Site-Specific Metallization of Multiple Metals on a Single DNA Origami

Jan 10, 2014 - Bibek Uprety , John Jensen , Basu R. Aryal , Robert C. Davis , Adam T. Woolley ... Elisabeth P. Gates , Andrew M. Dearden , Adam T. Woo...
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Site-Specific Metallization of Multiple Metals on a Single DNA Origami Template Bibek Uprety,† Elisabeth P. Gates,‡ Yanli Geng,‡ Adam T. Woolley,‡ and John N. Harb*,† †

Department of Chemical Engineering and ‡Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States S Supporting Information *

ABSTRACT: This work examines the selective deposition of two different metals on a single DNA origami template that was designed and assembled to direct the deposition. As a result, we were able to direct copper and gold to predesignated locations on the template, as verified by both compositional and morphological data, to form a heterogeneous Cu−Au junction. Seeding and deposition were performed in sequential steps. An enabling aspect of this work was the use of an organic layer or “chemical mask” to prevent unwanted deposition during the deposition of the second metal. In light of recent efforts in the field, the ability to localize components of different composition and structure to specific sections of a DNA template represents an important step forward in the fabrication of nanostructures based on DNA templates.

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form a heterogeneous metal−metal junction. Our previously demonstrated ability to perform site-specific deposition of a single metal on an origami template provides the foundation for this work.4 An overview of process steps required for the formation of the junction is provided in Figure 1. The objective of this study was to fabricate the desired junction and to identify the technical issues and challenges associated with its fabrication. Prior to performing the steps shown in Figure 1, it was necessary to create an origami design suitable for the study. Consequently, a bar-shaped DNA origami template was designed with attachment points for one metal group on half of the structure and a second metal group on the other half, as described in the Materials and Methods section. The second and third steps illustrated in Figure 1 can then be completed reliably by seeding with gold particles and depositing gold via electroless deposition to create a continuous structure.4 Given our experience and success in this area, we decided to use gold for half of the desired junction. Step D, although not trivial, was not expected to present major challenges because the seeding of the second half of the template should not be impacted significantly by the presence of gold on other sections of the template. Therefore, the principal challenge was how to deposit a second metal on the remaining half of the template (step E) selectively without depositing on the gold section of the junction. Two different approaches were considered for step E. The first approach involved the deposition of a seed material on which the desired second metal would selectively plate. For this

elf-assembly has shown considerable promise as a potential way of reducing cost, decreasing size, and enabling the fabrication of complex nanoassemblies. Self-assembly essentially seeks to utilize the recognition capability of single molecules to self-assemble those molecules into useful conformations of nanometer resolution.1−5 DNA, with its small size, functional groups, and complementary base pairs, is emerging as a desirable template for fabricating components of nanodevices via self-assembly.6,7 In this regard, the advent of DNA origami8 has enabled the fabrication of nanostructures for use in nanofabrication by folding single-stranded DNA into different 2D8−10 and 3D6,11−13 shapes. In addition, DNA origami designs can be made with attachment points for different functional groups at specific locations on the template. This can be done by extending the staple strands in the DNA origami template with additional nucleotides to serve as attachment sites for complementary sequences bound to the desired functional groups. Using this technique, a variety of materials such as metal nanoparticles4,14−17 and carbon nanotubes18 can be controllably attached to specific DNA origami sites. DNA-templated metallic structures hold potential for broad use in electronic and plasmonic applications.17 For such applications, continuous and conductive metallized DNA structures are required.4 The bulk of the work in this field has focused on the metallization of λ-DNA,19−23 and the continuous metallization of a DNA origami template was only recently reported.3 Furthermore, the selective deposition of metal at specific sites on origami templates is needed for the utilization of the full potential of these templates. Such sitespecific metallization has now been demonstrated for a single metal4,17 and was used to form conductive nanowires,4 which has opened up a spectrum of possibilities. In this study, we demonstrate the deposition of two different metals at designated locations on a single origami template to © 2014 American Chemical Society

Received: September 20, 2013 Revised: December 24, 2013 Published: January 10, 2014 1134

