Bottom-up Nanofabrication Using DNA Nanostructures - Chemistry of

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Bottom-up nanofabrication using DNA nanostructures Zhenbo Peng, and Haitao Liu Chem. Mater., Just Accepted Manuscript • DOI: 10.1021/acs.chemmater.5b04218 • Publication Date (Web): 06 Jan 2016 Downloaded from http://pubs.acs.org on January 12, 2016

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Chemistry of Materials

Bottom-up nanofabrication using DNA nanostructures Zhenbo Peng1,2 and Haitao Liu2* 1

Chemical Engineering College, Ningbo Polytechnic, 1069 Xinda Road, Economical & Technical Development Zone, Ningbo, 315800, P. R. China 2 Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, Pennsylvania, 15260 USA ABSTRACT: DNA nanostructures are ideal templates for bottom-up assembly and fabrication of nanomaterials. Their structures can be tailored for a given application and modified with pin-point precision. They offer the best of top down and bottom up assembly. We highlight recent progresses in DNA nanotechnology and in particular advances that are relevant to materials chemistry community. Examples of using DNA nanostructure to address materials chemistry challenges are highlighted.

Introduction. The past 10 years have witnessed a tremendous growth in the field of DNA nanotechnology. First pioneered by Seeman in the 1980s,1,2 the idea of using DNA to form well-defined structures has now become a broad research topic impacting biology, materials, photonics, and nanofabrication. Among many other advances, the landmark work by Rothemund in 2006 transformed the field by offering highly complex, tunable, and addressable DNA origami nanostructures.3 A key enabling feature of DNA nanostructure is the possibility to program its shape and to position molecules and nanoscale objects within itself with nanometer scale precision. Even compared with traditional top-down processes, such as photolithography, DNA nanostructure can already offer comparable or even higher spatial resolution. An additional benefit of using DNA nanostructure lies in the easy of materials integration, due to the presence of individually addressable DNA strands within the nanostructure. Once modified with a single DNA strand, small molecules, biomolecules, polymers, and inorganic nanoparticles can all be positioned on a DNA nanostructure with precise control of their location. The ability to program shape and address arbitrary part of the nanostructure is also unparalleled among all selfassembled nanostructures. Most bottom-up assembled nanoscale structures, such as phase separated block copolymers, micro/nanocrystal super-lattices, and virus particles, only offer limited design space in terms of the morphology they can offer. With the exception of virus particles, it is not possible to pinpoint chemical modification on these nanostructures. The unique benefits offered by DNA nanostructure do come with a huge price tag. The size and complexity of a DNA nanostructure is directly correlated with the number of DNA

strands used in its construction. It is common to use several hundreds and even thousands of unique DNA strands to produce a 2D DNA nanostructure about 100 nm in size. A larger DNA nanostructure will require proportionally large number of unique DNA strands. Such a requirement makes DNA nanostructure extremely expensive and also created a perceived barrier in adopting DNA nanostructure for materials research. It is worth pointing out that for applications in surface patterning, the cost of DNA nanostructure is in fact not a concern. In theory, only a monolayer amount of 2D DNA nanostructure is needed for surface patterning. It has been estimated that the cost of DNA template can be as low as $6/m2.4 On the other hand, the DNA nanotechnology community is also developing ways to mass-produce DNA nanostructures using biological machineries in bacteria and virus.5,6 It is conceivable that grams or even larger quantities of DNA nanostructures can be produced this way at much reduced cost. Below we highlight some recent progresses in DNA nanotechnology and in particular, the ones that are relevant to material chemistry research community. Examples of using DNA nanostructure to address challenges in materials research are discussed. Due to space limitation, we will not discuss research effort in using DNA nanostructure for applications in biology or therapeutics. This perspective is not a comprehensive review but rather an introduction of DNA nanotechnology and how it may benefit material chemists. The readers are suggested to refer to several recent focused reviews on the self-assembly of DNA nanostructures7-13 and their applications in photonics,14,15 therapeutics,16,17 nanofabrication,18-20 and mechanics.21 1. Fabrication of DNA nanostructures.

