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C: Physical Processes in Nanomaterials and Nanostructures

Connecting Nanoparticles with Different Colloidal Stability by DNA for Programmed Anisotropic Self-Assembly Li Yu, Shota Shiraishi, Guoqing Wang, Yoshitsugu Akiyama, Tohru Takarada, and Mizuo Maeda J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b02863 • Publication Date (Web): 14 May 2019 Downloaded from http://pubs.acs.org on May 14, 2019

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The Journal of Physical Chemistry

Connecting Nanoparticles with Different Colloidal Stability by DNA for Programmed Anisotropic Self-Assembly Li Yu,†,‡ Shota Shiraishi,‡ Guoqing Wang,‡,§ Yoshitsugu Akiyama,‡,|| Tohru Takarada,*,‡ and Mizuo Maeda†,‡

†Department

of Advanced Materials Science, Graduate School of Frontier Sciences, The

University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8561, Japan ‡Bioengineering

Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako,

Saitama 351-0198, Japan §College

of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao

266003, China ||Faculty

of Industrial Science and Technology, Tokyo University of Science, 102-1 Tomino,

Oshamambe-cho, Yamakoshi-gun, Hokkaido 049-3514, Japan

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ABSTRACT: A strategy is described to produce an anisotropic assembly of isotropic particles. To generate the anisotropy, local-structure-sensitive colloidal stability of double-stranded DNAmodified gold nanoparticles was exploited; namely, fully matched (F) particles are spontaneously aggregated at high ionic strength, whereas terminal-mismatched (M) particles continue to stably disperse. Linear trimers prepared by aligning both the F and M particles on a DNA template in a strictly defined order undergo highly directed assembly, as revealed by electron microscopy. Importantly, the identity of the central particle controls the structural anisotropy. The trimers containing the M or F particle at the center selectively assemble in an end-to-end or side-by-side manner, respectively. Further, similar trimers having a central M larger than the peripheral F form assemblies that have small particles between the large particles. By contrast, the trimers with a central F larger than the peripheral M form an assembled structure in which the large particles are surrounded by the small particles. The anisotropy is programmable by the rule that an interparticle attractive force emerges between the F particles, probably due to blunt-end stacking of the surface-grafted DNA. This methodology could be useful to fabricate nanodevices.


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INTRODUCTION Nanoparticle assemblies with an ordered structure have unique collective properties that have elicited both practical and theoretical interest.1 To fabricate these assemblies, the base-pairing specificity of DNA sequences has been effectively exploited.2,3 For example, gold nanoparticles modified with single-stranded DNA (ssDNA–AuNPs) were cross-linked through DNA hybridization to produce 1D chains,4–9 2D arrays,10–12 and 3D superlattices.13–17 However, facile methods to construct highly directed assemblies have not yet been fully established. In general, anisotropic particles readily self-assemble into an anisotropic structure by virtue of an entropic advantage;18 however, the creation of anisotropic structures from isotropic building blocks is a technical challenge. For this purpose, Janus and patchy particles with an isotropic core surrounded by different compositional corona have been developed.19–22 This strategy was successfully applied to asymmetric DNA modification of AuNP surfaces to construct highly directed assemblies.23–31 This paper describes an alternative method to produce an anisotropic assembly of isotropic particles. Specifically, we use spherical AuNPs almost uniformly modified with ssDNA as an isotropic particle to construct their linear trimers. We then prepare various anisotropic AuNP assemblies by orienting the trimers. To induce the self-assembly of the trimers, we make use of local-structure-sensitive colloidal behaviors of double-stranded (ds) DNA–AuNPs; namely, fully matched dsDNA–AuNPs aggregate spontaneously at high ionic strength, whereas the particles having a single-base mismatch32 or a single-nucleotide protrusion33 at the outermost surface disperse stably under the same conditions. An investigation using colloidal probe atomic force microscopy has suggested that the interparticle attractive forces were dominated by - stacking interaction between the terminal base pairs of the surface-grafted dsDNA.34 The interparticle attraction has been employed to induce structural changes of the AuNP assemblies. 3 ACS Paragon Plus Environment


We demonstrated that fully matched dsDNA–AuNP dimers and trimers were spontaneously shrunk in a non-cross-linking manner.35,36 We also identified the folding of fully matched dsDNA–AuNP chains into an island-like 2D array structure.37 Notably, terminal-mismatched dsDNA–AuNP dimers, trimers, and chains exhibited no structural changes. These results have prompted us to design a series of trimers consisting of the fully matched and terminalmismatched dsDNA–AuNPs in a strictly defined order. In the present study, we investigate the non-cross-linked assembly of these trimers with transmission electron microscopy (TEM).