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Figure 1. Process used for making a heterogeneous metal junction on a DNA origami template. (A) DNA origami template. (B) Seed particles for the first metal group on a select segment of the template. (C) Electroless plating of the seeded section. (D) Seed particles for the second metal group on the adjacent section of the template. (E) Electroless plating on the second seed layer to make the desired metal junction.

structure. An examination of the 3D shape of the bar using the program CanDo indicated that the structure likely had an overall twist when in solution. A structure with a twist could appear bent in different places, depending on how it landed on the surface. Seeding for Gold Deposition. Each half of the template was functionalized with different DNA sequences as summarized in Figure 3. These binding sites were designed to hybridize

strategy to be successful, the second metal would need to be plated on the second seed layer only, not on the existing gold. The largest challenge associated with this strategy was not in finding a seed upon which the metals of interest would plate but rather in finding metals that would not plate on the existing gold layer. In the second approach, a chemical mask was proposed to protect the gold from additional deposition while plating the second metal. This approach was potentially applicable to a variety of metals but involved additional process steps. It was the second approach that was used in this study.

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RESULTS AND DISCUSSION Template Assembly. A bar-shaped template with a length of 410 nm and a width of 17 nm was designed for use in this study as described in the Materials and Methods section. Figure 2A shows the bar-shaped DNA origami after assembly. As seen

Figure 3. Bar-shaped DNA template functionalized with attachment strands for gold nanoparticle deposition.

with DNA-coated metal nanoparticles that were to serve as seed particles for site-specific electroless deposition. The origami template was seeded with 5 nm gold nanoparticles by exposing it to a solution of DNA-functionalized Au NPs (2 nM) for 40 min in a humid chamber in order to allow the T-functionalized particles to hybridize with complementary sites on the template. After Au NP attachment (Figure 2B), the average height of the DNA origami template in the seeded region increased to 7.0 nm with a standard deviation of 0.7 nm (n = 30), compared to the unseeded DNA origami height of ∼1 nm. Gold particles attached to half of the origami template, as expected. In addition, Au NPs were occasionally observed to stick to the opposite end of the origami in some samples. A possible explanation for this is that the extra scaffold strand at the end of the assembled origami template may have led to particle attachment by physically wrapping around the nanoparticle. Electroless Gold Deposition. After seeding, origami templates were plated with gold for 1 min. The average height of the plated origami was 24 nm with a standard deviation of 2.7 nm (n = 30). The plating time used was based on previous experience with the fabrication of continuous gold-plated structures.4 Figure 2C shows the result of electroless gold plating on the bar-shaped template. SEM images of the samples (Figure 2D) after gold plating showed continuous structures with distinct grains, consistent with previously observed

Figure 2. (A) Bar origami. (B) Au seeding on half the length of the origami. (C) Au plating on the Au-seeded section of the template. (D) SEM image of Au-plated structures. The height scale is 10 nm, and the scale bar is 500 nm.

in the figure, most of the DNA origami deposited on the surface had folded properly to yield the desired shape. The average length of the folded origami was 415 nm (from AFM images) with a standard deviation of 2.3 nm (n = 30), which is consistent with the design size. Some of the origami structures appeared to have one or more kinks or bends in the folded 1135

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Figure 4. (A) Au-plated bar-shaped DNA. (B) Structure in A masked with thiolated DNA and introduced into the copper plating bath. (C) EDX analysis of the structure in B using a spot scan. Scale bars are 200 nm.

