RSC Advances
PAPER
DNA assembly of silicon quantum dots/gold
nanoparticle nanocomposites†
Cite this: RSC Adv., 2016, 6, 63933

Asuka Inoue,a Hiroshi Sugimoto,a Hidenobu Yakub and Minoru Fujii*a
Silicon quantum dots (Si-QDs) dispersible in water and exhibiting bright near infrared (NIR) luminescenceare a very attractive nano-light-emitter usable in bioimaging and biosensing. Here, we demonstrate thefabrication of NIR luminescent nanocomposites composed of Si-QDs and gold nanoparticles (Au-NPs)
Received 25th May 2016
Accepted 24th June 2016

by DNA hybridization. We ﬁrst develop processes to functionalize the surface of Si-QDs with diﬀerent
types of silane coupling agents without notably aﬀecting the water solubility and the luminescence
properties, and then conjugate the functionalized Si-QDs with single-stranded DNA (ssDNA). DNA

DOI: 10.1039/c6ra13565j

hybridization with a Au-NP with complementary ssDNA results in the formation of Si-QDs/Au-NP

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nanocomposites.

Semiconductor quantum dots (QDs) with size-tunable photoluminescence (PL) have been intensively studied as nanoprobes
for biomedical applications1–4 due to the suitable chemical andphotophysical properties compared to organic dyes and uorescent proteins.5 However, toxic heavy metal elements incommercially available CdX and PbX (X ¼ S, Se and Te) QDs
raise concern for their application in biomedical elds. Silicon(Si) QDs are considered to be a promising alternative to the CdX
and PbX QDs because of the high biocompatibility andbiodegradability.6,7
Numerous eﬀorts have been made to develop waterdispersible and brightly luminescent Si-QD targeting forbiomedical applications.6–18 In the development of Si-QDs,
a crucial step is the functionalization of the surface withbiomolecules such as proteins and nucleic acids.18–21 Jonghoon
et al. achieved coupling of streptavidin with Si-QDs using
a multistep photoassisted reaction.18 Wang et al. conjugated 1–2
nm diameter Si-QDs to DNA through formation of a carboxamide bond.19 Romuald et al. reported conjugation of Si-QDs
with DNA by pulsed laser ablation in liquid.20 In theseprevious work, the luminescence wavelength is in the 400–600
nm range,18–21 which is much shorter than that commonly reported for hydrogen or oxygen terminated Si-QDs.22,23 The
mechanism of the short wavelength shi by organic capping is
still controversial.24–30 For the application of biomoleculefunctionalized Si-QDs in bioimaging and biosensing, theaDepartment of Electrical and Electronic Engineering, Graduate School of Engineering,
Kobe University, Rokkodai, Nada, Kobe 657-8501, Japan. E-mail: fujii@eedept.kobe-u.
ac.jp

b

Advanced Research Division, Panasonic Corporation, 3-4, Hikaridai, Seika-cho,Souraku-gun, Kyoto, 619-0237, Japan† Electronic supplementary information (ESI) available: Details are shown in
Fig. S1–3. See DOI: 10.1039/c6ra13565j

