DNA-programmed Glaser-Eglinton reactions for the synthesis of conjugated molecular wires

Article abstract of DOI:10.1002/anie.201105095

Wire self-assembly: Short oligo(phenylene ethynylene) modules (black structures, see picture) are assembled by attached DNA strands, which also direct the formation of 1,3-diyne linkages between the modules by the Cu-mediated Glaser-Eglinton reaction to selectively form dimer, trimer, and tetramer conjugated wires of up to 8 nm in length.

Full text of DOI:10.1002/anie.201105095

DOI: 10.1002/anie.201105095
DNA-Directed Chemistry
DNA-Programmed Glaser–Eglinton Reactions for the Synthesis of
Conjugated Molecular Wires**
Jens B. Ravnsbæk, Mikkel F. Jacobsen, Christian B. Rosen, Niels V. Voigt, and Kurt V. Gothelf*
The development of novel molecular fabrication methods
may lead to the production of complex functional nano-
materials and devices with discrete and monodisperse struc-
tures. Today, a large variety of small organic molecules with
potentially useful electronic properties are available through
classical synthetic approaches.[1] However, one of the major
obstacles for taking advantage of the unique properties of
individual molecular components for, for example, electronics
is our lacking ability to connect such components to each
other and to metallic contacts in a manner that is controllable
at the molecular scale.[2] It is very difficult to assemble
individual molecular components by top-down methods such
as scanning probe microscopy and even more challenging to
introduce covalent linkages between the components by these
techniques. Herein we report a method to apply DNA-
programmed assembly and covalent coupling of oligo(phe-
nylene ethynylene) building blocks to form monodisperse
conjugated molecular wires connected by carbon–carbon
bonds and with a length of up to 8 nm.
link is labile in aqueous media. In spite of its coplanar ground
structure it is structurally flexible. Furthermore, it is ques-
tionable if the linkage is electronically conducting.
We have therefore been exploring alternative coupling
strategies to irreversibly form linear and conjugated linkages
between molecular modules. Inspired by previous endeavors
in the synthesis of conductive modules,[8] we speculated that
1,3-diyne linkages would be well suited to meet these
demands. The 1,3-diynes can be obtained through the classic
Glaser and Eglinton reactions, in which oxidative homocou-
pling reactions of terminal alkynes are promoted by a CuI or
CuII source, and an amine base.[9,10] Glaser–Eglinton reactions
in water have previously been reported.[11] Encouraged by
these findings, we sought to develop a DNA-directed version
that could form 1,3-diyne linkages between conjugated
molecular building blocks. Unlike the classical Glaser–
Eglinton reactions (GE reactions), it is possible to selectively
perform heterocouplings of terminal alkynes by using DNA
to direct the formation of nonsymmetrical products.
DNA has proven to be a powerful tool for the self-
assembly of complex nanostructures and the programmable
organization of molecules and materials other than DNA
itself.[3] Furthermore, DNA-programmed chemistry offers the
opportunity to control chemical reactions between individual
molecules and the formation of covalent linkages between
molecular building blocks.[4] This approach has been demon-
strated by the synthesis of encoded combinatorial libraries of
organic molecules applied in the identification of new drug
leads.[5] Only few examples of controlled assembly of
molecular components into functional nanostructures utiliz-
ing DNA have been described.[6] We have previously reported
on the DNA-programmed assembly and coupling of molec-
ular wire fragments that consist of oligo(phenylene ethyny-
lene) (OPE) units conjugated to DNA strands in different
ways. Our previous chemical coupling strategy was based on
the coupling of salicylaldehydes to form metal–salen linkages
as was first reported by Czlapinski and Sheppard.[7] However,
formation of the metal–salen complex is reversible and the
For initial tests, we designed a model system based on a
simple end-of-helix architecture (Scheme 1) that consists of
two aryl-alkyne modified 18-mer oligonucleotide sequences,
O1 and O2. The two oligonucleotide sequences were synthe-
sized from the corresponding amino-modified oligonucleo-
tide sequences using N-hydroxysuccinimide(NHS)-ester
chemistry (see the Supporting Information). Upon annealing
and subsequent GE reaction the ligated product O3 would be
obtained.
[*] J. B. Ravnsbæk, M. F. Jacobsen, C. B. Rosen, N. V. Voigt,
Prof. K. V. Gothelf
Danish National Research Foundation: Center for DNA Nano-
technology, Department of Chemistry and iNANO
Aarhus University
Scheme 1. DNA-directed Glaser–Eglinton reaction utilizing the end-of-
helix architecture.
Langelandsgade 140, 8000 Aarhus C (Denmark)
E-mail: kvg@chem.au.dk
[**] The work was supported by the Danish National Research
Foundation.
To investigate the effects of the pH value, the copper
source, and copper ligand, a series of experiments were
carried out (Figure 1). Oligonucleotides O1 and O2 were
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201105095.
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10851