Figure 5. (A) AFM images and height analysis of unmetallized bar DNA. (B) AFM image and height analysis of the palladium-seeded section of bar DNA. The height scale is 6 nm, and the scale bars are 500 nm.

structures for gold-plated samples.4 The average length of the Au-plated area was 200 nm with a standard deviation of 6 nm (n = 15), which is close to the design length of ∼205 nm. EDX analysis of the structure showed the presence of Au. Choice of Second Metal. Two metals, copper and nickel, were considered for use as the second metal in the heterogeneous metal junction. Both of these metals are considerably more active than gold and thus provide increased versatility. For example, we recently demonstrated the galvanic displacement of these two metals to form DNA-templated Te and Bi2Te3 nanowires.5 Our previous work with these metals on DNA templates was performed on SiO2 surfaces that had been passivated with a hydrophobic alkylsilane.5 Because passivating layers were not used in this study, the surfaces were tested in the electroless plating baths to make sure that they were stable (did not plate) in the absence of seed particles. It was found that nickel was not stable without the passivating silane layer, whereas the copper plating solution remained stable. Consequently, copper was chosen as the second metal for the junction targeted in this study. Seeding for Cu Deposition. Although we recognized that we would almost certainly need to protect the gold surface from further metal deposition, it was hoped that a different seed material would provide some selectivity. Consequently, copper deposition on both silver- and gold-seeded samples was

investigated. After seeding with either silver or gold, the origami samples were exposed to the copper plating bath. AFM images of samples taken before and after exposure to the plating bath showed no significant plating as evidenced by no significant change in height for either type of seed particle (Figure S1 in Supporting Information). These results were unexpected because we had previously plated gold successfully on both Au and Ag nanoparticles with the use of a modified commercial gold plating solution.4 When we considered potential causes for the lack of Cu deposition on the Au or Ag nanoparticles, we concluded that the DNA strands attached to the surface of the nanoparticles were the most likely possibility (Figure 3). To test this hypothesis, we introduced our gold-plated origami samples, which did not have DNA attached to the exposed surface of the gold, into the copper plating bath. We found that copper readily deposited on the gold surfaces, causing a substantial change in the size and morphology of the initial structures. In addition, EDX analysis confirmed the presence of copper. Finally, we exposed the gold-plated structures to the same thiolated DNA strands used to attach to the Au and Ag nanoparticles (Materials and Methods section). After coating with DNA, we introduced the gold samples into the Cu plating bath and found that the size and morphology of the samples did not change (Figure 4), indicating that no plating occurred. There was also no evidence of Cu on the surface in EDX 1136

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measurements. Apparently, the bath that we prepared for copper plating was not able to plate with DNA on the surface whereas the commercial plating bath used for gold was able to do so. The difference in the success of the two baths is most likely due to an additive in the commercial bath. Similar behavior was observed previously with the electroless plating of gold where it was necessary to plate initially with a commercial bath prior to switching to another bath that provided improved plating morphology.4 Because nanoparticles functionalized with DNA strands were not suitable for seeding electroless copper deposition from our current bath, an alternative method of seeding was sought. Geng et al. recently demonstrated copper deposition on origami templates ionically seeded with palladium,2 and a similar procedure was used to seed the remaining half of the template in this study. Previous experiments with the ionic seeding of palladium revealed no visible difference between seeding on origami structures that had extended strands for sequence-specific attachment and those that did not.24 Therefore, we were able to use the same origami template, which had additional GTGCGTGT strands that were originally designed for the sequence-specific attachment of nanoparticles. Figure 5 shows a comparison of the height of the DNA origami before and after palladium seeding for samples where gold has already been deposited on half of the origami template. Pd seeding changed the average height of the unplated DNA to 2.8 nm (standard deviation = 0.5 nm, n = 10), consistent with the values reported by Geng et al.2 The image is saturated in order to highlight the change on the unplated section of the origami. Samples seeded with palladium by this process readily plated when introduced into the Cu plating bath. Note that the modification of the plating bath to facilitate Cu deposition on DNA-coated surfaces was not attempted in this study and is an area for future work. Protecting Gold-Plated Structure with an Organic Layer. With a suitable method of seeding samples for copper deposition, the next challenge was to find a way to restrict copper deposition to the second half of the template. Unfortunately, the difference between the rate of copper deposition on gold and that on palladium was not sufficient to provide the needed selectivity. Consequently, it was necessary to mask the existing gold-plated section of the bar in order to deposit Cu selectively on the remaining part of the template. The potential effectiveness of a masking monolayer was demonstrated inadvertently by the DNA-coated surface described above, which was resistant to the electroless plating of copper. However, DNA strands are not a viable material for masking gold because palladium ions interact with DNA bases during seeding to form a Pd seed layer. This seed layer would facilitate copper deposition onto the gold that we are trying to protect (Figure S2 in Supporting Information). Self-assembled monolayers (SAMs) of n-alkanethiol have been shown to protect Au substrates from reacting in aqueous Br− solutions.25 Consequently, we explored the possibility of masking gold-plated origami with octadecanethiol (C18−SH) to prevent copper deposition on gold during the second plating step. Gold-plated origami samples were reacted with octadecanethiol (Materials and Methods) and introduced into the copper plating bath to determine if the surface layer formed on the gold would prevent additional plating on the gold. No change in the size and morphology of the samples was observed, indicating that no plating occurred (Figure 6). There was also no evidence of Cu on the surface in EDX

