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University of Groningen
DNA-based asymmetric catalysis
Boersma, Arnold
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Chapter 1
An introduction to DNA-based
asymmetric catalysis
An emerging field in catalysis is the use of hybrid biomolecules for asymmetric catalysis. A
variety of transition-metal catalyzed reactions can proceed in an enantioselective manner
due to the presence of proteins. But also polynucleotides such as RNA and DNA can be
harnessed for chiral recognition and asymmetric catalysis. This chapter aims to provide a
literature survey on these concepts which form the foundation of DNA-based asymmetric
catalysis.
Chapter 1
1.1 Asymmetric catalysis and water
1.1.1 Asymmetry in catalysis
Molecules can have different three-dimensional structures even though they have the same
combinations of bonds between the atoms.1 If these molecules are non-superimposable
mirror images, they are considered to be chiral, and are called enantiomers. In 2007, 70% of
the new small-molecule approved drugs contained at least one stereogenic center.2 The
isolation of a single enantiomer is highly desirable, because the function of the drug in
biological systems is related to its chiral configuration. This has resulted in the
development of several methodologies for the preparation of enantiopure drugs. The three
main strategies to obtain enantiopure compounds are i) resolution techniques, i.e. separating
enantiomers by changing their physical properties upon interaction with other chiral
molecules, ii) synthesis using enantiopure starting materials available from nature’s chiral
pool, and iii) asymmetric synthesis and catalysis. Resolution techniques are widely used,
but are costly and often a bottleneck in multistep synthesis due to the limiting yield of
50%,3 which in turn can be overcome by recycling the unwanted enantiomer. In asymmetric
synthesis, a prochiral substrate is transformed into a single enantiomer by inducing a
relative change in Gibbs energy between the two activated complexes by the formation of
diastereomeric transition-state structures. In order to obtain an enantiomerically enriched
compound, either a chiral auxiliary can be attached to the substrate, or a chiral catalyst can
be employed. Since in a catalytic event the catalyst by definition lowers the Gibbs energy
of the activated complex, the latter is an ideal tool to create diastereomeric transition states.
1.1.2 Asymmetric catalysis in water
The asymmetric catalysts can roughly be divided in two groups; enzymes and small
molecule catalysts, both having advantages and disadvantages. Enzymes generally function
as highly enantioselective catalysts for their natural substrates,4-6 and are generally applied
in water. Most enzymes however, with some notable exceptions such as lipases, display a
high substrate selectivity, which limits the scope of the substrates. This can be overcome by
engineering an enzyme, by means of mutagenesis techniques, or post-synthetic
modification. Most enzymes require mild conditions, although engineered and wild-type
enzymes have been used at higher reaction temperatures (70-110 °C), in organic solvents,
and at non-physiological pH. Wild-type enzymes are used for the transformation of their
natural substrate on industrial scale. For example, fumarase catalyzes the asymmetric
hydration of fumarate to provide maleate. This process is performed with 400 g/L
concentrations for the synthesis of maleate.7
The small molecule catalysts have the advantage over enzymes that they are generally
easier to modify, have larger substrate scopes, and perform chemistry that is not available
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An introduction to DNA-based asymmetric catalysis
with enzymes. Although small molecule catalysts can have high catalytic activity, they are
generally still outperformed by enzymes. However, the possibility to catalyze a wide
variety of reactions, renders small molecule catalysts very important for applications of
asymmetric catalysis in industry,8 and on smaller scale in total synthesis.9 The solvents of
choice for small molecule catalysis have been organic solvents, due to the complications
associated with water as solvent, i.e. the insolubility of many small molecule catalysts in
water, the deactivation of several catalysts by water, loss of non-bonding interactions in
water, and the often low substrate solubility in water. On the other hand, the use of water as
a solvent has been subject to numerous research efforts, since water is arguably the most
non-toxic and cheapest solvent. Indeed, several examples of small molecule catalysts to
accomplish asymmetric catalysis in water as a solvent have been described.10 The often low
solubility of small molecule catalysts in water is overcome by using micellar media,11
attaching solubilizing ionic groups to the catalyst,12,13 or attaching the catalyst to a solid
support.14 Examples of these strategies are the rhodium catalyzed hydrogenations,11 the
rhodium catalyzed hydrogen transfer reductions,14 Sharpless dihydroxylations,15 and the
proline-catalyzed C–C bond forming reactions.16 In these examples, the reaction occurs “in
water”, but the role of the water in the catalytic event is not always clear: does the catalysis
occur “in water”,17 “on water”,18 or “with water”?19 This is often not known because
concentrations of reactants are used that exceed the solubility limits in water.
