DNA-based asymmetric catalysis

Article abstract of DOI:10.1002/anie.200500298

(Chemical Equation Presented) A twist in catalysis! The chirality of DNA is transferred directly to a Diels-Alder reaction by using a DNA-tethered catalyst. A catalytically active copper complex with achiral ligands self-assembles with DNA to give products with up to 90% ee, as is the case for the exo isomer of product 1.

Full text of DOI:10.1002/anie.200500298

Communications
Asymmetric Catalysis
DNA-Based Asymmetric Catalysis**
Gerard Roelfes* and Ben L. Feringa*
The ubiquitous right-handed double helix of DNA is arguably
the most elegant example of chirality in nature, yet chirality in
biocatalysis is almost exclusively the domain of the enzymes
encoded by DNA.[1] The direct transfer of chiral information
from DNA to chemical reactions will require the use of DNA-
based catalysts. In marked contrast to catalytic RNAs, which
have been employed successfully in a wide range of reactions
including enantioselective catalysis,[2,3] the synthetic reper-
toire of “DNAzymes” is still very modest.[4] The limited
applicability of catalytic DNA has occasionally been attrib-
uted to the absence of the 2’-OH functional group in the
sugar-phosphate backbone and the propensity for natural
DNA to adopt a double-helical duplex structure, which
precludes the formation of catalytically competent tertiary
structures.[4] Although the catalytic power of DNA has been
enhanced by the incorporation of nucleotide bases with
extended functionality,[5] enantioselective catalysis based on
DNA has yet to be reported. However, the reported chirality
transfer from DNA in stoichiometric DNA-templated syn-
thesis, which leads to diastereoselectivity in chemical reac-
tions and enantioselection of chiral substrates,[6] suggests the
potential of DNAzymes in asymmetric catalysis.
Herein, we demonstrate that the chirality of the DNA
double helix can be transferred directly to a metal-catalyzed
reaction, in the present case the copper(ii)-catalyzed Diels–
Alder reaction (Figure 1). This can be done by positioning a
nonchiral or racemic catalyst in intimate contact with DNA
and using the chiral information of the DNA double helix to
generate reaction products with an excess in one of their
enantiomers. These artificial DNAzymes can be generated
through the propensity of small aromatic molecules to
intercalate in a noncovalent, yet kinetically stable and
Figure 1. Schematic representation of the asymmetric Diels–Alder
reaction of cyclopentadiene (2) with aza-chalcone 3, catalyzed by
copper complexes of ligand 1 in the presence of DNA.
stereoselective fashion, which enables the anchoring of
metal complexes to DNA.[7] This noncovalent and modular
approach allows rapid structural variation and optimization of
the catalytic system.
The catalyst is a complex formed in situ from copper(ii)
with ligand 1, which contains three key structural features: a
DNA-intercalating moiety such as 9-aminoacridine, a spacer
component, and a metal-binding group. The ligands were
prepared in an efficient and straightforward fashion starting
from monoprotected diamines (Supporting Information).[8]
The copper(ii) complex has a characteristic green color, with
a weak UV/Vis spectroscopic absorbance at lmax = 620 nm
(e = 50mÀ1 cmÀ1) in the case of ligand 1a (Supporting Infor-
mation). This absorption, which is typical for copper di- and
polyamine complexes,[9] is slightly red-shifted in the presence
of DNA (lmax = 660 nm). The addition of extra copper salt did
not give a significant increase in this absorption. The
combination of DNA with either Cu(NO3)2 or the free
ligand does not have discernable features in this wavelength
region, which demonstrates that DNA does not sequester the
copper(ii) ion from the ligand. Although complexation of
these achiral ligands to copper generates chiral complexes,
they are formed as a racemic mixture; thus any enantiomeric
excess found in the product of the catalyzed reaction
originates from DNA.[10]
[*] Dr. G. Roelfes
Department of Organic Chemistry, Stratingh Institute and
Department of Biochemistry
Groningen Biomolecular Sciences and Biotechnology Institute
University of Groningen
Nijenborgh 4, 9747 AG Groningen (The Netherlands)
Fax: (+31)50-363-4296
E-mail: j.g.roelfes@rug.nl
The Diels–Alder reaction between cyclopentadiene (2)
and the aza chalcone 3 in water[11] was catalyzed by copper(ii)
complexes of ligand 1 in the presence of salmon testes or calf
thymus DNA, both of which are readily available and
inexpensive. The reaction was allowed to proceed until
> 80% conversion. Product 4 was obtained as a mixture of
the endo (major) and exo (minor) isomers, both with a
significant enantiomeric excess, depending on the ligand used
(Table 1). A series of control experiments established that the
combination of ligand, copper salt, and DNA is required to
obtain both efficient catalysis and enantioselectivity (Sup-
porting Information).