METHODS General. All reagents were purchased from Wako Pure Chemical unless otherwise specified. Citric acid-coated AuNPs with nominal diameters of 5 nm and 15 nm were obtained from BBI Solutions. Bis(p-sulfonatophenyl)phenylphosphine (BSPP) dihydrate dipotassium salt was purchased from Strem Chemicals. Tris-borate-EDTA (TBE) buffer was obtained from Nippon Gene. Ultra pure water (>18 M cm) was prepared using a Milli-Q pure water purification system (Millipore) and was sterilized for all experiments. Agarose (L03) was obtained from Takara Bio. All chemically synthesized DNA strands were purchased from Tsukuba Oligo Service and Eurofins Genomics. All DNA sequences used in this study are provided in Figure S1. Synthesis of ssDNA–AuNP Monomers. AuNPs were functionalized with ssDNA by following the reported procedure with some minor modifications.35 Briefly, the AuNP stabilized with BSPP was functionalized with 3´-dithiol-modified 59-nucleotide (nt)-long ssDNA (anchor DNA) through Au–S coordinate bond formation. The anchor–DNA–AuNP was purified by agarose gel electrophoresis. After electrophoretic extraction from the corresponding gel pieces, the anchor–DNA–AuNP was further modified with 3´-monothiol-modified 16-nt ssDNA (cover 4 ACS Paragon Plus Environment

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DNA) by the salt-aging method;35 the NaCl concentration was gradually increased at intervals of 45 mM, and finally brought to 300 mM over 3 h. The average number of cover DNAs on the AuNP surface was determined using the method reported elsewhere (Figure S2).38 Preparation of ssDNA–AuNP Trimers. A mixture (10 L) of ssDNA–AuNPs, 174-nt ssDNA (template DNA), and NaCl was allowed to stand at room temperature overnight after incubation at 60 ºC for 5 min. The ratio of each ssDNA–AuNP to its corresponding binding site on template DNA was 2:1 and the concentration of NaCl was 150 mM. For 5 nm and 15 nm ssDNA–AuNPs, the stock concentrations were 2 M and 0.5 M, respectively, in 0.5 × TBE containing 25 mM NaCl and 0.33 mg/mL BSPP dehydrate dipotassium salt. To purify the trimers, the mixture was subjected to 3% agarose gel electrophoresis (135 V, 30 min, and 4 °C). Representative images of the gels showing the separation of the trimers from the monomers, the monomers with the template DNAs, and the dimers are provided in Figure S3. 20 mM NaCl was immediately added to the isolated solution to avoid the dehybridization of the trimer. UV–vis Spectroscopy. The concentrations of ssDNA, AuNPs, ssDNA–AuNPs, and ssDNA–AuNP trimers were measured by UV–vis spectroscopy. As an example, an aliquot of the dispersion of ssDNA–AuNP trimers in TBE buffer containing 20 mM NaCl (198 L) was added to a 1 mL–tube containing 1% w/v Tween 20 (2 L). Background spectrum and extinction spectra were scanned with a Cary 50 UV–vis spectrophotometer (Varian). The concentration was calculated by Lambert–Beer’s Law. Transmission Electron Microscopy (TEM). An elastic-carbon-coated copper grid (ELSC10) from Okenshoji was hydrophilized with the UV/ozone treatment. A dispersion of the precursory ssDNA–AuNP trimer was mixed with 16-nt ssDNA (complementary DNA), whose sequence was complementary to cover DNA (8 equivalents of the total amount of the surfacegrafted ssDNA in the ssDNA–AuNP trimer), followed by incubation at room temperature for 10 5 ACS Paragon Plus Environment


min to allow DNA hybridization. The resulting mixture (2 L) was dropped onto the grid. After incubation at ambient temperature for 1.5 min, the excess solution was removed by using a capillary tube. Then, the sample was dried under a vacuum for 3 min. The measurements were performed on a JEM 1230 TEM (JEOL) operated at an accelerating voltage of 80 kV. TEM image analysis was conducted using an image analysis software (Particle Analyzer ver. 3.5, NSST). DFM Imaging and Scattering Spectroscopy. An aliquot (1 L) of the mixture of the ssDNA–AuNP trimer, the complementary DNA, and NaCl was dropped on an aminosilanecoated slide glass (Matsunami) and held by a cover slip. The sample was excited using the halogen white light source to generate plasmon resonance scattering light. An oil immersion objective lens (100x/1.30 Oil Iris, Zeiss) was used to collect the scattering light. A 5-megapixel color camera (AxioCam ICc5, Zeiss) was employed to capture the dark-field color images. The scattering light by the AuNP alone or by the assemblies adsorbed on the surface of the slide glass was split by a spectrometer (Solid Lambda CCD UV-NIR, Spectra Coop) equipped with a backthinned-type CCD (Hamamatsu). The scattering spectra were corrected by subtracting the background spectra taken from the adjacent dark regions.

