# Patterning of Gold Nanoparticles on  DNA Self-Assembled Scaffolds

Authors: Immensee Cheng; Bryan Wei; Xunyun Zhang; Yongjian Wang; Yongli Mi
Journal: Research Letters in Nanotechnology
 (2008)

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## Abstract

We report a method of patterning the 1D and 2D arrays of gold nanoparticles on the DNA self-assembled scaffolds. The 5 nm gold nanoparticle was well positioned at the center of each4×4 tile motif of the DNA scaffold. The precisely located gold particles can form 1D and 2D arrays. This controllable scaffolding technology may become a promising tool for nanoscaled fabrication of electronics and photonic devices.


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## Body

## 1. Introduction

In recent years, people have shown tremendous interest in
developing electronic, photonic, and spintronic devices with nanoparticles
(NPs). Since the top-down approach requires expensive equipment and expertise,
the bottom-up self-assembly approach has the advantage of massive parallelism. The
challenge of the bottom-up assembly is to build well-defined structures with
considerable rigidity to scaffold NP assemblies. Lately, substantial attention
has been drawn to self-assembled DNA suprastructures because DNA and DNA-based
nanostructures are programmable and rigid enough. Meanwhile, DNA can be easily
grafted to the surface of the NPs, so that the self-assembled DNA suprastructures
can be used as templates for patterning NPs [1, 2].Although the concept of using DNA to scaffold NPs was first proposed by Robinson and Seeman
about two decades ago [3], the development of
DNA self-assembly, as scaffolds for functional nanomaterials, is still in its
early stages. To follow the idea of DNA-based nanopatterning, researchers have
developed a variety of motifs for DNA self-assemblies, such as the double
crossover (DX) [4, 5], the triple crossover (TX) [6, 7], the paranemic crossover
(PX) [8–10], 4×4 tile [11]. Many of them have been used as scaffolds for protein
and NP arrays [1, 2, 12–14]. In particular, Yan et al. have successfully obtained
gold NPs matrix scaffolded by DNA lattice [12, 13].Here we report our
results of 1D and 2D arrays of gold NPs using DNA arrays as scaffolds. The4×4
tile, as the building block of the arrays, is modified from the one developed
by Yan et al. [11]. One of the component strands of the motif was biotin modified,
so it had a strong affinity to streptavidin modified 5 nm gold NP. By mixing
the DNA array with the streptavidin modified gold NPs, the metallic array was
formed on the DNA template. The 4×4 array was examined by atomic force
microscopy (AFM) and the metallic arrays were observed by transmission electron
microscope (TEM).


## 2.  Materials and Experimental

Custom DNA strands, for the4×4 tiles (sequence design shown in Figure 1), were purchased from
Integrated DNA Technology (Leuven, Belgium). Strands
were purified by electrophoresis; bands were tailored out of 15% denaturing
polyacrylamide gels and eluted in a solution containing 500 mm ammonium
acetate, 10 mm magnesium acetate, and 1 mm EDTA. Five nm gold NP labeled with
streptavidin solution is purchased from Sigma Aldrich (Mo,  USA).The sequence design of the4×4 tiles. (a) The 4×4 tile motif of the DNA template for the 1D gold
NP array. (b) The 4×4 tile motif of the DNA template for the 2D gold NP
array.
(a)(b)DNA arrays were
formed by mixing a stoichiometric quantity of corresponding strands, quantified
by OD260, in 1×TAE/Mg (20
mm Tris, 2 mm EDTA, and 12.5 mm MgCl2) buffer. The final
concentration of each DNA strand was 1.0 μM and the final volume was 50 μL. DNA strand mixtures were cooled slowly from
95°C to 4°C in a heating block for 51 hours to facilitate hybridization.A small drop of
the DNA lattice sample (2μL) was deposited on the freshly cleaved mica
surface. 1×TAE/Mg
buffer (400 μL) was then added to the drop on the mica. The DNA lattice was
imaged in a fluid cell in semicontact mode on a Ntegra Aura atomic force
microscope (NT-MDT Co., Moscow, Russia)
using MSCT/Au tips (Veeco Inc., NY, USA).The hybridized DNA scaffold sample
was mixed with 5 nm gold NPs labeled with streptavidin overnight. TEM images were
obtained with a Jeol JEM 2010 microscope. A holey carbon film coated copper grid was
placed floating on a 5μL droplet of the mixture of the DNA scaffold and the NPs
for 5 minutes. The excess liquid was then removed from the grid by lightly
touching the edge of a filter paper. The sample grid was put in a desiccator
overnight, before the TEM examination.