This journal is © The Royal Society of Chemistry 2016

emission wavelength is preferably within the transparent
window of tissues (700–1000 nm).31
One of the purposes of this work is to develop biomoleculefunctionalized Si-QDs exhibiting PL in the NIR range. We
employ B and P codoped all-inorganic Si-QDs as a starting
material.32 The codoped Si-QDs have negative surface potential
and are dispersible in water almost perfectly without organic
ligands.33 They exhibit size tunable and stable PL in the NIR
range in water.33 First, we functionalize the surface by three
types of silane coupling agents via the surface Si–OH bonds andstudy the inuence on the solution dispersibility and the PL
properties. We then conjugate Si-QDs and single-stranded DNA(ssDNA) and demonstrate the formation of nanocomposites
composed of Si-QDs and gold (Au) nanoparticles (NPs) by DNA
hybridization. By this process, the distance between Si-QDs and
Au-NPs can be controlled with high accuracy. We also show theformation of similar structures by using Au–S bonding.
First, we briey summarize the structural and optical properties of B and P codoped all-inorganic Si-QDs used in this work.
The size of the Si-QDs can be controlled by the growthtemperature (Ta) in a wide energy range (0.9–1.85 eV).34 In thiswork, we employ two samples grown at 1150 and 1200  C. Notethat the structural and chemical properties of the two samples
are almost identical except for the luminescence wavelength.
Fig. 1(a) shows the optical transmittance spectra of water
solutions of codoped Si-QDs grown at 1150 and 1200  C. In both
samples, the transmittance in the NIR range is almost 100%,
indicating that Si-QDs are perfectly dispersed in water. In fact,from the photograph in Fig. 1(b), the solution is very clear andcharacters behind the bottle can clearly be seen. The high water
dispersibility is due to the negative surface potential (zeta
potential: 35 mV at pH 7) and electrostatic repulsion
between QDs.32 Fig. 1(c) shows a transmission electron microscope (TEM) image of Si-QDs grown at 1150  C. For the TEM

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observations, the water solution is dropped on a carbon-coated
Cu mesh. Si-QDs are aligned two dimensionally and no threedimensional agglomerates are observed. The average diameter(dave) is 4.8 nm with the standard deviation of 1.4 nm (Fig. 1(d)).
In the high-resolution image in the inset, lattice fringes corresponding to {111} planes of Si crystal (0.314 nm) can be seen.
The TEM image and the size distribution of Si-QDs grown at
1200  C are shown in Fig. 1(e) and (f), respectively. In this case,the average diameter is 6.7 nm and the standard deviation is 1.2
nm.
Fig. 1(g) shows infrared (IR) absorption spectra of codoped
Si-QDs grown at 1150 and 1200  C stored in methanol for about
two months aer preparation. A major peak around 1080 cm1(a) Optical transmittance spectra of water solutions of B and P
codoped Si-QDs (Ta ¼ 1150, 1200  C). (b) Photograph of Si-QDsdispersed water (Ta ¼ 1200  C). (c) TEM image and (d) size distributionof Si-QDs grown at 1150  C. The inset shows a high resolution TEM
image. (e) TEM image and (f) size distribution of Si-QDs grown at 1200
C. The inset shows a high resolution TEM image. (g) IR absorption
spectra of B and P codoped Si-QDs (Ta ¼ 1150, 1200  C) after storage
in methanol for about 2 months. (h) Normalized PL spectra of codoped
Si-QDs (Ta ¼ 1150, 1200  C).

Paper

is Si–O–Si stretching mode. Small peaks around 1300–1500cm1 and 2100–2200 cm1 are assigned to B–O–B stretching
and Si–H stretching modes, respectively. Note that, just aer
preparation, the surface is mainly H-terminated,35 and oxidation slowly proceeds during storage in methanol. Aer a monthof storage in methanol, the surface is dominated by Si–O bonds.
Fig. 1(h) shows the PL spectra of codoped Si-QDs in water.
Depending on the size, the PL wavelength is changed from 900
to 1000 nm. It should be noted that the PL wavelengths are
longer than those of conventional Si-QDs with comparable
sizes.34 The long wavelength shi is due to the formation ofdonor and acceptor states in the band gap by B and P
codoping.34
For the surface functionalization, we use surface Si–O bonds,
which are abundant aer storage in methanol (Fig. 1(g)), tofunctionalize Si-QDs. In order to introduce amino and thiolgroups onto the surface via the Si–O bonds, 3 diﬀerent types ofsilane coupling agents, (A) (3-mercaptopropyl) trimethoxysilane, (B) (3-ethoxydimethylsilyl) propylamine and (C) (3aminopropyl) trimethoxysilane, are employed (Fig. 2). First, 10
ml of silane coupling agent was added to methanol solution of
Si-QDs (200 ml). The concentration of Si-QDs was 0.3 mg ml1,
while that of silane coupling agent was chosen so that the
number ratio of the molecules per a Si-QD becomes 250, 500

