Modular assembly of plasmonic nanoparticles assisted by DNA

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Interface-Rich Materials and Assemblies

Modular assembly of plasmonic nanoparticles assisted by DNA origami Chenggan Zhu, Meng Wang, Jinyi Dong, Chao Zhou, and Qiangbin Wang Langmuir, Just Accepted Manuscript • DOI: 10.1021/acs.langmuir.8b01933 • Publication Date (Web): 12 Jul 2018 Downloaded from http://pubs.acs.org on July 13, 2018

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Modular assembly of plasmonic nanoparticles assisted by DNA origami Chenggan Zhu,†‡§ǁ Meng Wang,† Jinyi Dong,†§ Chao Zhou,†and Qiangbin Wang*†‡ †

CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab, Suzhou

Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China. ‡

University of Chinese Academy of Sciences, Beijing 100049, P. R. China

§

School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, P. R.

China ǁ

Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai

200050, P. R. China KEYWORDS: Plasmonic Structure, DNA Origami, Gold Nanoparticle, Self-assembly

ABSTRACT

Arraying noble metal nanoparticles at the nanoscale features an important way towards plasmonic devices with novel optical properties such as plasmonic chiral metamolecules, optical waveguides, etc. Along with top-down methods of fabricating plasmonic nanostructures, solution-based self-assembly provides an alternative approach. There are mainly two routes of

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organizing metal nanoparticles via self-assembly. One is directly linking nanoparticles through some linker molecules, while the other one is decorating nanoparticles on a pre-formed template. We combine these two routes and herein report a strategy of DNA origami-assisted modular assembling

of

gold

nanoparticles

into

homogeneous

and

heterogeneous

plasmonic

nanostructures. For each module, we designed a W-shaped DNA origami with two troughs as two domains. One domain is used to host a gold nanoparticle and the other domain is designed to capture another gold nanoparticle hosted on a different module. By simply tuning the sequences of capture DNA strands on each module, gold nanoparticles including spherical and rod-shaped gold nanoparticles (denoted as AuNPs and AuNRs) could be well organized in a pre-defined manner to form versatile plasmonic nanostructures. Since the inter-particle distances could be precisely controlled at the nanoscale, we also studied the plasma coupling among the assembled plasmonic nanostructures. This modular assembly strategy represents a simple, yet general and effective design principle for DNA-assembled plasmonic nanostructures.

INTRODUCTION To assemble nano objects into desired configurations at the nanoscale is an important challenge in nanoscience.1 Especially, the assembly of noble metal nanoparticles such as gold nanoparticles has drawn great attention since they show substantial optical phenomena when they are placed in close proximity.2,3 There are mainly two routes to assemble gold nanoparticles. One is directly linking discrete nanoparticles via inter-molecule interactions after the surface modification of gold nanoparticles.4,5 Many inter-molecule interactions were successfully employed for linking gold nanoparticles, such as DNA hybridization,6-9 peptide interaction,10-12 and hydrophobic


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interaction.13-15 The other way is decorating discrete gold nanoparticles on pre-formed templates like peptide16-18 or polymeric fibers19-21 to form specific patterns. Compared to the former “linking” method that normally yields to simple polymers or periodic arrays, template-based assembly offers much more possibilities of building complex gold nanoparticle nanostructures. Among diverse templates for assembling gold nanoparticles, DNA nanostructures, especially DNA origami, is arguably the most versatile template for assembling gold nanoparticles.22-27 By folding a long scaffold DNA strand with hundreds of sequence-specific short staple strands in a programmed way, DNA origami could be engineered into nearly arbitrary nanoarchitectures with full addressability.28-31 Gold nanoparticles modified by oligonucleotides therefore can be positioned on DNA origami through DNA hybridization with nanometer precision.32-35 For instance, helical structures with plasmonic chiral responses comprised of spherical gold nanoparticles (AuNPs)36-38 or anisotropic gold nanorods (AuNRs)39-41 were fabricated respectively in the guidance of DNA origami templates, and different chirality could be achieved by tuning the spiral direction of AuNPs or AuNRs. Another example is optical waveguide formed by AuNP chain organized on DNA origami.42-44 Though DNA-templated gold nanoparticle nanostructures could be very versatile thanks to the programmability of DNA origami, one specific template needs to be designed and engineered for each case and the dimension of nanostructures is limited by the size of DNA templates. Here we propose a modular strategy of assembling gold nanoparticles into homogeneous and heterogeneous nanostructures with the help of DNA origami. We first designed a W-shaped DNA origami as the basis of each module. The W-shaped DNA origami has two juxtaposed troughs that work as two domains. One domain is expected to host one gold nanoparticle and the other one is designed to capture gold nanoparticle hosted on a different module by extended


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DNA strands. The basic structure for each module are the same while the sequences of DNA strands on gold nanoparticles as well as the capture strands on origami could be tailored. Therefore, each module could be independently controlled to host either a spherical AuNP or an anisotropic AuNR. Also, one module can only be linked to the very module with the correct capture strands. So the composition and the module number could be readily tailored simply by tuning the sequences of each module. With this strategy, we successfully assembled a series of gold nanoparticle arrays with finite number of spherical AuNPs and/or AuNRs.