In some cases, water has a beneficial effect on the catalytic event. For example in the case
of concerted reactions such as the Diels-Alder reaction20 and the Claisen rearrangement.21
The rate increase has been ascribed to both hydrophobic effects and hydrogen bonding of
water with the activated complex. The first report of a chiral Lewis-acid catalyst that was
able to catalyze an asymmetric transformation in water was a copper(II)-amino acid catalyst
(Scheme 1).22
Scheme 1: Asymmetric catalysis in water using a small molecule catalyst.22
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Chapter 1
The copper(II) ion was shown to act as a Lewis acid, and catalysed the Diels-Alder reaction
between aza-chalcone 1 and cyclopentadiene 2.23 Here, the water did not only increase the
rate of Diels-Alder reactions, but also increased the enantioselectivity. It was postulated
that π-stacking interactions of the aromatic side group of the α-amino acid were enhanced
due to hydrophobic effects.24 The π-stacking of the arene on the dienophile or copper(II)25
is important for the enantioselectivity since it provides shielding of one face of the
dienophile.
1.2 Asymmetric catalysis with biohybrid catalysts
A catalyst that can combine the attractive properties of biocatalysis and chemocatalysis
would be highly desirable. An emerging approach is to modify a protein posttranslationally with a catalytically active metal complex, resulting in a hybrid or artificial
metalloenzyme.26 In this way, the scope and promiscuity are adopted from the transition
metal catalyst, and the high enantioselectivity from the protein. These features can be
optimized separately by chemical and molecular biology techniques. Variations in the
primary coordination sphere provided by the metal complex have the most significant effect
on the enantioselectivity, while the fine tuning of the enantioselectivity is governed by the
modification of the secondary coordination sphere provided by the protein.27 These two
parameters combined should in principle give an additional advantage over the two
conventional approaches. The enantioselectivity does not need to originate from the metal
complex, since the protein acts as a chiral scaffold also. This excludes the need of an
enantiopure metal complex, and prevents the formation of different diastereomers upon
combination of the metal complex with the protein. The application of the biohybrid
catalysts in asymmetric catalysis was pioneered by Wilson & Whitesides,28 who showed
that a protein can act as a source of enantioselectivity when a biotin-containing rhodiumphosphine catalyst was anchored into avidin. An asymmetric hydrogenation was performed
with a modest selectivity of 41% ee (Scheme 2).
Scheme 2: Asymmetric hydrogenation using a biohybrid catalyst by Wilson & Whitesides.28
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Later, Ward and co-workers improved this design and obtained selectivities up to >95% ee,
using a combination of chemical and genetic engineering.29-31 A critical choice in the design
of a biohybrid catalyst is the mode of attachment of the catalyst to the protein, which can be
in a covalent, dative, or non-covalent fashion.32
1.2.1 Covalent anchoring strategies
The catalyst can be bound to the protein via a covalent bond, in which the metal-binding
ligand contains a reactive moiety that binds selectively to an α-amino acid such as cysteine.