Fig. 163934 | RSC Adv., 2016, 6, 63933–63939(a)–(c) Optical transmittance spectra, (d)–(f) PL spectra excited
at 405 nm, and (g)–(i) PL decay curves of Si-QDs (Ta ¼ 1150  C)
functionalized by three kinds of molecules, (A) (3-mercaptopropyl)
trimethoxysilane, (B) (3-ethoxydimethylsilyl) propylamine and (C) (3aminopropyl) trimethoxysilane (detected at 890 nm). The nominal
numbers of molecules per a Si-QD are 250 (red), 500 (green) and 2500
(blue). The data of untreated Si-QDs are shown by black symbols. All
the measurements are performed in water.
Fig. 2This journal is © The Royal Society of Chemistry 2016

Paperand 2500. Hereaer, we distinguish samples with a symbol
representing the molecules (A, B and C in Fig. 2) and thenumber ratio, e.g., A250. Aer mixing, 10 ml of deionized (DI)water was added and sonicated for 30 min to promote hydrolysis. To remove unreacted molecules, the solution was lteredusing Amicon Ultra-0.5 centrifugal lter units (3 kDa cut-oﬀ)(Millipore) at 14 000g for 30 min and Si-QDs collected on thelter were dispersed in DI water. The procedure was repeated
twice. Finally, the solution was heated at 70  C for 15 min toenhance covalent bonding of silane coupling agent with SiQDs.36–40
Fig. 2(a)–(c) shows optical transmittance spectra of aqueous
solution of functionalized Si-QDs (Ta ¼ 1150  C). In the case of(3-mercaptopropyl) trimethoxysilane (A250-A2500), the water
dispersibility of Si-QDs is not degraded and the spectra are
identical to that of untreated Si-QDs (black curve). In the case of(3-ethoxydimethylsilyl) propylamine (B250-B2500), the situationis slightly diﬀerent. The transmittance spectrum changes
slightly in the highest mixing ratio (B2500). This is due toagglomeration of Si-QDs and partial precipitation to thebottom. The precipitation is very serious in (3-aminopropyl)
trimethoxysilane (C250-C2500). Even in the smallest mixing
ratio (C250), the transmittance spectrum is completely diﬀerent
from that of the untreated ones.
The diﬀerent behaviour between A and others (B and C) is
explained by the kinds of functional group. Thiol group in A
keeps the dispersibility, while amino group in B and C induces
agglomeration. The diﬀerence can be explained by the surface
potential. As described above, the surface of codoped Si-QDs is
negatively charged. Functionalization by negatively charged
thiol group enhances the surface charges and keeps Si-QDs
dispersible in water. On the other hand, positively charged
amino group cancels negative surface charges of Si-QDs andweakens the electrostatic repulsion between Si-QDs. Within B
and C, more serious agglomeration in C can be explained by thelarger number of silanol group, i.e., 3 per a molecule instead of
1 per a molecule in B. The larger amount of silanol group makes
cross linking of Si-QDs possible, which promotes theagglomeration.
In many of previous work on organic functionalized Si-QDs,
PL properties are strongly modied by the functionalization
process.24–28,30,41 Quite oen red to NIR emission disappears andblue or green emission appears aer functionalization. This is
not the case in this work. The PL spectra of all the samples are
summarized in Fig. 2(d)–(f), together with the decay curves(Fig. 2(g)–(i)). In all the cases, the PL spectral shape is not
aﬀected by the functionalization. The extremely high insensitiveness of the PL properties on the functionalization process isa characteristic feature of B and P codoped Si-QDs. It should be
stressed here that comparison of PL intensities between
samples is not straightforward due to precipitation of Si-QDs insome samples.
In contrast to the PL intensity, the PL lifetime is not strongly
aﬀected by the degree of the agglomeration. In A, the lifetime isslightly shortened, which is accompanied by the intensity
decrease. This suggests that non-radiative processes are introduced by the functionalization process, although they are not