Figure 6. (A) SEM image of Au-plated T-shaped DNA. (B) EDX analysis performed on the DNA in A using a spot scan. (C) SEM image of Au-plated T-shaped DNA plated with copper. (D) EDX analysis performed on the DNA in C using a spot scan. (E) Au-plated T-shaped DNA masked with octadecanethiol and exposed to copper plating solution. (F) EDX analysis performed on the DNA in E using a spot scan. The scale bars are 200 nm.

measurements. “Blank” origami templates were also exposed to the octadecanethiol solution prior to seeding and metallization, and the solution did not appear to affect subsequent processing steps adversely to any appreciable extent. It was observed, however, that the substrate surface was less hydrophilic after exposure to octadecanethiol, as evidenced by the interaction of the substrate with the aqueous processing solutions; again, this did not appear to affect the subsequent metallization of the DNA origami templates for samples that had not previously been plated. Following these initial tests, gold-plated bar origami samples were immersed in 2 mM octadecanethiol solution for 24 h. No obvious changes in the origami shape, size, or density on the surface were observed by AFM (Figure S3 in Supporting Information). However, the contact angle between subsequent seeding and plating solutions and the surface did change significantly. Even so, the large volume of liquid used for seeding and plating relative to that used for the DNA origami ensured complete coverage of the samples (Materials and Methods). Fabrication of the Final Junction. Now that a method for masking the gold had been identified, the DNA bar templates upon which gold had previously been deposited were masked with octadecanethiol, seeded with palladium ions, and introduced into the copper plating solution. Figure 7 shows SEM images of samples after 2 min of electroless copper plating, the last step in the formation of the desired Au−Cu 1137

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in each image consists of smaller grains that were plated much more unevenly and, in general, more heavily than the left side. EDX analysis was performed on the two different sections and showed that the left side was indeed gold and the right side was copper (Figure 7G,H). The size and continuity of the copper section of the structures was in all cases less uniform than the gold. In fact, some copper structures appeared to be overplated (Figure 7A) whereas others appeared to be discontinuous (Figure 7E) or shorter (Figure 7F) than the design length of ∼200 nm. Some of the shorter structures may have resulted from the presence of bends in the origami template. The electroless copper-plating reaction was fast as evident from the visual change in the surface to brown after ∼1 min in the plating bath; however, samples were kept in the bath for 1−3 min to facilitate continuous plating. The images and the composition data establish the successful fabrication of Au−Cu metal junctions on the DNA template. There is, however, opportunity to improve the morphology and continuity through the optimization of electroless copper deposition and, to a lesser extent, the electroless deposition of gold. Uneven Copper Deposition. The samples shown in the previous section were from the center portion of the substrate where distinct gold and copper deposition were evident. We also observed that there were areas on the substrate surface with little or no copper deposition and areas with heavy copper deposition as shown in Figure 8. Almost no copper deposition was observed in the center of the substrates (Figure 8A), where only the gold-plated structures that had been deposited prior to copper deposition were observed. In contrast, substantial nonselective copper deposition was observed around the edges of the substrate (Figure 8C). In between, we observed the successful formation of the targeted heterometal junctions as well as some nonselective copper deposition. The images shown (Figure 7) of metal junctions in the DNA template were from the middle region. The copper deposition time was varied between 1 and 3 min and did not appear to change the observed nonuniform distribution of copper, which remained similar to that shown in Figure 8. To understand the above observations further, a series of full surface experiments without DNA origami were performed to test the variability of the copper deposition on the substrate. To test for the impact of the octadecanethiol exposure step on the background deposition of copper, several SiO2 substrates were immersed in the octadecanethiol solution overnight and then seeded with palladium and plated with copper. Results from these substrates were compared to results from substrates seeded with palladium and plated with copper but without the octadecanethiol step. It was observed that the background deposition of copper increased substantially as a result of the

