CONTENTS
10.2 DNA Nanostructures as a Self-Assembled Template
10.2.1 Nanoscale Patterning of Metal
10.2.2 Alignment of Molecules, Nanocrystals, and Carbon Nanotubes
10.3 DNA Nanostructures as a Catalytically Active Mask for Patterning SiO2
10.3.1 Conventional Methods for SiO2 Etching
10.3.2 Mechanism of SiO2 Etching by HF
10.3.3 DNA-Mediated Etching of SiO2
10.4 Applications and Future Directions
The development of integrated circuits and microchips has led to a new paradigm of smart computing and Internet devices. Photolithography, the most commonly used lithography method in industry, has made possible the scaling of integrated circuits all the way from several microns in the 1970s to tens of nanometers in current manufacturing [1]. The number of transistors that can be placed on an integrated circuit has doubled approximately every two years, obeying Moore’s law. This development has fueled continuous improvement in the tools used in the photolithography process. However, state-of-the-art photolithography process has reached a saturation point and faces technological and economic challenges to produce features less than 22 nm. Therefore over the last few years, alternative lithography processes that can produce features with sizes in the range of tens of nanometers have been developed.
Nanolithography is a lithography process that can produce nanometer-scale features on the surface. The technique of nanolithography can be divided into two types depending upon whether the pattern is transferred using a mask, referred to as masked lithography, or without a mask, referred to as maskless lithography. The forms of masked nanolithography include photolithography [2,3,4,5,6,7,8], nanoimprint lithography [9,10,11,12,13,14,15,16], and soft lithography [17,18,19,20]. Maskless nanolithography includes methods such as electron beam lithography [21,22,23,24,25,26,27], x-ray lithography [28,29], focused ion beam lithography [30,31,32,33], and scanning probe lithography [34,35,36,37,38,39,40] that fabricate patterns by serial writing without the use of a mask. Since this chapter focuses on the use of DNA nanostructures as the mask for lithography, the maskless lithography methods will not be discussed.
Among various masked nanolithography methods, soft lithography processes are gaining interest due to their lower cost, effectiveness, availability, and ease of use compared to the photolithography process. In a soft lithography process, elastomeric stamps, molds, or masks with patterns on their surface are used to generate micro- or nanostructure patterns [20]. The elastomeric stamp is a key component of the soft lithography process, and a variety of elastomers such as polydimethoxysilane, polyurethanes, polyimides, cross-linked Novolac™ resins, and their chemically modified derivatives have been used by researchers to fabricate stamps [20,41,42,43,44]. The stamps are commonly fabricated by pouring the pre-polymer of the elastomer over a master having the desired pattern on its surface, followed by the curing (cross-linking of the polymer) and peeling off steps. The master is fabricated using photolithography, micromachining, or e-beam lithography.
The different types of soft lithography techniques include microcontact printing (µCP), replica molding (REM), microtransfer molding (µTM), micromolding in capillaries (MIMIC), solvent-assisted micromolding (SAMIM), phase-shift photo-lithography cast molding, embossing, and injection molding [20,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59]. The µCP method is different from other printing methods in that it uses self-assembly to form micropatterns. A pattern with SAMs on the surface of the PDMS stamp is brought in contact with the substrate surface to form micropatterns of SAMs on the substrate surface.
The soft lithographic techniques offer advantages in several applications. For example, one of the major advantages of soft lithographic techniques is the ability to pattern a nonplanar surface. The other advantages include patterning solid materials other than photoresist, patterning materials in liquid phase, patterning functional molecules, and the formation of 3D microstructures and systems. Compared to photolithography, soft lithography is advantageous in applications where the capital cost of equipment is a concern or where precise alignment, uniformity, and continuity of the final pattern are not required. Examples of such applications include microelectrodes, microelectromechanical systems (MEMS), sensors, biosensors, microreactors, and plastic electronics. In these cases, soft lithography is economical and easy to implement compared to photolithography.