EXPERIMENTAL SECTION Materials: Single-stranded M13mp18 viral genomic DNA was pruchased from New England Biolabs. Non-thiolated DNA sequences were purchased from Genewize, and thiolated DNA sequences with HPLC purification were purchased from Sangon Biotech. Tetrachloroauric acid (HAuCl4) was obtained from Alfra Aesar. Cetyltrimethylammonium bromide (CTAB), sodium borohydride, ascorbic acid, silver nitrate, sodium dodecyl sulfate (SDS), sodium citrate, and tannic acid were purchased from Sigma. Bis(psulfanatophenyl)phenyl-phosphine dihydrate dipotassium salt (BSPP) was supplied by Strem Chemicals. Synthesis of 11 nm-sized spherical AuNPs: A general seed-mediated growth route was employed to synthesize larger AuNPs. First, 6 nm of AuNPs were synthesized as seed. 20 mL solution of 0.01% (w/v) HAuCl4 was added into 100 mL flask and stirred quickly. The gold salt solution was heated to boiling in 5 min. The reducing solution (400 µL of 1% dehydrate sodium citrate and 90 µL of 1% (w/v) freshly prepared tannic acid) was then rapidly injected into the boiling solution. Kept the solution boiling for 10 min, and then the solution was slowly cooled to


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room temperature. The citrate-stabilized 11 nm AuNPs were synthesized through kinetic control of the reaction conditions as described previously.45 Functionalization of AuNPs with Thiolated ssDNA: AuNPs were first treated by BSPP for phosphorylation to increase its stability. Then they were incubated with excess thiolated ssDNA with the molar ratio of DNA : AuNP of 200:1 in 0.5 × Tris-Broate-EDTA (TBE) buffer (89 mM Tris base, 89 mM boric acid, 2 mM EDTA, pH 8.0) and 50 mM NaCl for 20 h at 25 oC. The excess thiolated ssDNA were removed from the DNA-modified AuNPs by 2% agarose gel electrophoresis in 0.5 × TBE running buffer. Synthesis of AuNRs: 13 × 38 nm AuNRs were synthesized following the published protocol.46 In general, (1) Synthesis of Seeds: 0.125 mL solution of 10 mM HAuCl4 was added into 5 mL of 0.1 mM CTAB solution and stirred vigorously. 0.30 mL of ice-cold 0.01 M NaBH4 was rapidly injected to the mixture and kept stirring the seed solution for 2 min, then kept it at 25 °C. (2) Growth of AuNRs: 270 µL solution of 0.06 mM AgNO3 was mixed into 40 mL of 0.1 mM CTAB solution at 25 °C and stirred evenly. Then, added 2 mL of 0.010 M HAuCl4 and 0.45 mL of 0.064 M ascorbic acid into the mixture in order. Finally, 450 µL of the previously prepared seed solution was injected to the growing solution. The mixture was kept undisturbed to grow AuNRs for several hours. Functionalization of AuNRs with Thiolated ssDNA: 10 µL of 500 µM thiolated ssDNA was added to 1 mL of 0.95 nM AuNRs solution in 1 ×TBE buffer containing 0.01% SDS, and the mixture solution was incubated at 25 °C for several hours. 10 µL of 5 M NaCl was added to the mixture solution for ten times in 10 h. The ssDNA-modified AuNRs were purified by 2% agarose gel electrophoresis in 0.5 × TBE running buffer.