Communications
Figure 1. Denaturating PAGE analysis of the DNA-directed Glaser–
Eglinton reactions.
Figure 2. a) Schematic representation of the incorporated organic
module. b) Oligomerization of ODM monomers by multiple Glaser–
Eglinton reactions.
annealed at three different pH-values: 5.0, 7.1, and 9.6, and a
mixture that consists of a copper(II) source (CuSO4 or
Cu(OAc)2) and a ligand for copper (THTA[12] or BPDS[13]
)
was added. It should be noted that in analogy to CuI alone,
CuI–phenanthroline complexes react rapidly with oxygen, and
are well documented to generate oxygen species that can
damage biomolecules such as DNA.[14] Extensive decompo-
sition of DNA is observed when using CuI or CuI-phenanthro-
line. On the other hand, the THTA ligand is known to protect
DNA from CuI-mediated degradation.[15] Denaturing PAGE
analysis of the reactions showed no formation of O3 for the
reactions at acidic or neutral pH values (Figure 1, lanes 3 and
4, respectively); performing the reaction at basic pH led to
major product formation (Figure 1, lane 2). These observa-
tions are consistent with the fact that both Glaser and
Eglinton reactions require the presence of a base, which
facilitates the formation of the reactive Cu–acetylide inter-
mediate.[16] Further improvement is possible by switching to
CuSO4, which facilitates the almost complete conversion to
O3 (Figure 1, lane 1). The crucial role of the ligand for copper
is clearly demonstrated by the absence of product when
BPDS was employed (Figure 1, lane 5).
required OPE molecule must be equipped with functionalities
for incorporation into DNA.
In our strategy, the target molecule 9 is equipped with 4,4’-
dimethoxytrityl (DMTr) and phosphoramidite functionalities
for incorporation into a DNA oligonucleotide by automated
DNA synthesis (Scheme 2). The synthesis of the organic
module starts from 5-bromo-2-iodobenzoic acid 1. Introduc-
tion of a molecular handle was achieved by an amide coupling
with tert-butyldimethylsilyl(TBS)-protected 3-aminopropanol
2 in the presence of 1-ethyl-3-(3-dimethylaminopropyl)-
carbodiimide(EDC)·HCl
and
1-hydroxybenzotriazol
(HOBt) to give amide 3 in 75% yield. By utilizing the
À
À
preference for C I over C Br bond insertion by the metal in
Pd-catalyzed Sonogashira reactions,[17] we were able to react
amide 3 selectively with 0.55 equiv of 1,4-diethynylbenzene
To confirm the identity of the observed product, a
reaction mixture corresponding to lane 1 (Figure 1) was
subjected to reversed phase (RP-)HPLC analysis, which
showed nearly full conversion to a new product in consistency
with the denaturing PAGE analysis. Moreover, MALDI-TOF
mass analysis of the RP-HPLC purified product gave a mass
of 11601 Da, in good agreement with the calculated mass for
the GE product O3 of 11602 Da.
In extension of the DNA-directed GE reaction between
two molecules, the next step was to synthesize an OPE
molecule that contains two terminal acetylene groups, since
this will enable the assembly and coupling of more molecules
to form conjugated linear oligomers (Figure 2a). By employ-
ing multiple DNA-directed GE reactions, we envisioned that
several OPE molecules could be attached at their ends to
form one conjugated entity of predetermined length (Fig-
ure 2b). These oligomeric products are calculated to span
lengths of 4 nm, 6 nm, and 8 nm for the dimer (W-2), trimer
(W-3 a or W-3 b), and tetramer (W-4), respectively. The
Scheme 2. Synthesis of OPE phosphoramidite 9; TEA=triethylamine.
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Angew. Chem. Int. Ed. 2011, 50, 10851 –10854