RESULTS AND DISCUSSION Design and Preparation of AuNP Trimers. Figure 1 shows the method used to prepare dsDNA–AuNP trimers. First, we synthesized ssDNA–AuNP monomers according to the previously reported method.35 All DNA sequences used in this study are provided in Figure S1. We functionalized 5 and 15 nm-diameter AuNPs with thiol-modified ssDNA through Au–S bond formation. The 3´-dithiol-modified 59-nucleotide (nt)-long ssDNA (anchor DNA) was used to immobilize the AuNP onto 174-nt ssDNA (template DNA). In the present study, we used two 6 ACS Paragon Plus Environment

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types of anchor DNA (anchor DNA-a and anchor DNA-t). The other surface-bound DNA was the 3´-monothiol-modified 16-nt ssDNA (cover DNA), which served to induce the non-crosslinking assembly. We designed two types of cover DNA (cover DNA-a and cover DNA-t) with sequences that differed only by a single nucleobase (A or T) at the solution-facing terminus. We modified AuNP with strictly one anchor DNA per particle (5-nm and 15-nm AuNPs) and then on average 9 cover DNA-t strands per particle (5-nm AuNP), 10 cover DNA-a strands per particle (5-nm AuNP), and 180 cover DNA-a strands per particle (15-nm AuNP) to produce an ssDNA– AuNP monomer (Figure S2). In this study, we prepared a pair of the monomers: one having anchor DNA-t and cover DNA-t and the other having anchor DNA-a and cover DNA-a. The former and latter particles are referred to as T and A, respectively (Figure 1). We considered the T and A particles nearly completely isotropic. This is because their colloidal stability was governed by one kind of cover DNA tethered uniformly to the particle surface in sharp contrast against Janus and patchy particles. We then attached the T and A particles to template DNA through hybridization between anchor DNA and template DNA. We separated the ssDNA–AuNP trimer from the by-products composed of the monomer, the monomer with the template, and the dimer by using agarose gel electrophoresis (Figure S3) and extracted the trimer from the small gel band.35 TEM statistical analysis using Figures S4 and S5 revealed that the number fraction of the trimer thus obtained was almost 90% (Table S1), albeit the total yield of the ssDNA–AuNP trimer based on the bare AuNP was less than 1%. Subsequently, we added 16-nt ssDNA, whose sequence was complementary to cover DNA, to form DNA duplexes on the particle surface. The oligonucleotides complementary to cover DNA-a and cover DNA-t are termed complementary DNA-t and complementary DNA-a, respectively. The sequences of complementary DNA-t and complementary DNA-a differed only in terminal single base (Figure S1). The addition of 7 ACS Paragon Plus Environment


complementary DNA-t or complementary DNA-a to an ssDNA–AuNP trimer with any particle composition resulted in the production of a trimer having fully matched dsDNA–AuNP (referred to as F) or terminal-mismatched dsDNA–AuNP (M) as a constituent particle (Figure 1). Directed Assembly of AuNP Trimers. As shown in Figure 2a, we first synthesized a trimer having one central A particle and two peripheral T particles by using 5-nm AuNP (T5-A5-T5). We added complementary DNA-a and complementary DNA-t to the T5-A5-T5 dispersion to prepare F5-M5-F5 and M5-F5-M5, respectively. An aliquot of the dispersion of F5-M5-F5 and M5-F5-M5 with 20 mM NaCl was dropped onto a TEM grid and dried in preparation for microscopic observation. During the drying of the sample solutions, the ionic strength was gradually augmented to induce the non-cross-linking assembly of F5-M5-F5s and M5-F5-M5s. We determined the initial NaCl concentration such that formation of larger assemblies composed of more than two trimers was sufficiently suppressed for unambiguous discrimination of the assemblies. We observed only isolated trimers with 4 mM NaCl (Figure S6a) and the large assemblies with 50 mM NaCl (Figure S6b). For F5-M5-F5 with 20 mM NaCl, we observed assemblies caused by attraction between peripheral F5 particles in an end-to-end manner (Figure 2b and Figure S7). We also found a small number of cyclic assemblies (Figure S7a). For M5-F5M5, we found side-by-side assemblies due to attraction between central F5 particles (Figure 2c and Figure S8). The guidelines for the classification of the TEM images into the end-to-end and side-by-side configuration were as follows. (i) The assemblies composed of 6 AuNPs were excluded from the image analysis. (ii) The selected assemblies (5 or 6 AuNPs) were categorized as end-to-end or side-by-side according to the morphology. (iii) The undirected assemblies were classified into "others". TEM statistical analysis revealed a high number ratio of the end-to-end and side-by-side assembly (Figure 2b, c). However, this classification cannot avoid ambiguity because the template DNA was unable to be identified with the conventional 8 ACS Paragon Plus Environment