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Self-Assembly and Purification of the DNA Origami: the DNA origami was self-assembled by annealing the single-stranded M13mp18 viral genomic DNA with the staple strands at ratio of 1:15 from 94℃ to 25 °C over 12h in 1×TAE-Mg2+ buffer (pH 8.0, made from 40 mM Tris base, 2 mM EDTA, 12.5 mM magnesium acetate (MgAc2·4H2O), and 20 mM acetic acid). The DNA origami products were stained using SYBR-Green and purified by 1% agarose gel electrophoresis to separate from excess staple strands and capture strands in 1×TAE-Mg2+ running buffer. The gel band of the DNA origami was cut out under UV light and recovered by electroelution with dialysis membrane (8000–14 000 MWCO). Construction of building blocks with spherical AuNPs or AuNRs: DNA origami was mixed with DNA-functionalized AuNPs together at a molar ratio of [DNA origami]:[AuNPs] of 1:2.5. The mixture of DNA origami and DNA-functionalized AuNPs was then annealed from 40 ℃ to 25 °C over 8 h. The DNA origami-AuNP building block was separated from excess AuNPs by 1% agarose gel electrophoresis in 1×TAE-Mg2+ running buffer. The gel band of the DNA origami-AuNP was cut out and recovered by electroelution with dialysis membrane (8000–14 000 MWCO). Fabrication of the gold nanoparticle assemblies: For each type of assembly, the building blocks with respective gold nanoparticle and capture strands were first purified by gel as abovementioned. Then all of the building blocks needed were mixed at equal ratio. The mixture was then annealed from 40 °C to 25 °C over 12 h to obtain the assemblies. TEM and absorption spectra characterization: The sample was dropped on carbon-coated grid and negative stained using uranyl acetate. A Tecnai G2 F20 S-Twin TEM (FEI, USA) was used for sample observation. The absorption spectra were measured by using PerkinElmer


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lambda-25 UV–vis spectrometer. The measurement was carried out at the wavelength range of 425–900 nm at room temperature in a 1.0 cm length cell. All the products were diluted to 200 µL in 1 × TAE-Mg2+. The scanning speed is 240 nm min−1. The baseline was corrected using 1 × TAE-Mg2+ buffer.

RESULTS AND DISCUSSION Construction of modular building blocks. The DNA origami template has two juxtaposed troughs-like domains which are connected by the middle ridge and further constrained by three hinges on the back surface of the middle ridge, as shown in Fig. 1a. Each trough domain is 41 nm long, 20 nm wide and 9 nm high. For each modular building block, one trough hosts either a spherical AuNP or an AuNR by two lines of capture DNA strands. In total, six capture strands are employed for capturing an 11 nm spherical AuNP as 10 capture strands for one AuNR (Fig. 1b). With this trough design, the AuNPs and AuNRs are expected to be aligned in a parallel way and only one side of each nanoparticle is exposed for connecting to a different trough on another DNA origami. Monodispersed build blocks capturing spherical AuNPs or AuNRs were obtained by gel purification and then characterized by TEM, as shown in Fig. 1c and Fig. 1d-e. The TEM results confirm that only one gold nanoparticle was hosted for each DNA origami template. These building blocks hosting spherical AuNP or AuNR were then used for assembling various gold nanoparticle nanostructures.


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Figure 1. (a) Schematic of DNA origami template; (b) Schematic of modular building blocks hosting a spherical AuNP or an AuNR; (c) Gel electrophoresis images of assembling the building blocks under visible light (left) and UV light (right): lane 1: M13 single-stranded DNA, lane 2: DNA origami template, lane 3: the building blocks with spherical AuNPs, lane 4: the building blocks with AuNRs. (d) TEM images of DNA the building blocks with spherical AuNPs. (e) TEM images of the building blocks with AuNRs. Modular assembly of spherical AuNPs with definite number. We first employed the building blocks with spherical AuNPs to demonstrate our modular assembly strategy. The free trough without hosting AuNP was engineered for controlling the modular assembly behavior. For example, spherical AuNP dimer structures were assembled simply by mixing two building blocks in which the capture strands in the free trough of the first building block were complementary with strands on AuNP hosted by the second building block (Fig. 2a). Similarly,


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to get trimer structure, the free trough of the second building block was functionalized by different sequences that are complementary with AuNP on a third building block. Following this simple rule, we also prepared AuNP tetramers and pentamers (Fig. 2b-e, more TEM images could be seem in Fig. S2). From TEM images of these assembled AuNP chains, we analyzed that the average distance between two adjacent AuNPs is 16 ± 4.4 nm, which is consistent with the structure of DNA origami template. There were no obvious difference for the absorption spectra from these different AuNP assemblies (Fig. 2f), suggesting that the plasma coupling among these particles was extremely weak. This is understandable considering the size of AuNPs (11 nm in diameter) and the distances (around 16 nm between two adjacent particles) among them.

Figure 2. Assembly of spherical AuNPs. (a) schematic of fabricating spherical AuNP trimers; (b-e) TEM images of spherical AuNP dimers, trimers, tetramers and pentamers (all scale bars are 50 nm); (f) absorption spectra of the AuNP assemblies.


