Amphiphilic DNA-dendron hybrid: A new building block for functional assemblies

Article abstract of DOI:10.1039/c1sm06028g

A new kind of amphiphilic DNA-dendron hybrid consisting of a highly hydrophobic dendron and a single stranded DNA is synthesized. The hybrid could assemble into long nanofibers in aqueous phase. The hybridization property of DNA at the shell of fibers ass

Full text of DOI:10.1039/c1sm06028g

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Amphiphilic DNA-dendron hybrid: a new building block for functional
assemblies†
a
a
b
a
b
a
a
Liying Wang, Yu Feng, Yawei Sun, Zhibo Li, Zhongqiang Yang, Yan-Mei He, Qing-Hua Fan*
and Dongsheng Liu*b
Received 2nd June 2011, Accepted 20th June 2011
DOI: 10.1039/c1sm06028g
1
0
A new kind of amphiphilic DNA-dendron hybrid consisting of
a highly hydrophobic dendron and a single stranded DNA is
synthesized. The hybrid could assemble into long nanofibers in
aqueous phase. The hybridization property of DNA at the shell of
fibers associated with the encapsulation ability of dendron at the
inner core enable further functionalization, offering a unique class of
supramolecular building block.
supramolecular chemistry and functional materials. Covalently
conjugation of both perfect architectures, DNA and dendrimer,
certainly provides a new class of promising supramolecular building
block with the potential to fabricate smart soft materials with
11
controlled structures and functions. Although a few kinds of DNA–
12
dendrimer hybrids have been constructed, these primary attempts
12a–d
mainly focused on fabrication methods,
and mostly employed
hydrophilic dendrimers. To the best of our knowledge, there is no
report on the hierarchical assembly of such hybrids in aqueous
solution. Herein, we report the synthesis of a new kind of amphiphilic
DNA–dendron hybrid composed of a highly hydrophobic dendron
and a hydrophilic single-stranded DNA (ssDNA). We studied their
self- assembly behavior, a possible assembly mechanism and further
investigated their functions.
Precise molecular design becomes more and more important to
achieve well-defined supramolecular assemblies with functions.
Besides designing completely new molecules, combining available
components with different structures and functions, for example,
biomacromolecules and organic polymers, to get new hybrid mole-
cules is definitely efficient and consistently needed, and also chal-
First, we chose poly(benzyl ether) dendron peripherally function-
1
lenging. In the past decades, DNA with its inherent base-pairing
alized with dichlorobenzene (G Cl, 2 represents the generation of the
2
fidelity, structure diversity, hydrophilicity and biocompatibility, has
2
become an excellent supramolecular building block. DNA based
3
nanostructures, nanomachines, biosensors and hydrogels have
dendron) in this study. In addition to its hydrophobicity, this type of
13
dendron may possess multiple interactions, such as p–p stacking,
4
5
6
14
van der Waals interactions and halogen bonding interactions,
15
been extensively studied. To achieve more versatile and multiple
7
functions, DNA has also been combined with other materials, in
which are expected to play important roles in the self-assembly of
such DNA–dendron hybrids. The synthesis route to our designed
DNA–dendron hybrid is outlined in Scheme 1. The dendron was
synthesized using the divergent method via repetitive ester reduction
and Mitsunobu reaction (for detailed synthetic procedures, see ESI†).
particular, DNA block copolymers composed of DNA and organic
8
polymers, are examples of this exciting soft material. Recently, some
of them have been developed to assemble into tunable nanostructures
with potential applications in nanoscience, diagnostics and bio-
8a–c,f,g
medicine.
The resulting G Cl reacted with phosphoramidite chloride under
2
However, owing to the wide molecular weight distri-
room temperature for 30 min, after methanol precipitation, affording
bution of the polymeric segments, rational design of more
controllable and precise DNA hybrids is highly desirable.
the key reagent, G Cl-P, for further coupling with DNA. In a typical
2
8b
solid phase synthesis experiment, a mixture containing G Cl–P, 5-
2
Dendrimers/dendrons are synthetic molecules with well-defined
highly branched nanostructures and almost monodisperse molecular
ethylthiotetrazole (ETT) and the controlled pore glass (CPG) beads
9
weights. A variety of dendrimers with precisely designed cores and
periphery groups have been constructed and widely applied in
a
Beijing National Laboratory for Molecular Sciences, CAS Key
Laboratory of Molecular Recognition and Function, Institute of
Chemistry and Graduate School, The Chinese Academy of Sciences,
Beijing, 100190, China. E-mail: fanqh@iccas.ac.cn
b
Optoelectronics & Molecular Engineering of the Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing, 100084, China.
