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Angewandte
Eine Zeitschrift der Gesellschaft Deutscher Chemiker
Chemie
www.angewandte.de
Akzeptierter Artikel
Titel: Valence-Engineering of Quantum Dots Using Programmable
DNA Scaffolds
Autoren: Jianlei Shen, Qian Tang, Li Li, Jiang Li, Xiaolei Zuo,
Xiangmeng Qu, Hao Pei, Lihua Wang, and Chunhai Fan
Dieser Beitrag wurde nach Begutachtung und Überarbeitung sofort als
"akzeptierter Artikel" (Accepted Article; AA) publiziert und kann unter
Angabe der unten stehenden Digitalobjekt-Identifizierungsnummer
(DOI) zitiert werden. Die deutsche Übersetzung wird gemeinsam mit der
endgültigen englischen Fassung erscheinen. Die endgültige englische
Fassung (Version of Record) wird ehestmöglich nach dem Redigieren
und einem Korrekturgang als Early-View-Beitrag erscheinen und kann
sich naturgemäß von der AA-Fassung unterscheiden. Leser sollten
daher die endgültige Fassung, sobald sie veröffentlicht ist, verwenden.
Für die AA-Fassung trägt der Autor die alleinige Verantwortung.
Zitierweise: Angew. Chem. Int. Ed. 10.1002/anie.201710309
Angew. Chem. 10.1002/ange.201710309
Link zur VoR: http://dx.doi.org/10.1002/anie.201710309
http://dx.doi.org/10.1002/ange.201710309
10.1002/ange.201710309
Angewandte Chemie
COMMUNICATION
Valence-Engineering of Quantum Dots Using Programmable DNA
Scaffolds
Abstract: Precise control over quantum dots (QDs) valency is
critical and fundamental for quantitative imaging in living cells.
However, prior approaches on valence control of QDs remain
restricted to single types of valences. Here we report a DNAprogrammed general strategy for valence engineering of QDs with
high modularity and high yield. By employing a series of
programmable DNA scaffolds, we generated QDs with tunable
valences in a single step with near-quantitative yield (> 95%). We
further demonstrated the use of these valence-engineered QDs to
develop 12 types of topologically organized QDs-QDs and QDsAuNPs and 4 types of fluorescent resonance energy transfer (FRET)
nanostructures. Quantitative analysis of the FRET nanostructures
and live-cell imaging reveal the high potential of these nanoprobes in
bioimaging and nanophotonic applications.
Quantum dots (QDs) are widely used for probing cell
components both in vitro and in vivo due to their strong and
stable luminescence[1]. However, the lack of valence control of
functionalized QDs hampers their bioimaging abilities since
interparticle cross-linking may interfere with internalization[2],
trafficking[3], motility[4], and signaling of membrane receptors [5].
There have been many efforts to develop QDs with controlled
valency[6], primarily on monovalent and divalent biofunctionalized QDs[7]. In a straightforward approach, QDs were
titrated with monovalent streptavidin (mSA) of different ratios
followed by purification using gel electrophoresis to obtain
monovalent QD-mSA conjugates[5]. However, the yield of this
approach is often low because of the recovery step of the QDs
from the gel with typical extraction efficiencies of 30-50%[8].
Improvement of the yield was realized using the principle of
[*]
steric exclusion which is applicable to both modified nucleic
acids and polymers of low dispersity and controlled chemical
functionality[9]. In these previous methods, precise control of QD
valency in a quantitative manner still remains challenging. Of
note, the controllability is highly important for studying
multivalent protein–ligand interactions and even tailoring them
for many important biological events, including viral infection,
immune response, cell signaling, and its regulation.
Over the past two decades, DNA nanotechnology has attracted
intense interest owing to their unparalleled self-recognition
properties that offer flexibility and convenience for the ‘bottomup’ construction of exquisite DNA nanostructures with high
controllability and precision. The DNA nanostructures have been
shown to possess low cellular toxicity and excellent cell
permeability[10]. Given the highly precise and programmable
nature, DNA is well suited for creating QDs of customized
valency with precise controllability and high yield [11]. More
recently, Kelley and co-workers reported a strategy that allows
one-step and purification free functionalization of CdTe QDs
using a chimeric DNA molecule as a single biomolecular
receptor[7c]. The resulting DNA-passivated monovalent QDs
exhibited high specific binding to protein, however, quantitative
control of multi-valency remained unsolved. It is therefore highly
desirable to develop a general approach to produce QDs of
customized valency capable of quantitative bio-analysis.