Figure 7. (A−F) SEM images of the Au−Cu junction on bar origami. (G) EDX analysis using the spot scan on left section of the origami. (H) EDX analysis using the spot scan on the right section of the origami. The scale bar is 200 nm.

junction. Two distinct morphologies are evident in the images. The section on the left of each image consists of larger distinct grains whose morphology is similar to that observed previously for gold (e.g., Figure 2D). In contrast, the section on the right

Figure 8. (A) Section of the substrate with no copper deposition. (B) Section of the substrate with gold and copper structures. (C) Section of the substrate with heavy copper deposition. The scale bar is 500 nm. 1138

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nanosystems. Toward this end, we recently demonstrated the formation of Te and Bi2Te3 segments on DNA templates by the galvanic displacement of metals that had been previously deposited onto the templates.5 The combination of metal deposition and galvanic displacement is an example of compatible processes that exploit the molecular recognition properties of the template for sequential and/or parallel deposition of multiple materials onto single DNA templates. Significant effort is needed to develop such processes in order to enable the molecularly directed assembly of future devices based on engineered DNA templates.

overnight octadecanethiol treatment (Figure S5 in Supporting Information). The experiments just described showed an increased background deposition of Cu due to treatment of the surface with octadecanethiol; however, that background deposition occurred uniformly over the entire surface. In contrast, nonuniform copper deposition was observed for origami that had been partially plated when gold was present on the surface. To explore the impact of gold, SiO2 substrates (without DNA origami) were seeded with Au NPs using the same procedure used previously to seed the DNA origami. Next, these particles were plated with gold for 1 min. The substrates were then immersed in octadecanethiol solution overnight and subsequently seeded with palladium and plated with copper. The results showed the same type of nonuniform deposition that was observed earlier with the DNA templates (Figure S6 in Supporting Information). Almost no copper deposition was observed toward the center of the substrate (compare to Figure 8A), whereas heavy deposition of copper around the edges was observed (compare to Figure 8C). Additional experiments were performed to investigate the cause of the nonuniform copper plating (Table S1 in Supporting Information). Although the precise mechanisms are not understood, it was found that the nonuniform copper plating occurred when gold was present on a surface that was subsequently exposed to octadecanethiol. The hydrophobic nature of the C18 is believed to be a primary factor in the nonuniform deposition. Our success rate for gold deposition onto half of the origami bar templates was close to 100%, and the resulting gold structures were continuous and consistent with our design parameters. Copper deposition was less consistent as shown in Figure 7, and optimization of the copper morphology is needed. Nonuniform Cu deposition on the substrate surface makes it difficult to quantify our rate of success for copper deposition on the origami templates. However, in the middle region where copper plating was possible without high background deposition, we were able to form heterogeneous Au−Cu metal structures successfully on DNA origami templates by taking advantage of site-specific metal deposition. To conclude, the fabrication of a Cu−Au metal junction on a single DNA origami template was successfully demonstrated. Specifically, we were able to direct copper and gold to predesignated locations on a template designed for this study, as verified by both compositional and morphological data. To our knowledge, this is the first demonstration of a dissimilar metal junction on a DNA origami template. In addition to the successful fabrication of the structure itself, the use of an organic layer or chemical mask to prevent unwanted deposition during the metallization is another important aspect of this work. In light of recent efforts in the field, the ability to localize components of different composition and structure to specific sections of a DNA template represents an important step forward in the fabrication of nanostructures based on DNA templates. We envision that the work demonstrated here for metal− metal junctions includes specific applications for devices such as thermocouples. More importantly, the general approach demonstrated in this work can be used for the site-specific deposition of a much broader set of materials including semiconductors, energetic materials, and perhaps even structural materials to enable circuits, sensors, energy storage, and mechanical components for hybrid DNA-templated