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Figure 1. Scaffold-free construction of 2D and 3D DNA nanostructures. (A) Structure and assembly of SSTs and their assembly to form 2D nanostructures. (B) AFM images of folded structures. The size of each image is 150 nm x 150 nm. Reprinted by permission from Macmillan Publishers Ltd: Nature 2012, 485, 623. Copyright 2012. (C) Structure and assembly of SSTs and their assembly to form DD nanostructures. (D) 3D model, expected 2D projection, and transmission electron micrograph (TEM) image of 3D DNA nanostructures. Reprinted by permission from Science 2012, 338, 1177. Copyright 2012.

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In 2006, Rothemund demonstrated that DNA nanostructures having well-defined shapes could be made by repeated folding of a long (ca. 7k bases) single-stranded DNA (also known as scaffold) with hundreds of short (ca. 30 – 40 bases) synthetic single-stranded DNA (also known as staple strands).3 These DNA nanostructures, also called DNA origami, are 2 dimensional objects about 100 nm in size. Several research groups have released freely available computer programs to facilitate the design of these DNA origami structures.22-24 Although hugely successful (over 2600 citations in less than 10 years), the original DNA origami approach does have its limitations, most significantly, the size of the nanostructure is limited by that of the scaffold. With the popular M13mp18 scaffold, the size of the origami is ca. 100 nm. While some studies have explored alternative scaffold strands in an effort to produce super-sized origami structures,25-27 others have explored alternative assembly concepts and we briefly review them below. 1.1 Scalable, scaffold-free construction of DNA nanostructures. A key component of DNA origami structure is the scaffold strand that runs through the whole structure. From its name, one may assume that a scaffold strand is required to hold the staple strands together. Large nanostructure will naturally require a longer scaffold strand. The availability of a suitable scaffold strand will limit the size of the nanostructure one can make. Yin and coworkers recently showed that DNA nanostructures could be constructed without a scaffold strand.28 In their approach, a DNA nanostructure is fabricated from many ‘single-stranded tiles’ (SST) that are each 42 bases long. A key concept is that each SST only hybridizes with its nearest neighbors (Figure 1A). Thus each SST can be viewed as a ‘pixel’ and the location of each ‘pixel’ is encoded in its sequence. Therefore, a collection of distinct SSTs will assemble into a desired 2D shape by designing their inter-connectivity (Figure 1B). This approach does not require a scaffold strand and therefore can be scaled up in size by increasing the number of SSTs in the structure. This SST concept has been further developed by other group to prepare ring structures.29 The same group later used the SST approach to construct 3D DNA objects. In this case, the basic constructing unit is a 32 bases single strand tile that has four 8-strand binding domain.30 In the 2D assembly, all SSTs are in the same plane after hybridization with their nearest neighbors. To enable 3D assembly, the new SSTs were designed such that they are perpendicular to each other after the hybridization (Figure 1C). This new geometry provides connectivity between the layers to enable assembly of 3D objects. Using ca. 1000 SSTs, the group demonstrated the fabrication of various 3D objects that are ca. 25 nm x 25 nm x 27 nm in size (Figure 1D). Using the 32 base pair, 4 domain strands, the theoretical size limit for the nanostructure is 524,288 strands, or a cube of ca. 160 nm in each dimension. In reality, the yield begins to drop significantly at much smaller strand pools (e.g. 24,576), likely due to kinetics and defects. The SST approach can be used to prepare super-lattices by using two or more sets of SSTs structures that can bind each other. During annealing, the SSTs polymerize to form extended structures.31 Both extended 1D and 2D structures have been demonstrated.

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Figure 2. Assembly of DNA polyhedra. (A) Design of a tripod. (B) Connection between tripods. (C) Connection scheme for assembling a tetrahedron. (D) TEM image of assembled DNA tetrahedron, triangular prism, and cube. Adapted with permission from Science 2014, 344, 65. Copyright 2014.

