Modulation of chiroptical properties by DNA-guided assembly of fluorenes

Article abstract of DOI:10.1039/c0cc05125j

The supramolecular organization of fluorene building blocks in a DNA scaffold is described. The molecular assembly into ordered π-aggregates leads to distinct changes in the electronic properties.

Full text of DOI:10.1039/c0cc05125j

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COMMUNICATION
Modulation of chiroptical properties by DNA-guided assembly
of fluorenesw
¨
Daniel Wenger, Vladimir L. Malinovskii and Robert Haner*
Received 23rd November 2010, Accepted 10th January 2011
DOI: 10.1039/c0cc05125j
The supramolecular organization of fluorene building blocks
in a DNA scaffold is described. The molecular assembly into
ordered p-aggregates leads to distinct changes in the electronic
properties.
Hybrid stability was analyzed by thermal denaturation
(ESIw). All curves show sharp transitions which indicates a
high cooperativity of the de- and renaturation processes.
Furthermore, heating and melting cycles were superimposable
revealing no signs of hysteresis (ESIw). The Tm values of the
different hybrids are summarized in Table 1. Fluorene modifi-
cation generally leads to an increase in hybrid stability. A
single fluorene pair has a positive effect of approximately 1 1C,
whereas introduction of two units leads to a stabilization of up
to 3 1C per modification. The gain in duplex stability can be
attributed to good stacking interactions between the extended
aromatic systems of the alkynyl substituted fluorenes, which is
in agreement with observations made previously with other
aromatic moieties.32
DNA serves as an advanced engineering tool for the modular
construction of nanomaterials.1–3 Nucleic acids based nanoobjects
of remarkable complexity have been reported.4,5 Further
expansion of the functionality and applicability of DNA-based
assemblies6–14 will largely depend on the availability of novel
types of responsive building blocks. Different types of non-
nucleosidic aromatic derivatives have been described as artificial
substitutes of the natural nucleosides.15 Fluorene derivatives are
intensively investigated as components of organic materials with
advanced and diverse optical and electronic properties.16–19
Polymeric and oligomeric fluorenes are systematically studied
for their electronic aspects,20–25 for photovoltaic applications26,27
or for use in electroactive devices.28,29 In addition to their
chemical structures also the supramolecular arrangement of the
individual units has a significant influence on the spectroscopic
features of fluorene-based materials.19,30 Here, we describe the
electronic effects that originate from the molecular assembly of
dialkynyl fluorene molecules in a DNA scaffold. The formation of
ordered p-aggregates leads to distinct changes in the absorbance,
fluorescence and chiroptical properties of the chromophores.
The preparation of the fluorene building blocks is shown
in Scheme 1. Starting from 2,7-dibromofluorene, the alkynyl
chains were introduced via the Sonogashira reaction. Two
different chain lengths (butynol, n = 1 and hexynol, n = 3)
were chosen. The two diols 1a and 1b were converted to
the corresponding mono-DMT protected alcohols 2a
and 2b. Phosphitylation resulted in the formation of the
phosphoramidites 3a and 3b. The obtained building blocks
were incorporated into oligonucleotides by phosphoramidite
chemistry.31 The different oligomers (ON1-8) containing one
or two fluorenes are shown in Scheme 1, along with the two
unmodified reference oligonucleotides (R1 and R2).
The linker length did not affect the hybrid stability in a
significant way. The main absorption band of the fluorene
moiety at 330 nm is also suitable for monitoring the denatura-
tion process (ESIw). The so obtained Tm values are in agreement
with the ones determined at 260 nm, which provides further
evidence that the substitution of a natural base pair by a
fluorene pair does not disturb the cooperativity of the melting
process. The hyperchromicity of the 330 nm band is, however,
considerably larger (50–60%, see also ESIw) than the one at
260 nm. This is illustrated in Fig. 1 showing the tempera-
ture dependence of the UV-absorption spectrum of hybrid
ON1*ON2. A high degree of hypochromicity was observed
Department of Chemistry and Biochemistry, University of Bern,
Freiestrasse 3, CH-3012 Bern, Switzerland.
E-mail: robert.haener@ioc.unibe.ch; Tel: +41 31 631 4382
w Electronic supplementary information (ESI) available: Synthetic
and analytical details; additional fluorescence and CD spectra. See
DOI: 10.1039/c0cc05125j
Scheme 1 Fluorene building blocks and oligomers; DMT = 4,40-
dimethoxytrityl; CEP = 2-cyanoethyl-N,N-diisopropyl-phosphoramidite.
c
3168 Chem. Commun., 2011, 47, 3168–3170
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Table 1 Tm values of fluorene-containing DNA hybrids
Duplex
Tma/1C
DTmb/1C
DTm/modc/1C
R1*R2
70.7
72.0
75.9
72.0
76.7
71.3
71.3
76.0
76.1
—
—
ON1*ON2
ON3*ON4
ON5*ON6
ON7*ON8
ON1*ON6
ON2*ON5
ON3*ON8
ON4*ON7
+1.3
+5.2
+1.3
+6.0
+0.6
+0.6
+5.3
+5.4
1.3
2.6
1.3
3.0
0.6
0.6
2.7
2.7
Fig.
2
Temperature dependent fluorescence spectra of hybrids
a
Conditions: 1.0 mM oligonucleotide (each strand), 10 mM phosphate
