Synthesis of new building blocks for use in supramolecular DNA architectures

Article abstract of DOI:10.1080/10610270903304418

New nucleoside building blocks for the synthesis of functional DNA are presented. A porphyrin-bis nucleoside dU-porphyrin-dU was synthesised from a di-acetylene-substituted porphyrin using Sonogashira coupling with 5-iodo deoxy uridine. The same strategy

Full text of DOI:10.1080/10610270903304418

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Synthesis of new building blocks for use in
supramolecular DNA architectures
Thomas Rühl a & Eugen Stulz a
a School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1EW, UK
Published online: 18 Jan 2010.
To cite this article: Thomas Rhl & Eugen Stulz (2010) Synthesis of new building blocks for use in supramolecular DNA
architectures, Supramolecular Chemistry, 22:2, 103-108, DOI: 10.1080/10610270903304418
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Supramolecular Chemistry
Vol. 22, No. 2, February 2010, 103–108
Synthesis of new building blocks for use in supramolecular DNA architectures
Thomas Ru¨hl and Eugen Stulz*
School of Chemistry, University of Southampton, Highfield, Southampton SO17 1EW, UK
(Received 19 May 2009; final version received 14 August 2009)
New nucleoside building blocks for the synthesis of functional DNA are presented. A porphyrin-bis nucleoside
dU-porphyrin-dU was synthesised from a di-acetylene-substituted porphyrin using Sonogashira coupling with 5-iodo deoxy
uridine. The same strategy was used to obtain a new terpy-functionalised nucleoside dUterpy. This building block can be
metallated with ruthenium(II) either to make a mono-nucleoside ruthenium complex (dUterpy)RuII(terpy), or to connect two
building blocks to create a bis-nucleoside (dUterpy)2RuII. The terpy nucleoside building block dUterpy was incorporated into
short strands of DNA to give TXT, TXXT and TXXXT as sequences (X ¼ dUterpy). The functionalised DNA has the
potential to create supramolecular assemblies through metal complexation.
Keywords: porphyrin; terpy metal complex; nucleoside; DNA scaffold; functional DNA
Introduction
supramolecular array strongly depend on the structure
of the modification, and the interactions can thus be
fine-tuned simply by reprogramming the DNA synthesizer.
In particular, the attachment of the porphyrins on
complementary strands, which leads to a stable zipper
array, allows the reversible creation of photonic wires
when using different porphyrins (26). Other work has
also been concerned with the attachment of porphyrins to
DNA as CD markers (27–30), or for both internal (31)
(base replacement) and external (32–34) modifications of
the DNA. Here, we now present the synthesis of new
nucleotide building blocks, which have great potential in
the design of DNA-based supramolecular functional
assemblies. The building blocks are based on either a
porphyrin or a terpy metal complex (Figure 2).
The development of synthetic protocols for modified
nucleotides and their incorporation into DNA via
phosphoramidite chemistry has made it possible to
establish the use of oligonucleotides as a supramolecular
scaffold for the synthesis of new functional molecules.
In this way, substituents such as metal complexes (1, 2),
small organic molecules (3–7) and chromophores (8–12)
can be attached to the DNA in a sequence-specific manner
and – upon duplex formation – placed in a predetermined,
three-dimensional arrangement. The substituents are thus
located either in the major or the minor groove of the
DNA, and can lead to stacked arrays of chromophores.
The substituents can be incorporated into the DNA either
in one strand or in complementary strands (13) where new
supramolecular assemblies are obtained after hybridis-
ation. Also, the substitution of the nucleobase can lead to
new supramolecular arrays (14–16). The detailed analysis
of the thus obtained functional DNA and the exploration of
the new tailor-made molecules through sequence-specific
incorporation of the modifications are, however, still in its
infancy. Nevertheless, given the diversity of the building
blocks already available, this will lead the concept of using
DNA as a supramolecular scaffold forward (17–19), and
open the way to a field which may be termed DNA
architectonics (Figure 1).
Synthesis of the bis-nucleoside-substituted porphyrin
The porphyrin dinucleoside building block 1 was
synthesised according to the route outlined in Scheme 1.
The porphyrin itself is synthesised from the correspond-
ing dipyrromethane 6 by 2þ2 condensation with the
protected acetylene-derivatised benzaldehyde 5 (35), and
obtained as free-base porphyrin after column chromatog-
raphy. Metallation using zinc acetate in refluxing
chloroform–methanol is quantitative, and the metallated
porphyrin 7 can be isolated after evaporation of the
solvent and filtration with DCM. Deprotection of the
acetylene using KOH in refluxing toluene gives the free
bis-acetylene porphyrin 8. According to our previous
protocol to connect an acetylene porphyrin to deoxy-
uridine, the bis-nucleotide was synthesised by
We are exploring the use of DNA as a supramolecular
scaffold to create helical porphyrin arrays and established
a general synthetic route to porphyrin–DNA (20–23).
The successful incorporation of different porphyrins, i.e.
tetra phenyl porphyrin (TPP) (24) and diphenyl porphyrin
(DPP) (25), shows that the electronic properties of the
*Corresponding author. Email: est@soton.ac.uk
ISSN 1061-0278 print/ISSN 1029-0478 online
q 2010 Taylor & Francis
DOI: 10.1080/10610270903304418
http://www.informaworld.com