This journal is © The Royal Society of Chemistry 2016

RSC Advances

very serious considering the small degree of the PL quenching.
The lifetime shortening and PL quenching are slightly larger in
B. It may be possible that positive charges of the amino groupaﬀect the PL properties. Note that the strong decrease of the PL
intensity in B2500 is not merely due to the introduction of nonradiative processes, but simply due to precipitation of QDs tothe bottom. In C, the lifetime shortening and the quenching ismore serious than others.
In order to conrm successful functionalization of Si-QDs
surface, we produce nanocomposites of Si-QDs and Au-NPs byusing thiol functionalized Si-QDs. Since thiol group forms
chemical bonds with Au, nanocomposites are expected to beformed spontaneously by simply mixing aqueous solution of
thiol functionalized Si-QDs (Ta ¼ 1150  C) with citrate-stabilized
Au-NPs (dave ¼ 40 nm) in diameter. Fig. 3(a) and (b) shows TEM
images of the nanocomposites. The high-resolution TEM
images are shown in Fig. 3(c) and (d). The dark regions about 40
nm in diameter are Au-NPs. Si-QDs are attached to the surfaceof the Au-NPs as conrmed by the high-resolution TEM images.
Fig. 3(e) shows the energy-dispersive X-ray spectroscopy (EDS)
mapping of a nanocomposite. We can clearly see that Au-NPs
are surrounded by Si. The TEM observations and the EDS(a), (b) TEM images, (c), (d) high-resolution TEM images and (e)STEM-EDS element mapping of a Si-QDs/Au-NP nanocomposite
formed by Au–S bonds by using thiol terminated Si-QDs (Ta ¼1150  C). (f) Normalized PL spectra of thiol terminated Si-QDs (black)and Si-QDs/Au-NP nanocomposites (red). The excitation wavelengthis 365 nm.
Fig. 3

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mapping conrm the formation of nanocomposites. Note thatthe size and shape of Au-NPs are not modied by the composite
formation process (see ESI, Fig. S1(a),† a TEM image of a Au-NP
before the composite formation). Fig. 3(f) shows the PL spectraof the nanocomposites. The spectral shape is almost identicalwith that of Si-QDs before the composite formation. It should be
stressed here that the nanocomposites were not formed whenuntreated Si-QDs were used. This indicates that they are formedby the Au–S bonds.
Now we proceed to self-assembly of nanocomposites via DNA
hybridization. The procedure is schematically shown in
Fig. 4(a). First, amine terminated Si-QDs (Ta ¼ 1200  C) andcarboxyl-modied ssDNA are conjugated by peptide bonding
using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholium
chloride (DMT-MM) as a condensing agent.42 The Si-QDs arethen annealed with Au-NPs (dave ¼ 80 nm) having thePaper

complementary ssDNA in hybridization buﬀer (ESI Fig. S1(b)†).
Fig. 4(b)–(e) show the TEM images of the nanocomposites. The
high resolution TEM images around the surface of Au-NPs areshown in Fig. 4(f)–(i). A STEM-EDS element mapping is shownin Fig. 4(j). The TEM images and a STEM-EDS mapping are
similar to those in Fig. 3, and the formation of nanocomposites
can clearly be recognized. In the ESI (Fig. S2†), STEM-EDS
mappings of individual elements, i.e., Au, N and Si, areshown. The N mapping image conrms the nanocomposite
formation by DNA hybridization. An important diﬀerence fromthe case of Au–S bonding in Fig. 3 can be seen in the highresolution TEM images. In Fig. 4(f)–(i), Si-QDs are indicatedby circles and the distance between Si-QDs and Au-NPs is shownin the images. In contrast to Fig. 3, where Si-QDs are almost
directly attached on the surface of Au-NPs, there are distances
between Si-QDs and Au-NPs in Fig. 4. The distance isFig. 4 (a) Schematic illustration of the fabrication process of Si-QDs/Au-NP nanocomposites (Ta ¼ 1200  C) by DNA hybridization. (b)–(e) TEM
images, (f)–(i) high-resolution TEM images and (j) STEM-EDS element mapping of a Si-QDs/Au-NP nanocomposite formed by DNA hybridization.
(k) Normalized PL spectra of thiol terminated Si-QDs (black) and Si-QDs/Au-NP nanocomposites (red). The excitation wavelength is 405 nm. (l)Summary of the evolution of the PL intensity during the nanocomposites formation process in solution. (i) Untreated Si-QDs, (ii) functionalizationby amino group, (iii) conjugation with ssDNA and (iv) Si-QDs/Au-NP nanocomposites by DNA hybridization. (v)–(viii) Are control samples, (v)ssDNA conjugated Si-QDs and citrate-stabilized Au-NPs, (vi) untreated Si-QDs and ssDNA, (vii) untreated Si-QDs, ssDNA and citrate-stabilized
Au-NPs and (viii) untreated Si-QDs, ssDNA and DNA functionalized Au-NPs.