The advantages of a covalent mode of attachment are i) precise knowledge of the location
of the metal complex, ii) access to different sites on the protein, and iii) no dependence on
the binding affinity of the complex to the protein. An important drawback of this design is
that the optimization is time-consuming due to the necessity of extra synthesis and
purification steps. This could be a reason why examples of successful asymmetric catalysis
with a covalently attached catalyst are less prevalent in the literature compared to the dative
and the non-covalent approaches. The most notable example using this strategy is an
asymmetric sulfoxidation reaction catalyzed by a manganese salen complex anchored to
myoglobin with moderate ee’s up to 51%.33 The covalent approach has among others also
been employed for rhodium-catalyzed hydrogenations using papain as host, which induced
rate accelerations or enantioselectivities up to 65%.34,35
1.2.2 Dative anchoring strategies
In the dative anchoring strategy, the catalytically-active metal is bound to the protein by
coordination of one of the α-amino acid side chains, e.g. a cysteine or a hystidine. Several
examples exist in which high ee is generated. A prominent example is the combination of
bovine serum albumin (BSA) and copper(II) phthalocyanine, which was inspired by the
earlier work by Otto & Engberts (vide supra) and the first generation DNA-based catalysts
(vide infra).36 The copper(II)phthalocyanine is most likely anchored to the BSA via a dative
bond, originating from a tyrosine (Tyr161) that binds to the axial coordination site on the
copper(II). Ee’s up to 98% were obtained in the Diels-Alder reaction between aza-chalcone
4 and cyclopentadiene 2 (Scheme 3). Surprisingly, the use of a tetradentate chelating ligand
such as phthalocyanine, which leaves only the axial coordination site on the copper
available, still renders the copper ion active in catalysis. The authors propose that the azachalcone was activated via the coordination of the ketone to the free axial coordination site
on copper. The issue that a low pH of 4 is beneficial for the ee and conversion, is very
important because the Diels-Alder reaction can also be Brønsted-acid catalyzed,23 however,
the authors do not comment on this issue. Another important observation is that the rate of
the catalysis by copper(II) phthalocyanine decreased due to the presence of the BSA. This
means that the copper(II) complex has to be bound tightly since any unbound copper(II)
complex will have a strong negative effect on the ee.
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Scheme 3: A copper(II)phthalocyanine/BSA conjugate for catalytic asymmetric Diels-Alder
reactions.36
1.2.3 Non-covalent anchoring strategies
The non-covalent, or supramolecular, approach is based on the binding of a transition metal
complex to a protein via hydrophobic interactions, hydrogen bonding, or electrostatic
interactions. Most successful examples of asymmetric catalysis using a hybrid enzyme were
reported following this approach. The main advantage of the non-covalent approach is the
modular assembly of the catalyst, which makes the optimization process less timeconsuming. Different transition-metal complexes can be tested, and the protein can be
modified using mutagenesis. The non-covalent approach based on the biotin-avidin
technology was first reported by Wilson and Widesides,28 and further developed by Ward.37
The biotin-streptavidin approach induced high ee’s in hydrogenations,31
ketone
reductions,38 alcohol oxidations,39 and allylic alkylations.40 The ruthenium catalyzed ketone
reduction has been optimized successfully using both chemical and genetic optimization
(Scheme 4).27 The chemical optimization of the ruthenium complex, i.e. the primary
coordination sphere, affected the ee and the conversion most.38 This was exemplified by the
sensitivity of the catalysis to the substitution pattern of the aryl group in the linker, since
only the para substitution resulted in a catalytically active complex. Also, the ee and the
enantiopreference, i.e. which enantiomer is obtained in excess, were influenced to a large
extend by the nature of the aryl group in the piano-stool complexes. When, for example,
benzene was applied as capping arene instead of cymene, the other enantiomer of the
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An introduction to DNA-based asymmetric catalysis
product was obtained. The ee in the reduction of acetophenone 6 ranged between 56% of
the S-enantiomer and 57% of the R-enantiomer, when employing wild-type streptavidin.
Scheme 4: A ruthenium-piano stool complex non-covalently attached to streptavidin via biotin for
enantioselective ketone reductions.38 S112Y Sav is a mutant streptavidin with serine S112 substituted
for tyrosine.