E-mail: liudongsheng@tsinghua.edu.cn
†
Electronic Supplementary Information (ESI) available: The detailed
1
synthetic routes, additional cryo-TEM and TEM images and H NMR,
C NMR and MALDI-TOF charaterizations See DOI:
0.1039/c1sm06028g
13
1
Scheme 1 The solid phase synthesis of the G
2
Cl-18 hybrid.
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loaded with DNA was transferred into a flask followed by addition of
anhydrous tetrahydrofuran (THF). The reaction proceeded under
The average diameter of the G Cl-18 fibers was 16.5 ꢁ 1.3 nm in
2
cryo-TEM, about twice of the molecule length, 9.2 nm (the contour
length of the 18-mer ssDNA is approximately 7.7 nm at a 0.43 nm
nitrogen atmosphere overnight. Then the unreacted G Cl–P and
2
1
6
ETT were removed from the system by rinsing the CPG beads with
rise per base, and the G
2
Cl was 1.5 nm in the CPK model). Due to
1
5 mL anhydrous THF. The newly formed phosphite-triester group
the electrostatic repulsion, the DNA strands are almost completely
8c
was oxidized with iodine solution for 30 s; the CPG beads were rinsed
again with 15 mL THF and 15 mL acetonitrile. After the ammonium
deprotection and cleavage from the CPG beads, the target product
stretched. We propose that in the nanofiber the dendrons aggregate
to form a hydrophobic core while the hydrophilic DNA strands
assemble at the corona. The average diameter of the fibers in TEM
image was similar to that in the cryo-TEM images. We note that the
height of the fibers in AFM images was only 9.4 ꢁ 1.7 nm (Fig. 1C),
about 7 nm smaller than the diameters observed in TEM and cryo-
TEM, possibly due to sample compression by the AFM tip.
2
G Cl-18 (18 represents the DNA length) was purified by poly-
acrylamide gel electrophoresis (PAGE). This solid phase synthetic
method can be used for preparation of DNA–dendron hybrids on
a large scale. The molecular weight and structural assignment were
confirmed by MALDI-TOF mass spectroscopy (Table S1†), and the
obtained result was in good agreement with the calculated value. The
purity of the product was confirmed by gel electrophoretic migration-
shift assay (Fig. S1†), combined with the results above, indicating
that the DNA–dendron hybrid was indeed formed with high purity.
With this hybrid in hand, we then investigated its self-assembly
In order to explore the universality of the designed DNA–dendron
system, other hybrids with different dendron generations and DNA
lengths were also synthesized and assembled in aqueous solution
(Chart S2†). Under the same assembly conditions as G
more sterically demanding G Cl-18 could also assemble into nano-
Cl-18,
2
Cl-18, the
3
fibers with a diameter of 17.3 ꢁ 0.9 nm (Fig. S5†). Notably, G
1
behavior. G Cl-18 was dissolved into 100 mL water to get a concen-
2
with such a small hydrophobic part (hydrophobic/hydrophilic weight
ratio equals to 0.079), could also form long nanofibers (Fig. S5†),
suggesting that other interactions besides hydrophobic aggregation
existed in the dendrons as mentioned previously. On the other hand,
as the DNA length became shorter, from 18 to 9 bases, nanofibers
tration of 20 mM. In the presence of 5 mL dichloromethane, the
ꢀ
solution was heated to 90 C for 30 min and subsequently cooled to
room temperature in 2 h. The TEM results clearly showed that
nanofibers existed almost exclusively and extended tens of microns in
length (Fig. 1A). An amorphous network would be formed without
annealing (Fig. S2†), indicating the heating process can destroy these
undesired aggregates, and the hybrids could reassemble during
cooling. Therefore, the annealing process was necessary for the fiber
formation. In order to make sure that the nanofibers were not formed
during the drying or the negative staining process of the TEM sample
preparation, cryo-TEM (Fig. 1B) and tapping mode AFM (Fig. 1C)
were also performed. The morphologies observed are in good
agreement with the TEM results. We also measured the critical
still predominantly existed in the aqueous solution of G Cl-9
2
(Fig. S5†). Certainly, the diameter was smaller than that of the G Cl-
2
18 fibers. These results demonstrate the aggregation behavior of such
designed amphiphilic DNA–dendron hybrids is general due to
structure similarity.