Prof. Dr. B. L. Feringa
Department of Organic Chemistry, Stratingh Institute
University of Groningen
Nijenborgh 4, 9747 AG Groningen (The Netherlands)
Fax: (+31)50-363-4296
E-mail: b.l.feringa@rug.nl
[**] The authors thank W. R. Browne and Professor D. B. Janssen for
valuable discussions. This research was supported by a Veni grant
from the Netherlands Organization for Scientific Research (NWO)
to G.R.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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DOI: 10.1002/anie.200500298
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Angewandte
Chemie
Table 1: Results of the catalytic Diels–Alder reaction with 1-naphthyl-
methyl- and 3,5-dimethoxybenzyl-substituted ligand 1.[a]
37% ee for the endo and 78% ee for the exo isomer (Table 1,
entry 10).
The difference in behavior of the catalyst based on ligands
Ligand 1
Diels–Alder Product 4
Entry Ligand
R
n
Dienophile endo/ endo
exo [% ee]
exo
[% ee]
1a and 1 f is also evident from the reactions with substrates 3b
and 3c, which contain a nitro and a methoxy group,
respectively, on position 4 of the phenyl ring. Although the
conversions observed with these substrates were generally
lower ( ꢀ 50%) than those obtained with 3a (a possible result
of their lower solubility), similar results with 3c and slightly
lower ee values with 3b were obtained with ligand 1a
(Table 1, entries 4 and 5). In contrast, the complex with
ligand 1 f gave a much improved enantiomeric excess for both
substrates; in the case of the methoxy-substituted substrate
3c, up to 53 and 90% ee were observed for the endo and exo
isomers, respectively (entry 15). These values represent the
highest ee values obtained thus far with this system. These
results provide strong evidence that the interaction of the
substituent R with the dienophile is important for the
stereochemical outcome of the reaction. However, the exact
nature of this interaction and in particular, the differences
between R = 1-naphthylmethyl and R = 3,5-dimethoxybenzyl
are the subject of further study.
Neither the substrate/catalyst ratio, which could be
increased to 4 mm:0.18 mm dienophile/catalyst (that is, cata-
lyst at 4.5 mol% with respect to substrate, giving up to 22
turnover events; Table 1, entries 2 and 11) nor the source of
the DNA used (salmon testes versus calf thymus DNA;
entries 3 and 12) had a significant effect on the results. A
small synthetic dsDNA (the self-complementary 16-mer
d(GACT)2(AGTC)2) also gave a similar enantioselectivity
for 1 f (entry 13), which rules out any possible residual
impurity in the DNA from natural sources as influencing the
catalytic reaction. Interestingly, in this case the exo product
was favored even more.
The results presented herein demonstrate that the chir-
ality of DNA can be transferred directly to a catalytic
reaction. Despite the invariance of the chirality of the DNA
employed, both enantiomers of the Diels–Alder product are
accessible by a judicious choice of ligand. The key strengths of
the present system are its modular nature, which together
with the noncovalent binding of the catalytic moiety to DNA
and the use of achiral ligands, allows rapid structural variation
and optimization of catalysts for new reactions. An additional
advantage of the present approach is the isolation of the
product from the reaction mixture. The use of a DNA
intercalator in the catalytic system creates a very tightly
bound Cu–ligand–DNA complex, which remains in the
aqueous phase during extraction of the products. The
possibility to address specific DNA sequences in both natural
and synthetic DNA, for example, by using a selective DNA
binding moiety tethered to the catalyst, is particularly
appealing for the future design of DNA-based catalysts.