1.2 Assembly of DNA nanostructures. An alternative approach to access large DNA nanostructure is to assemble preformed, smaller nanostructures into a super-structure. Such assembly can be achieve by programming the interaction between DNA nanostructures, through base-pairing or other none-covalent interactions. Base-paring mediated assembly. Perhaps the most straightforward approach to assemble DNA nanostructures is by baseparing. In this case, the DNA nanostructures are constructed with sticky ends to enable interconnect.32,33 Yin and coworkers fabricated large scale DNA polyhedra from pre-assembled DNA tripods.33 These DNA tripods were prepared using the origami approach and assembled using multiple 30 base pairs ‘connector’ strands (Figure 2A-B). Each connector strand has a 28 base pair portion on one tripod and 2 base pair on the other. By adjusting the inter-arm angle, a variety of polyhedra can be assembled (Figure 2C-D). Non-base-pairing mediated assembly. Rothemund and coworker showed that DNA nanostructure could be assembled through attractive base stacking interaction between bluntends (i.e., the termini of a DNA duplex.34 The location of the blunt-ends were geometrically encoded into the edges of 2D DNA origami structures; structures with complementary shape can recognize each other and form super-structures (Figure 3A). Using a similar principle, Dietz and co-workers recently demonstrated assembly of 3D DNA nanostructures.35 In this case, the interaction between DNA nanostructures mimics that

Figure 3. (A) Recognition based on blunt-end interactions. The diagram shows a DNA nanostructure with geometrically encoded blunt-ends on the edge: 1 and 0 indicate presence and absence of blunt-ends, respectively. The AFM image shows a linear chain produced by assembly of DNA nanostructure units. Adapted with permission from Nature Chem., 2011 3, 620, (B) Using shape complementarity to direct 3D DNA assembly. DNA domain protrusions and recessions are highlighted in red and blue, respectively. The images are average negative stained TEM micrograph of the assembled super-structure. Scale bar: 20 nm. Adapted with permission from Science, 2015, 347, 1446.

between Ribonuclease P and pre-transfer RNA (Figure 3B). Large-scale DNA nanostructure assemblies, in one case up to 14 microns long, were fabricated. More interestingly, dynamic structures that respond to the ionic strength of the solution can also be made in this way. Combining the base-paring and non-base-paring strategies, Endo and Sugiyama demonstrated an assembly of DNA nanostructures using DNA ‘jigsaw’ pieces.36 The jigsaw pieces recognize each other through matching convex connectors and

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Figure 4. (A-B) AFM images of DNA 2D array produced by surface-mediated assembly. Adapted with permission from J. Am. Chem. Soc., 2009, 131, 13248. (C-D) AFM images + of origami checkboard lattice produced by Na -assisted surface diffusion and assembly. The origami units interact through blunt-end interactions. Adapted with permission from Nature Comm. 2014, 5, 4889. (E-F) AFM images of rectangular DNA origami tile (E) in the absence of NaCl and (F) in the presence of 200 mM NaCl. The insets are the Fourier transforms of the image. Adapted with permission from Angew. Chem. Int. Ed. 2014, 53, 7665.

concavities. The jigsaw assembly is mediated by a combination of base-paring and non-base-pairing interactions. Large scale, complex 2D patterns can be achieved through this approach.37 Surface-mediated assembly. For surface patterning, it is often desirable to created deterministic deposition or closepacking structure on a solid substrate. The deposition of DNA nanostructure onto mica and SiO2 substrates are mediated by Mg2+ ion, which serves as a salt bridge.38 In an early study, Mao and coworkers showed that the strong interaction between DNA and the substrate can be exploited for selective formation of DNA super-lattice on a mica substrate (Figure 4 A-B).39 However, for pre-formed DNA origami structures, the strong ionic interaction makes the deposited DNA nanostructure immobile and therefore the deposition is random. Deterministic deposition of DNA nanostructure can be achieved by using a substrate having pre-defined hydrophilic binding