(4) to give bromide 5 in 72% yield. The introduction of the
terminal alkyne functionalities was achieved by a subsequent
Sonogashira reaction with ethynyltrimethylsilane leading to 6
in an excellent yield. Global deprotection of the four silyl
protection groups was accomplished under mild conditions
with Et3N·3HF, resulting in 4 in 89% yield. Notably,
deprotection using tetra-n-butylammonium fluoride (TBAF)
instead failed and led to extensive decomposition. A stat-
istical mono-DMTr protection of the two equivalent alcohol
functionalities upon treatment of 4 with 4,4’-dimethoxytrityl
chloride (DMTrCl) in pyridine gave a mixture of di-DMTr
product, mono-DMTr product 8, and diol 6. However, column
chromatography provided excellent separation of the product
mixture and allowed for recycling of unreacted 6. The desired
mono-protected product 8 could be isolated in 34% yield
after one reaction. Treatment of 8 with chloride 7 in dry
dichloromethane and N,N-diisopropylethylamine (DIPEA)
gave the desired phosphoramidite 9 in 83% yield. Due to the
unstable nature of 9, all automated DNA synthesis was
carried out with freshly prepared samples.
A series of four 30mer oligonucleotides was prepared by
automated DNA synthesis. During the synthesis, the phos-
phoramidite 9 was incorporated into the middle of each of the
30mer oligonucleotides. The synthesis thus gave four oligo-
nucleotide-functionalized diacetylene modules (ODMs) con-
sisting of the organic moiety with two 15mer oligonucleotides
flanking its terminal regions (Figure 2). Low yields were
observed in the couplings of phosphoramidite 9 and therefore
prolonged coupling times and additional capping cycles were
introduced to avoid truncated sequence byproducuts. The
four ODMs were purified using RP-HPLC and were charac-
terized by MALDI-TOF mass analysis (see the Supporting
Information).
Performing the DNA-directed GE reactions between
ODM sequences using slightly altered conditions compared
to the model system proved beneficial. A mixture of a CuI and
a CuII source was applied, and the reaction time was increased
from 2 to 24 h. As observed by denaturing PAGE analysis
(Figure 3a) oligomerization to dimers and trimers proceeds to
a high degree (Figure 3a, lanes 2–4). The observed mobility
difference between pure ODM-1 (Figure 3a, lane 1) and the
unreacted ODM monomers after GE reactions (Figure 3a,
lanes 2–5) is caused by a difference in salt concentrations in
the samples. It is possible to form the two unique trimers W-
3a (lane 3) and W-3 b (Figure 3a, lane 4) in comparable
yields. However, when the number of GE reactions is
increased for the formation of the tetramer W-4, the yield
decreases (Figure 3a, lane 5), and considerable amounts of
dimer and trimer products are also observed. Various
conditions such as different salt concentrations and temper-
atures were tested, but in all experiments, the tetramer was
formed in unproportional low yields compared to the trimer.
We propose that the increased electrostatic repulsion and
steric hindrance between the increasing number of DNA
oligonucleotides in the assemblies cause the dramatic
decrease in yield of the tetramer. For future studies, potential
solutions to this obstacle could be to use PNA instead of DNA
to avoid charge repulsion or to increase the length of the
organic modules.
Figure 3. a) Denaturing PAGE analysis of DNA-directed Glaser–Eglin-
ton oligomerization of ODM sequences. b) Denaturing PAGE analysis
of purified ODM di-, tri-, and tetramer products.
It is noteworthy that the oligomers have much higher
retention than linear oligonucleotides with the same base
count, as seen by comparing lane 1–5, Figure 3b, with DNA
ladder lane L. This observation may be explained by the more
compact organization of the DNA in the ODM wires than in a
linear DNA sequence. The oligomeric products of the DNA-
directed GE reactions could be isolated by excision of the
corresponding gel bands followed by extraction of the
oligomers. The products are obtained in high purity as evident
from denaturing PAGE analysis (Figure 3b). The identity of
the dimer product W-2 a was further confirmed by MALDI-
TOF mass analysis (see the Supporting Information).
In summary, we have demonstrated that DNA-directed
GE reactions are feasible and can proceed in high yield. The
DNA-directed approach allows for the formation of non-
symmetric GE products, which cannot be obtained in the
classical intermolecular reaction. Furthermore, we have
extended the scope of this novel DNA-directed reaction to
the formation of molecular rods based on oligomerization of
oligonucleotide-functionalized dialkyne modules (ODMs).
This methodology enables the preparation of molecular rods
of predetermined lengths ranging from 4 to 8 nm, which are
potential conducting nanowires. The single-stranded DNA
(ssDNA) sequences at the two termini of the wires may be
utilized to specifically position the molecular wires in a more
complex DNA structure such as DNA origami.[18,19] The ideal
distance between ssDNA sequences extending from the same
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Communications
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Potentially such short wires positioned on DNA origami
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Received: July 20, 2011
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Keywords: DNA · Eglinton reaction · Glaser reaction ·
nanotechnology · nanowires
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