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TEM analysis. For example, the observed assembly composed of 6 AuNPs was actually undistinguishable into two AuNP trimers or three AuNP dimers, even though the probability of two trimers was expected to be higher because the number ratio of the precursory ssDNA–AuNP trimer (T5-A5-T5) was 92%, whereas the ratio of the by-product dimer was only 7% (Table S1). To compensate for the unavoidable ambiguity about characterization of each assembly, we additionally made a careful comparison of different shapes of the assemblies in a quantitative manner. Specifically, we introduced circularity, the degree to which an object is round, to discuss the structural difference (Figure S9).39 The circularity e is defined as follows: e = 4 (area)/(perimeter)2 Both the area and the perimeter length for each assembly image were determined with the image analysis software. The average circularity value for the assemblies of F5-M5-F5s (Figure 2d) was smaller than that of M5-F5-M5s (Figure 2e) with a p-value of less than 0.001. This result indicated that T5-A5-T5s assembled into differently shaped structures when the complementary DNAs differing only in the terminal base were added. We also calculated the particle number per 100 nm2 (the particle density) by using the area described above and the number of the particles involved in the assembly (Figure 2f, g). The assembly of M5-F5-M5s was more densely packed than the assembly of F5-M5-F5s, even though the number of F5 particles of M5-F5-M5 was smaller than that of F5-M5-F5. Next, we synthesized asymmetric T5-A5-A5 with the same method. Complementary DNA-a and complementary DNA-t were added to the trimer dispersion to prepare F5-M5-M5 and M5F5-F5, respectively (Figure 3a). For F5-M5-M5, we observed the end-to-end assemblies caused by attraction between terminal F5 particles (Figure 3b and Figure S10). TEM statistical analysis revealed a high number ratio of the end-to-end assembly (Figure 3b). We found the absence of cyclic assemblies and larger assemblies consisting of more than two trimers. For M5-F5-F5, the 9 ACS Paragon Plus Environment


side-by-side assemblies emerged with a similar high ratio (Figure 3c and Figure S11). The average circularity value for the assemblies of F5-M5-M5s (Figure 3d) was smaller than that of M5-F5-F5s (Figure 3e) with a p-value of less than 0.001. This result demonstrated that T5-A5A5s also assembled into differently shaped structures with the complementary DNAs differing only in the terminal mononucleotide. The particle number per 100 nm2 for the assemblies of F5M5-M5s was smaller than that of M5-F5-F5s (Figure 3f, g); namely, the assemblies of M5-F5F5s were more highly packed than those of F5-M5-M5s. In this case, the particle density was roughly proportional to the F5 particle number. Basis of Anisotropic Structures. For comparison, we also synthesized a homo-trimer T5T5-T5, and then prepared F5-F5-F5 and M5-M5-M5 (Figure S12). As predicted, F5-F5-F5s assembled randomly (Figure S12b), while M5-M5-M5s dispersed stably (Figure S12c). We determined the average circularity value of the random F5-F5-F5 assemblies to be 0.61 ± 0.18 (Figure S12d), and the particle number per 100 nm2 to be 0.84 ± 0.26 (Figure S12e). Comparisons of this homo-trimer with the preceding hetero-trimers allowed us to point out the following. (1) Substitution of central M5 in M5-M5-M5 with F5 generated the side-by-side assembly. (2) Substitution of one terminal M5 in M5-M5-M5 with F5 generated the end-to-end assembly. (3) Substitution of central F5 in F5-F5-F5 with M5 made the transition from the undirected assembly to the end-to-end assembly. (4) Substitution of one terminal F5 in F5-F5-F5 with M5 made the transition from the undirected assembly to the side-by-side assembly. Taken together, these results indicate that when the trimers were prepared by aligning the F5 and M5 particles in a strictly defined order, the resultant assembled structures were endowed with the anisotropy; namely, highly directed assemblies of the structurally isotropic particles were achieved in a programmed manner. The connection between the particles by DNA was essential for the anisotropic assembly. 10 ACS Paragon Plus Environment