Dr. J. Shen[+], Prof. X. Zuo
Institute of Molecular Medicine, Renji Hospital, School of Medicine
and School of Chemistry and Chemical Engineering, Shanghai Jiao
Tong University
Shanghai 200127 (China)
E-mail: zuoxiaolei@sjtu.edu.cn
Dr. J. Shen[+], Profs. J. Li, L. Wang, X. Zuo, C. Fan
Division of Physical Biology and Bioimaging Center, Shanghai
Synchrotron Radiation Facility, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences
Shanghai 201800 (China)
Prof. C. Fan
School of Life Science and Technology, ShanghaiTech University,
Shanghai 201210 (China)
Dr. Q. Tang[+], Prof. L. Li[+], Prof. X. Qu, Prof. H. Pei
Shanghai Key Laboratory of Green Chemistry and Chemical
Processes, School of Chemistry and Molecular Engineering, East
China Normal University
Shanghai 200241 (China)
[+]
These authors contributed equally to this work
Supporting information for this article is given via a link at the end of
the document.
Figure 1. Preparation of QDs of customized valency by the principle of steric
exclusion and electrostatic repulsion. (a) Schematic showing that the
modification of surface chemistry generates monovalent QDs. The neutral
mPEG reduces the negative surface charge, favoring the subsequent DNA
approaching; whereas ptDNA molecules of appropriate size wrap the QD,
preventing the reaction of a second strand owing to steric exclusion. Agarose
gel electrophoresis showing QDs at three stages: MPA protected QD (MPAQD), MPA/mPEG co-protected QD (PEG-QD), and monovalent QD (Mono-VQD). The surface zeta potentials confirm the modification of surface chemistry
at three stages. (b) DNA scaffolds self-assembled from different sets of
chimeric DNA strands for valence-engineered QDs. The phosphorothioate (ps)
portion of the sequence serves as a nanocrystal ligand, while the phosphate
(po) potion of the sequence remains free for recognition. (c) The agarose gel
electrophoresis confirming the formation of multivalent QDs. The DNA: QD
This article is protected by copyright. All rights reserved.
Accepted Manuscript
Jianlei Shen+, Qian Tang+, Li Li+, Jiang Li, Xiaolei Zuo*, Xiangmeng Qu, Hao Pei, Lihua Wang,
Chunhai Fan
10.1002/ange.201710309
Angewandte Chemie
COMMUNICATION
In this work, we report a single-step and purification-free method
to create QDs of customized valency with precise control and
high yield. The approach relies on the programmable design of
DNA scaffolds that exploits a dual steric hindrance and
electrostatic repulsion strategy. Four types of functional QDs
with four different valencies, including monovalent, divalent,
trivalent, and tetravalent, were created in high yield (higher than
96%, 95%, 80%, and 85%, respectively). The resulting
functional QDs hold great promise for precise construction of
complex nanostructures. Moreover, the highly controllable DNA
distributions on QD also provided an unprecedented platform to
study the resonant energy transfer from QDs to acceptor dyes
which was of great importance and interest for quantitative bioanalysis. Lastly, the monovalent QDs was used for bio-imaging
which exhibited reduced background due to minimized
oligomerization during QDs-target interaction.
First, we prepared monovalent QDs in high yield using surface
electrostatic repulsion and steric exclusion effects. The
CdSe/ZnS QDs suspended in chloroform (emission wavelength
at 590 nm) were transferred into aqueous solution through the
modification of mercaptopropionic acid (MPA) (Figure 1a). Then,
in order to facilitate the approaching of negatively charged DNA,
we reduced the surface charges of MPA protected QDs (MPAQD) by replacing a portion of MPA with neutral
2,5,8,11,14,17,20-heptaoxadocosane-22-thiol
(mPEG,
with
seven repeated units). Since the competitively adsorption of
mPEG on QD to form disulfide bond, the ratio of and MPA and
mPEG on QD can be tuned by mPEG concentration and
reaction time. To implement the steric exclusion strategy, the
resulting MPA/mPEG co-protected QDs (PEG-QD) were then
incubated with the chimeric DNA containing a 50-adenosine
phosphorothioate DNA (ptDNA) fragment that serves as both a
nanocrystal ligand and a steric hindrance component [12]. The
surface modification process was verified by the surface zeta
potential measurements and gel electrophoresis (Figure 1a).
