Well-defined DNA nanoparticles templated by self-assembled M 12L24 molecular spheres and binding of complementary oligonucleotides

Article abstract of DOI:10.1021/ja108334g

Perfectly monodisperse DNA nanoparticles were prepared via the self-assembly of 12 Pd(II) ions and 24 bidentate ligands functionalized with oligonucleotides of varying length (n = 1-3). The DNA nanoparticles formed hydrogen bonds with cDNA strands and an

Full text of DOI:10.1021/ja108334g

Published on Web 10/27/2010
Well-Defined DNA Nanoparticles Templated by Self-Assembled M12L24
Molecular Spheres and Binding of Complementary Oligonucleotides
Takashi Kikuchi, Sota Sato, and Makoto Fujita*
Department of Applied Chemistry, School of Engineering, The UniVersity of Tokyo, and JST-CREST, 7-3-1 Hongo,
Bunkyo-ku, Tokyo 113-8656, Japan
Received September 15, 2010; E-mail: mfujita@appchem.t.u-tokyo.ac.jp
Abstract: Perfectly monodisperse DNA nanoparticles were pre-
pared via the self-assembly of 12 Pd(II) ions and 24 bidentate
ligands functionalized with oligonucleotides of varying length
(n ) 1-3). The DNA nanoparticles formed hydrogen bonds with
cDNA strands and an insoluble aggregate formed only with
matching trimeric nucleotide strands (tri-A).
DNA-coated nanoparticles1 are promising materials as biological
sensors in DNA/RNA detection,2 gene regulation,3 and biological
screening.4 Recent applications have focused on their use in material
applications where the subsequent recognition and binding of cDNA
strands can template further structural elaboration.5 Gold clusters2a-k,3,4,5a-e
and polymer micelles2l,m are typically utilized as platforms for DNA
nanoparticles, but as the starting templates are ill-defined and
structurally disperse, the resultant DNA nanoparticles exhibit a
larger range of properties. If the DNA nanoparticles were isostruc-
tural, an enhancement of material properties and functions should
result.
Here we report well-defined, perfectly monodisperse DNA
nanoparticles exploiting self-assembled coordination nanospheres
as nanoparticle templates to control the number, spacing, and
alignment of the peripheral DNA strands. The assembly of M12L24
Figure 1. Self-assembly of DNA-displaying coordination nanospheres. (a)
Structures of ligands 1a-c. (b) Self-assembly of DNA-conjugated molecular
complexes6 from 12 Pd(II) ions (M) and 24 bidentate ligands (L)
sphere 2c from 12 Pd(II) ions and 24 1c ligands. Ligands 1a and 1b also
give the corresponding M12L24 spheres (consisting of 12 Pd(II) ions and 24
ligands).
is well established. Our present strategy relies on the attachment
of a single DNA strand at the convex of the bidentate ligands and
their subsequent assembly into a nanosphere coated by precisely
24 DNA oligonucleotides (Figure 1).
Ligands 1a-c were synthesized by coupling the desired
protected oligo-thymine (T) derivative, prepared by the liquid-
phase phosphoramidite method7 (see Supporting Information),
to the -OCH2CH2OH tether of the bispyridyl ligand. Protecting
the phosphate is necessary, as the unprotected anion interferes in
the self-assembly process. M12L24 sphere 2a was constructed by
treating ligand 1a (10 µmol) with Pd(NO3)2 (6 µmol) in DMSO-d6
(1 mL) at 70 °C for 2 h. The quantitative formation of M12L24
1
coordination nanosphere 2a was suggested by H NMR spectros-
copy (Figure 2) as the downfield shifts of the pyridine R and ꢀ
proton signals (∆δ ) 0.82 and 0.59 ppm, respectively) are indicative
of metal coordination. The phosphodiester tethers survived the
complexation reaction, but ∼10% of the terminal TBS protecting
groups were hydrolyzed. Spheres 2b and 2c were also prepared in
the same way.
Cold-spray ionization mass spectrometry (CSI-MS)8 of com-
plexes 2a and 2b in CH3CN revealed molecular weights of 21 693
-
and 30 267, respectively, after anion exchange of nitrate (NO3
)
for tetrafluoroborate (BF4-) ions (see Supporting Information) and
clearly demonstrated sphere identity and their precise fidelity. The
low solubility of 2c in CH3CN precluded CSI-MS experiments,
Figure 2. 1H NMR spectra of (a) 1a and (b) 2a (500 MHz, DMSO-d6,
300 K). Spectra displaying all the protons at a range of -1 to 12 ppm are
shown in the Supporting Information.
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15930 J. AM. CHEM. SOC. 2010, 132, 15930–15932
10.1021/ja108334g  2010 American Chemical Society