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pockets.38,40,41 Attempts have also been made to use electrophoresis to trap DNA nanostructures.42 Rothemund and Simmel groups recently showed that by introducing Na+ ion, the surface mobility of DNA nanostructure can be greatly increased.43,44 This approach was used to produce DNA nanostructure assemblies with designed connectivity (Figure 4 C-D) or close packed super-lattices (Figure 4 EF). Although not been demonstrated yet, this approach has the potential to produce large-scale super-lattice of DNA nanostructures, which will be useful for lithographic patterning of surfaces. As an alternative to using solid substrate, DNA nanostructures, either used as is or after modification with cholesterol molecules, can be adsorbed onto a supported lipid bilayer.45-48 The liquid bilayer support offers the DNA nanostructure high mobility and dynamics of assembly/disassembly can be visualized by using a high-speed atomic force microscope (AFM) or a fluorescence microscope. 2. DNA-based assembly of molecules and nanomaterials. As highlighted in the introduction, one of the most unique and powerful features of DNA nanostructure is its ability to position molecular and nanoscale objects with high spatial precision. Such a capability is much needed in addressing many fundamental science questions in charge/energy transfer, light-matter interaction, photonics, sensing, and catalysis. For example, DNA nanostructures have been used to produce ‘standard’ samples for many types of single-molecule studies.49,50 Below we highlight some of the recent efforts in this direction. 2.1 Inorganic nanomaterials. Inorganic nanocrystals can be modified with single stranded DNA on the surface and attached to a DNA nanostructure modified with complimentary DNA binding strands. Besides the DNA-based linkers, another popular choice is biotin-streptavidin combination. The relative distance between nanocrystals can be easily controlled by adjusting the location of the anchoring ligands in the DNA nanostructure. In addition to being used as a , the inorganic nanomaterial itself is used as a structural component to assemble the DNA nanostructures into 1D and 2D lattices.51 Many of the reported self-assemblies were demonstrated using gold nanocrystals, most likely due to their easy of surface functionalization and characterization. Gold nanocrystals also have interesting optical properties that are sensitive to interparticle distance and orientation. Liu and Yan groups assembled gold nanorods with defined inter-rod angles; these structures were prepared with >70% yield and exhibited tunable plasmonic properties (Figure 5A).52 Kuang and coworkers fabricated nanoparticle linear waveguide by patterning 10 nm gold nanocrystals onto a linear DNA template.53 Liedl and coworkers prepared chiral plasmonic structures by patterning gold nanocrystals into a helical pattern.54 Mao and coworkers used a DNA tetrahedron framework to build nanoparticle assemblies that resemble the topography of common molecules (Figure 5B).55,56 Gang and coworkers used an octahedral DNA wireframe structure to assemble nanoparticles of different sizes into 3D clusters and further crosslinked these clusters into 1D and 2D arrays (Figure 5C).51

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Figure 5. (A) Schematic and TEM images of DNAassembled gold nanorod dimers. Scale bars: 100 nm. Adapted with permission from J. Am. Chem. Soc. 2011, 133, 17606. (B) Schematics and TEM images of CH4-like (left) and SF6-like gold nanocrystal clusters assembled by DNA nanostructure. Adapted with permission from J. Am. Chem. Soc. 2015, 137, 4320. (C) Gold nanocrystals assembled by an octahedron DNA frame. Shown are TEM images taken at different tilting angles. Adapted with permission from Nature Nanotech. 2015, 10, 637. (D) AFM image of quantum dots assembled onto a 1D DNA origami array. Scale bar: 1 µm. Adapted with permission from Chem. Commun. 2014, 50, 3413. (E) AFM image of individual polymer chain on a DNA nanostructure. Scale bar: 200 nm. Adapted with permission from Nature Nanotech. 2015, 10, 892.

The same approach used for assembling gold nanocrystals has been applied to other types of inorganic nanomaterials,