However, soft lithography is still in its infancy. The technique relies on a mask/mold for pattern transfer. The deformation and distortion of the elastomeric stamp needs to be very well understood and studied. Optimization of the properties of elastomer for faithful pattern transfer, especially for small size features, is important. Other factors, such as density of defects in the final pattern, high-resolution patterns, uniformity of the patterns, and compatibility with the techniques used in production of microelectronics, also need to be optimized and improved.
A single-stranded DNA is a long polymeric chain made up of repeating units of nucleotides. The nucleotide contains both the backbone of the molecule and a base. The backbone is made of alternating phosphate and sugar residues, while the base can be one of the four molecules: adenine (A), cytosine (C), guanine (G), and thymine (T). These bases form the alphabet of DNA and encode information.
In living organisms, DNA exists as a pair of molecules called double-stranded DNA that are held together tightly in the shape of a double helix. In a double helix, A bonds preferentially to T, and C bonds preferentially to G. The DNA double helix is stabilized by hydrogen bonds and hydrophobic interactions between the bases. Since the hydrogen bonding is noncovalent, the double-stranded DNA can be broken and rejoined by controlling the temperature of the solution [60,61,62].
The DNA nanostructure is a complex arrangement of single-stranded DNA molecules that are partially hybridized along their subsegments. Fabrication of DNA nanostructures is mainly based on the self-assembly process. The idea is to design a stable motif with sticky ends first that can hybridize to form DNA nanostructures [60,61,63,64,65,66]. For example, four motifs with sticky ends are assembled to form a quadrilateral with additional sticky ends on the outside, further allowing the structure to form a two-dimensional (2D) lattice [60,65]. Some of the useful motif types found in DNA nanostructures are stem loop (also called hairpins), Holliday junction, and sticky ends. Stem loop is a single-stranded DNA that loops back to hybridize on itself and is often used to form patterns on DNA nanostructures. Sticky end is an unhybridized single-stranded DNA that protrudes from the end of a double helix and is often used to combine two DNA nanostructures via hybridization. Holliday junctions are formed by two parallel DNA helices with one strand of each DNA helix crossing over the other DNA helix. Holliday junctions are often used to hold together various parts of DNA nanostructures. To achieve complicated DNA assemblies, it is important to design stable motifs. The use of branched DNA junctions with sticky ends to construct 2D arrays often did not yield the desired stable nanostructure due to the flexible nature of branched DNA junctions. To address this challenge, Seeman and coworkers constructed branched complexes with greater rigidity called crossover tiles, such as double-crossover tiles (DX) [67,68]. Inspired by the DX motif, several other motifs were engineered, such as triple-crossover (TX) motif, paranemic crossover tiles (PX), three-, five-, and six-point star motifs, and T-junctions, to provide more options to fabricate DNA nanostructures. Examples of these structures are shown in Figure 10.1 [67,68,69,70,71,72,73,74,75,76,77,78,79].
Another breakthrough in the design of the DNA nanostructure was achieved when Rothemund developed the concept of DNA origami [81,82]. Unlike the conventional crossover strategy, which is a two-step process that involves self-assembly of single building blocks (or motifs) into large structures, DNA origami provides a simple and versatile one-pot method in which a large single strand of DNA is folded into the desired shape using numerous short single strands. A very complex and arbitrary shape can be made by this DNA origami approach. However, scaling up the size of DNA origami is a critical challenge. Recently, Zhao et al. developed a new strategy to construct large-scale 2D origami [83]. They used rectangular-shaped DNA tiles instead of traditional staple strands that resulted in a DNA origami structure of a larger dimension than the structure obtained using staple strands.
FIGURE 10.1 Two-dimensional (2D) DNA nanostructures. (a) 2D hexagonal lattices formed from three-point-star motifs [69]. (b) 2D periodic arrays formed from symmetric six-point-star motifs [71]. (c) 2D pseudohexagonal trigonal arrays formed from bulged junction triangle [80]. (d) 2D arrays assembled from six-helix bundle tube [76]. (Reprinted from He, Y., et al., Journal of the American Chemical Society 2005, 127, 12202; He, Y., et al., Journal of the American Chemical Society 2006, 128, 15978; Mathieu, F., et al., Nano Letters 2005, 5, 661; and Ding, B., et al., Journal of the American Chemical Society 2004, 126, 10230. With permission.)