## 3. Results and Discussion

### 3.1. 1D Gold NP Array

The4×4 DNA tile, modified from the motif developed by Yan et al. [11], was used
to build the 1D scaffold. The sequence of the 4×4 tile motif with nine strands
is shown in Figure 1(a). The modified sticky end matching enabled motifs to
form a ribbon-like 1D DNA scaffold as shown in Figure 2(a). The 1D scaffold was
used to obtain the 1D gold NP array after adding the streptavidin labeled gold
NPs as shown in Figure 2(a). The strand mixture in TAE/Mg buffer was slowly
cooled down to facilitate the self-assembly process. Referring to Figure 1(a),
there was a biotin group grafted on one of the TTTT segments of the center
strand, so the motif was able to capture the streptavidin labeled 5 nm gold NP.
By mixing streptavidin labeled gold NPs with the 4×4 tile array in the buffer
solution, the gold NP array was then obtained (as shown schematically in Figure
2(a)). According to the TEM images
(Figures 2(b) and 2(c)), the gold NPs were 5.0±0.8 nm in diameter and the center-to-center distances of the gold NPs were in a
range of 15.8 to 19.4 nm, which is within the design parameter of the DNA
template. The red dots in Figures 2(b) and 2(c)
represent the missing NPs due to the imperfect binding efficiency. The future
task of such research is on how to enhance the binding efficiency in order to
achieve more perfect NP arrays in larger scale.The 1D DNA template and the
derivative 1D gold NP array. (a) The pathway of 1D gold NP array from the 1D
DNA template. The yellow dots denote streptavidin
labeled NPs, which were able to be anchored at the center of each4×4 tile
by the binding between biotin and streptavidin.  (b), (c) The TEM image of the 1D
gold NP array. The scale bars in both (b) and (c) are 20 nm.
(a)(b)(c)


### 3.2. 2D Gold NP Array

The 2D gold NP array was obtained by the pathway strategically similar to that of the
1D NP array. The4×4 tile motif, shown in Figure 1(b), with chosen lattice-forming
sticky end matching strategy, was used to form the 2D DNA scaffold for positioning
gold NPs in a 2D array. The 2D DNA scaffold was formed in the cooling down
process and was examined by AFM in liquid. The streptavidin labeled gold NPs were mixed
with the 2D DNA scaffold in the buffer solution to form the 2D gold NP array as
shown in Figure 3(a). The AFM image of the 2D DNA scaffold is shown in Figure 3(b).
The 2D gold NP array was examined by TEM. According to the TEM images (Figures
3(c) and 3(d)), the gold NPs were 5.0±0.8 nm in diameter and the
center-to-center distances of the gold NPs were in a range of 15.4 to 18.6 nm,
which is within the design parameter of the 2D DNA template. Again, the red
dots in Figures 3(c) and 3(d) represent the missing NPs due to the imperfect
binding efficiency. Although Figures 3(c) and 3(d) are not perfect arrays of
gold NPs, this study shows that such DNA scaffolding technique has the
potential to position gold NPs in nanoscale rather precisely. Our future study
will be focused on developing DNA scaffolds in larger scale and enhancing
better binding between DNA scaffolds and the gold NPs. We are also trying to
bind the magnetic NPs on the DNA scaffolds, which should have applications in
information storage technology.The 2D DNA template and the derivative 2D gold NP array. (a) The pathway of
2D gold NP array from the 2D DNA scaffold. The yellow dots
denote streptavidin labeled NPs to be anchored at the center of each4×4 tile motif
by the binding between biotin and streptavidin. (b) The AFM image of the 2D DNA scaffold. (c), (d) The
TEM images of the 2D gold NP arrays. The scale bar of (c) is 50
nm and the scale bar of (d) is 20 nm.
(a)(b)(c)(d)