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MATERIALS AND METHODS

Materials. M13mp18 DNA was purchased from New England Biolabs (Ipswich, MA). Staple strands at a concentration of 100 μM in TE (Tris-EDTA (ethylenediamine tetraacetic acid)) buffered solution for DNA origami folding were obtained from Eurofins MWG Operon (Huntsville, AL). Single-stranded DNA functionalized with thiol to enable attachment to metal nanoparticles was also purchased from Eurofins MWG Operon with PAGE purification and diluted to 1 mM in water. PCR primers to make scaffolds for DNA origami were also ordered from Operon. PCR purification kits were acquired from Qiagen (Valencia, CA). DNA polymerase and PCR buffers were purchased from either Invitrogen (Grand Island, NY) or New England Biolabs. TAE-Mg2+ buffer (1X) was made from 40 mM Tris base, 20 mM acetic acid, 1 mM EDTA, and 12.5 mM magnesium acetate (MgAc2·4H2O). BSPP (bis-sulfonatophenyl phenylphosphine dehydrate dipotassium salt) for concentrating the gold nanoparticle solution was obtained from Strem Chemicals (Newburyport, MA). Gold nanoparticles (Au NPs, 5 nm) were obtained from Ted Pella (Redding, CA). Amicon ultra 0.5 mL centrifugal filters (30 kDa) were obtained from Millipore (Billerica, MA). NH4Cl was obtained from EM Science (Gibbstown, NJ). MgCl2, MgAc2, and acetic acid were obtained from EMD Chemicals (Gibbstown, NJ). HEPES (4-(2hydroxyethyl)-1-piperazineethanesulfonic acid), KNaC4H4O6·4H2O (99.0%), CuSO4·5H2O (99.1%), HCHO (37.4%), and boric acid were purchased from Mallinckrodt Baker (Phillipsburg, NJ). NaOH (97%) was obtained from Spectrum Chemical Mfg. Corp (New Brunswick, NJ). Ethyl alcohol (200 proof) was purchased from Decon Laboratories, Inc. (King of Prussia, PA). PdCl2, DMAB (dimethylamine borane), 1-octadecanethiol, and methanol (99.9%) were purchased from Sigma-Aldrich (St. Louis, MO). Tris base (tris(hydroxymethyl)aminomethane) was obtained from Fisher Scientific Inc. EDTA was obtained from Life Technologies (Carlsbad, CA). Gold plating solution (GoldEnhance EM, catalog no. 2113) was obtained from Nanoprobes (Yaphank, NY). Water (18.3 MΩ cm) treated with an EASYPure UV/UF purification system was used for all rinsing and aqueous solution preparations. Bar Origami Design. Of the 7249 bases in M13mp18 scaffold, a total of 7085 bases were used to produce a bar-shaped structure with a length of 410 nm and a width of 6 helices (∼17 nm). This left a short tail of unfolded scaffold at the end of the origami. Staple strands were modified to contain an additional length of nucleotides on the 3′ end to enable the site-specific attachment of nanoparticles as metal seeds. Staple strands used to assemble the bar origami were modified with a sequence of 10 adenine nucleotides on one-half of the bar and a GTGCGTGT sequence on the other half of the bar. Specific staple strand sequences are included in the Supporting Information. Additional Origami. T-shaped origami from a previous study was also used in this study for screening experiments.4,10 This origami utilizes a 2958-base scaffold amplified from M13mp18. For Au NP attachment, staple strands in the origami were modified to contain a sequence of 10 adenine nucleotides on the 3′ end. Only the top section of the T shape (67 strands in total) was modified. Hence, seeded and metallized samples appear as bar shapes that are approximately 240 nm in length. DNA Origami Folding. T and bar structures were made by heating a mixture of the scaffold and staple strands (2 nM scaffold and 1139