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When no template DNA was added to a mixture of F5 and M5 with a given ratio, we found only isolated AuNPs in the TEM images (Figure S13). Our previous study demonstrated that regionselective DNA modification of circular-shaped ends and a side region of Au nanorod (15 nm × 45 nm) either with fully matched or terminal-mismatched dsDNA produced the non-cross-linked end-to-end or side-by-side assemblies of the Au nanorods.40 The present results strongly suggested that the directed assemblies were also available with the AuNP trimers. Emphasis is placed on the technical advantage of the current approach; the modularity of F5 and M5 could allow one to design and fabricate a variety of anisotropic nanostructures. The identity of the central particle (F5 or M5) of the trimer controlled the structural anisotropy of the self-assembly. The circularity gradually increased in the following order: M5M5-F5 < F5-M5-F5 < F5-F5-M5 < M5-F5-M5. The circularity values for the trimers having the central F5 were larger than those having the central M5. Figure 4 shows the relationship between the particle density and the circularity. The particle density for the assemblies of the trimers having the central F (M5-F5-M5 and F5-F5-M5) with the side-by-side structure was as dense as that for the random assemblies of F5-F5-F5s, irrespective of the circularity value. In contrast, the particle density for those having the central M5 (F5-M5-F5 and M5-M5-F5) was augmented with increasing circularity. Therefore, the identity of the central particle determined the orientation of the trimer and the particle density. The importance of the central particle was presumably due to the fact that the mobility of the central particle was more restricted than that of the peripheral ones. For example, two F5-M5-F5s assembled into the end-to-end structure rather than the sideby-side structure. The side-by-side configuration made by attraction between the peripheral F5 particles should compel the central M5 particles to exist in close proximity, thereby inducing the repulsion to impose substantial thermodynamic penalties to self-assembly. On the other hand, two M5-F5-M5s were able to assemble into the side-by-side structure, because the repulsion 11 ACS Paragon Plus Environment


between the peripheral M5 particles placed opposite to each other was avoidable due to greater flexibility. Self-Assembly of Differently Sized Trimers. Based on this consideration, we next synthesized the ssDNA–AuNP trimer consisting of a central large AuNP and peripheral small AuNPs (T5-A15-T5) (Figure S5). We then added complementary DNA to prepare F5-M15-F5 and M5-F15-M5 (Figure 5a). TEM observation revealed that two F5-M15-F5s self-assembled into an anisotropic structure, which had the F5 particle(s) between two M15 particles (Figure 5b and Figure S14). This structure is termed Interior. On the other hand, two M5-F15-M5s assembled into the inverted structure that contained the F15 particles surrounded by the M5 particles (Figure 5c and Figure S15). The structure is referred to as Exterior. The guidelines for the classification of the TEM images into Interior and Exterior are described in Figure S16. Interior and Exterior were morphologically analogous to the end-to-end and side-by-side assembly, respectively. Interior essentially corresponded to the cyclic version of the end-to-end assembly (Figure S7a), whereas about 30% of Interior partially exhibited the linear end-to-endlike structure (Figure S14b). TEM statistical analysis revealed that the number ratio of Interior of F5-M15-F5s and Exterior of M5-F15-M5s was extremely high (Figure 5b, c). A distinct difference in size between F and M for F5-M15-F5 and M5-F15-M5 enabled us to unambiguously discriminate between Interior and Exterior and thus perform detailed image analysis. Specifically, we focused our attention on the interparticle center-to-center distance between the central 15-nm AuNPs. We found that the distance for Interior (Figure 5d) was 1.7 times longer than that for Exterior (Figure 5e). Further, we confirmed that the observed value for Exterior (23 nm) was almost the same as the calculated one (25.9 nm) by using the contour length of the 16-base-pair-long B-form dsDNA and the AuNP diameter (Figure S17). The result was in line with our working hypothesis 12 ACS Paragon Plus Environment

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that the non-cross-linking assembly of the AuNP trimers was induced by the blunt-end stacking between the terminal base pairs of the surface-grafted dsDNA.34 Finally, we attempted to address the question as to whether the evaporation of the samples was required to produce the difference of the interparticle distance between the central 15-nm AuNPs for the F5-M15-F5 assemblies and the M5-F15-M5 assemblies. For this purpose, we carried out the surface plasmon scattering measurement without the sample drying under a darkfield microscope (Figure 6 and Figure S18).41,42 However, it was practically impossible to control the number of the trimers that composed the assembly in solution. It should be noted that the assembling number of the trimers in solution at high ionic strength for the dark-field microscopy was probably larger than that in the dried sample for the TEM analysis. Only the scattering light by large 15-nm AuNPs involved in the individual trimers and the trimer assemblies was detectable, owing to the limited sensitivity of the current system. Therefore, we performed the surface plasmon scattering measurement in order to test our hypothesis that the plasmon coupling among the 15-nm AuNPs involved in the trimer assemblies in solution varied according to the type of the terminal nucleobase of the complementary DNA. First, we selected the NaCl concentration of the sample solutions as 0.2 M. No remarkable difference was found between the spectra of F5-M15-F5 and M5-F15-M5 (Figure 6a, b). This result strongly suggested that their isolated states were almost identical. Next, the NaCl concentration was increased to 1.5 M to induce the non-cross-linking assembly. We expected that F5-M15-F5s and M5-F15-M5s self-assembled into an oligomeric Interior-like structure as shown in Figure S14c and an oligomeric Exterior-like structure as shown in Figure S15c, respectively. For comparison, we measured the scattering light from the F15 and M15 particles alone. The free F15 particles were expected to form random assemblies in a non-cross-linking manner, while the free M15 particles were expected to disperse stably. The scattering spectra 13 ACS Paragon Plus Environment


were collected for the samples (Figure 6c–f), which were ordered according to the average resonance wavelength: M15 < F5-M15-F5 < M5-F15-M5 < F15. This result agreed with the TEM data, indicating that the distance between the central 15-nm AuNPs of Exterior was shorter than that of Interior (Figure 5d, e). It is thus strongly suggested that the sample drying was not responsible to make the difference in shape between the assemblies, which was indeed caused by the terminal single-base difference of the cover DNA.