Optimization of the secondary coordination sphere, i.e. the protein, is less straightforward,
since the α-amino acids which comprise the active site need to be identified. From docking
studies it was found that serine S112 was placed close to ruthenium catalyst. Hence,
position 112 was subjected to saturation mutagenesis giving 20 mutants of streptavidin.41
The mutants gave rise to changes in the enantiomeric excess as well as the
enantiopreference, and a relation was found between the charge or the hydrophobicity of
the α-amino acid side group and the enantiopreference. Using saturation mutagenesis at
position 112, several mutants were identified that gave rise to an increased ee for a variety
of aromatic ketones. In the case of acetophenone 6, the mutant containing a tyrosine at
position 112 increased the ee to 90%. For more challenging substrates, for example dialkyl
ketones, a more elaborate modification of the protein was needed. With the availability of
the X-ray structure of the mutant streptavidin in combination with a ruthenium complex,
two new locations that were in close contact with the catalyst were identified, i.e. K121 and
L124.42 Saturation mutagenesis of these two positions gave 114 mutants, which were tested
in the reduction of dialkyl ketones. Also in this case, the primary coordination sphere had
the largest effect on the ee, but by optimization of the second coordination sphere the ee
could be increased, as is illustrated by an increase from 30% to 90% ee for a dialkyl ketone.
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Chapter 1
1.3 RNA and DNA enzymes
1.3.1 RNAzymes
The use of biopolymers in catalysis is not restricted to proteins.43 Cech44 and Altman45
discovered the catalytic properties of RNA, for which they were awarded the Nobel Prize in
chemistry in 1989. In Nature, RNA catalyzes reactions as part of the ribosome in the
synthesis of proteins, and RNA cleaves phosphodiester bonds of other RNAs. Artificial
RNAzymes have been isolated from random pools of RNAs, via rational and iterative
methods such as in vitro selection procedures, e.g. SELEX-type methodologies.46,47 These
RNAzymes have been subject to continuous simplification and modification. Artificial and
natural RNAzymes often form a tertiary structure called a hammerhead, which consists of
three double stranded regions, and a pocket in the middle containing unpaired bases. Many
reactions have been catalyzed by artificial RNAzymes, including C-C bond forming
reactions such as the Diels-Alder reaction48 and the aldol reaction.49 Using an RNAzyme, a
Diels-Alder reaction between anthracene 8 and maleimide 9 was performed in an
asymmetric fashion, with an ee of 90% in the corresponding Diels-Alder product 10
(Scheme 5).50,51
Scheme 5: Ribozyme catalyzed enantioselective Diels-Alder reaction.50,51 Crystal structure
reproduced with permission from the Nature Publishing Group.
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In this reaction, the mechanism for both the induction of the ee and the catalytic activity
relies on the presence of a preformed catalytic pocket in the central part of the RNAzyme.
Upon reaction with maleimide, the anthracene undergoes a large structural change from a
planar to a bent structure. The preformed catalytic pocket complements the bent shape of
the activated complex of the Diels-Alder reaction, resulting in an increase in the rate of the
reaction and an enantioselective cycloaddition.
1.3.2 DNAzymes
In contrast to RNAzymes, natural occurring DNAzymes have not been found to date. The
absence of DNAzymes in Nature is maybe not surprising since DNA is the most important
carrier of genetic information. Artificial DNAzymes, on the other hand, have become more
common recent years.52 The examples of catalytic DNAs are highly related to the
RNAzymes, as the design is based on similar tertiary structures.53 DNA can also form a
variety of different topologies such as loops, junctions, etc., and these tertiary structures can
be programmed by means of the DNA sequence.54 Other similarities between RNAzymes
and DNAzymes is that i) the stability of these tertiary structures is often increased by the
presence of divalent metal ions such as magnesium(II), and ii) the possibility to use in vitro
selection procedures of random pools of oligonucleotides. The first example of a
DNAzyme was capable of cleaving RNA.53 Several other types of reactions have been
catalyzed using catalytic DNA,52 of which the majority is nucleotide chemistry. Recently, a
Diels-Alder reaction was catalyzed by a DNAzyme.55 The RNAzyme capable of catalyzing
the Diels-Alder reaction between anthracene and maleimide was taken as a starting point
for the optimization of the DNAzyme, resulting in the catalysis of the same Diels-Alder
reaction as efficiently as the RNAzyme. Previously, DNAzymes were considered to be an
inferior catalyst compared to RNAzymes due to absence of the 2’-OH. The Diels-Alder
case proves that DNA can be as good as a catalyst as RNA. To date, the ee of the DielsAlder product was not reported.