The zeta potential was increased from -46.2 mV to -18.6 mV
after mPEG replacement process, and was decreased to -48.6
mV after modification with chimeric DNA. The change of surface
zeta potential was further validated by the agarose gel
electrophoresis results. As shown in Figure 1a, only one new
band appeared in the agarose gel electrophoresis for each step,
suggesting that nearly all bare QDs were consumed. It should
be noted that DNA decorated QDs (Mono-V-QD) migrated
slower than MPA protected QDs (MPA-QD) despite their lower
surface potential, which can be attributed to the increased
resistance force of the extended ssDNA during migration of QDs.
We next investigated the effect of salt concentration and pH on
the assembly process (Figures S1 and S2). We found that the
0.1 M of sodium citrate buffer and pH 5 resulted in the highest
yield of >96%. This assembly strategy can be generalized to
QDs with different sizes. As confirmed by the agarose gel
electrophoresis (Figure S3), we demonstrated the preparation of
monovalent QDs with the size of approximately 4 nm (emission
wavelength at 560 nm) to exemplify the generality of this
assembly strategy.
In order to verify the formation of monovalent QDs, we
constructed QD dimers by assembling two Mono-V-QD with
complementary strands. Two chimeric DNA strands with the
same sequence in ptDNA fragment (50-adenosine) and
complementary sticky ends were assembled onto QDs (denoted
as QD1 and QD2 in Figure S4, Supporting Information),
respectively. After the assembly, suspensions with two
complementary monovalent QDs were mixed together without
purification. As shown in Figure S4, a new band with slower
migration speed appeared in the agarose gel electrophoresis
which was mainly composed of QD dimers and negligible
higher-order nanostructures, including trimers (<1%) and
tetramers (<0.2%) (TEM image in Figure S4).
We further explored the effect of the stoichiometric ratio between
DNA and QDs on the preparation of monovalent QDs. Figure S5
displays the electrophoresis results of QDs incubated with DNA
under different molar ratios ranging from 0:1 to 100:1. As can be
clearly seen from digital image and corresponding gray values
(quantified by Image J analysis), a new band appeared with
adding 0.2-fold DNA; a further increase in DNA ratio only led to
the consumption of bare QDs and generation of modified QDs.
The positions of newly formed band remained unchanged even
with 100-fold DNA. This result suggested that no stoichiometry
was needed for the preparation of monovalent QDs, which was
of critical importance for the subsequent preparation of
multivalent QDs.
We further investigated the steric hindrance effect on the
preparation of monovalent QDs. The chimeric DNA with different
lengths in ptDNA fragment (the total length of ssDNA was kept
unchanged) was incubated with QDs at different molar ratios. As
shown in Figure S6, the bands of monovalent QD appeared
when the number of phosphorothioate adenosine was more than
20; whereas with shorter ptDNA fragment, many bands were
observed in gel electrophoresis, indicating that more than one
DNA was adsorbed on the surface due to relatively weaker
steric exclusion effect. To identify the non-specific adsorption of
DNA, ssDNA with the same sequence as that of chimeric DNA
but without phosphorothioate modification was also incubated
with QDs. Negligible non-specific adsorption was found during
the assembly (Figure S7). Furthermore, we monitored the
assembly dynamics through agarose gel electrophoresis. The
gel results showed that the assembly process can be completed
within 40 min (Figure S8). Taken together, these results
elucidated that our assembly strategy allowed the one-pot,
purification-free, and fast preparation of monovalent QDs with
high yield and insensitivity to the stoichiometric ratio of
DNA/QDs.
The preparation of monovalent QDs with a remarkably high yield
can be ascribed to the sufficiently charged surface of QDs.
