraacetic
acid (EDTA) [10]. The primary CD signals of the G-triplex were positive
peaks at 253 and 289 nm. The CD spectra of ODN-1 were obtained in
water, MOPS (pH = 7.0) buffer containing 70-mM KCl and 10-mM
KH2PO4, and MOPS buffer containing only 10-mM KH2PO4 (Fig. S1).
EDTA was not added to the buffer because of its possibility to chelate
with the copper ions. Strong signals were observed at 253 and
289 nm when ODN-1 was in the buffer containing 70-mM KCl and
10-mM KH2PO4 (Fig. S1). This result confirmed that the G-triplex
structure would not form in the absence of EDTA and that 10-mM
KH2PO4 would affect the formation of the G-triplex. The results suggested
that the G-triplex forms only in high concentrations of potassium chlo-
ride. When copper ions were added to the buffer, the CD signals did not
change appreciably, producing typical peaks at 289, 253, and 265 nm, in-
dicating the formation of G-triplex structures (Fig. S1). Furthermore, 1H
NMR spectroscopy was performed to confirm the formation of G-triplex
when Cu2+ ions were added. As reported in the literature [10], the signals
in the 11.0–12.5-ppm region of the 1H NMR spectrum confirmed the
presence of four well-defined exchangeable protons, which is typical of
DNA structures with Hoogsteen hydrogen bonds, validating the forma-
tion of the G-triplex structure. Hence, all the experiments were
3. Results and discussion
In this study, G-triplex DNA (ODN-1, 5′-GGTTGGTGTGG-3′) was
used as a catalyst scaffold in D–A reactions. Because of the G-triplex,
DNA also becomes water-soluble. Water was used as the major solvent
because it is environmentally friendly and inexpensive [11]. First, a
model D–A reaction between aza-chalcone (1a) and cyclopentadiene
(2) was chosen as the model substrate to explore the catalytic perfor-
mance of ODN-1. As expected, ODN-1 promoted the D–A reaction,
affording the endo isomer 3a in a 14% enantiomeric excess (ee) albeit
with low conversion (Table 1).
Table 2
Kinetic parameters of ODN-1, Cu2+ and ODN-1–Cu2+ a
.
b
c
Entry
Catalyst
kapp [M−1S−1
]
krel
1
2
3
4
None
(2.5 0.5) × 10−3
(3.2 0.4) × 10−3
(1.4 0.2) × 10−2
(2.5 0.9) × 10−2
1.0
1.3
5.6
ODN-1
Cu2+
ODN-1 + Cu2+
10.0
a
D–A reactions of 2 (1 mM) and 1a at fixed concentrations (10, 15, 25, 35, and 50 mM)
were executed without catalyst and with ODN-1 (25 μM), Cu2+ (25 μM) and ODN-1–Cu2+
(ODN-1 (25 μM) and Cu2+ (25 μM)) catalysts. All of the reactions were performed in
MOPS buffer (20 mM pH = 6.6) containing 70 mM KCl and 10 mM KH2PO4 at 298 K.
b
The apparent second-order rate constant (kapp) was estimated from the initial rates
Fig. 1. The correlation of the enantioselectivity for the D–A reaction between the molar
ratio of Cu2+/ODN-1 and ee value. The conversions are all over 95% except that 13% con-
version (Cu2+/ODN-1 = 0).
(kapp = Vinit ∕ ([1a]0 · [2]0)).
Rate acceleration (krel) was calculated by the ratio of kappcatalyst/kappuncatalyzed, in which
kappuncatalyzed is the apparent second-order rate constant in the absence of the catalyst.
c

18
X. Xu et al. / Catalysis Communications 74 (2016) 16–18
Table 3
Substrate specifity of ODN-1–Cu2+ for the Diels–Alder reaction. All of the data are the average of two experiments.
Entry
Substrate
Conversion [%]a
Isolated yield
endo/exob
ee [%]b
1
2
3
4
1a
1b
1c
1d
99
96
90
99
90
85
86
92
91:9
91:9
85:15
99:1
−51
−18
28
64
a
Determined for the crude product by HPLC analysis on a chiral stationary phase; results are reproducible within 10%.
Determined for the endo isomer by HPLC analysis on a chiral stationary phase; results are reproducible within 10%.
b
performed in MOPS buffer (20 mM, pH = 6.6) containing 70-mM KCl
and 10-mM KH2PO4.
have other applications in chemical synthesis and biology, and more
research on reactions catalyzed by this unique DNA structure are ongo-
ing in our laboratory.
Then, the effects of the Cu2+/ODN-1 ratio on the reaction were
further explored. The product's ee values resulting from various
Cu2+/ODN-1 ratios were compared. The highest ee value (−51%) was
obtained when the Cu2+/ODN-1 ratio was 1:2 (Fig. 1). Therefore, this
ratio was used as a parameter in the subsequent optimization. Notably,
the G4DNA catalyst reported by Li consisted of DNA (two equivalents)
and Cu2+ ions (one equivalent).
Acknowledgments
This work was supported by the National Basic Research Program of
China (973 Program) (2012CB720600, 2012CB720603) and the National
Natural Science Foundation of China (Nos. 91213302, 21072115, and
21272181).
In order to further examine the catalytic activity of ODN-1–Cu2+, the
initial rate (Vinit) of the D–A reactions catalyzed by ODN-1, Cu2+, and
ODN-1–Cu2+ was measured. Apparent second-order rate constant
(kapp) with ODN-1 as catalyst was 1.3-fold higher than that of the reac-
tion without catalyst (Table 2, entry 2 vs. entry 1).
Therefore, ODN-1 only slightly accelerated the D–A reaction. The
kapp had a 5.6-fold increase when the reaction was catalyzed by Cu2+
(Table 2, entry 3), and the ODN-1–Cu2+ complex remarkably increased
the kapp almost 10-fold relative to the catalyst-free reaction (Table 2,
entry 4 vs. entry 1). These results illustrated that ODN-1–Cu2+ acceler-
ated the D–A reaction significantly. Compared with Cu2+ alone, ODN-
1–Cu2+ accelerated the D–A reaction almost twofold, which was attrib-
uted to the presence of G-triplex ligand.
Appendix A. Supplementary data
Supplementary data to this article can be found online at http://dx.
doi.org/10.1016/j.catcom.2015.09.012.
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