1
1a
1a
1a
1a
1a
1b
1c
1d
3
3
3
3
3
4
5
2
3a
3a
3a
3b
3c
3a
3a
3a
98:2 49
97:3 49
98:2 47
96:4 37
98:2 48
98:2 33
18
23
23
16
24
19
<5
À37
2[b]
3[c]
4
5
6
7
8
97:3
<5
96:4 À48
9
10
1e
1 f
3
2
2
2
2
2
2
3a
3a
3a
3a
3a
3b
3c
98:2 À37
92:8 À37
92:8 À34
92:8 À35
82:18 À34
88:12 À47
À7
À78
À74
À82
À80
À78
À90
11[b] 1 f
12[c] 1 f
13[d] 1 f
14
15
1 f
1 f
91:9
À53
[a] All experiments were carried out with salmon testes DNA under the
standard conditions (see Experimental Section) unless noted otherwise.
[b] Conditions: catalyst (0.18 mm), dienophile (4 mm), cyclopentadiene
(34 mm). [c] Calf thymus DNA. [d] DNA=synthetic duplex d(GACT)2-
(AGTC)2 (0.39 mm), cyclopentadiene (21 mm), buffer contained NaCl
(75 mm).
The substituent R and the spacer length n of the ligand are
crucial for both the observed enantioselectivity and the
enantiopreference (that is, which enantiomer is formed in
excess). A screen of ligands with a fixed spacer length (n = 3)
revealed the importance of the R group and specifically, the
requirement for it to contain an aromatic (arylmethyl) group
(Supporting Information). This suggests the involvement of
p–p interactions between the substituent and the dienophile,
as was previously described in the case of catalysts based on
amino acids.[11] The best results in the series examined were
obtained for ligands with R = 1-naphthylmethyl (1a), for
which an endo/exo ratio of 98:2 and 49% ee for the endo
isomer were found (Table 1, entry 1). Comparison of these
results with those from ligand with R = 2-naphthylmethyl,
which did not produce any significant enantiomeric excess,
demonstrates the subtlety of the interaction of the substituent
of the ligand with the dienophile.
Elongation of the spacer in 1a resulted in a rapid decrease
of the enantioselectivity; for n = 5 (1c) no significant enan-
tiomeric excess was observed (Table 1, entry 7). In contrast, a
decrease in spacer length to n = 2 (1d) gave a value similar to
1a (48% ee), but surprisingly of the opposite enantiomer
(entry 8). These findings demonstrate that intimate contact
between the DNA double helix and the catalyst is required
for efficient chirality transfer. They therefore offer compel-
ling evidence for DNA as the source of chirality in these
reactions.
Experimental Section
The special case of R = 3,5-dimethoxybenzyl gave the
same enantiomer of the product in excess regardless of spacer
length (n = 2 or 3). In the case of ligand 1 f (n = 2) relatively
more of the exo isomer was formed (endo/exo = 92:8), with
Catalytic Diels–Alder reactions: DNA-bound catalyst in buffered
solution (salmon testes DNA (1.3 mgmLÀ1), catalyst (0.3 mm, ligand/
Cu2+ = 1.3), and MOPS (20 mm, pH 6.5))[12] was prepared by mixing
salmon testes DNA (2 mgmLÀ1) in solution with MOPS (30 mm) in a
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volume of 10 mL (prepared 24 h in advance) with a solution of the
preformed catalyst: Cu(NO3)2 (0.9 mm) and ligand 1a (1.17 mm) in a
volume of 5 mL. An aliquot of a stock solution of dienophile 3a in
CH3CN (0.5m, 30 mL) was added to a final concentration of 1 mm and
the mixture was cooled to 58C. The reaction was started with the
addition of cyclopentadiene (5 mm, 7 mL) and mixed by continuous
inversion for 3 days, followed by extraction of the product with
diethyl ether. After 1H NMR spectroscopic analysis the percent ee
value was determined by chiral HPLC (Daicel chiralcel-ODH
column, elution with heptane/iPrOH 98:2). Selected products were
purified by column chromatography and analyzed on an Daicel
chiralpak-AD column to confirm the results obtained from analysis of
the crude product.
Received: January 26, 2005
Published online: April 21, 2005
Keywords: asymmetric catalysis · copper · cycloaddition ·
.
deoxyribozymes · DNA
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