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T. Ruhl and E. Stulz
104
Figure 1. Concept of using DNA as a supramolecular scaffold to create functional molecules (DNA architectonics) with a modelled
multiporphyrin array as an example.
Pd–Cu-catalysed Sonogashira cross-coupling with 5-iodo
deoxy-uridine 9. Product 1 was obtained pure after
column chromatography and re-crystallisation from
DCM–methanol at 48C in 64% yield. This new
compound could well serve as a cross-linking agent in
DNA synthesis, or by self-condensation lead to helical-
stacked porphyrin arrays, both of which we are currently
investigating.
complexes. Terpy ligands were attached to the sugar
moiety of the nucleoside via propargyl amine linkers, but
our type of attachment gives a more rigid arrangement, in
line with other reports (38–40).
The acetylene-substituted terpy (36, 37) was synthesised
from commercially available 2-acetyl pyridine 10 and
4-bromobenzaldehyde 11 (Scheme 2) in 45% yield.
The acetylene was introduced into 12 via Pd–Cu-catalysed
Sonogashira cross-coupling with the protected acetylene
2-methylbut-3-yn-2-ol 13 (21% yield). After deprotection of
the acetylene 14 using potassium hydroxide in refluxing
toluene (61% yield), the terpy 15 was attached to the
dimethoxy-trityl (DMT) protected iodo deoxy uridine 9 by
Sonogashira coupling to give dUterpy 2 in 62% yield. All the
terpy-containing products can easily be visualised on TLC
due to their characteristic blue luminescence upon UV
irradiation, or by staining with a saturated ethanolic FeIII
solution, giving a brown colour of the iron terpy complex.
Synthesis of the dUterpy building block
The second new set of building blocks is based on
terpyridine as a potential chelating metal ligand.
Bipyridyl-derived building blocks have been synthesised
previously (1, 2), and the successful incorporation of their
ruthenium complexes was reported. The terpy ligand,
however, would offer the possibility to form complexes in
a linear fashion to form directional supramolecular
Figure 2. Porphyrin-nucleotide and terpy-nucleotide building blocks.

Supramolecular Chemistry
105
Scheme 1. Synthesis of 1.
Scheme 2. Synthesis of the terpy-substituted deoxy-uridine dUterpy
.

