Toward a catalytic site in DNA: Polyaza crown ether as non-nucleosidic building blocks in DNA conjugates

Article abstract of DOI:10.1080/15257770701539260

A number of functionalized polyaza crown ether building blocks have been incorporated into DNA-conjugates as catalytic Cu2+ binding sites. The effect of the DNA-conjugate catalyst on the stereochemical outcome of a Cu2+-catalyzed Diels-Alder reaction will

Full text of DOI:10.1080/15257770701539260

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Toward a Catalytic Site in DNA: Polyaza
Crown Ether as Non-Nucleosidic Building
Blocks in DNA Conjugates
Ulla Jakobsen a , Katja Rohr a & Stefan Vogel a
a Nucleic Acid Center, Department of Chemistry , University of
Southern Denmark , Odense M, Denmark
Published online: 05 Dec 2007.
To cite this article: Ulla Jakobsen , Katja Rohr & Stefan Vogel (2007) Toward a Catalytic Site in DNA:
Polyaza Crown Ether as Non-Nucleosidic Building Blocks in DNA Conjugates, Nucleosides, Nucleotides
and Nucleic Acids, 26:10-12, 1419-1422, DOI: 10.1080/15257770701539260
To link to this article: http://dx.doi.org/10.1080/15257770701539260
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Nucleosides, Nucleotides, and Nucleic Acids, 26:1419–1422, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701539260
TOWARD A CATALYTIC SITE IN DNA: POLYAZA CROWN ETHER AS
NON-NUCLEOSIDIC BUILDING BLOCKS IN DNA CONJUGATES
Ulla Jakobsen, Katja Rohr, and Stefan Vogel
Nucleic Acid Center, Department
2
of Chemistry, University of Southern Denmark, Odense M, Denmark
A number of functionalized polyaza crown ether building blocks have been incorporated into
2
DNA-conjugates as catalytic Cu2+ binding sites. The effect of the DNA-conjugate catalyst on the
stereochemical outcome of a Cu2+-catalyzed Diels-Alder reaction will be presented.
Keywords Polyaza crown ether; catalysis; DNA-conjugates
INTRODUCTION
Due to its architecture, DNA is an ideal scaffold for the construction of
hybrid materials including catalytic systems (e.g., DNAzymes).[1−7] Feringa
et al. recently introduced a new modular assembled DNA-based catalyst.[11]
The catalytic Cu2+binding site intercalates into dsDNA due to their polyaro-
matic nature. The Cu2+ binding site is thereby brought into proximity of the
chiral environment of the dsDNA, which in turn leads to transfer of chirality
from the dsDNA to the reaction products with an ee of up to 99% for the ma-
jor (endo) isomer. We report in this communication another approach based
on covalent incorporation of catalytic polyaza crown ether based Cu2+ bind-
ing sites into ssDNA.[12]
RESULTS AND DISCUSSION
The synthetic route toward the desired building blocks (monomer W, X,
and Y) is very flexible and can be easily adapted for a series of macrocyclic
building blocks for automated DNA synthesis based on the phosphoramidite
approach (Scheme 1).[8,12] Macrocycle 8 served as universal building block
for the N-functionalization by acylation (W) or reductive amination (X, Y).
Funding of this work was provided by The Nucleic Acid Center (NAC).
Address correspondence to Stefan Vogel, Nucleic Acid Center, Department of Chemistry, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. E-mail: snv@chem.sdu.dk
1419

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U. Jakobsen et al.
SCHEME 1 Synthesis of polyaza crown ether phosphoramidite building blocks and monomer substitu-
tion patterns: W: R = H, X: R = C16H33 (palmityl), Y: R = CH2C5H4N (2-pyridyl).
Synthesis of ONs (oligonucleotides) was performed in 0.2 µmol scale on
an automated DNA synthesizer using the phosphoramidite approach. Incor-
poration of monomers W, X, and Y opposite to a complementary 17-mer ss-
DNA sequence resulted in a destabilization (-10–12◦C, Table 1, entries 2–4).
This can be explained by the steric distorsion of the corresponding dsDNA
(W, X, and Y are ∼2 × larger than A, G, C, and T). Juxtapositioned incor-
porations of W, X, and Y are well tolerated (+8◦C, for X, Table 1, entry 5)
despite the steric demand and non-nucleosidic structure of the monomers.
The remarkable increase in thermal stability displayed by modification X
is likely due to undisturbed interstrand base distances in the duplex and
additional strong hydrophobic forces (C16-palmityl chains). The chosen re-
action (Scheme 2) has been used for comparison with the system reported
by Feringa et al.[11]
The 2,6-diamino-pyridine unit in the core of 8 is binding Cu2+ efficiently
accompanied by the appearance of a characteristic UV band at 668 nm. UV-
titration with increasing conc. of Cu2+ revealed a 1:1 stochiometry of the
complex.
The initially performed catalytic reactions have shown that all DNA-
conjugates are able to catalyse the Diels-Alder reaction but only one of
the DNA-conjugates displayed a very weak asymmetric induction (10% ee,

A Catalytic Site in DNA
1421
TABLE 1 Influence of monomer W-Y on thermal DNA
duplex stability
Entry
1
Sequence
Tm [◦C]a
5ꢁ-TGT-GGA-AGA-AGT-TGG-TG
3ꢁ-ACA-CCT-TCT-TCA-ACC-AC
5ꢁ-TGT-GGA-AGA-AGT-TGG-TG
3ꢁ-ACA-CCT-TCW-TCA-ACC-AC
5ꢁ-TGT-GGA-AGA-AGT-TGG-TG
3ꢁ-ACA-CCT-TCX-TCA-ACC-AC
5ꢁ-TGT-GGA-AGA-AGT-TGG-TG
3ꢁ-ACA-CCT-TCY-TCA-ACC-AC
5ꢁ-TGT-GGA-AGX-AGT-TGG-TG
3ꢁ-ACA-CCT-TCX-TCA-ACC-AC
56.0
44.0
44.5
45.5
64.0
2
3
4
5
a10 mM sodium phosphate, 100 mM NaCl, 0.1 mM EDTA, ad-
justed to pH 7.0, concentration of 1 µM for each DNA strand.
SCHEME 2 Cu2+ catalyzed Diels-Alder reaction: DNA-conjugates W, X, and Y were used as catalysts.
Figure 1) under the conditions used by Feringa et al. (measured values of
9 and 11% have been averaged to 10%). We have not investigated the in-
fluence of the juxtapositioned base (e.g., T, G, C, instead of A) due to pro-
hibitive amounts of ONs needed for further experiments. From our initial
results and the putative structure of the catalytic center we assume that the
reaction center is not close enough to the chiral environment to induce a
stronger asymmetric induction, the use of a considerably smaller catalytic
center is therefore the next step towards improved asymmetric induction.
A flexible synthetic strategy toward functionalized polyaza crown ether
amidites as well as an efficient incorporation of the respective building

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U. Jakobsen et al.
FIGURE 1 HPLC traces for a) racemic mixture, b) reaction catalyzed with dsDNA (Table 1, entry 3)
with 10% ee (no effect on ee for W and Y), c) schematic model of the catalytic center embedded in a
17-mer dsDNA.
blocks into DNA sequences has been achieved. The results from the cat-
alyzed Diels-Alder reactions have shown that a more rigid catalytic center in
close proximity to the helical DNA regions is required to achieve significant
asymmetric induction.
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