Conceptually, there is no difference between 2D and 3D assembly. Still, 3D DNA nanostructures are significantly more challenging to design than 2D structures because of the limited rigidity of the DNA motifs. With the development of rigid and unique 3D motifs as well the assembling strategies, a variety of 3D DNA nanostructures are fabricated and reported in the literature [61,63,66,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98].
10.2 DNA NANOSTRUCTURES AS A SELF-ASSEMBLED TEMPLATE
Assembly of interconnected nanoscale components in a controlled fashion is one of the key challenges in nanotechnology. The top-down lithographic patterning method is approaching its feature-size limitations, and so researchers are exploring bottom-up lithographic patterning methods as an alternative. DNA nanostructures are promising bottom-up alternatives because of their ease with which predesigned shapes/patterns can be obtained and their rich surface chemistry that can be used for precise positioning of nanoscale materials using a variety of covalent and noncovalent interactions. The most common way to use DNA nanostructures as templates for self-assembly is to pattern the DNA on the substrate and then use it to bind, nucleate, or mask other materials.
10.2.1 NANOSCALE PATTERNING OF METAL
DNA templated synthesis of metallic nanowires involves adsorption of positively charged metal ions on the negatively charged DNA backbone, followed by reduction of the adsorbed metal ions, resulting in metal nanowires grown on DNA templates. There are several reports on the synthesis of a variety of metallic nanowires, such as gold, platinum, silver, palladium, and nickel, using DNA as templates [79,99,100,101,102,103,104,105,106,107,108]. However, the metallization process results in nanowires that are at least 10 times thicker than the DNA templates. Also, the metallic nanowires obtained are linear structures, and features with specific shapes and patterns that are normally required for technological applications are challenging. To circumvent this issue, Deng and Mao reported the use of DNA as a mask to fabricate nanoscale gold patterns on the surface [109]. The method involved deposition of thick metal films over DNA nanostructures on mica to create imprinted metal replicas of the DNA features (negative tone pattern) with the nanometer-scale resolution. In another such technique, Becerril and Woolley reported the use of DNA molecules aligned on the substrate as shadow mask templates to obtain features with a spatial resolution in the sub-10 nm range [110]. The method involved alignment of DNA nanostructures on the surface, followed by vapor deposition of metal film at a certain angle relative to the surface, which resulted in films with nanometer-sized gaps corresponding to the DNA shadow mask. Anisotropic etching of these features resulted in transfer of these patterns into the substrate in the form of trenches.
10.2.2 ALIGNMENT OF MOLECULES, NANOCRYSTALS, AND CARBON NANOTUBES
DNA nanostructures have also been used as templates to assemble a variety of organic and inorganic moieties (Figure 10.2) [111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128]. The most common strategy is to incorporate functional moieties into DNA nanostructure architecture and use that as a binding site to organize nanoscale organic and inorganic moieties. For example, Zhang et al. demonstrated the incorporation of a single gold nanoparticle into a DNA nanostructure building block and used it for self-assembly of 2D nanoparticle arrays with well-defined periodic patterns and interparticle spacing [111]. Pinto et al. demonstrated the periodic arrangement of nanoparticles of different sizes [114]. Yan et al. reported the possibility for designing complex assemblies of multicomponent nanomaterials by using peptides with specific affinity for particular inorganic materials. By coupling gold binding peptide to self-assembling DNA strands, they assembled gold nanoparticles suggesting the possibility of achieving mixed nanoparticle systems depending upon the peptide location within the self-assembling DNA nanostructure [79]. Hung et al. reported a combination of lithography and self-assembly to selectively deposit DNA origami structures hybridized with gold nanoparticles on lithographically patterned substrate resulting in a spatially ordered 2D assembly of 5 nm gold particle, demonstrating a versatile approach for large-scale nanoparticle patterning [129].