1.4 Applications of DNA in chiral recognition and catalysis
DNA has found many applications in vitro, in addition to its role as the principle carrier of
genetic information in Nature, and its recent use as a DNAzyme (vide supra). Due to the
programmability of the hybridization event and its structural robustness, many of its
applications are found in nanotechnology.56 The applications that are relevant to the
research described in this thesis are the enantiomeric selection of chiral molecules, and the
attempts to modify DNA with small molecule catalysts. It must be noted that the majority
of the latter applications were published after our initial reports of DNA-based asymmetric
catalysis as described in this thesis.
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1.4.1 Chiral recognition of molecules containing stereogenic carbons
The chirality of DNA’s right handed helix can be exploited to distinguish between
enantiomers of DNA-binding molecules. In fact, a common observation is an increased
binding affinity for one of both enantiomers, or diastereomers, to the DNA.57 For example,
daunarubicin intercalates preferentially in B-DNA, but when the opposite enantiomer of
daunarubicin was employed, a higher affinity for Z-DNA, i.e. DNA with a left handed
helical conformation, was observed.58 Also, oxidized polycyclic aromatic hydrocarbons
(PAH) interact with DNA via a reaction of the DNA with the epoxide ring.59 The epoxide
ring reacts with an exocyclic amino group of a nucleobase leading to a covalent adduct of
the drug with the DNA. This reaction occurs in a stereoselective fashion, as a result of the
fact that both enantiomers of the PAH bind in a different orientation to the DNA. The most
successful example with respect to clinical applications is the anti-cancer drug oxaliplatin,
of which the chirality of its ligand is important for its toxicity.60
Scheme 6: Structures of daunarubicin, an oxidized polycyclic aromatic hydrocarbon, and oxaliplatin.
1.4.2 Chiral recognition of octahedral metal complexes
The majority of research on the recognition of enantiomers by DNA has been performed on
the chiral octahedral metal complexes. When combined with bi- or tridentate ligands, these
complexes can form right (∆) or left handed (Λ) propellor-like shapes (Scheme 7). Nordén
and Tjerneld showed that the addition of the conformationally labile iron(II) tris(bipyridyl)
to DNA resulted in a preferred binding of the ∆-enantiomer, while the complex remaining
in the bulk solution racemized.61 Stable chiral octahedral complexes of ruthenium, rhodium,
or cobalt have been studied extensively.62 The group of Barton has developed several
applications for these complexes, such as DNA-light switch,63 and DNA cleavage agents.64
All these applications rely on which enantiomer of the complex is applied, because the
symmetry of the complex matches that of the double helix. Moreover, small changes in the
ligands changed the symmetry of the complex, resulting in binding to different sites in the
DNA. Hence, the dependence on the chirality of the binding affinity of a molecule to DNA
is a common observation, and is in some cases critical.
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Scheme 7: Structures of the octahedral complexes iron(II) (bpy)3, and the ∆-enantiomer of
ruthenium(II) (phi)(bpy)2.
1.5 Applications of DNA in catalysis
DNA is a very suitable chiral scaffold in synthesis, since it is chemically stable,
commercially available in large quantities, and the costs are in the range of small molecule
catalysts. The chiral features of DNA are predictable to a certain extent: the relatively stable
right handed helix of B-DNA is the predominant conformation, while variations in the
conformation of the helix can be expected when a variety of parameters are changed, such
as the DNA sequence, the extend of hydration of the grooves, the ionic strength of the
solvent, and the presence of DNA-binding molecules.54 Moreover, many examples exist in
which DNA is bound by molecules in an enantioselective fashion (vide supra). DNA has
several other advantages, such as the possibility to design other topologies, the
programmability of the hybridization by its sequence, and the possibility to modify it
covalently or non-covalently with a catalytically active molecule.
It is important to distinguish between the different forms of DNA catalysis, which
accelerate reactions based on different principles.52 The different classes are DNAzymes
(vide supra), DNA-templated synthesis, DNA-based catalysis, DNA-directed catalysis, and
finally DNA-based asymmetric catalysis. These approaches will be discussed in more detail
in the remainder of this chapter.