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Modular assembly of AuNRs with definite number. We then applied this modular assembly strategy for assembling anisotropic AuNRs. The assembly of AuNRs is more challenging due to their relative larger size and anisotropy. However, the AuNRs can perfectly fit in our W-shaped DNA origami template. The AuNRs can be well aligned with one half embedded in the trough and the other half exposed for linking with a different building block (Fig. 3a). Following the same design principle of assembling spherical AuNPs, we also successfully prepared dimers, trimers, tetramers and pentamers of AuNRs (Fig. 3b-e, more TEM images could be seen in Fig. S3). Slight deformations were observed in the TEM images due to the drying effect in the TEM sampling process. Different from the assemblies of spherical AuNPs, here we observed the plasma couple among AuNRs from their absorption spectra. As shown in Fig. 3f, their longitudinal resonance peak showed gradually red-shift from 713 to 727 nm along with the incensement of number of AuNR from one to five. The half band widths of absorption spectra of assembled AuNR oligomers are distinctly wider than that of AuNR monomer, also indicating the strong plasma couple among the assembled AuNRs.


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Figure 3. Assembly of AuNRs. (a) schematic of fabricating AuNR trimers; (b-e) TEM images of AuNR dimers, trimers, tetramers and pentamers (all scale bars are 50 nm); (f) absorption spectra of the AuNR assemblies. Modular assembly of AuNPs and AuNRs into heterogeneous plasmonic nanostructures. With successful assemblies of spherical AuNPs and AuNRs at hand, we further employed this approach for assembling more complex plasmonic nanostructures with both spherical AuNPs and AuNRs. We designed a diagram consisting of nine different arrangements of spherical AuNPs and AuNRs and then assembled the respective structures following the above mentioned design principle (schematics and TEM images in Fig. 4a-i). With two different kinds of nanoparticles, we can examine the arrangement order of these oligomers formed by our modular assembly strategy. The nine-pattern diagram could be divided into three rows as shown in Fig 4. For each row, the right one is formed by adding one more building block on the one at its left. For example, in the first row, we first assembled trimers formed by two spherical AuNPs separated by one AuNR in the middle (Fig. 4a). Another AuNR was added at the side of the trimers to form the tetramers in Fig. 4b, and then another spherical AuNP was added to form the pentamers. All of these oligomers showed the alternate arrangement of spherical and rod-shaped gold nanoparticles as expected. In the second and the third row, the arrangements of gold nanoparticles were also consistent with our design. From TEM images of these heterogeneous plasmonic nanostructures, we analyzed that the average distance between spherical AuNPs and AuNRs is 14.5± 5.2 nm, which is consistent with the structure of DNA origami template. We also measured the spectra of these assemblies, which are presented in Fig. 4j-l. From the spectra of the assemblies in the first row (Fig. 4j), the longitudinal resonance peak of AuNRs had no red-shift since there were


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separated by small spherical AuNPs. Instead, for the spectra of the assemblies in the second row (Fig. 4k) and the third row (Fig. 4l), the longitudinal resonance peak of AuNRs both showed redshift to some extent, indicating there were some AuNRs arranged closely. All of these results confirmed that the assembly of gold nanoparticles could be fine turned by our modular assembly strategy.

Figure 4. Assembly of heterogeneous plasmonic nanostructures. (a-i) schematic and TEM image diagrams of nine different heterogeneous assemblies of AuNPs and AuNRs (all scale bars are 50 nm); (j) absorption spectra of the assemblies in a-c; (k) absorption spectra of the assemblies in df; (l) absorption spectra of the assemblies in g-i.

CONCLUSIONS


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In summary, we proposed a modular assembly strategy for assembling complex plasmonic nanostructures with the help of DNA origami. Employing this strategy, we fabricated a series of plasmonic nanostructures consisting of definite numbers and types of gold nanoparticles with precisely controlling their distance and arrangement. All of these assemblies were based on a simple DNA origami template which can host one gold nanoparticle as well as capture one gold nanoparticle from a different origami template. This modular assembly strategy represents a simple, yet general and effective design principle for DNA-assembled plasmonic nanostructures. With further modulation of this origami template, we believe it could be developed to build more complicated and functional metal nanostructures. For example, each modular building blocking with its own structural and optical features could be assembled to form supra-nanostructures with precisely controlled numbers and arrangements. In addition, this modular assembly strategy can also be used for building diverse nanoscale architectures beyond metal nanoparticles.

ASSOCIATED CONTENT Supporting Information More TEM and AFM images and DNA sequences. This material is available free of charge via the Internet at http://pubs.acs.org. AUTHOR INFORMATION Corresponding Author * E-mail: [email protected]


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Notes The authors declare no competing financial interest.

ACKNOWLEDGMENT The authors acknowledge funding by the Chinese Ministry of Science and Technology (Grant No. 2016YFA0101503, 2017YFA0205503), the National Science Foundation of China (Grant No. 21425103, 21673280).

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TOC

DNA origami-assisted modular assembling of gold nanoparticles into homogeneous and heterogeneous plasmonic nanostructures


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Modular assembly of plasmonic nanoparticles assisted by DNA

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