Firstly, it allows only a small amount of DNA to approach the
surface sequentially. Once one sulfur atom of ptDNA fragment is
anchored on the surface, the whole ssDNA in ptDNA fragment
would wrap around QDs (the persistence length of ssDNA is
approximately 2 nm and the ptDNA fragment is much longer)
and block the remaining active anchor sites, which can impede
This article is protected by copyright. All rights reserved.
Accepted Manuscript
molar ratio was 2:1. Monovalent: Mono-V-QD; divalent QD: Di-V-QD; trivalent
QD: Tri-V-QD; tetravalent QDs: Tetra-V-QD. S1: MPA-QD, S2: PEG-QD, S3:
DNA-QD.
10.1002/ange.201710309
Angewandte Chemie
subsequently approaching ssDNA. Secondly, the surface charge
could stabilize QDs under harsh reaction condition where high
concentration salt is typically involved.
Having successfully prepared monovalent QDs, we next sought
to control over the valences of QDs with pre-designed DNA
scaffolds. As schematically illustrated in Figure 1b, we can
generate divalent QDs (Di-V-QDs) using a linear DNA
nanostructure comprising a 30-adenosine ptDNA fragment and
two recognition sites at two opposite positions. The assembly
process was conducted following the same protocol to prepare
monovalent QDs. The electrophoresis results suggested a
remarkable assembly efficiency (with yield higher than 95%),
which well agreed with above results that ptDNA of more than
20-adenosine was sufficient for achieving high assembly
efficiency. Likewise, as shown in Figure 1b, Y-shaped and
cross-shaped DNA scaffolds were designed for the fabrication of
trivalent and tetravalent QDs, respectively. Specifically, the Yshaped DNA nanostructure comprises a 45-adenosine ptDNA
fragment and three recognition sites topologically arranged on
the loop; the cross-shaped DNA nanostructure comprises a 48adenosine ptDNA fragment and four recognition sites
topologically arranged on the loop. Each DNA scaffold contains
a ptDNA domain consisting of a single strand “loop” that could
interact with QDs. The gel electrophoresis results confirmed that
the Y-shaped DNA nanostructure was successfully prepared
with yield of 95.3% (Figure 1c) and its three sticky ends can well
hybrid with different complementary DNA strands to produce the
trivalent QDs (Figure S9-11). Similarly, the gel electrophoresis
results also verified the formation of the cross-shaped DNA
nanostructure (yield: 98.7%) and its hybridization capability with
four different complementary DNA strands (Figure 1c and Figure
S9-11). Significantly, we found that Y-shaped and cross-shaped
DNA nanostructures led to the formation of trivalent and
tetravalent QDs in high yields of ~80-85%.
Figure 2. QDs-QDs and QDs-Au clusters fabricated with multivalent QDs.
Assembly of monovalent, divalent, trivalent, and tetravalent QDs with
complementary AuNPs of 5, 10, and 15 nm, respectively. The AuNPs used
here were fully decorated with complementary thiolated DNA and were added
into the QDs solution excessively. Red arrows in figures indicate the position
of QDs.
The valency control of QDs offers great potential for bottom-up
construction of nanostructures with high precision. We first
tested our strategy by construction of heterodimers assembled
from monovalent QDs with AuNPs of 5, 10, and 15 nm,
respectively (Figure 2 and Figure S12). The precise structure of
the heterodimers can be visualized in the transmission electron
microscopy (TEM, Figure 2). The AuNPs used here were fully
modified with complementary ssDNA and added excessively to
ensure that the hybridization was dominated by the valences of
QDs. To demonstrate the generalizability of nanostructure
construction, we further assembled trimers by mixing divalent
QDs with two monovalent QDs, or two AuNPs of the same sizes
(5 nm and 5 nm) or distinct sizes (5 nm and 10 nm), respectively.
As shown in Figure 2 and Figure S13, the decorated two
recognition sites were anchored at the opposite positions of QDs,
resulting in a “headset”-like configuration. Similarly, we can
obtain tetramers by mixing trivalent QDs with three monovalent
QDs, or three AuNPs of the same sizes (5, 5, and 5 nm) or
distinct sizes (5, 10, and 15 nm), respectively (Figure 2 and
Figure S14). Interestingly, all AuNPs were found to lay at one
side of QDs, indicating that three DNA arms of Y-shaped DNA
nanostructure were extended at the same side after assembly.