notably semiconductor quantum dots and carbon nanotubes. Yan and Liu groups prepared many examples of such assemblies to control energy or charge transfer as well as tuning the optical properties of quantum dots.50,57-59 Rahman et al. reported the assembly of quantum dots and carbon nanotubes on linear DNA origami arrays (Figure 5D).60,61 Very recently, Zhang et al. used DNA nanostructure to assemble fluorescence nanodiamond.62 Despite these advances, an area that needs much improvement is the yield and/or accuracy. Although an assembly yield of 99% has been reported for the DNA-directed assembly of streptavidin,60 the yield of most nanoparticle assemblies were in the range of 70% to 90% or even lower.51,55 Achieving high yield, high precision assembly is the prerequisite for their future applications. Unfortunately, there has been no systematic study to understand the origin of the low yield. 2.2 Small molecules, polymers, and biomolecules. Efforts have been made to attach small organic molecules to DNA nanostructures, mostly for studies related to their emission and energy transfer properties. Yurke and Knowlton groups recently demonstrated a fluorescence-based AND logic assembled on a rectangle shaped DNA nanostructure template.63 The ability to precisely control the distance between fluorophores has lead to the fabrication of standard samples for superresolution imaging. For example, Tinnefeld group recently reported a super-resolution imaging study on DNA nanostructures having two organic dyes installed just 6 nm apart.64 Dong, Gothelf, and coworkers modified a conjugated polymer, (2,5-dialkoxy) paraphenylene vinylene, with many short DNA strands along the polymer chain.65 This DNA-modified polymer can then self-assemble into predefined routes on 2D and 3D DNA templates (Figure 5E). The photo-physics of many conjugate polymers is sensitive to their confirmation. This report is the first to demonstrate the ability to manipulate individual polymer chains over long distance. A number of studies have focused on patterning protein on a DNA nanostructure template. A particular interesting concept here is to tune the kinetics of enzymatic reactions by controlling the spatial arrangement of enzymes. For example, Yan group prepared multi-enzyme complexes to enhance coupling between enzymatic reactions, either through enhanced diffusion or using a swinging arm to transfer substrates.66,67,51,55,60 3. DNA-based nanofabrication and nanolithography 3.1 Metallization of DNA nanostructures. Solution phase metallization of DNA was first demonstrate on individual λDNA by reducing adsorbed Ag+.68 Harb, Woolley, LaBean, Finkelstein, and Leidl groups have demonstrated metallization of DNA nanostructure in a similar fashion using electroless deposition of metals.54,69,70 In particular, site-specific metallization was achieved by using DNA nanostructures decorated with metal nanocrystal seeds.71 Woolley and Harb groups recently also demonstrated a two-stage metallization process that produces an Au-Cu heterojunction.69 These metal nanostructures was shown to have good electrical conductivity and interesting optical properties (e.g. chiral plasmonic response). Metalized DNA nanostructures have also been used as a mask to pattern other inorganic materials, such as graphene and 2D transition metal dichalcogenides.72

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A major challenge in solution phase metallization has been the loss of resolution. This is because solution phase metallization typically does not produce a conformal coating of metal onto the DNA template. Instead, nanoscale metal grains with sizes around several tens of nanometers were typically produced. Such uncontrolled growth severely limits the quality of the final metal nanostructure. However, high quality, almost conformal metallization of DNA nanostructure was recently demonstrated by Strano and Yin groups.73 In their study, a thin (ca. 4 nm) layer of gold was deposited onto DNA nanostructure templates, resulting in a high quality gold nanostructure. The gold nanostructure was then used as a hard mask for patterning graphene. Sub-20 nm features were obtained in some cases. A somewhat different approach to metallization was recently explored by Yin and Bathe groups. Instead of covering DNA nanostructure with metal, they used DNA nanostructure as a container to confine the growth of metal nanoparticle. The shape of the resulting gold nanoparticle mimics that of the cavity of DNA nanostructure template. Using this approach, a high level of shape and composition control can be achieved in the metal nanostructures.74 3.2 Direct pattern transfer from unmodified DNA nanostructures. Our group recently showed that unmodified DNA nanostructure modulates both gas phase etching and deposition of inorganic oxides with high spatial resolution.

Figure 6. (A) AFM images of (left) DNA triangle nanostructure template, (middle) negative-tone pattern transfer to SiO2 through DNA-enhanced HF etching of SiO2 in a high relative humidity environment, and (right) positive-tone pattern transfer to SiO2 due to a slowing down of HF etching of SiO2 by DNA at low relative humidity environment. Reproduced with permission from J. Am. Chem. Soc. 2011, 133, 11868. (B) AFM images of (left) DNA triangle nanostructure templates, (middle) negative-tone pattern transfer due to selective deposition of SiO2 on SiO2 surface., and (right) positive-tone pattern transfer due to selective deposition of SiO2 on DNA nanostructures. Adapted with permission from J. Am. Chem. Soc. 2013, 135, 6778.