FIGURE 10.2 Assembly of gold nanoparticles using (a) a square lattice [111] and (b) a DX-triangle tile [112]. (Reprinted from Zhang, J., et al., Nano Letters 2006, 6, 248, and Zheng, J., et al., Nano Letters 2006, 6, 1502. With permission.)
Carbon nanotubes have been studied extensively because of their unique mechanical, thermal, electronic, and optical properties. However, some of the major challenges in the widespread use of carbon nanotubes are their sorting, sizing, and arrangement to fabricate economical devices. DNA self-assembly offers the possibility for efficient arrangement of carbon nanotubes into composite structures. The early studies on assembly of carbon nanotubes using DNA relied on either a common moiety that would noncovalently link DNA and carbon nanotubes or covalent coupling of amino DNA to carboxylic groups on carbon nanotubes. During the last few years, a variety of methods were developed to assemble carbon nanotubes [113,130,131,132,133,134,135,136,137,138,139]. For example, Keren et al. combined DNA self-assembly with other biomolecular recognition processes to construct a carbon nanotube field effect transistor [133]. In another report, Maune et al. used DNA origami templates mixed with DNA-functionalized nanotubes to align nanotubes into cross-junctions [113]. They synthesized rectangular origami templates with two lines of single-stranded DNA hooks in a cross-pattern; this origami served as a template for two different types of nanotubes, each functionalized noncovalently with a distinct DNA linker molecule. The mixing of DNA origami templates and functionalized nanotubes resulted in alignment of nanotubes into cross-junctions that also demonstrated stable field effect transistor-like behavior.
10.3 DNA NANOSTRUCTURES AS A CATALYTICALLY ACTIVE MASK FOR PATTERNING SIO2
10.3.1 CONVENTIONAL METHODS FOR SIO2 ETCHING
SiO2 is the most commonly used dielectric material in silicon integrated circuits. The oxide growth on Si substrates can be divided into two categories: thermal and chemical vapor deposition (CVD). In the case of thermal oxide growth, bulk silicon is oxidized either in dry oxygen or in wet water vapor atmosphere at temperatures above 900°C, while in the case of the CVD process the oxide is formed by chemical reaction of silicon containing precursor vapor and oxygen. CVD oxides offer the advantage of lower deposition temperature than the thermal oxide process, and the deposition can be carried out either at atmospheric pressure (APCVD), low pressure (LPCVD), or by plasma activation (PECVD) [140,141].
The etching of SiO2 can be carried in a wet, dry, or vapor phase process. In a typical wet etching process, liquid phase etchants are used where the wafer is immersed in the bath of etchants (e.g., hydrofluoric acid (HF) solution). In the case of dry etching, the wafer is exposed to plasma of some reactive ion (such as Cl and F) that can react with SiO2. Dry etching requires expensive plasma instrumentation; it also has limitations on the etch rate. As a result, the wet etching method is most commonly used, as it offers the advantage of low cost, speed, and simplicity. However, one of the major challenges of using the wet etching process is the stiction problem [142,143,144,145,146,147,148]. Typically a wet etching process involves etching with a liquid etchant followed by a rinsing step. The rinse liquid eventually needs to be dried out. However, the capillary force at the menisci formed during the final drying step pulls the micro-structures down to the substrate. The deformed structure will adhere to the surface due to strong van der Waals and electrostatic interactions. Various techniques have been developed to alleviate or remove the stiction problem, such as using low surface tension liquid or dimples to reduce contact area, or using a rough surface to reduce effective surface energy, or eliminating the formation of a liquid-gas interface through sublimation, plasma ashing, or supercritical drying [142,149,150,151,152,153,154,155,156].
The vapor phase etching is attractive in that it eliminates the elaborate rinsing and drying steps. Vapor phase etching can faithfully transfer lithographically defined photoresist patterns into the underlying layers with both isotropic and anisotropic etch methods. Compared to wet etching, vapor phase etching offers the advantage of better control of process variables, such as temperature, pressure, relative composition of gas phase etchants, and ease of automation. Importantly, vapor phase etching can be carried out under mild conditions that will not lift off or destroy the DNA-based templates.