Based on this, the generated nanostructure of trivalent QD with
three AuNPs of different sizes could adopt a tetrahedron
configuration with intrinsic chirality, which was confirmed by the
circular dichroism (CD) spectrum (Figure S15). The weak CD
signal can be ascribed to the slightly uneven distribution of sulfur
atoms at two sides (Figure 2). Compared with Y-shaped DNA
nanostructure, cross-shaped DNA nanostructure led to less
distortion of planar geometry after assembly. As shown in Figure
2 and Figure S16, tetravalent QDs lay in the middle of the
nanostructure with QDs or AuNPs surrounding in a cross shape.
The difference of the assembly behaviors between Y-shaped
and cross-shaped DNA nanostructures was probably due to the
difference of the shape of loops at the center of each
nanostructure. As described above, the loop in cross-shaped
DNA nanostructure has rather larger inscribed circle (with
average diameters of approximately 3.7 nm for Y-shaped and
6.4 nm for cross-shaped DNA nanostructures) and weaker
rigidity than those of triangular loop in Y-shaped DNA
nanostructure. These results substantiate the potential of
multivalent QDs for bottom-up construction of heterogeneous
oligomeric nanostructures with high precise valency control as
atoms and molecules do.
The established multivalent QDs provide an unprecedented
platform to study the resonant energy transfer between QDs and
their acceptors in a quantitative and precise manner. Here, the
stoichiometric fluorescence resonance energy transfer (FRET)
between QDs (emission wavelength at 530 nm) and discrete
number of organic dyes (Cy3) was explored as a test bed. As
schematically illustrated in Figure 3a, tetravalent QDs can hybrid
with four complementary DNA strands each labeled with Cy3.
The introduce of complementary DNA strands enabled FRET
from QDs to fluorophore and turned on the fluorescence. By
introducing different complementary DNA, the energy of donor
was accessible to different number of acceptors. As shown in
Figure 3b, the fluorescence signal of Cy3 was found to increase
monotonically with increasing number of acceptors. The energy
transfer efficiency (EQD-dye) from QDs to Cy3 was calculated
based on the following equation[13]:
E QD dye 
FD  FD  A
FD
This article is protected by copyright. All rights reserved.
Accepted Manuscript
COMMUNICATION
10.1002/ange.201710309
Angewandte Chemie
COMMUNICATION
6
EQD  dye 
nR0
6
nR0  r 6
where n is the number of acceptors around the donor, r is the
real distance between the donor and acceptor, R 0 is the
calculated Fӧrster distance, with
R0  0.98  103[k 2 n 4QD J ]1 / 6
where k2 is the dipole orientation factor which was usually
approximated as 2/3, n is the refractive index of the medium
(n=1.33 for water), QD is the quantum yield of QDs and J is
designated as the spectral overlap integral. Figure 3c displays
the experimental ET efficiency values, which were consistent
with theoretical prediction. The minute deviation can be ascribed
to the impurities during the DNA assembly since no purification
process was conducted after the preparation of tetravalent QDs.
Compared with several previously reported FRET systems
constructed via stoichiometric addition of dye-labeled protein or
ssDNA[14], valence-engineering of QDs using programmed DNA
scaffolds offers precise controllability in the number of acceptor
dyes.
Figure 3. Quantitative FRET study between QDs and fluorophore Cy3. (a)
Schematic demonstration of the fluorescence resonance energy transfer
(FRET) between QD and four acceptors around its core with equal distance.
The number of the acceptor dyes can be tuned via the hybridization of four
types of different DNA sequence (complementary DNA 1-4 in supporting
information). (b) The fluorescence spectra with different donor-acceptor ratios.
The excitation wavelength at 370 nm was chosen to reduce the direct
excitation of Cy3. (c) The experimental (calculated from b) and theoretical
energy transfer efficiencies. The table shown as inset lists theoretical
parameters for the calculation of energy efficiencies. (d) The agarose gel
electrophoresis confirming the surface modification of monovalent QDs. 1 and
0 represent the presence and absence of reagents, which are BSA DNA
,
decorated primary antibody and QD, respectively (from top to bottom). The
optical images of (e) microtubules using monovalent QDs as imaging tag and
(f) the control sample without adding secondary antibody. Both images in (e)
and (f) were taken under the same conditions.