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Nanoscale wetting plays a key role in the pattern transfer process and is briefly discussed here. When deposited onto a solid substrate, the presence of DNA can change the amount of adsorbed water from the gas phase. For example, DNA can absorb more than 100% (w/w) of water at high humidity levels, much more than pristine SiO2 surface does. However, at very low humidity level, SiO2 retains more water than DNA does.75 Therefore, if a vapor phase reaction is sensitive to the amount of adsorbed water, the reaction rate can be modulated with high spatial resolution and the selectivity can be controlled by relative humidity. In an early demonstration of this concept, we showed that a DNA nanostructure can modulate the vapor phase HF etching of SiO2 to produce either positive-tone or negative-tone pattern transfer, depending on the reaction conditions.75 The vapor phase HF etching of SiO2 is catalyzed by water and therefore, if DNA nanostructures adsorb more water than the SiO2 substrate, the SiO2 underneath DNA will be etched faster than the rest of the substrate. Under such a condition, a negativetone pattern transfer is achieved. If the presence of DNA does not enhance water adsorption, a positive-tone pattern transfer is produced instead (Figure 6A) With a careful optimization of reaction conditions, lateral linewidth (full width at half max) as small as 15 nm can be achieved; in addition, even a single strand of DNA is shown to produce a pattern, suggesting an ultimate lateral resolution of less than 5 nm might be possible.76 This wetting mediated HF-etching reaction can be applied to a wide range of nanoscale templates, such as carbon nanotubes, graphene oxide, peptides, and inorganic salt particles.77 The same mechanism can be applied to chemical vapor deposition of metal oxide materials.78 In this case, the watersensitive reaction is the hydrolysis of a suitable metal oxide precursor. For example, the hydrolysis of Si(OEt)4 can be carried out at room temperature when using NH3 as a catalyst. The reaction rate will be positively correlated with the amount of water adsorbed on the surface. By controlling the adsorption of water, we demonstrated both positive-tone and negative-tone deposition of SiO2 with sub-50 nm lateral features (Figure 6B).78 Using the negative-tone SiO2 pattern as the mask, Toppari, Kostiainen, and coworkers recently fabricated metal nanostructures using metal evaporation followed by liftoff.79 Very recently, we showed that unmodified DNA nanostructures could mask the deposition of organic silanes from the gas phase. As a result, the presence of DNA nanostructure on a SiO2 substrate blocks the formation of silane self-assembled monolayer (SAM) underneath it. Lifting-off the DNA templatee produced negative-tone patterns in the SAM, with a lateral resolution of sub-50 nm.80 3.3 Application of DNA nanostructures under extreme chemical conditions. The applications of DNA nanostructures are traditionally limited to low temperature and/or aqueous environments. However, recent result from others and us suggest that the application window of DNA nanostructure in nanofabrication and nanolithography is likely much wider than previously believed. In aqueous solutions, the thermal stability of most unmodified DNA nanostructures is limited by the denaturing of double-stranded DNA at above ca. 55 oC. Sugiyama and cowork-

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0 1 2 3 µm µm Figure 7. (A) AFM images and height profiles of rectanguo lar DNA nanostructures after being heated to 150 C (top) o and 250 C (bottom) for 10 min. Note in the latter case, there is significant loss of fine details in the DNA nanostructure. Reproduced with permission from J. Vac. Sci. Technol. B, 2014, 32, 040602. (B) AFM images and height profiles of triangular shaped DNA nanostructures before (left) and after (right) exposure to UV/O3 for 20 min. Reproduced with permission from Chem. Mater. 2014, 26, 5265.

ers showed that photocrosslinking of DNA nanostructure using 8-methoxypsoralen expands the thermal stability window to ca. 85 to 90 oC.81 Later, other crosslinking chemistries were also demonstrated, such as photocrosslinking using 3cyanovinylcarbazole and psoralen82,83 alkylation using bis(2chloroethyl)amine,84 and alkyne-azide click chemistry.85 When supported on a dry substrate, the thermal stability of DNA nanostructure will be limited by the decomposition of DNA at ca. >250 oC. Lieberman and coworkers recently showed that DNA nanostructures deposited on mica retain their physical and chemical integrity even after being heated to 150 oC for 45 min;86 pyrolysis of DNA was observed at 180 oC by using X-ray photoelectron spectroscopy (XPS). The authors used a rectangle DNA nanostructure that has two fine structure details: a small loop of single-stranded DNA, and a letter “L” fabricated within the nanostructure with bulky staple strands. Upon heating to 250 oC, the authors observed loss of the fine structure features; however, the overall shape of the rectangle DNA nanostructure was still maintained (Figure 7A). In a parallel study, our group also reported that the shape of DNA nanostructures on a SiO2 substrate can survive very