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reduction to form seeds. For activation, 20 μL of Pd(II) solution (1 mM PdCl2 and 1 M NH4Cl in HEPES buffer, pH 6.5) was pipetted onto the surface upon which DNA origami templates had been previously deposited and was left to stand for 1 h in a humid chamber at room temperature. Compared to the palladium activation time (about 3 h) in the literature, the activation time was shortened to ∼1 h because that time was adequate for our experiments. Next, the liquid on the surface was removed using a spin coater by rotating at 1200 rpm for 12 s. Then, 20 μL of reducing agent (40 mM DMAB) was pipetted onto the activated DNA samples and allowed to react for 1 min. The reaction was quenched by rinsing the samples with 4 mM MgAc2 for 3 to 4 s, followed by rinsing with water for 1 to 2 s and drying with air. The seeding process was repeated three times to ensure larger seed sizes and a sufficient number of seeds on the DNA origami. Electroless Au Plating. Gold plating solution was prepared according to the manufacturer’s instructions. To this mixture, an equal volume of 10 mM MgCl2 was added to stabilize DNA origami under the plating solution. Plating was done by putting 40 μL of plating solution onto a SiO2 sample surface at room temperature. The plating was allowed to proceed for 1 min. The plating solution covered the entire area of the hydrophilic substrate. The sample was then rinsed with 4 mM MgAc2 solution for 3 to 4 s and then with water for 1 to 2 s and finally dried with a stream of filtered air. Electroless Cu Plating. The electroless copper plating solution26 consisted of 5 g/L CuSO4, 25 g/L KNaC4H4O6·4H2O, 7 g/L NaOH, and 10 g/L 37 wt % HCHO. Plating was done by putting 70 μL of plating solution onto a sample surface at room temperature for 2 to 4 min. The sample was then rinsed with 4 mM MgAc2 solution for 3 to 4 s and with water for 1 to 2 s. Following rinsing, the sample was dried with a stream of filtered air. AFM Imaging. The samples were imaged using tapping mode on a Digital Instruments Nanoscope IIIa MultiMode AFM (Veeco) with aluminum-coated conical silicon tips (Vistaprobes, 3 N/m, 45−75 kHz). Aluminum-coated tips have a thin film of aluminum on the back side that helps increase the reflection of the laser in the AFM. SEM Imaging. The DNA samples on the SiO2 surfaces were imaged in high-vacuum mode on a Philips XL30 ESEM FEG. EDX analysis was also performed with the same instrument.