To verify the proposed assembly mechanism of DNA–dendron
hybrids, we employed DNA modified gold nanoparticles (AuNPs)
2
containing complementary strands to hybridize with G Cl-18
(Fig. 2A). The ssDNA was first modified with thioctic acid and then
conjugated with 5 nm AuNPs adopting the published method and
micelle concentration (cmc) of G Cl-18 by using Nile Red as a fluo-
2
17
rescence probe (Fig. S3†), and it is shown that the cmc value is 0.7
characterized by agarose gel electrophoresis. AuNPs modified with
0
8a,c
0
mM, similar to other DNA block copolymer systems. Interestingly,
G Cl-18 nanofibers were all observed at the concentration range of 1
multiple complementary ssDNA (5 -TACACATCTACTTCA-3 )
were mixed with the pre-formed G Cl-18 nanofibers in 50 mM Tris-
2
2
to 50 mM (Fig. S4†), and the fibers exhibited high stability, retaining
ꢀ
HCl buffer (pH 8.0) and 50 mM NaCl at room temperature over-
night to ensure the hybridization. As shown in Fig. 2B, AuNPs
the same morphology even after six months under 4 C.
Fig. 2 (A) Schematic illustration of the hybridization of DNA modified
Fig. 1 Images of nanofibers formed by self-assembly of G
2
Cl-18 in
2
AuNPs with G Cl-18 nanofibers. TEM images of the hybridization of
aqueous solution. (A) Negatively stained TEM image, (B) cryo-TEM
image and (C) AFM image, including cross-section height analysis. The
scale bar is 200 nm.
G Cl-18 nanofibers with 5 nm AuNPs containing (B) complementary
2
ssDNA and (C) non-complementary ssDNA. Inset is the enlarged image.
The scale bar is 200 nm.
7
188 | Soft Matter, 2011, 7, 7187–7190
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particularly aggregated around G Cl-18 nanofibers and AuNP
2
recognition and modification properties of DNA, gold nanoparticles
and fluorescent molecules were particularly decorated onto fibers; in
addition, the hydrophobic core was capable of encapsulating
hydrophobic species as a reservoir; taken together, we believe the
DNA–dendron hybrids could be used as promising building blocks
for constructing functional materials and open up a wide range of
applications in drug delivery, supramolecular templates, biosensors
and hydrogels.
chains as long as several microns were observed; in contrast, the
0
control experiment used non-complementary ssDNA (5 -
0
TTTCGCAATGACTGTACT-3 ) modified AuNPs in Fig. 2C,
resulting in a random dispersion of AuNPs. Both observations
2
suggest that the accumulation of AuNPs along G Cl-18 nanofibers
was induced by DNA hybridization instead of non-specific interac-
tions. The diameter of the chains was about 25 nm, approximately 10
2
nm wider than that of the G Cl-18 nanofiber, this is reasonable
considering the 5 nm diameter of AuNPs. These results support the
assembly mechanism that the hydrophilic ssDNA forms a shell
surrounding the hydrophobic core. In addition, it provides a new
platform for functionalization and fabrication of DNA–dendron
nanofibers through DNA hybridization. For example, we employed
a carboxyfluorescein modified complementary strand FAM-15 to
Acknowledgements
The authors thank National Basic Research Program of China (973
program, No. 2007CB935900 & 2011CB935701), the National
Natural Science Foundation of China (No. 20725309 & 91027046)
and NSFC-DFG joint project TRR61 for financial support.
2
hybridize with G Cl-18, and a large amount of green nanofibers were
observed under fluorescence microscopy, indicating the fluorescent
FAM group was successfully loaded onto the fiber through DNA
hybridization (Fig. S6†). Due to the peculiar sequence programmable
and modifiable feature of DNA, we believe other functional groups/
species could also be incorporated into the fiber with the same
strategy, realizing a smart multifunctional system.
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f
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