buffer (pH 7.4) and 100 mM NaCl. In comparison to the unmodified
ON1*ON2 (left) and ON3*ON4 (right); lex: 300 nm, detector: 800 V,
ex slit: 2.5 nm; em slit: 5 nm; conditions as in Table 1.
b
c
duplex R1*R2. DTm per pair of fluorenes.
previously in fluorene oligomers and was attributed to a dense
packing of the p-electron systems.22
The fluorescence spectra of hybrids ON1*ON2 and
ON3*ON4 are shown in Fig. 2 as representative examples.
The duplex containing one fluorene unit in each of the strands
(Fig. 2, left) exhibits a broad, structureless band around 400 nm
which is typical for excimer emission.22,33 Upon melting, the
excimer band vanishes and the structured monomer emission
appears. The change from interstrand excimer to single strand
monomer emission is accompanied by a remarkable increase
in signal intensity. As expected, excimer emission is the
dominant feature over the whole temperature range in hybrid
ON3*ON4 which contains two fluorene moieties in each
strand (Fig. 2, right). The transition from inter- to intra-
molecular excimer, which takes place between 70 and 80 1C
(see also Tm values in Table 1), is associated with an increase
in emission. Intramolecular excimer formation in fluorene
oligomers has been described recently in oligofluorenes of
defined length22 as well as in spiro derivatives.33d On the other
hand, reports on intermolecular excimer formation by fluorene
derivatives are rare.33a,34 Quantum yields at 25 1C (ESIw)
range from 1 to 3% for the different oligomers and hybrids.
At higher temperature (85 1C) a significant increase (2–4 fold)
is observed.
Fig. 3 CD spectra of hybrids ON1*ON2 and ON5*ON6 showing a
switch in the conformational arrangement of the fluorene chromophores
induced by the different linkers (illustration: blue, right-handed; red,
left-handed).36 Conditions: as Table 1; 5.0 mM oligomer (each strand).
(butynyl vs. hexynyl) did not have an influence on hybrid stability,
it significantly affects the molecular interactions between the
fluorenes. In hybrid ON1*ON2 the negative signal at 336 nm
is followed by two positive bands (316 and 305 nm), whereas
for hybrid ON5*ON6 the pattern is inverted (positive signal
followed by two negative bands). Furthermore, the signal at
336 nm is red-shifted by 5 nm compared to the maximum of
the UV-absorption.
These two observations are strong evidence for exciton
coupling of the fluorene molecules35 originating from a twisted
arrangement of the chromophores.36 Thus, the change in the
linker induces a switch in the helical twisting of the fluorenes.
To the best of our knowledge, this is the first demonstration
that the chirality of a chromophore stack in a DNA frame-
work can be controlled by a seemingly simple change in the
linker length. In the hybrids containing two fluorenes per
strand, the CD signal in the 330 nm area is less pronounced.
Furthermore, the shape corresponds to an induced CD which
indicates a different arrangement of the fluorenes in these
hybrids (ESIw).37
Molecular interactions between the fluorene moieties were
further investigated by circular dichroism (CD) spectro-
scopy. The spectra of hybrids ON1*ON2 and ON5*ON6
(Fig. 3) reveal distinct stacking interactions of the fluorenes.
Interestingly, while the different length of the alkynyl linkers
The present communication shows that DNA serves as a
molecular frame for the formation of intermolecular fluorene
excimers, which are not readily accessible otherwise. Further-
more, this strategy allows the assembly of defined aggregates
in the aqueous medium. In addition, the observations described
above are in contrast to the behaviour of previously described
artificial building blocks, such as PDI15j,l or alkynylpyrene.32d
While the high tendency to form aggregates renders those
derivatives attractive for certain applications it may also be
problematic for others, e.g. in cases when the formation of a
Fig. 1 Temperature dependent UV absorbance of hybrid ON3*ON4;
inset: hyperchromicity observed at 330 nm; conditions as in Table 1.
c
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Chem. Commun., 2011, 47, 3168–3170 3169

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complex structure proceeds through a stepwise conformational
search via consecutive assembly–disassembly processes. In
contrast to the above mentioned building blocks, the fluorenes
described here do not exhibit any signs of hysteresis. This
adaptive behaviour is also illustrated by the finding that a
relatively small change in the linker length (butynol vs. hexynol)
results in a complete switch in the chiroptical properties of the
double helical hybrid.
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In conclusion, we have demonstrated the molecular organi-
zation of fluorene molecules by hybridization of complementary
DNA strands. The fluorene units support the formation of
stable hybrids and show optical properties which are charac-
teristic for ordered p-aggregates. While the nature of the linker
did not affect the hybrid stability, it had a pronounced effect
on the chiroptical properties of the chromophore assembly.
The fluorene derivatives described herein represent a promising
class of novel building blocks for the modular assembly of
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