ssDNA templated self-assembly of chromophores

Article abstract of DOI:10.1021/ja0711967

A single strand of DNA templates a supramolecular strand of chromophores, yielding a new type of DNA hybrid. In this hybrid construct, an oligothymine is used as the template to which a supramolecular stack of naphthalenes or oligo(phenylene)vinylenes equ

Full text of DOI:10.1021/ja0711967

Published on Web 04/21/2007
ssDNA Templated Self-Assembly of Chromophores
Pim G. A. Janssen, Joke Vandenbergh, Joost L. J. van Dongen, E. W. Meijer,* and
Albertus P. H. J. Schenning*
Laboratory of Macromolecular and Organic Chemistry, EindhoVen UniVersity of Technology, P.O. Box 513,
5600 MB EindhoVen, The Netherlands
Received February 19, 2007; E-mail: e.w.meijer@tue.nl; a.p.h.j.schenning@tue.nl
Scheme 1a
DNA is a promising building block to organize molecules in a
“bottom-up” approach for construction of functional nanosized
objects.1,2 For example, organic molecules have been covalently
attached to DNA for a precise nanoscale organization of chro-
mophores.3 Noncovalent approaches such as intercalation and
groove binding have also been reported,4 while discrete metal arrays
in artificial DNA were recently constructed by using metal-ligand
interactions.5 We have similarly organized chromophores by
sandwiching them between two strands of oligoadenine (dAn) via
hydrogen bonding.6 We now demonstrate an approach where only
a single strand of DNA templates a supramolecular strand of
chromophores, yielding a new type of DNA hybrid.7 In this hybrid
construct, an oligothymine (dTn, n ) number of thymines) is used
as the template to which a supramolecular stack of chromophores
a Schematic representation of ssDNA templated self-assembly of chro-
mophores (black strand, ssDNA; blue bar, chromophores; red bar, hydrogen-
bonding unit) and molecular structures of dTn, NT and OPVT.
is hydrogen-bonded via the complementary diamino triazine unit.
We report that, in case of dT40, 40 naphthalenes (NT) can be bound
and show that this approach can be extended to organize a
π-conjugated oligo(p-phenylene)vinylene (OPVT) (Scheme 1).
The two chromophores have been synthesized analogously to
alkyl equipped derivatives8 and have been fully characterized.9
OPVT and NT are both molecularly dissolved in chloroform, giving
absorption maxima at λ ) 403 and 315 nm, respectively. Concen-
tration-dependent UV-vis measurements show that NT is molecu-
larly dissolved in water up to a concentration of 0.6 mM (Figure
2b). OPVT is aggregated at 5 µM, indicated by the blue shift in
absorption to 390 nm and a red-shifted, quenched photolumines-
cence. Remarkably, aggregates of chiral OPVT do not possess
preferred helical order, concluded from the lack of Cotton effect
in the circular dichroism (CD) spectra.
We first studied the complexation and the stoichiometry between
NT and dT40. When NT is added to dT40, the absorption spectra
of NT revealed a red shift from 311 to 318 nm at 268 K (Figure
1b). In addition, CD spectroscopy (Figure 1a) shows an induced
positive bisignate Cotton effect with a positive maximum at 269
nm and a negative maximum at 244 nm with the zero-crossing at
λmax ) 258 nm. In the region where only the achiral NT absorbs,
a positive Cotton effect is present with the maximum at 327 nm,
showing that NT binds to dT40 and that the chirality present in
the template is expressed in the supramolecular organization of the
NTs.10 Titration experiments at 263 K show that the absorption
changes before the CD intensity increases, suggesting that the helical
organization of NT occurs at a later stage than the binding to dT40
(Figure 1c). The Job plot performed at 263 K clearly shows that
each NT binds to one thymine (Figure 1d).11
g/mol) bound, showing that the supramolecular complex dis-
assembles under these mild conditions. The formation of nano-
droplets could cause the formation of dT10-NT complexes with
more than 10 NT molecules.
The formation and the stability of the NT-dT40 complex was
monitored with temperature-dependent UV and CD spectroscopy
measurements by cooling at 6 K/h (Figure 1f). Binding of NT to
dT40 is fully reversible, and the shape of the curves indicates a
nucleation growth mechanism.12,13 NT first binds to dT40 (absorp-
tion at 269 nm) before NT is organized in a helical fashion (CD
intensity at 269 nm).
When dT40 is replaced with the noncomplementary strand dA40,
no Cotton effect is present above 300 nm, which demonstrates that
NT binds specifically to dT40. In an exchange experiment where
an equivalent amount of dA40 is added to the dT40-NT complex,
the Cotton effect above 300 nm disappears and the CD spectrum
of dT40-dA40 arises, meaning that the stack of NT is replaced
by dA40 (Figure 2a). This suggests that binding occurs via hydrogen
bonding and that the dT40-NT complex is less stable than dT40-
dA40.
Concentration-dependent UV and CD measurements of the NT-
dT40 (40:1) complex show a linear relationship at low concentra-
tions ([NT] < 0.6 mM) between the ln[NT] and Te-1 (temperature
at which the elongation starts), yielding an enthalpy ∆He ) -68
kJ/mol (Figure 2b). A similar linear relation has been found for
dsDNA.14 At high concentrations ([NT] > 0.6 mM), the Te deviates
from the straight line because NT itself already aggregates, showing
a linear relationship between the ln[NT] and Te-1, with a ∆He )
-26 kJ/mol (Figure 2b).
With electrospray ionization mass spectrometry (ESI-MS), we
were not able to detect the NT-dT40 complexes since the detected
signals could not be deconvoluted and therefore could not be
assigned. Complexes of dT10 and a number of NT molecules have
been detected (Figure 1e). The deconvoluted mass spectrum shows
dT10 (MdT40 ) 2978.5 g/mol) with 2-11 NT molecules (443.2
In order to create functional materials, we also studied binding
of OPVT with dTn. Complexes of OPVT (0.27 mM) with dT40
showed a Cotton effect above 300 nm, which is not present in the
absence of dT40 (Figure 3a). The positive Cotton effect at high
9
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J. AM. CHEM. SOC. 2007, 129, 6078-6079
10.1021/ja0711967 CCC: $37.00 © 2007 American Chemical Society

C O M M U N I C A T I O N S
With ESI-MS, up to five OPVT molecules bound to dT10 were
detected (Figure 3b).
In conclusion, new DNA hybrids have been constructed in which
the number of chromophores is controlled by the template. Binding
of chromophores to ssDNA occurs via hydrogen bonding and is
stabilized by π-π interactions. This approach can, in principle, be
applied to any functional molecule equipped with an appropriate
hydrogen-bonding moiety to create uniform well-organized nanos-
cale objects that are potentially useful in the emerging field of
supramolecular electronics.15
Acknowledgment. The authors wish to acknowledge X. Lou
for the MALDI-TOF spectra, and EURYI scheme for financial
support.
Supporting Information Available: Experimental methods, syn-
thetic details, and characterization of NT and OPVT (PDF). This
material is available free of charge via the Internet at http://pubs.acs.org.
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Figure 1. (a) CD and (b) absorption spectra and (f) the normalized UV
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Figure 2. (a) CD spectra at 263 K of a mixture of dT40 (12.5 µM) and
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wavelengths suggests a right-handed helical arrangement of OPVT
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due to extended π-π interactions in the supramolecular strand.
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