CONCLUSIONS In this study, the programmable assemblies were constructed from trimers composed of two types of dsDNA–AuNP (F and M) that exhibited remarkably different colloidal stabilities. The observed anisotropic structures were simply deduced from the rule that an interparticle attractive force emerged only between the F particles, whereas no attraction occurred between the M particles, as well as between the F and M particles.34 This rule was in line with our working hypothesis that interparticle attraction in the non-cross-linking assembly of dsDNA–AuNPs arose from the blunt-end stacking. More importantly, we succeeded in constructing anisotropic self-assemblies from isotropic nanoparticles. The anisotropy was achieved by connecting different colloids in a strictly defined order by exploiting the Watson-Crick complementary base pairing. This modularity may potentially be harnessed to design and fabrication of a wide variety of anisotropic nanostructures. Furthermore, it would be of fundamental interest to explore similarities in behavior among the present metallic nanoparticle oligomers, amphiphilic small organic molecules, amphiphilic copolymers, and recently reported colloidal surfactants.43 The increasing particle number and enhancing sequence diversity in the present particle chains could allow one to obtain various 3D assemblies. Such an attempt would be promising for prospective use of the current methodology in the fabrication of functional materials. 14 ACS Paragon Plus Environment

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ASSOCIATED CONTENT Supporting Information: The Supporting Information is available free of charge on the ACS Publications website. Particle-number distribution, DNA sequences, calibration curves to estimate the DNA number, gel electrophoresis images, additional TEM images, DFM images, and schematics. (PDF)

AUTHOR INFORMATION Corresponding Author *[email protected] ORCID Tohru Takarada: 0000-0001-6906-5812 Notes The authors declare no competing financial interest.

ACKNOWLEDGMENTS This study was supported by JSPS KAKENHI Grant Number JP25220204. L.Y. is a RIKEN International Program Associate. The authors thank Dr. Xu Shi at the Research Institute for Electronic Science, Hokkaido University, for his helpful discussion on the data of surface plasmon scattering.



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Page 21 of 34 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


A A

TA

A

TA

Complementary DNA-a

ssDNA–AuNP Monomers A

A

A

A

T

Cover DNA-a Anchor DNA-a

T

A

T

T T

T

T

T

ssDNA–AuNP Trimer

T

T

T

Template DNA for T-A-T

T

Cover DNA-t Anchor DNA-t

=

T

F

T

AT

A

A

T T

T

F

T T

AT

T

Complementary DNA-t

T

F

M

T

T

A T

T

T

A

=

A

Fully matched dsDNA–AuNP

M

=

M

F

M

Terminal-mismatched dsDNA–AuNP

Figure 1. Schematics for preparation of AuNP trimers having fully matched dsDNA and terminalmismatched dsDNA on the surface. As an example, two kinds of dsDNA–AuNP trimer are depicted, both of which are obtained from the precursory ssDNA–AuNP trimer composed of two peripheral AuNPs modified with cover DNA-t and a central AuNP modified with cover DNA-a (T-A-T). The addition of complementary DNA-a and complementary DNA-t to the dispersion of T-A-Ts yields the dsDNA–AuNP trimers, F-M-F and M-F-M, respectively.



(a)

d = 5 nm

T

A

×2

T

Complementary DNA-a

Complementary DNA-t

M F

M

F

F

M

F

M

End-to-end (ETE)

F F

M M

Side-by-side (SBS)

(b)

(c) Others

Others

ETE 86%

SBS 90%

n = 50

Probability

0.5 0.4

0.56 ± 0.16 n = 50

n = 50

(e)

0.5 Probability

(d)

0.3 0.2 0.1 0.0

0.4 0.2 0.1 0.0

0.6 0.5 0.4 0.3 0.2 0.1 0.0

0.64 ± 0.24 n = 50

0 0.3 0.6 0.9 1.2 1.5 Particle number/100 nm2

0.0 0.2 0.4 0.6 0.8 1.0 Circularity

(g)

0.6 0.5 Probability

(f)

0.76 ± 0.09 n = 50

0.3

0.0 0.2 0.4 0.6 0.8 1.0 Circularity

Probability

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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0.79 ± 0.19 n = 50