10.3.2 MECHANISM OF SIO2 ETCHING BY HF
The vapor phase etching of SiO2 using HF gas to produce SiF4 and H2O is a thermodynamically favorable reaction [157]:
where ΔG is the change in Gibbs free energy. However, HF alone does not etch SiO2, and so to lower the kinetic barrier, a polar molecule such as water is needed. It has been proposed that the adsorbed moisture on the oxide surface acts as a catalyst for the gas-solid reaction between HF and SiO2.
Several experimental and theoretical studies have been reported proposing the mechanism of vapor phase etching of SiO2 using HF and the significance of water in the etching reaction. For example, an in situ Fourier transform infrared (FTIR) spectroscopy study on the vapor phase etching suggested that the HF and H2O molecules form a HF-H2O complex that adsorbs on the SiO2 surface more strongly than either molecule alone [158]. Water consequently acts as a carrier or a medium for HF to stick on SiO2 and etch the surface [157]. A first principles molecular modeling study suggested that a concerted attack of HF and H2O molecules on the Si-O bond of surface silanol (SiOH) groups is the preferred etching pathway [160]. According to the model for gas phase etching of SiO2 proposed by Lee et al., HF vapor molecules and water molecules first adsorb physically onto the oxide [142,160].
An ionization reaction between the adsorbed HF and water results in a HF2– ion.
The ionized HF then reacts with the oxide by sequential substitution reactions to produce water and other by-products, as shown in the reaction below [157]:
The by-products are removed from the oxide surface by desorption [142,160]:
Thus irrespective of the variety of proposed mechanisms in the literature, all the mechanisms suggest the adsorption of water on the surface of the oxide playing an important role in controlling the etching kinetics. Therefore if the water adsorption on the surface is controlled with nanometer-scale resolution, it will be possible to control the etching of SiO2 at the same length scale. Since the etching reaction is autocatalytic, a small spatial variation in the initial concentration of surface-adsorbed water would be amplified by the reaction and will have a significant impact on the etching kinetics in the long run.
10.3.3 DNA-MEDIATED ETCHING OF SIO2
Several reasons make DNA nanostructures good candidates to control the adsorption of moisture and therefore to pattern the SiO2 surface. First, DNA nanotechnology offers the advantage of synthesizing a predetermined shape or pattern at the nanometer scale. Second, the chemical functionalities on the surface of DNA, such as phosphates, nitrogen, and oxygen, can hydrogen bond with water, and thus the moisture around the surface of DNA can be effectively controlled. Third, the etching is carried out in the vapor phase, eliminating the possibility of DNA being lifted off from the surface.
Both the DNA and the SiO2 surface will adsorb water; however, the amount of surface-adsorbed water on the clean SiO2 surface and the SiO2 surface underneath the DNA will depend on several factors, such as relative humidity, temperature, and partial pressure of water. Therefore by controlling the etching conditions, it is possible to etch/pattern the SiO2 surface at the nanometer-scale resolution. The resolution of the etching/pattern will be determined by the size of the DNA nanostructure.
We recently discovered that triangular DNA nanostructures deposited on the SiO2 surface when exposed to HF vapor under high-humidity conditions (~50% relative humidity) result in triangular-shaped trenches on the substrate surface (Figure 10.3a). This is due to high adsorption of water around DNA under high-humidity conditions that results in faster etching kinetics underneath DNA, resulting in a trench (negative tone etching). Under low-humidity conditions, the etching rate of SiO2 under DNA is less compared to DNA-free surface, resulting in DNA acting as a mask protecting the surface underneath it (positive tone etching). As shown in Figure 10.3a, triangular trenches in the range of 1–2 nm are obtained under high-humidity conditions while triangular ridges in the range of 2–3 nm are obtained under low-humidity conditions
The resolution limit of this technique was probed using a single double-stranded DNA (λ-DNA) as a template. As shown in Figure 10.3b, λ-DNA aligned on the SiO2 substrate, when exposed to HF vapors under high moisture conditions, resulted in trenches of width ranging from 10 to 30 nm on the SiO2 surface. Such a wide range of trench width is attributed to bundling of DNA with a single DNA strand producing features as small as 10 nm, while bundles produce features as large as 30 nm. Consistently, when λ-DNA aligned on the SiO2 substrate is exposed to HF vapors under low moisture conditions, this results in ridges on the SiO2 surface, indicating that even a single strand of DNA can slow the etching of SiO2 underneath it acting as a mask.