1.5.1 DNA-templated synthesis
Many examples exist in which the rate of the reaction is increased by increasing the
effective molarity of the reactants, making use of the hybridization of the DNA to which
they are attached, i.e. DNA-templated synthesis.65-68 But the reactants do not necessarily be
attached covalently to DNA: Dervan showed that in the case of the dimerization of two
DNA binding molecules the rate was enhanced by specific sequences of DNA, sequences
that brought the two reagents into close contact.69 The difference between DNA catalyzed
reactions and DNA-templated syntheses can be rather subtle, because in both cases the rate
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of the reaction is increased. Hence, the claim of catalytic DNA deserves a thorough
investigation. For example, the group of Wang and Li showed that under heterogeneous
conditions (20 mg/ml DNA) the presence of unmodified natural DNA had a favourable
effect on the conversions observed in an Aldol and a Henry reaction.70,71 These reactions
occur most likely due to an increase in the effective concentration of the reactants.
The first examples in which template-directed synthesis displayed stereoselectivity dealt
with the polymerization of nucleotides that hybridized on a nucleotide strand, such as
DNA.72 The growth of the polymer was faster when the same enantiomer of the nucleotides
was used as the template strand, whereas the growth was inhibited when the opposite
enantiomer was employed. In another example, DNAzymes were found to cleave RNA
upon hybridization of the RNA strand with enantiopreference for D-ribonucleotides.73
Liu et al. showed that in DNA-templated synthesis one enantiomer was preferred over the
other (Scheme 8).74 The SN2 displacement of an S-bromide by a thiol nucleophile
proceeded 4 times faster compared to the reaction with an R-bromide. Moreover, when the
reaction was performed with Z-DNA, the selectivity reversed, and the rate towards the Rbromide was 2 times higher compared to the S-bromide. Hence the conformation of the
DNA can be used to control the diastereoselectivity.
Scheme 8: Enantioselective displacement of an S-bromide with DNA-templated synthesis.
1.5.2 DNA-directed catalysis
In DNA-directed catalysis the DNA is used to increase the effective concentration of the
catalyst and the reactant, and is thus necessary for the catalysis. This strategy has mainly
been employed for site specific cuts in a complementary DNA strand using a localized
catalytically active metal complex.75-77 An example is the approach followed by Sheppard
et al., in which a nickel(II) salen complex is incorporated into a single strand of DNA.76
Upon combination with a complementary strand, the complementary strand is cleaved by
the nickel(II) salen complex.
Also C-C bond forming reactions have been performed using DNA-directed catalysis, using
proline as a catalyst attached covalently to the 5’-end of DNA (Scheme 9).78 An aldehyde
was attached to the 3’-end of the complementary strand, bringing it in close contact with
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the proline via hybridization, which effectively increases of the concentration of the
aldehyde. Combining proline with a ketone such as acetone gave the enamine ion, which
reacted with the aldehyde furnishing the corresponding aldol product is obtained. By
heating the duplex above its melting temperature, and subsequently cooling the mixture, the
proline modified strand recombined with a strand containing an unreacted aldehyde, and
catalytic turnover was achieved. The same catalytic aldol reaction was also feasible using
another design, in which the aldehyde was attached to a porphyrin.79 Porphyrins stabilize
the G-quadruplex conformation of a DNA strand via intercalation, and by attaching a
proline to the G-quadruplex, the reactants were brought again into close contact. No
enantioselectivity has been reported in these two examples.
oligo1
NH
H
O
O
O
oligo2
+
NH
O
N
H
oligo1
NH
O
O
OH
Scheme 9: DNA-directed catalysis of an aldol reaction.
1.5.3 DNA-based catalysis
As in the case of the hybrid enzymes, hybrid constructs of catalytic small molecules and
DNA can also be applied in catalysis. The strategies for anchoring the small molecule
catalyst to the DNA are the same as in the case of the proteins, i.e. covalent, dative, or noncovalent anchoring. An example of the dative anchoring strategy is the combination of an
iron porphyrin with a G-quadruplex forming oligomer.80 The porphyrin intercalates in the
G-quadruplex, and the iron is chelated by a guanine.81 The peroxidase activity of the iron
porphyrin was increased for a variety of substrates due to the presence of the DNA, albeit
that in the case of chiral substrates no enantiomeric preference was displayed.82
Mechanistic studies indicated that the increase in catalytic activity was caused by a
favorable conformational change of the porphyrin during catalysis, which was stabilized by
the DNA.80
The covalent approach has been explored as well. Four groups have developed strategies to
modify the DNA post-synthetically with chelating moieties, of which three groups have
used modified nucleobases, providing a handle for selective functionalization (Scheme 10).