20 nM for each staple strand in 1 X TAE-Mg2+ buffer) to 95 °C for 3 min and then slowly cooling to 4 °C over 90 min in a TECHNE TC3000 thermocycler. Au NP Preparation. This procedure was similar to that previously reported by Pearson et al.4 Au NPs were first phosphinated and concentrated with BSPP. To do this, 1.5 mg of BSPP was added to 5 mL of Au NP solution as received and shaken overnight. The nanoparticles were precipitated by adding 100 mg of NaCl to the reaction mixture until the color changed from red to dark red/purple. The solution was centrifuged to separate the nanoparticles, and the supernatant was removed. Au NPs were then resuspended in 100 μL of a 2.5 mM aqueous BSPP solution. Methanol (100 μL) was added to the solution until the color changed to dark purple/brown, at which point the mixture was centrifuged to separate the Au NPs. Au NPs were again suspended in 100 μL of a 2.5 mM aqueous BSPP solution. The concentration of Au NPs was then estimated with a Nanodrop 1000 spectrometer using the absorption at 520 nm. Au NP−DNA Conjugates. Au NPs treated with BSPP and thiolated DNA in water were combined in a 1:200 concentration ratio and left to react at room temperature for at least 19 h. The Au NP DNA conjugates were filtered using 30 kDa Amicon filters to remove unbound thiolated DNA. Samples were rinsed twice using 450−500 μL of 0.5 X TBE (44.5 mM Tris base, 44.5 mM boric acid, 1 mM EDTA) buffer during filtration. About 40 μL of Au NP-DNA conjugates in 0.5 X TBE buffer was recovered with a concentration of around 1−3.5 μM. Depositing DNA Origami on SiO2 Surfaces. The procedure used in this study is similar to that previously reported in the literature.11 Silicon dioxide surfaces were plasma cleaned (Harrick Plasma Asher, PDC-32G) for 30 s at 18 W to remove impurities on the surface. DNA origami (3 μL, 0.22 nM) in 10× TAE−Mg2+ buffer was allowed to absorb onto the cleaned surface (roughly 1 cm × 1 cm) for 15 min in a humid chamber at room temperature. Because the plasma-cleaned substrates are hydrophilic, 3 μL of origami solution spreads over the entire surface area of the wafer. The sample was then rinsed with 4 mM MgAc2 solution for 3 to 4 s and water for 1 to 2 s. Finally, the surface was dried with a stream of filtered air and imaged in an AFM. Seeding with Au NPs. A seeding solution (12 μL, 2 nM Au NP− DNA conjugates in 10× TAE−Mg2+ buffer) was pipetted onto the SiO2 surface with DNA origami and allowed to seed DNA by complementary base pairing for 40 min at room temperature in a humid chamber. The seeding solution covered the entire surface area of the substrate. The sample was then rinsed with 4 mM MgAc2 solution for 3 to 4 s, followed by rinsing with water for 1 to 2 s. After being rinsed, the sample was dried with a stream of filtered air. Surface Masking with Octadecanethiol. Octadecanethiol was used to make an organic layer on the surface of the metals present to inhibit further plating. To do this, a 2 mM octadecanethiol solution in 100% ethanol was prepared. Plasma-cleaned silicon substrates (roughly 1 cm × 1 cm) with metallized DNA origami were placed inside a glass vial, and sufficient octadecanethiol solution was added to cover the surface of the wafer. The glass vials were kept at room temperature for about 24 h. During this time, the thiolated end of octadecanethiol binds to form an organic layer on the surface of the metals present. The samples were then rinsed with ethanol and air dried. Surface Masking with Single-Stranded Thiolated DNA. Thiolated DNA strands were also used to make an inhibition layer on the surface of the gold-plated DNA structure. DNA solution (12 μL, 0.4 μM in water) was pipetted onto the silicon surface with DNA origami and allowed to react for 5 h at room temperature in a humid chamber. During this time, the thiolated end of DNA binds to form a layer on the surface of the gold attached to the origami. The solution covered the entire surface area of the substrate. The sample was then rinsed with 4 mM MgAc2 solution for 3 to 4 s, followed by rinsing with water for 1 to 2 s. After being rinsed, the sample was dried with a stream of filtered air. Seeding with Palladium. The procedure used in this study was modified slightly from that reported previously in the literature.2 The seeding step consisted of activation with palladium solution and

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ASSOCIATED CONTENT

S Supporting Information *

AFM images of gold-seeded origami before and after copper plating, SEM images of gold-seeded origami masked with a thiolated layer and plated with copper, AFM images of goldplated origami before and after 24 h in C18 solution, additional SEM images of the Au−Cu junction, AFM and SEM images of the increased background due to octadecanethiol treatment, SEM images of uneven copper plating on SiO2 surface without DNA origami, and a summary of different control experiments and DNA staple strand sequences. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We gratefully acknowledge funding from the National Science Foundation (CBET-0708347), Brigham Young University and the Semiconductor Research Corporation (2013-RJ-2487). We also thank Jianfei Liu, John Hickey, Nitesh Madan, John S. Gardner, and Michael Standing for their help and valuable insights. 1140

dx.doi.org/10.1021/la403617r | Langmuir 2014, 30, 1134−1141

Langmuir

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Article

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dx.doi.org/10.1021/la403617r | Langmuir 2014, 30, 1134−1141