Kinetics study on the etching reaction under low moisture conditions further supports the hypothesis (Figure 10.4). In this case, the aligned λ-DNA on SiO2 substrates was etched for 5, 10, 15, and 20 min under low moisture conditions, and the heights of the ridge features were measured using an atomic force microscope (AFM) before and after the removal of λ-DNA. The difference in the two measurements (~0.7 nm) indicates the presence of the DNA throughout the reaction. It is important to note, however, that AFM cannot detect if the chemical structure of DNA is still intact. The etching reaction observes an initiation or induction period (~5 min), where no etching is observed, followed by a fast etching step, indicated by the rapid buildup of the ridge height (~5–15 min). As the reaction progresses further, enough water is produced by the reaction to saturate the surface, leading to a decrease in ridge height.
FIGURE 10.3 AFM images and cross section of (a) DNA nanostructures. (a′) DNA origami triangles self-assembled on SiO2 wafer. (b′) Triangular trenches produced upon exposure of (a′) to high relative humidity air and HF vapor; the inset shows a high-magnification AFM image of a triangular trench with a width of 25 nm. (c′) Triangular ridges produced upon exposure of (a′) to low relative humidity air and HF vapor. Arrows indicate the lines along which the cross sections were determined. Scale bars represent 100 nm. (b) Single-stranded DNA. (d′) λ-DNA aligned on the SiO2 substrate. (e′) Trenches produced after exposure of (d′) to high relative humidity air and HF vapor; the inset shows a high-magnification image of the trench. (f′) Ridges produced after exposure of (d′) to low relative humidity air and HF vapor. It should be noted that this AFM image was obtained at exactly the same location as the one in (d′). Arrows indicate lines along which the cross sections were determined. Scale bars represent 1 μm. (Reproduced from Surwade, S.P., et al., Journal of the American Chemical Society 2011, 133, 11868. With permission.)
FIGURE 10.4 Kinetics study on etching rate. AFM images of SiO 2 wafer with single-stranded DNA after etching under relatively low-humidity air and HF vapor for (a) 5 min, (a′) sample (a) after piranha wash; (b) 10 min, (b′) sample (b) after piranha wash; (c) 15 min, (c′) sample (c) after piranha wash; and (d) 20 min, (d′) sample (d) after piranha wash. (e) Plot showing the temporal evolution of the height of the ridges obtained under relatively low-humidity air and HF vapor. (Reproduced from Surwade, S.P., et al., Journal of the American Chemical Society 2011, 133, 11868. With permission.)
Substrate temperature also plays an important role in determining the etching kinetics. The etching rate is observed to decrease with increasing substrate temperature, possibly due to a decrease in water adsorption on the SiO2 surface at high temperatures.
10.4 APPLICATIONS AND FUTURE DIRECTIONS
DNA nanostructures hold great promise as a template for high-resolution nanofabrication. A lithography is essentially a process that can make arbitrary shaped patterns at arbitrary locations. In this regard, the DNA nanostructure is far superior to almost any other self-assembled material systems in that it can produce arbitrary-shaped patterns with 2–3 nm of resolution. However, its applications in lithography are greatly limited by its stability, both chemical and mechanical. The vapor phase etching scheme circumvented these stability issues by avoiding using liquid and plasma etchants. However, improving the chemical and mechanical stability of the DNA nanostructure will certainly make it compatible with a wide range of existing nanofabrication processes. In addition to being useful as a practical lithography process, ways to fabricate a large-scale DNA nanostructure and its deterministic positioning on the substrate need to be developed. Last but not least, the fidelity and reproducibility of DNA self-assembly needs to be understood and controlled before it can be used in any real-world manufacturing process.
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