63936 | RSC Adv., 2016, 6, 63933–63939

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Paperdistributed from 3.5 to 10 nm. The distribution is probably due
to the fact that TEM image is a two-dimensional projection ofa three dimensional object and the longest distance corresponds to the situation that a Si-QD is attached in the equatorial
plane of a Au-NP. The longest distance coincides with the lengthof DNA used in the work (10 nm). This is a clear evidence thatthe nanocomposites are formed by DNA hybridization. Fig. 4(k)compares PL spectra before and aer the DNA hybridization.
The spectral shape is again not modied by the nanocomposite
formation.
In Fig. 4(l), the evolution of the PL intensity during the wholeprocess is summarized. Functionalization of the surface byamino group decreases the PL intensity by 20% ((ii) in Fig. 4(l)).
By conjugation with ssDNA, the intensity drops to almost half of
the initial value ((iii) in Fig. 4(l)). The intensity goes up by DNA
hybridization ((iv) in Fig. 4(l)). The PL enhancement is considered to be due to the coupling with surface plasmons in AuNPs,43–46 although more detailed analyses including theoreticalmodelling is necessary for detailed understanding of theenhancement mechanism.
On the right side of Fig. 4(l), the PL intensities of several
control samples are shown, i.e., mixture of (v) ssDNA conjugated
Si-QDs and citrate-stabilized Au-NPs, (vi) untreated Si-QDs andssDNA, (vii) untreated Si-QDs, ssDNA and citrate-stabilized AuNPs and (viii) untreated Si-QDs, ssDNA and DNA functionalized
Au-NPs. Although the PL intensities are slightly diﬀerent
between them, all of them have much smaller PL intensity thanthat of the DNA-assembled nanocomposites. This supports
surface
plasmonenhanceduorescenceinthenanocomposites.
In conclusion, we have succeeded in producing water
dispersible and NIR luminescent Si-QDs functionalized by thiol
and amino groups. By using thiol functionalized Si-QDs, SiQDs/Au-NP nanocomposites, in which Si-QDs are attached tothe surface of Au-NPs, are formed. We also developed ssDNA
conjugated Si-QDs by using amino group functionalized Si-QDs,
and succeeded in fabricating Si-QDs/Au-NP nanocomposites by
DNA hybridization. In the DNA-assembled nanocomposites, thedistance between Si-QDs and Au-NPs are precisely controlled by
the length of DNA. The development of nanocomposites
composed of environmentally friendly Si-QDs by DNA hybridization pave the way for designing more complicated Si-QDsbased composites or hybrid structures useful for biosensing
such as DNA detection with very high accuracy andcontrollability.

Experimental procedure
Preparation of B and P codoped Si-QDs
B and P codoped Si-QDs were prepared by the previously reported procedure.47 Briey, Si-rich boronphosphosilicate glass(BPSG) lms were deposited on a stainless steel substrates bya co-sputtering method. The lms were peeled from the plates
and ground into powder, and then annealed in a N2 gas atmosphere at 1150 and 1200  C for 30 min, which results in thegrowth of B and P codoped Si-QDs about 5 and 7 nm in diameters, respectively. The annealed powder was etched byThis journal is © The Royal Society of Chemistry 2016