We then employed monovalent QDs as imaging tags to visualize
the microtubules in Hela cell. Specifically, monovalent QDs were
firstly hybridized with complementary DNA-primary antibody
conjugation (with averaged 1.5 to 2 DNA per antibody). Here,
monovalent QDs were added in excess during hybridization to
ensure that each QD can be labeled with one primary antibody.
As shown in Figure 3d, we found that only one new band with
larger molecular weight was formed after incubation with primary
antibody; whereas no complex structures can be found. The
mixture was then incubated with bovine albumin (BSA) solution
to reduce the non-specific adsorption during cellular imaging
(Figure 3d). The resulting monovalent primary antibody labeled
QDs were incubated with the antibody treated sample and the
control sample (without secondary antibody), respectively. As
shown in Figures 3e and 3f, monovalent QDs produced a clear
imaging of microtubules with low oligomerization and negligible
non-specific adsorptions.
In summary, by combing the surface electrostatic repulsion
and steric exclusion effects, as well as DNA nanotechnology, we
achieved a precise control over the valences of DNA on QDs.
This strategy offers several unprecedented advantages. First,
QDs of customized valency can be rapidly and reliably
synthesized with high yields, providing a readily available
building blocks for bottom-up construction of nanostructures with
high precision, and atom-like property. Second, rationally
valence engineered QDs provides a versatile platform for
studying the FRET effect in a quantitative manner, which is of
great importance for FRET based bioassay/bioimaging where
the discrete number and topological positions of acceptors are
critical influential aspects. We demonstrate the use of
monovalent QDs as imaging tags to label microtubules with
remarkable specificity. Third, given that the information of
assembly was pre-written by DNA nanotechnology, QDs with
more complex valences can also be achieved through this
method. The method established here presents a simple and
effective strategy towards arbitrary decoration of DNA on QDs,
which not only provides diverse functional “bricks” towards the
fabrication of nanophotonic nanostructures but also offers a new
paradigm in designing versatile bio-probes for applications in
biological diagnostics and bio-imaging.
Acknowledgements
This work was financially supported by NSFC (Grants 21422508,
31470960, 21390414, 21722502, 21505045, 21705048),
Shanghai Municipal Education Commission-Gaofeng Clinical
Medicine Grant Support (20171913), Ministry of Science and
Technology of China (2016YFA0201200, 2013CB933802,
2013CB932803), the Chinese Academy of Sciences (QYZDJSSW-SLH031).
This article is protected by copyright. All rights reserved.
Accepted Manuscript
Where FD and FD-A are referred to as the donor fluorescence in
the absence and presence of the acceptor, respectively (all
signals were extracted after an index weight analysis with a
simple customized program written in MATLAB software, see
supporting information and Figure S17). The EQD-dye can also be
theoretically calculated. For instance, when the acceptors are
uniformly arranged around the donor with equal distance, the
EQD-dye can be calculated as follows:
10.1002/ange.201710309
Angewandte Chemie
Keywords: DNA scaffold • valence-engineering • quantum dots
• programmable • atom-like valency control
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Accepted Manuscript
COMMUNICATION
10.1002/ange.201710309
Angewandte Chemie
COMMUNICATION
Entry for the Table of Contents
COMMUNICATION
J. Shen, Q. Tang, L. Li, J. Li, X. Zuo*, X.
Qu, H. Pei, L. Wang, C. Fan
Page No. – Page No.
Valence-Engineering of Quantum
Dots Using Programmable DNA
Scaffolds
Accepted Manuscript
We report a DNA-programmed
general
strategy
for
valence
engineering of QDs with high
modularity and high yield. By
employing a series of programmable
DNA scaffolds, we generated QDs
with tunable valences in a single step
with near-quantitative yield (> 95%).
We demonstrated the use of these
valence-engineered QDs to develop
12 types of topologically organized
QDs-QDs and QDs-AuNPs and 4
types of FRET) nanostructures.
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