0.4 0.3 0.2 0.1 0.0


Figure 2. Directed assembly of T5-A5-T5s in an end-to-end and side-by-side manner. (a) Schematics for the preparation of F5-M5-F5 and M5-F5-M5 from T5-A5-T5 for the end-to-end and side-by-side assembly, respectively. (b, c) The representative TEM images of F5-M5-F5 (b) and M5-F5-M5 (c). Scale bars are 20 nm. The number ratio of the end-to-end assembly (b) and the sideby-side assembly (c) is also depicted. (d, e) The circularity distributions for the assembly of F5M5-F5s (d) and M5-F5-M5s (e). (f, g) The particle density distributions for the assembly of F5M5-F5s (f) and M5-F5-M5s (g). ± denotes the standard deviation.


Page 23 of 34

(a)

d = 5 nm

T

A

×2

A

Complementary DNA-a

Complementary DNA-t

M

M

M

F

F

M

M M

End-to-end (ETE)

F

F

F

F

Side-by-side (SBS)

(b)

(c) Others

Others

ETE 94%

SBS 90%

n = 50

Probability

0.5 0.4

0.49 ± 0.12 n = 50

n = 50

(e)

0.5 Probability

(d)

0.3 0.2 0.1 0.0

0.4 0.2 0.1 0.0

0.6 0.5 0.4 0.3 0.2 0.1 0.0

0.34 ± 0.10 n = 50


0.0 0.2 0.4 0.6 0.8 1.0 Circularity

(g)

0.6 0.5 Probability

(f)

0.68 ± 0.12 n = 50

0.3

0.0 0.2 0.4 0.6 0.8 1.0 Circularity

Probability

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


0.76 ± 0.24 n = 50

0.4 0.3 0.2 0.1 0.0


Figure 3. Directed assembly of T5-A5-A5s in an end-to-end and side-by-side manner. (a) Schematics for preparation of F5-M5-M5 and M5-F5-F5 from T5-A5-A5 for the end-to-end and side-by-side assembly, respectively. (b, c) The representative TEM images of F5-M5-M5 (b) and M5-F5-F5 (c). Scale bars are 20 nm. The number ratio of the end-to-end assembly (b) and the sideby-side assembly (c) is also depicted. (d, e) The circularity distributions for the assembly of F5M5-M5s (d) and M5-F5-F5s (e). (f, g) The particle density distributions for the assembly of F5M5-M5s (f) and M5-F5-F5s (g). ± denotes the standard deviation.



Side-by-side Random F

F

F

F

F

M

M

F

M

1.5

Particle number /100 nm2

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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1.0 E

0.5 E

0.0

M

E

E

E

M

0.3

0.4

F

0.5

F

M

0.6 0.7 Circularity

0.8

0.9

F

End-to-end

Figure 4. Relationship between the particle density and the circularity for the AuNP trimer assemblies. The data shown in Figures 2, 3 and S12 are used. The error bars indicate the standard deviation of the mean. The gray bands are drawn as a guide to the eye.


Page 25 of 34

(a)

d = 15 nm d = 5 nm

T

A

×2

T

Complementary DNA-a

Complementary DNA-t

Exterior

Interior F

M

M

M

M

F

F

F

F

F M

M

(b)

(c) Interior

Exterior

Exterior 96%

Interior 92%

n = 50

n = 50

1.0 38 ± 11 nm 0.8 n = 50 0.6

F

M

F M

0.4

F

F

0.2 0.0

0

1.0

(e)

20 40 60 80 Distance (nm)

Probability

(d) Probability

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


23 ± 2 nm n = 50

0.8 0.6

M

0.4

M

M F

F M

0.2 0.0

0 20 40 60 80 Distance (nm)

Figure 5. Directed assembly of trimers of dsDNA–AuNPs with a different diameter (T5-A15-T5). (a) Schematics for preparation of F5-M15-F5 and M5-F15-M5 for the assembly having 5-nm AuNPs between 15-nm AuNPs (Interior) and the assembly having 5-nm AuNPs around the 15-nm AuNPs (Exterior), respectively. (b, c) The representative TEM images of the assembly of F5-M15F5s (b) and M5-F15-M5s (c). Scale bars are 20 nm. The number ratio of Interior and Exterior is also depicted. (d, e) Distributions of the center-to-center interparticle distance between the central 15-nm AuNPs for the assembly of F5-M15-F5s (d) and M5-F15-M5s (e). ± denotes the standard deviation.