RSC Advanceshydrouoric acid (HF) solution (46 wt%), and codoped Si-QDs
were extracted from the BPSG matrices. Finally, isolated SiQDs were transferred to methanol and stored.
Preparation of ssDNA conjugated Si-QDs
Carboxyl-modied ssDNA at the 50 end was purchased from
Tsukuba Oligo Service Co., Ltd.,. The sequence was 50 TCGTGTTCCCATCTGGTCCAGGTTTCGTGC-30 .48 The ssDNA
and amine terminated Si-QDs were conjugated by peptide
bonding using DMT-MM as dehydrating agent. DMT-MM
solution was added to amine terminated Si-QDs solution,then incubated for 4 h at room temperature.42 The solution wasltered using Amicon Ultra-0.5 centrifugal lter units (3 kDa
cut-oﬀ) (Millipore) at 14 000g for 30 min. Finally, ssDNA
conjugated Si-QDs were dispersed in DI water.
Preparation of citrate stabilized Au-NPs and ssDNA
conjugated Au-NPs
Citrate-stabilized Au-NPs (dave ¼ 40 nm) (see a TEM image
Fig. S1(a) in the ESI†) were fabricated by seeded growth
synthesis.49 For the preparation of ssDNA conjugated Au-NPs,
thiol-modied ssDNA at the 50 end was purchased from Tsukuba Oligo Service Co., Ltd. The sequence was 50 -GCA-CGA-AACCTG-GAC-CAG-ATG-GGA-ACA-GCA-30 , which was complementary to the ssDNA immobilized onto Si-QDs. The sequence is thesame as that used in ref. 48. The conjugation of Au-NPs (dave ¼
80 nm) with the thiol-modied ssDNA was performed by using
OligoREADY Gold Nanopaticle Conjugation Kit (Cytodiagnostics Inc.). This kit has been optimized for high eﬃciency
one-step conjugation of thiol-modied ssDNA directly to the AuNPs surface. A TEM image of a ssDNA conjugated Au-NP isshown in the ESI (Fig. S1(b)†).
DNA assembly of Si-QDs and Au-NPs
For DNA hybridization, ssDNA modied Si-QDs and Au-NPs
were mixed and heated in hybridization buﬀer (0.3 M NaCl,
10 mM phosphate (pH 7)).50 The temperature was raised to 90
C, held for 2 min, and then cooled down to room temperature
with a rate of 2  C min1.
Structural characterization
For IR absorption measurements (PerkinElmer, Spectrum GX),
Si-QDs solution was drop-cast on a Au-coated Si substrate.
Absorption spectra were obtained by a reection-absorption
geometry with the incident angle of 5 in dry air. The samples
for TEM observations were prepared by dropping solutions onto
carbon-coated copper grid. TEM, high angle annular dark-eldscanning TEM (HAADF-STEM), and STEM-EDS mapping images
were obtained by using JEM-2100F (JEOL) operating at 200 kV.
PL spectroscopy
PL spectra were measured using a spectrouorometer (Flurolog3, HORIBA Jovin Yvon) equipped with a photomultiplier (500–850 nm) and an InGaAs photodiode (800–1300 nm) or a single
spectrometer equipped with a liquid nitrogen cooled InGaAs

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diode array (OMA-V-SE, Roper Scientic). PL spectra obtainedby diﬀerent detectors were merged aer correcting the sensitivity. The excitation source was a monochromatized Xe lamp
(365 nm and 405 nm) or a semiconductor laser (405 nm). PL
decay curves were obtained using image intensied CCD (ICCD)(PI-Max, Princeton Instrument). The excitation source wasmodulated 405 nm light. PL lifetimes were determined by
ðN 
IðtÞ
s¼
dðtÞ; where I(t) is the PL intensity as a function ofI0
t0
time t and I0 is the initial intensity at time t0. All the measurements were performed at room temperature.

Acknowledgements
This work is partly supported by 2014 JSPS Bilateral Joint
Research Projects (Japan-Czech Republic), 2015 JST Visegrad
Group (V4)-Japan Joint Research Project on Advanced Materials
and KAKENHI (16H03828). HS acknowledges support fromGrant-in-Aid for JSPS Fellows (# 26-3120).

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