The group of Kamer modified a uridine nucleobase chemically with a diphenylphosphine
via a palladium(II) catalyzed cross coupling (Scheme 10).83 A single uridine nucleotide was
modified, as well as a uridine containing a flanking adenine and thymine. The
diphenylphosphine modified uridine was applied in the Pd(II)-catalyzed allylic amination,
inducing ee’s up to 82% in THF as solvent. The application of trimers containing the
modified base, and the presence of water, lead to a lower reactivity and a loss of ee. No
explanation has been put forward for this observation. The group of Jäschke showed that
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DNA could also be modified post-synthetically by reaction of a phosphane with an
oligonucleotide containing a reactive group (Scheme 10).84 The phosphanes contained an
activated ester, that coupled efficiently with the amine of the modified nucleobase. To date,
no catalysis using these modified oligomers has been reported, possibly due to the
competition by the nucleobases for the free coordination sites on the transition metal. The
group of Vogel connected a polyaza crown ether to an oligonucleotide, and incorporated a
copper(II) ion.85 Applying the hybrid catalyst in the Diels-Alder between aza-chalcone 1
and cyclopentadiene 2 did not lead to a significant ee (<10%).
O
a)
O
I
NH
N
P
O
NH
HP(C6H5)2
R1O
N
Pd(OAc)2
O
O
R1O
DMF, Et3N
R1 = adenine
R2 = thymine
O
OR2
OR2
NH2
b)
O
O
HN
4
O N
O
R 1O
4N
H
N
O
N
P(Ph)2
O
R1O
O
OR2
HN
(Ph)2P
N
N
O
O
R1 = GGAATTGTGACG
R2 = TGAGCTCC
OR2
Scheme 10: Synthesis of ligand modified oligonucleotides by the groups of a) Kamer and b) Jäschke
for potential asymmetric catalysis.
To date, incorporation of modified nucleobases into oligonucleotides did not lead to
enantioselectivity. A recently reported approach followed by Sancho Oltra and Roelfes
involved the attachment of a copper(II) complex to a single stranded DNA, via the 3’ or 5’
end of a commercially available modified oligomer (Scheme 11).86 This design is highly
modular, and the combination with different complementary single stranded DNAs gave a
variety of DNA based catalysts. Given the success of the Diels-Alder reaction of azachalcone 1 and cyclopentadiene 2 catalyzed by copper(II) in DNA-based asymmetric
catalysis (this thesis), the same reaction was performed in the presence of these catalysts,
resulting in ee’s up to 93%.
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Scheme 11: A modular DNA-based catalyst for asymmetric Diels-Alder reactions.
Critical features in the design were the length of the spacer between the bipyridine and the
DNA, and the sequence of the DNA close to the copper(II) bipyridine. The optimal spacer
length was found to be an n-propyl spacer. The sequence affected the ee to a large extend,
and the straightforward modular assembly with other strands made rapid optimization
feasible. The three bases closest to the copper complex were critical for the ee observed,
and it was found that the triplet GTA, TAC in the template strand, gave the highest ee of
93%.
1.6 DNA-based asymmetric catalysis87
1.6.1 Concept of DNA-based asymmetric catalysis
The key issue in DNA-based asymmetric catalysis is to perform a reaction in the vicinity of
the helix, which then provides the chiral information for the activated complex of the
reaction, resulting in the preferential formation of one of the enantiomers of the reaction
product. In analogy with the hybrid enzymes, the approach to perform DNA-based
asymmetric catalysis is to make use of a small-molecule catalyst anchored to the DNA. The
noncovalent approach leads to a modular self-assembly of the catalyst, leading to a rapid
optimization of the catalyst. A catalyst can be bound non-covalently to DNA for instance
via intercalation. Moreover, to ensure the chiral information originates from the DNA, the
catalyst should be non-chiral or racemic.