0.4 0.2 0.0

0.2

1.0

1.0

0.8

Probability

1.2

0.8 0.6 0.4 0.2 0.0

0.6 0.4

M15

0.8 0.6 0.4 0.2 0.0

0.8 0.6

480 ± 10 nm n = 22

[NaCl] = 1.5 M

F15

0.4 0.2

0.2 0.0

0.4 0.2 0.0

420 460 500 540 580 Wavelength (nm)

1.2

1.0

1.01

0.8 550

0.8 0.6 0.4

0.6 n

420 460 500 540 580

0.4 0.2

420 460 500 540 580 Wavelength (nm)

1.0

1.2

560 ± 3 nm n = 23 1.01 0.8 0.6 0.4

300 400 500 600 700 800 Wavelength (nm)

Wavelength (nm)

± 6 nm = 19

0.0

0.2 0.00

0.0

300 400 500 600 700 800 Wavelength (nm)

0.4

480 ± 8 nm n = 17

0.6

Wavelength (nm)

1.0

1.0

0.6

300 400 500 600 700 800

(f) 1.2

0.8

0.8

0.2 0.00

420 460 500 540 580 Wavelength (nm)

Probability

[NaCl] = 1.5 M

M5-F15-M5

0.0

Wavelength (nm)

(e)

530 ± 10 nm n = 37

[NaCl] = 1.5 M

0.2

300 400 500 600 700 800

1.0

1.0

300 400 500 600 700 800 Wavelength (nm)

(d) Normalized Scattering Intensity

F5-M15-F5

0.4

420 460 500 540 580 Wavelength (nm)

Wavelength (nm)

[NaCl] = 1.5 M

M5-F15-M5

0.0

300 400 500 600 700 800

(c)

0.6

1.2 Probability

0.6

Normalized Scattering Intensity

0.8

[NaCl] = 0.2 M

480 ± 8 nm n = 17

Probability

0.8

Probability

1.0


1.0


F5-M15-F5

1.2 Probability

[NaCl] = 0.2 M


(b)

(a)


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 26 of 34

0.8 0.6 0.4 0.2 0.0

420 460 500 540 580 Wavelength (nm)

Figure 6. Dark-field scattering image analysis for F5-M15-F5, M5-F15-M5, M15, and F15 in the presence of 0.2 M NaCl or 1.5 M NaCl. Each panel is composed of a representative scattering spectrum with a scattering image (left) and a histogram of the plasmon resonance wavelength (right). The arrows in (a) and (b) indicate the surface plasmon scattering peaks used for the statistical analysis. ± denotes the standard deviation.


Page 27 of 34 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


TOC

20 nm



ACS Paragon Plus Environment

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Page 32 of 34

0.8

0.8 0.8 0.6 0.6 0.4 0.4

0.6

(b)

0.2

0.00 300 400 500 600 700 800

0.0 420 460 500 540 580 Wavelength (nm)

1.0

1.01

0.8

1.2 1.2

0.2 0.2

0.2

0.00 300 400 400 500 600 700 700 800 800 300 500 600 Wavelength (nm)

0.0 420 460 500 540 580 Wavelength (nm)

1.2 1.2

1.0

1.01

0.8

0.8 0.8 0.6 0.6 0.4 0.4

0.6

480 ± 8 nm n = 17

0.4

1.01

0.8

0.8 0.8 0.6 0.6 0.4 0.4

0.2

0.00 300 400 500 600 700 800

0.0 420 460 500 540 580 Wavelength (nm)

M5-F15-M5

1.0

1.01

0.8

0.8 0.8 0.6 0.6 0.4 0.4

0.6

480 ± 10 nm n = 22

[NaCl] = 1.5 M F15

0.4

0.2 0.2

0.2

0.00 300 400 500 600 700 800 Wavelength (nm)

0.0 420 460

0.8 0.8 0.6 0.6 0.4 0.4

0.2 0.2 0.00 300 400 500 500 600 600 700 700 800 800

0.6

0.2 0.0 420 460

500 540 580

Wavelength (nm)

1.0

1.01

0.8

0.6 0.6 0.4 0.4

500 540 580

Wavelength (nm)

1.2 1.2 0.8 0.8

550 ± 6 nm n = 19

0.4

Wavelength (nm)

(f) 1.2 1.2 Probability

M15

0.4

0.2 0.2

Wavelength (nm)

[NaCl] = 1.5 M

0.6

[NaCl] = 1.5 M 530 ± 10 nm n = 37

Probability

1.0


1.2 1.2 Probability

F5-M15-F5


[NaCl] = 1.5 M

Probability

(d)

(c)

(e)

M5-F15-M5

0.4

0.2 0.2

Wavelength (nm)

[NaCl] = 0.2 M

480 ± 8 nm n = 17

Probability

1.0

1.01


F5-M15-F5

1.2 1.2


[NaCl] = 0.2 M

Probability

(a)


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60



Page 33 of 34

0.6

560 ± 3 nm n = 23

0.4

0.2 0.2

0.2

0.00 500 600 600 700 700 800 300 400 500 800 Wavelength (nm)

0.0 420 460

500 540 580

Wavelength (nm)

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