C O M M U N I C A T I O N S
Figure 3. Molecular models of DNA coordination nanospheres (a) 2a, (b)
2b, and (c) 2c.
but diffusion ordered NMR spectroscopy (DOSY) of 2c in DMSO
confirmed the formation of a single product with a diffusion
coefficient of (3.4 ( 0.2) × 10-11 m2 s-1. From the diffusion
coefficient, the estimated diameter of 2c is 4.4 ( 0.2 nm, larger
than the diameter of the core framework (3.5 nm in diameter) but
indicates the peripheral DNA strands are not fully extended.9
Optimized structures of 2a-c with 24 fully extended oligonucle-
otides predicted diameters of 6.5, 7.2, and 8.7 nm, respectively
(Figure 3). The calculated surface density of DNA chains (0.59
chains nm-2) is higher than the previously reported value for DNA-
covered gold nanoparticles (0.23 chains nm-2).3b
The peripheral DNA strands of 2c form Watson-Crick base pairs
with complementary oligodeoxyadenosine trimers (tri-A). When 24
equiv of tri-A 3c was added to a DMSO-d6/CDCl3 (1:2) solution
of 2c (0.167 mM), the signals of the thymine amide protons shifted
downfield (∆δ ) 0.06 ppm), indicating the formation of a base
pair between T and A (Figure 4a, red line).10,11 The downfield shift
increased linearly with 3c and was of comparable magnitude to
pairs of free tri-T and tri-A (Supporting Information). In contrast,
the amide proton signals of mono-T and di-T spheres, 2a and 2b,
showed no notable downfield shifts when mixed with the comple-
mentary mono-A 3a or di-A 3b, thus indicating that the singly or
doubly bound hydrogen bond pairs of 3a and 3b are insufficient
and that the triply bonded H-bond pairs of 3c are the minimum
under these conditions (Figure 4a, green and blue lines).
When the solvent polarity was decreased (DMSO-d6/CDCl3 )
1:4) and the concentration of complementary oligo-A 3a and 3b
increased, hydrogen bonds with spheres 2a and 2b were observed.
After 120 equiv of the di-A 3b were added to the solution of sphere
2b (0.167 mM), the signals of the thymine amide protons shifted
downfield (∆δ ) 0.51 ppm) (Supporting Information). At 120 equiv
the thymine amide signals of mono-T sphere 2a also shifted
downfield but to a lesser extent (∆δ ) 0.14 ppm) and indicate
mono-A 3a is only weakly bound (Figure 4b, red line).
Figure 4. (a) Values of downfield shifts of thymine proton signals after
the addition of oligo-A strand 3a-c to the solutions of corresponding oligo-T
spheres 2a-c as a function of the equivalent of the oligo-A strand (green
line: 2a + 3a; blue line: 2b + 3b; red line: 2c + 3c) ([2] ) 0.167 mM,
DMSO-d6/CDCl3 ) 1:2, 500 MHz, 300 K). (b) The values of downfield
shift of thymine proton signals of 2a after the addition of mono-A (3a), G
(4), C(5) (red line: 2a + 3a; blue line: 2a + 4; green line: 2a + 5) ([2] )
0.167 mM, DMSO-d6/CDCl3 ) 1:4, 500 MHz, 300 K).
In summary, we have achieved the facile preparation of the
M12L24 spherical complexes with their surface modified with 24
oligonucleotide chains by attaching the oligonucleotide to the
convex of the bidentate ligand. We have also succeeded in the
selective recognition of complementary oligonucleotides by using
the oligonucleotide-coated spheres through the formation of the
hydrogen bonds. The DNA nanoparticles prepared here have well-
defined platforms of perfect fidelity on which precisely 24 oligo-
nucleotide chains are densely arranged. In due course, the attach-
ment of longer DNA chains with anionic phosphate backbones will
lead to a new recognition platform for natural DNA in aqueous
media.
Upon the addition of tri-A 3c to sphere 2c in the DMSO-d6/
CDCl3 (1:4) solvent mixture, a white solid immediately precipitated.
Precipitation did not occur when 3a or 3b was added to 2c nor did
spheres 2a and 2b precipitate with 3c. Only spheres 2c and
trinucleotide 3c formed an insoluble hydrogen-bonded network
structure.12
The DNA nanospheres recognized and selectively formed
hydrogen bonds with the complementary nucleobase. Mono-T
sphere 2a bound mono-A 3a (120 equiv) in DMSO-d6/CDCl3 )
1:4 solution (∆δ ) 0.14 ppm; Figure 4b, red line). Hydrogen bonds
with mismatched G (4)13 or C (5)14 derivatives were not observed.
Even the addition of excess 4 or 5 (120 equiv) to a solution of 2a
(0.167 mM, DMSO-d6/CDCl3 ) 1:4) produced only minor shifts
in the thymine amide proton signals on 2a (∆δ ) 0.01 and 0.04
ppm; Figure 4b, blue line and green line, respectively). These results
show that oligonucleotide-modified spheres prepared here will be
promising materials as molecular DNA nanoparticles, which
selectively recognize cDNA strands.
Acknowledgment. This work was supported by the JST,
Strategic International Cooperation Program (SICP), MEXT, Global
COE Program “Chemistry Innovation through Cooperation of
Science and Engineering”, and MEXT, Grants-in-Aid for Young
Scientists (A) (21685007).
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C O M M U N I C A T I O N S
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B.; Deng, Z.; Yan, H.; Cabrini, S.; Zuckermann, R. N.; Boker, J. J. Am.
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Supporting Information Available: Synthesis and characterization
data of the compound and additional figures. This material is available
free of charge via the Internet at http://pubs.acs.org.
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