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1.6.2 Design of the first DNA-based catalyst
A catalytically active copper(II) ion was bound to DNA via its ligand (Scheme 12). The
ligand comprised a bidentate copper(II) ion binding site, a DNA-intercalating 9-amino
acridine, connected via a spacer. The advantage of this design is that the spacer length (n)
and the amine substituent (R) can be used to optimize the design. Notably, a stereogenic
center is created at the nitrogen upon binding of copper(II). In the absence of DNA the
complex will be formed as a racemate, but in the presence of DNA an enantiomeric excess
in the complex could in principle be induced, similar to the case of iron(II)(bipy)3 (vide
supra). In this way, the chirality transfer might proceed in two steps; first from the DNA to
the copper(II) complex, and then from the copper(II) complex to the product of the
reaction. The model reaction that was chosen for proof-of-principle was the copper(II) ion
catalyzed Diels-Alder reaction between aza-chalcone 1 and cyclopentadiene 2 in water,
furnishing the chiral Diels-Alder product 3. This reaction was chosen because it undergoes
efficient Lewis-acid catalysis in water,23 and enantioselective examples of this
transformation have been reported in water as a solvent, using α-amino acids as ligands.22
Scheme 12: The first generation of DNA-based asymmetric catalysts.
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1.6.3 Asymmetric catalysis with a DNA-based catalyst
Using the described DNA-based catalysis concept it is possible to obtain ee’s in the DielsAlder reaction. The results obtained in the presence of salmon testes DNA (st-DNA) and
ligands L1 – L6, indicated that the enantiomeric excess obtained is highly dependent on the
ligand employed. A crucial feature was the spacer length: the n-propyl and ethyl spacers led
to the highest ee’s, whereas longer spacers such as n-pentyl (L5) showed a diminishing ee.
Hence, close contact of the copper(II) ion to the DNA appears to be a necessity to induce
significant ee’s. Also the R substituent on the ligand influenced the stereochemical outcome
of the reaction to a large extend. The highest ee’s were obtained with R = 1methylnaphthyl, i.e. ee’s up to 49%, whereas a change in the positioning of the naphthyl
group with R = 2-methylnaphthyl L6 resulted in a racemic product. Moreover, in the case
of R = 1-methylnaphthyl, using an n-propyl spacer instead of an ethyl spacer led to the
formation of the opposite enantiomer of 3. Hence, although DNA consisted of only the
right handed helix, both enantiomers could be obtained by a judicious choice of the achiral
ligand.
1.7 Aims and Outline
The goal of the research described in this thesis is to develop the general concept and
methodology of DNA-based asymmetric catalysis, with the aim of using this concept to
discover novel reactivities, and to develop mechanistic understanding of successful
catalysts. This knowledge can be used to further improve the class of hybrid enzymes, and
might increase our insight into the mechanistic features of enzyme catalysis.
In Chapter 2, a new design of DNA-based asymmetric catalysts is introduced. The 2nd
generation DNA-based catalysts are presented, which are capable of catalyzing the DielsAlder reaction between aza-chalcone and cyclopentadiene with >99% ee. The key issue of
removal of the coordinating auxilairy is solved by the application of a new substrate class.
Chapter 3 provides mechanistic insight, describing a thorough kinetic and sequence
dependence study of the Diels-Alder reaction catalyzed by the 2nd generation catalysts. The
results provide the basis to explain why salmon testes DNA can give such high
enantioselectivities.
Chapter 4 describes a structural study of the DNA-based catalysts, in which the DNAbinding mode of the copper(II) complexes is investigated.
Chapter 5 deals with the second part of the structural studies, in which the binding of azachalcone to the copper(II) complexes, and its effect on the enantioselectivity of the reaction,
is investigated
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Chapter 6 describes the first asymmetric Friedel-Crafts reaction with an olefin in water.
This reaction was catalyzed by the 2nd generation DNA-based catalysts and provided ee’s
up to 93%.
Chapter 7 displays another example of novel reactivity, in which the first non-enzyme
catalyzed asymmetric syn-hydration of an α,β-unsaturated carbonyl compound is
demonstrated.
Finally, in chapter 8 the results described in this thesis are summarized in a comprehensive
fashion, and overall conclusions are drawn.
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