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T. Ruhl and E. Stulz
106
Scheme 3. Formation of the ruthenium complexes of dUterpy
.
Synthesis and properties of ruthenium(II) complexes of
dUterpy
and the terpy moiety. The absorbance of the nucleobase
shows a bathochromic shift of 24 nm, indicating some
electronic perturbation due to the attached aromatic terpy
system. This was so far not observed with other substituents
such as porphyrins. The ruthenium complex 3 shows
absorbances at 230 nm (log 1 ¼ 5.07), 273 nm (log 1 ¼
5.09), 308 nm (log 1 ¼ 5.15) and 486 nm (log 1 ¼ 4.71).
Both ruthenium-containing building blocks 3 and 4
showed decomposition upon recrystallisation from aceto-
nitrile–toluene (2:1), but not from acetonitrile–water
(2:1). Both NMR and MS analyses of the obtained
crystalline products revealed loss of the DMT-protecting
group, which normally occurs under acidic conditions.
In the case of 4, further decomposition to the deprotected
dUterpy was observed. Analysis of the supernatant showed
the formation of benzoic acid, which was detected by its
typical fragmentation pattern in the mass spectrum and
was not present before treatment of the solution with
dUterpy. We therefore do not rule out the possibility that the
dUterpy building blocks can catalyse the oxidation of
toluene to benzoic acid in the presence of oxygen.
Formation of the ruthenium complex with the preformed
terpy–ruthenium complex 16 proceeded smoothly from a
refluxing methanolic solution (37), yielding the ruthenium
terpy nucleoside (dUterpy)Ru(terpy) 3 (Scheme 3). Initially,
the ruthenium complex is isolated as chloride salt, which is
then converted to the more soluble PF6 salt by trituration of
an acetonitrile solution with aqueous ammonium hexa-
fluoro phosphate. The product was isolated in overall 52%
yield. Alternatively, the terpy nucleoside can be dimerised
with ruthenium trichloride in refluxing methanol, thus
giving access to the dinucleoside building block (dUterpy)2-
Ru 4. As with 3, the complex was initially formed as the
chloride salt and subsequently converted into the PF6 salt,
and the overall yield for this synthesis was 31%.
The UV–vis spectra of the terpy nucleosides measured
in acetonitrile are shown in Figure 3. The building block 2
shows two absorption maxima at 284 nm (log 1 ¼ 4.65) and
324 nm (log 1 ¼ 4.64), corresponding to the nucleobase
DNA synthesis with dUterpy
Initial studies with the terpy nucleoside for DNA synthesis
show that building block 2 can be incorporated into DNA
(Scheme 4). The formation of the phosphoramidite 17
was achieved according to standard phosphitylation
methods using CEP-Cl as the reagent in dry DCM.
The phosphoramidite was then used directly in a DNA
Figure 3. UV–vis spectra of dUterpy 2 (solid line) and of
(dUterpy)Ru(terpy) 3 (dashed line) (c ¼ 2.22 £ 1025 M in
acetonitrile).

Supramolecular Chemistry
107
Scheme 4. Solid-phase synthesis of terpy-containing DNA strands using standard phosphoramidite chemistry.
synthesizer for the synthesis of the short oligonucleotide
TXXXT (X ¼ dUterpy). Cleavage of the strands from the
solid supports using concentrated ammonia overnight and
subsequent preliminary purification using NAP-5 and
poly-pack columns gave a mixture of the strands TXT 18,
TXXT 19 and TXXXT 20, as confirmed by MALDI-ToF
and UV–vis spectroscopy. The presence of high amounts
of the shorter sequences with only one or two
modifications indicates that the capping step in the
synthesis after introduction of the modification is not as
efficient as anticipated. A control synthesis without
capping gave the same mixture of strands. In addition,
even though four coupling cycles were run with 17, only
three insertions of the terpy building block were observed.
The strands were also subjected to denaturing PAGE, but
the excised segments containing the terpy DNA which
appeared as a streaky band again showed mixtures of the
three DNA strands. Separation could so far not be achieved
satisfactorily due to the large streaking of the terpy DNA in
both PAGE and HPLC. The synthesis and purification of
these poly-terpy DNA strands need to be optimised, but the
preliminary experiments show that new supramolecular
architectures can eventually be obtained incorporating
terpy metal ligands for further complexation with various
metals.
to be optimised. The terpy unit can be used to form
complexes with ruthenium(II), though a variety of other
metals could be used as well. The exploration of the
potential of all building blocks is currently under way.
Acknowledgements
Financial support by the EPSRC and analysis by the EPSRC
National Mass Spectrometry Service Centre Swansea (UK) are
greatly acknowledged.
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