harsh thermal treatment, up to 10 min of heating at 300 oC in air.87 Similarly, the shape persisted when the DNA nanostructures were exposed to UV/O3 oxidation for 20 min (Figure 7B). It is likely that the organic moiety of DNA decomposed under these conditions and only inorganic salt residues remained. Surprisingly, the salt residue maintained the original shape of the DNA nanostructure and can be used as a mask for vapor phase HF-etching of SiO2.76 It might be possible to use this salt residue to direct high temperature solid-state reactions as well. 4. Outlook From the work highlighted above, it is fair to state that DNA nanostructures have already demonstrated themselves as a useful tool for material research. However, only a small number of material chemists are taking advantage of these fascinating materials. A major barrier to adopting DNA nanostructures by materials chemists lies in the (perceived) difficulty in sample preparation and the associated high cost. Although a large number of DNA strands are needed to make a DNA nanostructure, the most DNA nanostructures syntheses are actually very straightforward, reproducible, and do not require special training in chemical biology. The staple strands for a typical 2D origami structure, if purchased from a commercial supplier, cost ca. $1500 (25 nmol scale) as of Oct 2015. Nevertheless, the field will likely benefit from having a commercial supply of ready-to-use ‘standard’ DNA nanostructures that can be modified by end users for their specific applications. On the bright side, surface patterning is not sensitive to the cost of DNA template. As we pointed out earlier, the cost of DNA template can be as low as $6/m2, making DNA-based fabrication a potential candidate even for large-scale patterning. Although significant advances have been made in the pattern transfer from DNA template to various inorganic substrates, there has been no demonstration of device fabrication using DNA nanostructure templates. Here, a critical missing link is the deterministic deposition of DNA nanostructures onto bare substrates or existing patterns using processes that are compatible with subsequent pattern transfers.38 Such a capability will enable the mass production of aligned features and carrying out multi-step fabrications. On the other hand, using DNA nanostructure for generalpurpose nanomaterials fabrication will require much larger amount of template materials. Without significant advance in low-cost manufacturing processes, it is unlikely that DNAbased approaches will be able to compete with wet chemistry for the mass production of simple nanomaterials (e.g. shaped controlled nanocrystals). There has been extensive efforts in developing enzymatic (e.g. rolling circle amplification, or RCA) and cell-based amplification of single-stranded DNA or DNA nanostructures,88-90 and in some cases, in gram scale quantities.91 Nevertheless, there could be applications, such as sensing and therapeutics, which may require very small amount of DNA nanostructure materials. It remains to identify such a killer application that justifies the cost and structural complexity of DNA nanostructures. Corresponding Author * [email protected].

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Acknowledgement P.Z. is supported by a fellowship from Chinese Scholarship Council. H.L. acknowledges support from NSF (CHE1507629), ONR (N000141310575 and N000141512520), AFOSR (FA9550-13-1-0083), and University of Pittsburgh CDRF grant.

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TOC FIGURE

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AUTHOR BIOGRAPHY Dr. Zhenbo Peng received his BSc in chemistry in 2001 and his MSc in analytical chemistry in 2004 from the University of Science and Technology of China (Hefei, China). He obtained his PhD in material physics and chemistry at Ningbo Institute of Technology and Engineering, CAS in 2013. He is an associate professor in Ningbo Polytechnic and is currently a visiting scholar at the University of Pittsburgh. His research interest is on DNA-based nanofabrication and nanomaterials for lithium-ion battery.

Professor Haitao Liu graduated in 2001 with a bachelor’s degree in chemistry from the University of Science and Technology of China (Hefei, China). He was a graduate student at the University of California, Berkeley, in the group of Professor Paul Alivisatos and obtained his PhD in chemistry in 2007. He carried out postdoctoral research at Columbia University with Professor Louis Brus and Professor Colin Nuckolls. Since 2010, he has been an assistant professor in the chemistry department of the University of Pittsburgh. His research interests include DNA-based nanofabrication, surface properties of graphitic materials, and reaction mechanism of the synthesis of inorganic colloidal nanocrystals.


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Bottom-up Nanofabrication Using DNA Nanostructures - Chemistry of

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