## 3.1. 1D Gold NP Array

The4×4 DNA tile, modified from the motif developed by Yan et al. [11], was used
to build the 1D scaffold. The sequence of the 4×4 tile motif with nine strands
is shown in Figure 1(a). The modified sticky end matching enabled motifs to
form a ribbon-like 1D DNA scaffold as shown in Figure 2(a). The 1D scaffold was
used to obtain the 1D gold NP array after adding the streptavidin labeled gold
NPs as shown in Figure 2(a). The strand mixture in TAE/Mg buffer was slowly
cooled down to facilitate the self-assembly process. Referring to Figure 1(a),
there was a biotin group grafted on one of the TTTT segments of the center
strand, so the motif was able to capture the streptavidin labeled 5 nm gold NP.
By mixing streptavidin labeled gold NPs with the 4×4 tile array in the buffer
solution, the gold NP array was then obtained (as shown schematically in Figure
2(a)). According to the TEM images
(Figures 2(b) and 2(c)), the gold NPs were 5.0±0.8 nm in diameter and the center-to-center distances of the gold NPs were in a
range of 15.8 to 19.4 nm, which is within the design parameter of the DNA
template. The red dots in Figures 2(b) and 2(c)
represent the missing NPs due to the imperfect binding efficiency. The future
task of such research is on how to enhance the binding efficiency in order to
achieve more perfect NP arrays in larger scale.The 1D DNA template and the
derivative 1D gold NP array. (a) The pathway of 1D gold NP array from the 1D
DNA template. The yellow dots denote streptavidin
labeled NPs, which were able to be anchored at the center of each4×4 tile
by the binding between biotin and streptavidin.  (b), (c) The TEM image of the 1D
gold NP array. The scale bars in both (b) and (c) are 20 nm.
(a)(b)(c)


## 3.2. 2D Gold NP Array

The 2D gold NP array was obtained by the pathway strategically similar to that of the
1D NP array. The4×4 tile motif, shown in Figure 1(b), with chosen lattice-forming
sticky end matching strategy, was used to form the 2D DNA scaffold for positioning
gold NPs in a 2D array. The 2D DNA scaffold was formed in the cooling down
process and was examined by AFM in liquid. The streptavidin labeled gold NPs were mixed
with the 2D DNA scaffold in the buffer solution to form the 2D gold NP array as
shown in Figure 3(a). The AFM image of the 2D DNA scaffold is shown in Figure 3(b).
The 2D gold NP array was examined by TEM. According to the TEM images (Figures
3(c) and 3(d)), the gold NPs were 5.0±0.8 nm in diameter and the
center-to-center distances of the gold NPs were in a range of 15.4 to 18.6 nm,
which is within the design parameter of the 2D DNA template. Again, the red
dots in Figures 3(c) and 3(d) represent the missing NPs due to the imperfect
binding efficiency. Although Figures 3(c) and 3(d) are not perfect arrays of
gold NPs, this study shows that such DNA scaffolding technique has the
potential to position gold NPs in nanoscale rather precisely. Our future study
will be focused on developing DNA scaffolds in larger scale and enhancing
better binding between DNA scaffolds and the gold NPs. We are also trying to
bind the magnetic NPs on the DNA scaffolds, which should have applications in
information storage technology.The 2D DNA template and the derivative 2D gold NP array. (a) The pathway of
2D gold NP array from the 2D DNA scaffold. The yellow dots
denote streptavidin labeled NPs to be anchored at the center of each4×4 tile motif
by the binding between biotin and streptavidin. (b) The AFM image of the 2D DNA scaffold. (c), (d) The
TEM images of the 2D gold NP arrays. The scale bar of (c) is 50
nm and the scale bar of (d) is 20 nm.
(a)(b)(c)(d)


## 4. Conclusion

In summary, we have
successfully applied self-assembled DNA scaffold to pattern 5 nm gold NPs into the
1D and the 2D arrays. This study shows that it is possible to engineer a desired
NP pattern by designing a specific DNA scaffold (e.g., pattern, spacing, and
size). However, the efficiency of the binding between the scaffold and NPs is
still not high enough. It is difficult to obtain NP arrays in larger scale
insofar. The popular methods for NP and DNA binding are based on either DNA
base pairing or streptavidin-biotin binding, yet both bindings are not strong
enough. Therefore, it is desirable to find another stronger binding mechanism for
NPs to be anchored on DNA scaffolds. It is still quite intriguing to obtain
well-patterned NP arrays with the simple method of DNA nanotechnology. When DNA
arrays can be more controllable and the binding efficiency of the gold NPs on
the DNA scaffold is further enhanced, this DNA nanotechnology methodology will
be powerful to scaffold NPs into nanoscaled devices.



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*Source: 827174-2008-02-11.xml*